diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml new file mode 100644 index 000000000..9bb321f90 --- /dev/null +++ b/.github/workflows/deploy.yml @@ -0,0 +1,57 @@ +name: Deploy to Sonatype Central + +on: + push: + tags: + - 'v*' # Trigger the workflow when a tag starting with 'v' is pushed, like v1.0.0 + workflow_dispatch: + +jobs: + deploy: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v5 + + - name: Set up JDK 17 + uses: actions/setup-java@v5 + with: + java-version: '17' + distribution: 'adopt' + + - name: Cache Maven dependencies + uses: actions/cache@v4 + with: + path: ~/.m2/repository + key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }} + restore-keys: | + ${{ runner.os }}-maven- + + - name: Import GPG key + run: | + echo "${{ secrets.GPG_PRIVATE_KEY }}" | gpg --import --armor --batch --no-tty + + - name: Setup Maven settings + run: | + rm ${HOME}/.m2/settings.xml + + cat << EOF > ${HOME}/.m2/settings.xml + + + + central + ${{ secrets.SONATYPE_USERNAME }} + ${{ secrets.SONATYPE_PASSWORD }} + + + + EOF + + - name: Deploy to Sonatype Central + run: | + ./mvnw clean deploy -Prelease \ + --batch-mode \ + -Dgpg.keyname=${{ secrets.GPG_KEY_ID }} diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 083f78e39..a6b53e7f3 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -26,4 +26,4 @@ jobs: java-version: '17' distribution: 'adopt' - name: Build with Maven - run: mvn --batch-mode --update-snapshots verify + run: ./mvnw --batch-mode --update-snapshots verify diff --git a/.mvn/wrapper/maven-wrapper.properties b/.mvn/wrapper/maven-wrapper.properties index 0061e751e..72853742a 100644 --- a/.mvn/wrapper/maven-wrapper.properties +++ b/.mvn/wrapper/maven-wrapper.properties @@ -1 +1 @@ -distributionUrl=https://repo1.maven.org/maven2/org/apache/maven/apache-maven/3.6.0/apache-maven-3.6.0-bin.zip \ No newline at end of file +distributionUrl=https://repo1.maven.org/maven2/org/apache/maven/apache-maven/3.6.3/apache-maven-3.6.3-bin.zip \ No newline at end of file diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 2015ee0c3..c33478258 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -9,7 +9,7 @@ Changelog * Improve user guide, tutorial, and documentation. * Introduce *latest* and *stable* documentation branches * Add showcase of apps that use phenopacket-tools to add more code examples -* Run `MetaDataValidator` during base validation +* Run `MetaDataValidator` and `HpoUniqueValidator` during base validation * Finalize JSON and YAML format sniffing * Fix example phenopackets diff --git a/docs/conf.py b/docs/conf.py index 4997f4605..08fe983eb 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -6,24 +6,8 @@ # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -############# -# JR added: -import os -import sys - -sys.path.insert(0, os.path.abspath('../../')) -extensions = [ - 'sphinx.ext.autodoc', - 'sphinx.ext.githubpages', - 'sphinx_rtd_theme', - 'recommonmark' -] - -html_theme = 'sphinx_rtd_theme' -############## - project = 'phenopacket-tools' -copyright = '2022, Daniel Danis, Peter Robinson' +copyright = '2026, Daniel Danis, Peter Robinson' author = u'Daniel Danis, Peter Robinson' # The version info for the project you're documenting, acts as replacement for @@ -33,7 +17,7 @@ # The short X.Y version. version = '1.0' # The full version, including alpha/beta/rc tags. -release = '1.0.0-RC3' +release = '1.0.0' # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration @@ -48,7 +32,6 @@ # -- Options for HTML output ------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output -html_theme = 'alabaster' html_static_path = ['_static'] html_css_files = ['pxftools.css'] diff --git a/docs/validation.rst b/docs/validation.rst index c4f8a8cbc..1f8089dc0 100644 --- a/docs/validation.rst +++ b/docs/validation.rst @@ -353,6 +353,20 @@ library to parse the HPO JSON file. The `OntologyLoader` is part of `phenol-io `_ module, you may need to add an appropriate dependency into your build file. +.. _rstuniquephenotypevalidation: + +Unique phenotypic features +########################## + +The `HpoUniqueValidator` checks if the HPO terms used by a phenopacket are *unique* - present at most once. +If a term is not unique, the validator points this out along with the term's occurrence count. + +In code, we add the corresponding validator into the validation workflow by running: + +.. code-block:: java + + builder.addValidator(HpoPhenotypeValidators.Unique.phenopacketValidator(hpo)); + .. _rstancestryphenotypevalidation: diff --git a/phenopacket-tools-builder/pom.xml b/phenopacket-tools-builder/pom.xml index e7594d8e4..d8407f6dc 100644 --- a/phenopacket-tools-builder/pom.xml +++ b/phenopacket-tools-builder/pom.xml @@ -7,7 +7,7 @@ org.phenopackets.phenopackettools phenopacket-tools - 1.0.0-RC3 + 1.0.0 phenopacket-tools-builder diff --git a/phenopacket-tools-builder/src/main/java/org/phenopackets/phenopackettools/builder/builders/VariationDescriptorBuilder.java b/phenopacket-tools-builder/src/main/java/org/phenopackets/phenopackettools/builder/builders/VariationDescriptorBuilder.java index 55bcc5a29..96fb3eb07 100644 --- a/phenopacket-tools-builder/src/main/java/org/phenopackets/phenopackettools/builder/builders/VariationDescriptorBuilder.java +++ b/phenopacket-tools-builder/src/main/java/org/phenopackets/phenopackettools/builder/builders/VariationDescriptorBuilder.java @@ -100,6 +100,10 @@ public VariationDescriptorBuilder transcript() { return this; } + public VariationDescriptorBuilder moleculeContext(MoleculeContext context) { + builder.setMoleculeContext(context); + return this; + } public VariationDescriptorBuilder structuralType(OntologyClass structuralType) { builder.setStructuralType(structuralType); diff --git a/phenopacket-tools-builder/src/main/java/org/phenopackets/phenopackettools/builder/builders/VcfRecordBuilder.java b/phenopacket-tools-builder/src/main/java/org/phenopackets/phenopackettools/builder/builders/VcfRecordBuilder.java index 472c56b8c..c0b58fb4c 100644 --- a/phenopacket-tools-builder/src/main/java/org/phenopackets/phenopackettools/builder/builders/VcfRecordBuilder.java +++ b/phenopacket-tools-builder/src/main/java/org/phenopackets/phenopackettools/builder/builders/VcfRecordBuilder.java @@ -2,9 +2,14 @@ import org.ga4gh.vrsatile.v1.VcfRecord; +import java.util.ArrayList; +import java.util.List; + public class VcfRecordBuilder { private final VcfRecord.Builder builder; + private boolean passIsSet = false; + private List filters = null; private VcfRecordBuilder(String assembly, String chromosome, int position, String ref, String alt) { builder = VcfRecord.newBuilder() @@ -48,18 +53,46 @@ public VcfRecordBuilder qual(String qual) { } /** - * If this method is called, "PASS" is added to the FILTER column + * If this method is called, the FILTER column is set to "PASS" and any other previously added filters are cleared. + * Calling {@code pass()} is equivalent to calling filter("PASS"). */ - public VcfRecordBuilder pass() { - builder.setFilter("PASS"); + public synchronized VcfRecordBuilder pass() { + passIsSet = true; + if (filters != null) + filters.clear(); + return this; } /** - * @param filter FILTER field of VCF. calling {@link #pass()} is equivant to calling filter("PASS) + * Add a VCF filter field. + *

+ * The field can be a single value (e.g. q50) or several values joined by ; (e.g. q10;q50). + *

+ * Calling filter("PASS") is equivalent to calling {@link #pass()}. As a side effect, + * all previously added filter values are removed. + * + * @param filter add a FILTER field. + * @see #pass() */ - public VcfRecordBuilder filter(String filter) { - builder.setFilter(filter); + public synchronized VcfRecordBuilder filter(String filter) { + passIsSet = false; + if (filters == null) + filters = new ArrayList<>(); + + if ("PASS".equalsIgnoreCase(filter)) + return pass(); + else { + if (filter.contains(";")) { + for (String field : filter.split(";")) { + String trimmed = field.trim(); + if (!trimmed.isEmpty()) + this.filter(field); + } + } else + filters.add(filter); + } + return this; } @@ -71,7 +104,13 @@ public VcfRecordBuilder info(String info) { return this; } - public VcfRecord build() { + public synchronized VcfRecord build() { + if (passIsSet) + builder.setFilter("PASS"); + + else if (filters != null && !filters.isEmpty()) + builder.setFilter(String.join(";", filters)); + return builder.build(); } } diff --git a/phenopacket-tools-builder/src/test/java/org/phenopackets/phenopackettools/builder/builders/VcfRecordBuilderTest.java b/phenopacket-tools-builder/src/test/java/org/phenopackets/phenopackettools/builder/builders/VcfRecordBuilderTest.java new file mode 100644 index 000000000..b044187a8 --- /dev/null +++ b/phenopacket-tools-builder/src/test/java/org/phenopackets/phenopackettools/builder/builders/VcfRecordBuilderTest.java @@ -0,0 +1,30 @@ +package org.phenopackets.phenopackettools.builder.builders; + +import org.ga4gh.vrsatile.v1.VcfRecord; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.CsvSource; + +import static org.junit.jupiter.api.Assertions.*; +import static org.hamcrest.MatcherAssert.*; +import static org.hamcrest.Matchers.*; + +public class VcfRecordBuilderTest { + + @ParameterizedTest + @CsvSource({ + "PASS, PASS", + "pass, PASS", + "q50, q50", + "q50;q10, q50;q10", + "q50;pass, PASS", + "pass;q50, q50", + }) + public void addFilter(String filter, String expected) { + VcfRecord record = VcfRecordBuilder.builder("GRCh37", "chr1", 123_456, "C", "G") + .filter(filter) + .build(); + + assertThat(record.getFilter(), equalTo(expected)); + } +} \ No newline at end of file diff --git a/phenopacket-tools-cli/pom.xml b/phenopacket-tools-cli/pom.xml index 871fc4116..94c1bc260 100644 --- a/phenopacket-tools-cli/pom.xml +++ b/phenopacket-tools-cli/pom.xml @@ -7,7 +7,7 @@ org.phenopackets.phenopackettools phenopacket-tools - 1.0.0-RC3 + 1.0.0 phenopacket-tools-cli diff --git a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/Main.java b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/Main.java index 1de9e69ae..fade5c533 100644 --- a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/Main.java +++ b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/Main.java @@ -15,7 +15,7 @@ "phenopacket-tools (pxf)", "An application and library for building, conversion, and validation of GA4GH Phenopackets.\n" }, - version = "v1.0.0-RC3", + version = "v1.0.0", mixinStandardHelpOptions = true, subcommands = { // see https://picocli.info/autocomplete.html diff --git a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/ValidateCommand.java b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/ValidateCommand.java index 4dd8b3b0f..af9725847 100644 --- a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/ValidateCommand.java +++ b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/ValidateCommand.java @@ -3,8 +3,8 @@ import com.google.protobuf.MessageOrBuilder; import org.monarchinitiative.phenol.base.PhenolRuntimeException; -import org.monarchinitiative.phenol.io.OntologyLoader; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.io.MinimalOntologyLoader; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.monarchinitiative.phenol.ontology.data.TermId; import org.phenopackets.phenopackettools.core.PhenopacketElement; import org.phenopackets.phenopackettools.core.PhenopacketSchemaVersion; @@ -149,10 +149,10 @@ private List> configureSema // Right now we only have one semantic validator, but we'll extend this in the future. LOGGER.debug("Configuring semantic validators"); List> validators = new ArrayList<>(); - Ontology hpo = null; + MinimalOntology hpo = null; if (validateSection.hpJson != null) { LOGGER.debug("Reading HPO from {}", validateSection.hpJson.toAbsolutePath()); - hpo = OntologyLoader.loadOntology(validateSection.hpJson.toFile()); + hpo = MinimalOntologyLoader.loadOntology(validateSection.hpJson.toFile()); // The entire logic of this command stands and falls on correct state of `element` and the read message(s). // This method requires an appropriate combination of `T` and `element`, as described in Javadoc. @@ -163,18 +163,24 @@ private List> configureSema //noinspection unchecked validators.add((PhenopacketValidator) HpoPhenotypeValidators.Primary.phenopacketHpoPhenotypeValidator(hpo)); //noinspection unchecked + validators.add((PhenopacketValidator) HpoPhenotypeValidators.Unique.phenopacketValidator(hpo)); + //noinspection unchecked validators.add((PhenopacketValidator) HpoPhenotypeValidators.Ancestry.phenopacketHpoAncestryValidator(hpo)); } case FAMILY -> { //noinspection unchecked validators.add((PhenopacketValidator) HpoPhenotypeValidators.Primary.familyHpoPhenotypeValidator(hpo)); //noinspection unchecked + validators.add((PhenopacketValidator) HpoPhenotypeValidators.Unique.familyValidator(hpo)); + //noinspection unchecked validators.add((PhenopacketValidator) HpoPhenotypeValidators.Ancestry.familyHpoAncestryValidator(hpo)); } case COHORT -> { //noinspection unchecked validators.add((PhenopacketValidator) HpoPhenotypeValidators.Primary.cohortHpoPhenotypeValidator(hpo)); //noinspection unchecked + validators.add((PhenopacketValidator) HpoPhenotypeValidators.Unique.cohortValidator(hpo)); + //noinspection unchecked validators.add((PhenopacketValidator) HpoPhenotypeValidators.Ancestry.cohortHpoAncestryValidator(hpo)); } } @@ -191,7 +197,7 @@ private List> configureSema return validators; } - private static PhenopacketValidator prepareOrganSystemValidator(Ontology hpo, + private static PhenopacketValidator prepareOrganSystemValidator(MinimalOntology hpo, List organSystems, PhenopacketElement element) { // Organ system validation can only be done when HPO is provided. diff --git a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/BaseValidateCommand.java b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/BaseValidateCommand.java index d4ecad43f..11b487959 100644 --- a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/BaseValidateCommand.java +++ b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/BaseValidateCommand.java @@ -1,8 +1,8 @@ package org.phenopackets.phenopackettools.cli.command.validate; import com.google.protobuf.MessageOrBuilder; -import org.monarchinitiative.phenol.io.OntologyLoader; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.io.MinimalOntologyLoader; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator; import org.phenopackets.phenopackettools.validator.core.ValidationResult; import org.phenopackets.phenopackettools.validator.core.ValidationResults; @@ -109,7 +109,7 @@ protected List> configureSemanticValidators() { List> validators = new ArrayList<>(); if (hpJson != null) { LOGGER.debug("Reading HPO from '{}}'", hpJson.toAbsolutePath()); - Ontology hpo = OntologyLoader.loadOntology(hpJson.toFile()); + MinimalOntology hpo = MinimalOntologyLoader.loadOntology(hpJson.toFile()); validators.add(createHpoValidator(hpo)); } @@ -117,6 +117,6 @@ protected List> configureSemanticValidators() { return validators; } - protected abstract PhenopacketValidator createHpoValidator(Ontology hpo); + protected abstract PhenopacketValidator createHpoValidator(MinimalOntology hpo); } diff --git a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidateCohortCommand.java b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidateCohortCommand.java index 6355f625f..5e6f00d4a 100644 --- a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidateCohortCommand.java +++ b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidateCohortCommand.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.cli.command.validate; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator; import org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner; import org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators; @@ -30,7 +30,7 @@ protected ValidationWorkflowRunner prepareValidationWorkflow(Li } @Override - protected PhenopacketValidator createHpoValidator(Ontology hpo) { + protected PhenopacketValidator createHpoValidator(MinimalOntology hpo) { return HpoPhenotypeValidators.cohortHpoPhenotypeValidator(hpo); } diff --git a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidateFamilyCommand.java b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidateFamilyCommand.java index 25390c06b..05481da15 100644 --- a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidateFamilyCommand.java +++ b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidateFamilyCommand.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.cli.command.validate; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator; import org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner; import org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators; @@ -30,7 +30,7 @@ protected ValidationWorkflowRunner prepareValidationWorkflow(Li } @Override - protected PhenopacketValidator createHpoValidator(Ontology hpo) { + protected PhenopacketValidator createHpoValidator(MinimalOntology hpo) { return HpoPhenotypeValidators.familyHpoPhenotypeValidator(hpo); } diff --git a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidatePhenopacketCommand.java b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidatePhenopacketCommand.java index a16486d43..ceffd9083 100644 --- a/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidatePhenopacketCommand.java +++ b/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidatePhenopacketCommand.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.cli.command.validate; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator; import org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner; import org.phenopackets.phenopackettools.validator.core.metadata.MetaDataValidators; @@ -32,7 +32,7 @@ protected ValidationWorkflowRunner prepareValidationWorkfl } @Override - protected PhenopacketValidator createHpoValidator(Ontology hpo) { + protected PhenopacketValidator createHpoValidator(MinimalOntology hpo) { return HpoPhenotypeValidators.phenopacketHpoPhenotypeValidator(hpo); } diff --git a/phenopacket-tools-converter/pom.xml b/phenopacket-tools-converter/pom.xml index 2ec70089e..2d76af214 100644 --- a/phenopacket-tools-converter/pom.xml +++ b/phenopacket-tools-converter/pom.xml @@ -7,7 +7,7 @@ org.phenopackets.phenopackettools phenopacket-tools - 1.0.0-RC3 + 1.0.0 phenopacket-tools-converter diff --git a/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/V1ToV2ConverterImpl.java b/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/V1ToV2ConverterImpl.java index cf80e5d38..e044d8334 100644 --- a/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/V1ToV2ConverterImpl.java +++ b/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/V1ToV2ConverterImpl.java @@ -1,5 +1,6 @@ package org.phenopackets.phenopackettools.converter.converters; +import org.ga4gh.vrsatile.v1.MoleculeContext; import org.ga4gh.vrsatile.v1.VariationDescriptor; import org.phenopackets.phenopackettools.builder.builders.*; import org.phenopackets.phenopackettools.converter.converters.v2.*; @@ -209,7 +210,7 @@ private static Optional toV2Interpretation(org.phenopackets.sche diagnosis.addGenomicInterpretation(genomicInterpretation.build()); } - return Optional.ofNullable(InterpretationBuilder.builder(v1.getId()) + return Optional.of(InterpretationBuilder.builder(v1.getId()) .solved(diagnosis.build())); } @@ -220,8 +221,10 @@ private static Function toVariationDescriptor() { return switch (variant.getAlleleCase()) { case HGVS_ALLELE -> { var hgvsAllele = variant.getHgvsAllele(); + Optional moleculeContext = guessMoleculeContext(hgvsAllele.getHgvs()); yield VariationDescriptorBuilder.builder(hgvsAllele.getId()) .zygosity(v2zygosity) + .moleculeContext(moleculeContext.orElse(MoleculeContext.unspecified_molecule_context)) .hgvs(hgvsAllele.getHgvs()) .build(); } @@ -231,6 +234,7 @@ private static Function toVariationDescriptor() { vcfAllele.getChr(), vcfAllele.getPos(), vcfAllele.getRef(), vcfAllele.getAlt()) + .info(vcfAllele.getInfo()) .build(); yield VariationDescriptorBuilder.builder(vcfAllele.getId()) .vcfRecord(vcfRecord) @@ -247,6 +251,7 @@ private static Function toVariationDescriptor() { spdiAllele.getInsertedSequence()); yield VariationDescriptorBuilder.builder(spdiAllele.getId()) .spdi(spdi) + .genomic() .zygosity(v2zygosity) .build(); } @@ -254,6 +259,7 @@ private static Function toVariationDescriptor() { var iscnAllele = variant.getIscnAllele(); yield VariationDescriptorBuilder.builder(iscnAllele.getId()) .iscn(iscnAllele.getIscn()) + .genomic() .zygosity(v2zygosity) .build(); } @@ -263,4 +269,17 @@ private static Function toVariationDescriptor() { }; } + private static Optional guessMoleculeContext(String hgvs) { + if (hgvs.startsWith("NM_") || hgvs.startsWith("XM_") || hgvs.startsWith("ENST")) { + return Optional.of(MoleculeContext.transcript); + } else if (hgvs.startsWith("NP_") || hgvs.startsWith("XP_") || hgvs.startsWith("ENSP")) { + return Optional.of(MoleculeContext.protein); + } else if (hgvs.startsWith("NC_")) { + return Optional.of(MoleculeContext.genomic); + } else { + LOGGER.debug("Could not determine molecule context {transcript, protein, genomic} from HGVS string {}", hgvs); + return Optional.empty(); + } + } + } diff --git a/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/AgeConverter.java b/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/AgeConverter.java index 2a4c6a9dc..8e142c630 100644 --- a/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/AgeConverter.java +++ b/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/AgeConverter.java @@ -29,12 +29,11 @@ static Optional toAgeRange(org.phenopackets.schema.v1.core.AgeRange v1 if (start.isEmpty() && end.isEmpty()) return Optional.empty(); - else - return Optional.of( - AgeRange.newBuilder() - .setStart(start.orElse(Age.getDefaultInstance())) - .setEnd(end.orElse(Age.getDefaultInstance())) - .build() - ); + else { + AgeRange.Builder builder = AgeRange.newBuilder(); + start.ifPresent(builder::setStart); + end.ifPresent(builder::setEnd); + return Optional.of(builder.build()); + } } } diff --git a/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/DiseaseConverter.java b/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/DiseaseConverter.java index 4aead25d2..095f7251e 100644 --- a/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/DiseaseConverter.java +++ b/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/DiseaseConverter.java @@ -19,27 +19,29 @@ public static List toDiseases(List toDisease(org.phenopackets.schema.v1.core.Disease v1Disease) { + private static Optional toDisease(org.phenopackets.schema.v1.core.Disease v1Disease) { if (v1Disease.equals(org.phenopackets.schema.v1.core.Disease.getDefaultInstance())) return Optional.empty(); Optional term = OntologyClassConverter.toOntologyClass(v1Disease.getTerm()); + Optional onset = toDiseaseOnset(v1Disease); List stages = OntologyClassConverter.toOntologyClassList(v1Disease.getDiseaseStageList()); List tnm = OntologyClassConverter.toOntologyClassList(v1Disease.getTnmFindingList()); - Optional onset = toDiseaseOnset(v1Disease); - if (term.isEmpty() && stages.isEmpty() && tnm.isEmpty() && onset.isEmpty()) + if (term.isEmpty() && onset.isEmpty() && stages.isEmpty() && tnm.isEmpty()) return Optional.empty(); - return Optional.of(Disease.newBuilder() - .setTerm(term.orElse(OntologyClass.getDefaultInstance())) - .addAllDiseaseStage(stages) - .addAllClinicalTnmFinding(tnm) - .setOnset(onset.orElse(TimeElement.getDefaultInstance())) - .build()); + Disease.Builder builder = Disease.newBuilder(); + term.ifPresent(builder::setTerm); + // v1 has no excluded field, hence no builder.setExcluded(...) + if (!stages.isEmpty()) builder.addAllDiseaseStage(stages); + if (!tnm.isEmpty()) builder.addAllClinicalTnmFinding(tnm); + onset.ifPresent(builder::setOnset); + + return Optional.of(builder.build()); } - static Optional toDiseaseOnset(org.phenopackets.schema.v1.core.Disease v1Disease) { + private static Optional toDiseaseOnset(org.phenopackets.schema.v1.core.Disease v1Disease) { if (v1Disease.hasClassOfOnset()) return OntologyClassConverter.toOntologyClass(v1Disease.getClassOfOnset()) .map(onsetClass -> TimeElement.newBuilder().setOntologyClass(onsetClass).build()); diff --git a/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/EvidenceConverter.java b/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/EvidenceConverter.java index 128b6f7e4..c944edb62 100644 --- a/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/EvidenceConverter.java +++ b/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/EvidenceConverter.java @@ -22,7 +22,7 @@ static List toEvidences(List .toList(); } - static Optional toEvidence(org.phenopackets.schema.v1.core.Evidence v1Evidence) { + private static Optional toEvidence(org.phenopackets.schema.v1.core.Evidence v1Evidence) { if (v1Evidence.equals(org.phenopackets.schema.v1.core.Evidence.getDefaultInstance())) return Optional.empty(); @@ -32,9 +32,9 @@ static Optional toEvidence(org.phenopackets.schema.v1.core.Evidence v1 if (evidenceCode.isEmpty() && externalReference.isEmpty()) return Optional.empty(); - return Optional.of(Evidence.newBuilder() - .setEvidenceCode(evidenceCode.orElse(OntologyClass.getDefaultInstance())) - .setReference(externalReference.orElse(ExternalReference.getDefaultInstance())) - .build()); + Evidence.Builder builder = Evidence.newBuilder(); + evidenceCode.ifPresent(builder::setEvidenceCode); + externalReference.ifPresent(builder::setReference); + return Optional.of(builder.build()); } } diff --git a/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/PhenotypicFeatureConverter.java b/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/PhenotypicFeatureConverter.java index 4f761a37c..731ee5b91 100644 --- a/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/PhenotypicFeatureConverter.java +++ b/phenopacket-tools-converter/src/main/java/org/phenopackets/phenopackettools/converter/converters/v2/PhenotypicFeatureConverter.java @@ -78,7 +78,7 @@ static Optional toPhenotypicFeature(org.phenopackets.schema.v } private static Optional toPhenotypicFeatureOnset(org.phenopackets.schema.v1.core.PhenotypicFeature v1PhenotypicFeature) { - if (v1PhenotypicFeature.equals(TimeElement.getDefaultInstance())) + if (v1PhenotypicFeature.equals(org.phenopackets.schema.v1.core.PhenotypicFeature.getDefaultInstance())) return Optional.empty(); boolean isDefault = true; diff --git a/phenopacket-tools-converter/src/test/java/org/phenopackets/phenopackettools/converter/converters/V1ToV2ConverterTest.java b/phenopacket-tools-converter/src/test/java/org/phenopackets/phenopackettools/converter/converters/V1ToV2ConverterTest.java index 5e6d8dc8c..fc1ee8a99 100644 --- a/phenopacket-tools-converter/src/test/java/org/phenopackets/phenopackettools/converter/converters/V1ToV2ConverterTest.java +++ b/phenopacket-tools-converter/src/test/java/org/phenopackets/phenopackettools/converter/converters/V1ToV2ConverterTest.java @@ -1,6 +1,7 @@ package org.phenopackets.phenopackettools.converter.converters; import org.ga4gh.vrsatile.v1.Expression; +import org.ga4gh.vrsatile.v1.MoleculeContext; import org.ga4gh.vrsatile.v1.VariationDescriptor; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Nested; @@ -101,6 +102,7 @@ public void convertPhenopacketWithConvertingVariants() { .setSyntax("hgvs") .setValue("NM_001848.2:c.877G>A") .build()) + .setMoleculeContext(MoleculeContext.transcript) .setAllelicState(OntologyClass.newBuilder() .setId("GENO:0000135") .setLabel("heterozygous") diff --git a/phenopacket-tools-core/pom.xml b/phenopacket-tools-core/pom.xml index 8555d7569..8220af227 100644 --- a/phenopacket-tools-core/pom.xml +++ b/phenopacket-tools-core/pom.xml @@ -6,7 +6,7 @@ phenopacket-tools org.phenopackets.phenopackettools - 1.0.0-RC3 + 1.0.0 phenopacket-tools-core diff --git a/phenopacket-tools-io/pom.xml b/phenopacket-tools-io/pom.xml index 089bf7959..23b1f8e2f 100644 --- a/phenopacket-tools-io/pom.xml +++ b/phenopacket-tools-io/pom.xml @@ -6,7 +6,7 @@ phenopacket-tools org.phenopackets.phenopackettools - 1.0.0-RC3 + 1.0.0 phenopacket-tools-io diff --git a/phenopacket-tools-test/pom.xml b/phenopacket-tools-test/pom.xml index 71ed5c16e..7937f293e 100644 --- a/phenopacket-tools-test/pom.xml +++ b/phenopacket-tools-test/pom.xml @@ -5,7 +5,7 @@ phenopacket-tools org.phenopackets.phenopackettools - 1.0.0-RC3 + 1.0.0 4.0.0 diff --git a/phenopacket-tools-util/pom.xml b/phenopacket-tools-util/pom.xml index 0db1f0956..a5252cbb6 100644 --- a/phenopacket-tools-util/pom.xml +++ b/phenopacket-tools-util/pom.xml @@ -5,7 +5,7 @@ phenopacket-tools org.phenopackets.phenopackettools - 1.0.0-RC3 + 1.0.0 4.0.0 diff --git a/phenopacket-tools-util/src/main/java/module-info.java b/phenopacket-tools-util/src/main/java/module-info.java index b5ed35eac..8baadf63d 100644 --- a/phenopacket-tools-util/src/main/java/module-info.java +++ b/phenopacket-tools-util/src/main/java/module-info.java @@ -9,5 +9,6 @@ requires org.phenopackets.schema; exports org.phenopackets.phenopackettools.util.format; + exports org.phenopackets.phenopackettools.util.message; exports org.phenopackets.phenopackettools.util.print; } \ No newline at end of file diff --git a/phenopacket-tools-util/src/main/java/org/phenopackets/phenopackettools/util/message/MessageUtils.java b/phenopacket-tools-util/src/main/java/org/phenopackets/phenopackettools/util/message/MessageUtils.java new file mode 100644 index 000000000..137511d3f --- /dev/null +++ b/phenopacket-tools-util/src/main/java/org/phenopackets/phenopackettools/util/message/MessageUtils.java @@ -0,0 +1,66 @@ +package org.phenopackets.phenopackettools.util.message; + +import com.google.protobuf.MessageOrBuilder; + +import java.util.Collection; +import java.util.stream.Stream; + +/** + * A class with utility functions for working with protobuf messages. + */ +public class MessageUtils { + + private MessageUtils() { + // static utility class + } + + /** + * Find all instances of {@link T} in a given {@code message}. + *

+ * Protobuf messages are hierarchical structures where, depending on the schema, a component may be present + * at different places of the hierarchy. This function will stream all instances of the requested class. + * + * @param message protobuf message to search in + * @param clz target class + * @return a {@linkplain Stream} of all {@link T}s found in the {@code message} + * @param type of the target class + */ + @SuppressWarnings("unchecked") + public static Stream findInstancesOfType(MessageOrBuilder message, Class clz) { + Stream.Builder builder = Stream.builder(); + if (clz.isInstance(message)) { + /* + We suppress the warning regarding an unchecked cast of the message to T because we have checked + that `clz.isInstance(message)` holds. + */ + builder.add((T) message); + } + + for (Object field : message.getAllFields().values()) { + findAllInstances(field, clz, builder); + } + + return builder.build(); + } + + @SuppressWarnings("unchecked") + private static void findAllInstances(Object o, Class clz, Stream.Builder builder) { + if (clz.isInstance(o)) { + /* + We suppress the warning regarding an unchecked cast of `o` to T because we have checked + that `clz.isInstance(o)` holds. + */ + builder.add((U) o); + } else { + if (o instanceof MessageOrBuilder message) { + for (Object v : message.getAllFields().values()) { + findAllInstances(v, clz, builder); + } + } else if (o instanceof Collection collection) { + for (Object nestedField : collection) { + findAllInstances(nestedField, clz, builder); + } + } + } + } +} diff --git a/phenopacket-tools-util/src/main/java/org/phenopackets/phenopackettools/util/message/package-info.java b/phenopacket-tools-util/src/main/java/org/phenopackets/phenopackettools/util/message/package-info.java new file mode 100644 index 000000000..0d22cb63b --- /dev/null +++ b/phenopacket-tools-util/src/main/java/org/phenopackets/phenopackettools/util/message/package-info.java @@ -0,0 +1,4 @@ +/** + * Utility methods for working with protobuf messages. + */ +package org.phenopackets.phenopackettools.util.message; \ No newline at end of file diff --git a/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/format/TestResources.java b/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/TestResources.java similarity index 79% rename from phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/format/TestResources.java rename to phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/TestResources.java index fc70e3e1d..24ef11339 100644 --- a/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/format/TestResources.java +++ b/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/TestResources.java @@ -1,4 +1,4 @@ -package org.phenopackets.phenopackettools.util.format; +package org.phenopackets.phenopackettools.util; import java.nio.file.Path; diff --git a/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/format/ElementSnifferTest.java b/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/format/ElementSnifferTest.java index 153d53bd7..8b82ab72f 100644 --- a/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/format/ElementSnifferTest.java +++ b/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/format/ElementSnifferTest.java @@ -6,6 +6,7 @@ import org.phenopackets.phenopackettools.core.PhenopacketElement; import org.phenopackets.phenopackettools.core.PhenopacketFormat; import org.phenopackets.phenopackettools.core.PhenopacketSchemaVersion; +import org.phenopackets.phenopackettools.util.TestResources; import java.io.BufferedInputStream; import java.io.File; diff --git a/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/format/FormatSnifferTest.java b/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/format/FormatSnifferTest.java index 1584a31d5..462aca79b 100644 --- a/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/format/FormatSnifferTest.java +++ b/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/format/FormatSnifferTest.java @@ -3,6 +3,7 @@ import org.junit.jupiter.params.ParameterizedTest; import org.junit.jupiter.params.provider.CsvSource; import org.phenopackets.phenopackettools.core.PhenopacketFormat; +import org.phenopackets.phenopackettools.util.TestResources; import java.io.BufferedInputStream; import java.io.IOException; diff --git a/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/message/MessageUtilsTest.java b/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/message/MessageUtilsTest.java new file mode 100644 index 000000000..a87bb64b7 --- /dev/null +++ b/phenopacket-tools-util/src/test/java/org/phenopackets/phenopackettools/util/message/MessageUtilsTest.java @@ -0,0 +1,67 @@ +package org.phenopackets.phenopackettools.util.message; + +import com.google.protobuf.Message; +import com.google.protobuf.util.JsonFormat; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.phenopackets.phenopackettools.util.TestResources; +import org.phenopackets.schema.v2.Phenopacket; +import org.phenopackets.schema.v2.core.Biosample; +import org.phenopackets.schema.v2.core.OntologyClass; +import org.phenopackets.schema.v2.core.PhenotypicFeature; +import org.phenopackets.schema.v2.core.Resource; + +import java.io.BufferedReader; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.*; + +public class MessageUtilsTest { + + private static final Path TEST_DIR = TestResources.BASE_DIR.resolve("message"); + + + private static final Message.Builder COVID_PHENOPACKET = Phenopacket.newBuilder(); + + @BeforeAll + public static void beforeAll() throws IOException { + try (BufferedReader reader = Files.newBufferedReader(TEST_DIR.resolve("covid.json"))) { + JsonFormat.parser().merge(reader, COVID_PHENOPACKET); + } + } + + @Test + public void findAllOntologyClasses_PhenotypicFeatures() { + List pfs = MessageUtils.findInstancesOfType(COVID_PHENOPACKET, PhenotypicFeature.class) + .toList(); + assertThat(pfs, hasSize(8)); + List labels = pfs.stream() + .map(PhenotypicFeature::getType) + .map(OntologyClass::getLabel) + .toList(); + assertThat(labels, hasItems("Fever", "Flank pain", "Hematuria", "Stage 3 chronic kidney disease", "Myalgia", + "Diarrhea", "Dyspnea", "Acute respiratory distress syndrome")); + } + + @Test + public void findAllOntologyClasses_Resources() { + List resources = MessageUtils.findInstancesOfType(COVID_PHENOPACKET, Resource.class) + .toList(); + assertThat(resources, hasSize(2)); + List labels = resources.stream() + .map(Resource::getNamespacePrefix) + .toList(); + assertThat(labels, hasItems("NCIT", "MONDO")); + } + + @Test + public void findAllOntologyClasses_NoMatch() { + List resources = MessageUtils.findInstancesOfType(COVID_PHENOPACKET, Biosample.class) + .toList(); + assertThat(resources, is(emptyCollectionOf(Biosample.class))); + } +} \ No newline at end of file diff --git a/phenopacket-tools-util/src/test/resources/org/phenopackets/phenopackettools/util/format/covid.json b/phenopacket-tools-util/src/test/resources/org/phenopackets/phenopackettools/util/format/covid.json index 21125cb9d..52a8f2400 100644 --- a/phenopacket-tools-util/src/test/resources/org/phenopackets/phenopackettools/util/format/covid.json +++ b/phenopacket-tools-util/src/test/resources/org/phenopackets/phenopackettools/util/format/covid.json @@ -19,7 +19,7 @@ "phenotypicFeatures": [{ "type": { "id": "HP:0001945", - "label": "Fever " + "label": "Fever" }, "onset": { "timestamp": "2021-02-01T05:00:00Z" diff --git a/phenopacket-tools-util/src/test/resources/org/phenopackets/phenopackettools/util/message/covid.json b/phenopacket-tools-util/src/test/resources/org/phenopackets/phenopackettools/util/message/covid.json new file mode 100644 index 000000000..52a8f2400 --- /dev/null +++ b/phenopacket-tools-util/src/test/resources/org/phenopackets/phenopackettools/util/message/covid.json @@ -0,0 +1,317 @@ +{ + "id": "arbitrary.phenopacket.id", + "subject": { + "id": "P123542", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P70Y" + } + }, + "vitalStatus": { + "status": "DECEASED", + "causeOfDeath": { + "id": "MONDO:0100096", + "label": "COVID-19" + } + }, + "sex": "MALE" + }, + "phenotypicFeatures": [{ + "type": { + "id": "HP:0001945", + "label": "Fever" + }, + "onset": { + "timestamp": "2021-02-01T05:00:00Z" + } + }, { + "type": { + "id": "HP:0030157", + "label": "Flank pain" + }, + "onset": { + "timestamp": "2021-02-01T05:00:00Z" + } + }, { + "type": { + "id": "HP:0000790", + "label": "Hematuria" + }, + "onset": { + "timestamp": "2021-02-01T05:00:00Z" + } + }, { + "type": { + "id": "HP:0012625", + "label": "Stage 3 chronic kidney disease" + }, + "onset": { + "timestamp": "2021-02-01T05:00:00Z" + } + }, { + "type": { + "id": "HP:0003326", + "label": "Myalgia" + }, + "onset": { + "interval": { + "start": "2020-03-18T00:00:00Z", + "end": "2020-03-20T00:00:00Z" + } + } + }, { + "type": { + "id": "HP:0002014", + "label": "Diarrhea" + }, + "onset": { + "interval": { + "start": "2020-03-18T00:00:00Z", + "end": "2020-03-20T00:00:00Z" + } + } + }, { + "type": { + "id": "HP:0002094", + "label": "Dyspnea" + }, + "onset": { + "interval": { + "start": "2020-03-18T00:00:00Z", + "end": "2020-03-20T00:00:00Z" + } + } + }, { + "type": { + "id": "HP:0033677", + "label": "Acute respiratory distress syndrome" + }, + "onset": { + "timestamp": "2020-03-20T00:00:00Z" + } + }], + "measurements": [{ + "assay": { + "id": "LOINC:26474-7", + "label": "Lymphocytes [#/volume] in Blood" + }, + "value": { + "quantity": { + "unit": { + "id": "NCIT:C67245", + "label": "Thousand Cells" + }, + "value": 1.4 + } + }, + "timeObserved": { + "interval": { + "start": "2019-09-01T00:00:00Z", + "end": "2020-03-01T00:00:00Z" + } + } + }, { + "assay": { + "id": "LOINC:26474-7", + "label": "Lymphocytes [#/volume] in Blood" + }, + "value": { + "quantity": { + "unit": { + "id": "NCIT:C67245", + "label": "Thousand Cells" + }, + "value": 0.7 + } + }, + "timeObserved": { + "timestamp": "2020-03-20T00:00:00Z" + } + }], + "diseases": [{ + "term": { + "id": "MONDO:0005015", + "label": "diabetes mellitus" + }, + "excluded": true + }, { + "term": { + "id": "MONDO:0004994", + "label": "cardiomyopathy" + } + }, { + "term": { + "id": "MONDO:0100096", + "label": "COVID-19" + }, + "onset": { + "timestamp": "2020-03-17T00:00:00Z" + } + }], + "medicalActions": [{ + "procedure": { + "code": { + "id": "NCIT:C80473", + "label": "Left Ventricular Assist Device" + }, + "performed": { + "timestamp": "2016-01-01T00:00:00Z" + } + } + }, { + "treatment": { + "agent": { + "id": "NCIT:C722", + "label": "Oxygen" + }, + "routeOfAdministration": { + "id": "NCIT:C38284", + "label": "Nasal Route of Administration" + }, + "doseIntervals": [{ + "quantity": { + "unit": { + "id": "NCIT:C67388", + "label": "Liter per Minute" + }, + "value": 2.0 + }, + "scheduleFrequency": { + "id": "PATO:0000689", + "label": "continuous" + }, + "interval": { + "start": "2021-02-01T18:58:43Z", + "end": "2021-02-02T08:22:42Z" + } + }, { + "quantity": { + "unit": { + "id": "NCIT:C67388", + "label": "Liter per Minute" + }, + "value": 50.0 + }, + "scheduleFrequency": { + "id": "PATO:0000689", + "label": "continuous" + }, + "interval": { + "start": "2021-02-02T08:22:42Z", + "end": "2021-02-02T12:22:42Z" + } + }] + } + }, { + "treatment": { + "agent": { + "id": "CHEBI:41879", + "label": "dexamethasone" + }, + "doseIntervals": [{ + "quantity": { + "unit": { + "id": "UO:0000022", + "label": "milligram" + }, + "value": 6.0 + }, + "scheduleFrequency": { + "id": "NCIT:C125004", + "label": "Once Daily" + }, + "interval": { + "start": "2020-03-20T00:00:00Z", + "end": "2020-03-30T00:00:00Z" + } + }] + } + }, { + "procedure": { + "code": { + "id": "NCIT:C116648", + "label": "Tracheal Intubation" + }, + "performed": { + "timestamp": "2020-03-22T00:00:00Z" + } + } + }, { + "treatment": { + "agent": { + "id": "NCIT:C722", + "label": "Oxygen" + }, + "routeOfAdministration": { + "id": "NCIT:C50254", + "label": "Positive end Expiratory Pressure Valve Device" + }, + "doseIntervals": [{ + "quantity": { + "unit": { + "id": "NCIT:C91060", + "label": "Centimeters of Water" + }, + "value": 14.0 + }, + "scheduleFrequency": { + "id": "PATO:0000689", + "label": "continuous" + }, + "interval": { + "start": "2020-03-22T00:00:00Z", + "end": "2020-03-28T00:00:00Z" + } + }] + } + }, { + "treatment": { + "agent": { + "id": "NCIT:C84217", + "label": "Tocilizumab" + }, + "doseIntervals": [{ + "quantity": { + "unit": { + "id": "NCIT:C124458", + "label": "Milligram per Kilogram per Dose" + }, + "value": 4.0 + }, + "scheduleFrequency": { + "id": "NCIT:C64529", + "label": "Every Four Weeks" + }, + "interval": { + "start": "2020-03-24T00:00:00Z", + "end": "2020-03-28T00:00:00Z" + } + }] + } + }], + "metaData": { + "created": "2021-08-17T00:00:00Z", + "createdBy": "anonymous biocurator", + "resources": [{ + "id": "ncit", + "name": "NCI Thesaurus", + "url": "http://purl.obolibrary.org/obo/ncit.owl", + "version": "2019-11-26", + "namespacePrefix": "NCIT", + "iriPrefix": "http://purl.obolibrary.org/obo/NCIT_" + }, { + "id": "mondo", + "name": "Mondo Disease Ontology", + "url": "http://purl.obolibrary.org/obo/mondo.obo", + "version": "2021-11-26", + "namespacePrefix": "MONDO", + "iriPrefix": "http://purl.obolibrary.org/obo/MONDO_" + }], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [{ + "id": "DOI:10.1016/j.jaccas.2020.04.001", + "reference": "PMID:32292915", + "description": "The Imperfect Cytokine Storm: Severe COVID-19 With ARDS in a Patient on Durable LVAD Support" + }] + } +} \ No newline at end of file diff --git a/phenopacket-tools-validator-core/pom.xml b/phenopacket-tools-validator-core/pom.xml index f9790dd66..7d074cf7c 100644 --- a/phenopacket-tools-validator-core/pom.xml +++ b/phenopacket-tools-validator-core/pom.xml @@ -7,7 +7,7 @@ org.phenopackets.phenopackettools phenopacket-tools - 1.0.0-RC3 + 1.0.0 phenopacket-tools-validator-core @@ -37,6 +37,11 @@ org.monarchinitiative.phenol phenol-core + + com.fasterxml.jackson.core + jackson-databind + provided + org.monarchinitiative.phenol diff --git a/phenopacket-tools-validator-core/src/main/java/module-info.java b/phenopacket-tools-validator-core/src/main/java/module-info.java index 75fe7dc85..8fbcfef45 100644 --- a/phenopacket-tools-validator-core/src/main/java/module-info.java +++ b/phenopacket-tools-validator-core/src/main/java/module-info.java @@ -14,6 +14,8 @@ requires org.monarchinitiative.phenol.core; requires org.phenopackets.schema; + requires com.fasterxml.jackson.databind; + // There are many places where the protobuf classes are part of the API, e.g. as type parameter // of PhenopacketFormatConverter. requires transitive com.google.protobuf; diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidationResult.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidationResult.java index f8193cd69..95de51490 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidationResult.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidationResult.java @@ -1,8 +1,14 @@ package org.phenopackets.phenopackettools.validator.core; +import com.fasterxml.jackson.annotation.JsonGetter; +import com.fasterxml.jackson.annotation.JsonPropertyOrder; +import com.fasterxml.jackson.databind.annotation.JsonSerialize; + /** * {@code ValidationResult} contains results of a single validation step performed by a {@link PhenopacketValidator}. */ +@JsonSerialize(as = ValidationResult.class) +@JsonPropertyOrder({"validatorInfo", "level", "category", "message"}) public interface ValidationResult { /** @@ -36,21 +42,25 @@ static ValidationResult of(ValidatorInfo validatorInfo, /** * @return information about the validator used to create the {@link ValidationResult}. */ + @JsonGetter ValidatorInfo validatorInfo(); /** * @return level of the validation */ + @JsonGetter ValidationLevel level(); /** * @return an error category. */ + @JsonGetter String category(); /** * @return specific error message */ + @JsonGetter String message(); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidationResults.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidationResults.java index da4aa6334..4bb747a1b 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidationResults.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidationResults.java @@ -1,5 +1,10 @@ package org.phenopackets.phenopackettools.validator.core; +import com.fasterxml.jackson.annotation.JsonGetter; +import com.fasterxml.jackson.annotation.JsonIgnore; +import com.fasterxml.jackson.annotation.JsonPropertyOrder; +import com.fasterxml.jackson.databind.annotation.JsonSerialize; + import java.util.ArrayList; import java.util.List; @@ -11,6 +16,8 @@ * The results contain info regarding which validators were run ({@link #validators()}) and the issues found during * the validation ({@link #validationResults()}). */ +@JsonSerialize(as = ValidationResults.class) +@JsonPropertyOrder({"validators", "validationResults"}) public interface ValidationResults { static ValidationResults of(List validators, @@ -31,16 +38,19 @@ static Builder builder() { /** * @return a list of {@link ValidatorInfo} representing validators applied to the top-level element. */ + @JsonGetter List validators(); /** * @return a list of {@link ValidationResult} representing the issues found in the top-level element. */ + @JsonGetter List validationResults(); /** * @return {@code true} if no issues have been found and the validated item is valid. */ + @JsonIgnore default boolean isValid() { return validationResults().isEmpty(); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidatorInfo.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidatorInfo.java index 3714b4ae6..50b1c5eb4 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidatorInfo.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/ValidatorInfo.java @@ -1,8 +1,14 @@ package org.phenopackets.phenopackettools.validator.core; +import com.fasterxml.jackson.annotation.JsonGetter; +import com.fasterxml.jackson.annotation.JsonPropertyOrder; +import com.fasterxml.jackson.databind.annotation.JsonSerialize; + /** * A description of a {@link PhenopacketValidator}. */ +@JsonSerialize(as = ValidatorInfo.class) +@JsonPropertyOrder({"validatorId", "validatorName", "description"}) public interface ValidatorInfo { static ValidatorInfo baseSyntaxValidation() { @@ -25,16 +31,19 @@ static ValidatorInfo of(String validatorId, String validatorName, String descrip /** * @return string with a unique validator ID. */ + @JsonGetter String validatorId(); /** * @return human-friendly validator name. */ + @JsonGetter String validatorName(); /** * @return brief description of the validation provided by the validator. */ + @JsonGetter String description(); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/metadata/MetaDataValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/metadata/MetaDataValidator.java index 851e9673a..30dbea493 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/metadata/MetaDataValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/metadata/MetaDataValidator.java @@ -1,6 +1,7 @@ package org.phenopackets.phenopackettools.validator.core.metadata; import com.google.protobuf.MessageOrBuilder; +import org.phenopackets.phenopackettools.util.message.MessageUtils; import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator; import org.phenopackets.phenopackettools.validator.core.ValidationResult; import org.phenopackets.phenopackettools.validator.core.ValidatorInfo; @@ -11,7 +12,6 @@ import org.phenopackets.schema.v2.core.OntologyClass; import org.phenopackets.schema.v2.core.Resource; -import java.util.Collection; import java.util.List; import java.util.Optional; import java.util.Set; @@ -40,7 +40,7 @@ public List validate(T component) { Set validOntologyPrefixes = getOntologyNamespacePrefixes(metaData.get()); - return streamOfAllInstancesOfType(component, OntologyClass.class).sequential() + return MessageUtils.findInstancesOfType(component, OntologyClass.class).sequential() .flatMap(oc -> { // Curie should be something like `HP:1234567` or `NCIT_C123457`. String curie = oc.getId(); @@ -79,45 +79,6 @@ private static Set getOntologyNamespacePrefixes(MetaData metaData) { .collect(Collectors.toSet()); } - @SuppressWarnings("unchecked") - private static Stream streamOfAllInstancesOfType(MessageOrBuilder message, Class clz) { - Stream.Builder builder = Stream.builder(); - if (clz.isInstance(message)) { - /* - We suppress the warning regarding an unchecked cast of the message to T because we have checked - that `clz.isInstance(message)` holds. - */ - builder.add((U) message); - } - - for (Object field : message.getAllFields().values()) { - findAllInstances(field, clz, builder); - } - - return builder.build(); - } - - @SuppressWarnings("unchecked") - private static void findAllInstances(Object o, Class clz, Stream.Builder builder) { - if (clz.isInstance(o)) { - /* - We suppress the warning regarding an unchecked cast of `o` to T because we have checked - that `clz.isInstance(o)` holds. - */ - builder.add((U) o); - } else { - if (o instanceof MessageOrBuilder message) { - for (Object v : message.getAllFields().values()) { - findAllInstances(v, clz, builder); - } - } else if (o instanceof Collection collection) { - for (Object nestedField : collection) { - findAllInstances(nestedField, clz, builder); - } - } - } - } - static class PhenopacketMetaDataValidator extends MetaDataValidator { @Override diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/HpoPhenotypeValidators.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/HpoPhenotypeValidators.java index 40da8cb80..e23e1b03c 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/HpoPhenotypeValidators.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/HpoPhenotypeValidators.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.validator.core.phenotype; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.monarchinitiative.phenol.ontology.data.TermId; import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator; import org.phenopackets.phenopackettools.validator.core.phenotype.ancestry.CohortHpoAncestryValidator; @@ -12,6 +12,7 @@ import org.phenopackets.phenopackettools.validator.core.phenotype.primary.CohortHpoPhenotypeValidator; import org.phenopackets.phenopackettools.validator.core.phenotype.primary.FamilyHpoPhenotypeValidator; import org.phenopackets.phenopackettools.validator.core.phenotype.primary.PhenopacketHpoPhenotypeValidator; +import org.phenopackets.phenopackettools.validator.core.phenotype.uniq.HpoUniqueValidator; import org.phenopackets.schema.v2.*; import java.util.Collection; @@ -26,39 +27,39 @@ private HpoPhenotypeValidators() { } /** - * Get {@link PhenopacketValidator} to validate {@link Phenopacket} using provided {@link Ontology}. + * Get {@link PhenopacketValidator} to validate {@link Phenopacket} using provided {@link MinimalOntology}. * * @param hpo HPO ontology - * @deprecated use {@link Primary#phenopacketHpoPhenotypeValidator(Ontology)} instead + * @deprecated use {@link Primary#phenopacketHpoPhenotypeValidator(MinimalOntology)} instead */ // REMOVE(v1.0.0) @Deprecated(forRemoval = true) - public static PhenopacketValidator phenopacketHpoPhenotypeValidator(Ontology hpo) { + public static PhenopacketValidator phenopacketHpoPhenotypeValidator(MinimalOntology hpo) { return Primary.phenopacketHpoPhenotypeValidator(hpo); } /** - * Get {@link PhenopacketValidator} for validate {@link Family} using provided {@link Ontology}. + * Get {@link PhenopacketValidator} for validate {@link Family} using provided {@link MinimalOntology}. * * @param hpo HPO ontology - * @deprecated use {@link Primary#familyHpoPhenotypeValidator(Ontology)} instead + * @deprecated use {@link Primary#familyHpoPhenotypeValidator(MinimalOntology)} instead */ // REMOVE(v1.0.0) @Deprecated(forRemoval = true) - public static PhenopacketValidator familyHpoPhenotypeValidator(Ontology hpo) { + public static PhenopacketValidator familyHpoPhenotypeValidator(MinimalOntology hpo) { return Primary.familyHpoPhenotypeValidator(hpo); } /** - * Get {@link PhenopacketValidator} for performing primary validation {@link Cohort} using provided {@link Ontology}, + * Get {@link PhenopacketValidator} for performing primary validation {@link Cohort} using provided {@link MinimalOntology}, * as described in {@link org.phenopackets.phenopackettools.validator.core.phenotype.primary.AbstractHpoPhenotypeValidator}. * * @param hpo HPO ontology - * @deprecated use {@link Primary#cohortHpoPhenotypeValidator(Ontology)} instead + * @deprecated use {@link Primary#cohortHpoPhenotypeValidator(MinimalOntology)} instead */ // REMOVE(v1.0.0) @Deprecated(forRemoval = true) - public static PhenopacketValidator cohortHpoPhenotypeValidator(Ontology hpo) { + public static PhenopacketValidator cohortHpoPhenotypeValidator(MinimalOntology hpo) { return Primary.cohortHpoPhenotypeValidator(hpo); } @@ -69,30 +70,30 @@ public static PhenopacketValidator cohortHpoPhenotypeValidator( */ public static class Primary { /** - * Get {@link PhenopacketValidator} to validate {@link Phenopacket} using provided {@link Ontology}. + * Get {@link PhenopacketValidator} to validate {@link Phenopacket} using provided {@link MinimalOntology}. * * @param hpo HPO ontology */ - public static PhenopacketValidator phenopacketHpoPhenotypeValidator(Ontology hpo) { + public static PhenopacketValidator phenopacketHpoPhenotypeValidator(MinimalOntology hpo) { return new PhenopacketHpoPhenotypeValidator(hpo); } /** - * Get {@link PhenopacketValidator} for validate {@link Family} using provided {@link Ontology}. + * Get {@link PhenopacketValidator} for validate {@link Family} using provided {@link MinimalOntology}. * * @param hpo HPO ontology */ - public static PhenopacketValidator familyHpoPhenotypeValidator(Ontology hpo) { + public static PhenopacketValidator familyHpoPhenotypeValidator(MinimalOntology hpo) { return new FamilyHpoPhenotypeValidator(hpo); } /** - * Get {@link PhenopacketValidator} for performing primary validation {@link Cohort} using provided {@link Ontology}, + * Get {@link PhenopacketValidator} for performing primary validation {@link Cohort} using provided {@link MinimalOntology}, * as described in {@link org.phenopackets.phenopackettools.validator.core.phenotype.primary.AbstractHpoPhenotypeValidator}. * * @param hpo HPO ontology */ - public static PhenopacketValidator cohortHpoPhenotypeValidator(Ontology hpo) { + public static PhenopacketValidator cohortHpoPhenotypeValidator(MinimalOntology hpo) { return new CohortHpoPhenotypeValidator(hpo); } } @@ -115,29 +116,29 @@ private Ancestry() { } /** - * Get {@link PhenopacketValidator} to validate ancestry {@link Phenopacket} using provided {@link Ontology}. + * Get {@link PhenopacketValidator} to validate ancestry {@link Phenopacket} using provided {@link MinimalOntology}. * * @param hpo HPO ontology */ - public static PhenopacketValidator phenopacketHpoAncestryValidator(Ontology hpo) { + public static PhenopacketValidator phenopacketHpoAncestryValidator(MinimalOntology hpo) { return new PhenopacketHpoAncestryValidator(hpo); } /** - * Get {@link PhenopacketValidator} to validate ancestry {@link Family} using provided {@link Ontology}. + * Get {@link PhenopacketValidator} to validate ancestry {@link Family} using provided {@link MinimalOntology}. * * @param hpo HPO ontology */ - public static PhenopacketValidator familyHpoAncestryValidator(Ontology hpo) { + public static PhenopacketValidator familyHpoAncestryValidator(MinimalOntology hpo) { return new FamilyHpoAncestryValidator(hpo); } /** - * Get {@link PhenopacketValidator} to validate ancestry {@link Cohort} using provided {@link Ontology}. + * Get {@link PhenopacketValidator} to validate ancestry {@link Cohort} using provided {@link MinimalOntology}. * * @param hpo HPO ontology */ - public static PhenopacketValidator cohortHpoAncestryValidator(Ontology hpo) { + public static PhenopacketValidator cohortHpoAncestryValidator(MinimalOntology hpo) { return new CohortHpoAncestryValidator(hpo); } } @@ -160,48 +161,84 @@ private OrganSystem() { /** * Get {@link PhenopacketValidator} to validate annotation of organ systems in a {@link Phenopacket} - * using provided {@link Ontology} and a collection of organ system {@link TermId}s. + * using provided {@link MinimalOntology} and a collection of organ system {@link TermId}s. *

- * NOTE: the organ system {@link TermId} that is absent from the {@link Ontology} is disregarded + * NOTE: the organ system {@link TermId} that is absent from the {@link MinimalOntology} is disregarded * and not used for validation. * * @param hpo HPO ontology * @param organSystemTermIds a collection of HPO {@link TermId}s corresponding to organ systems. */ - public static PhenopacketValidator phenopacketHpoOrganSystemValidator(Ontology hpo, + public static PhenopacketValidator phenopacketHpoOrganSystemValidator(MinimalOntology hpo, Collection organSystemTermIds) { return new PhenopacketHpoOrganSystemValidator(hpo, organSystemTermIds); } /** * Get {@link PhenopacketValidator} to validate annotation of organ systems in a {@link Family} - * using provided {@link Ontology} and a collection of organ system {@link TermId}s. + * using provided {@link MinimalOntology} and a collection of organ system {@link TermId}s. *

- * NOTE: the organ system {@link TermId} that is absent from the {@link Ontology} is disregarded + * NOTE: the organ system {@link TermId} that is absent from the {@link MinimalOntology} is disregarded * and not used for validation. * * @param hpo HPO ontology * @param organSystemTermIds a collection of HPO {@link TermId}s corresponding to organ systems. */ - public static PhenopacketValidator familyHpoOrganSystemValidator(Ontology hpo, + public static PhenopacketValidator familyHpoOrganSystemValidator(MinimalOntology hpo, Collection organSystemTermIds) { return new FamilyHpoOrganSystemValidator(hpo, organSystemTermIds); } /** * Get {@link PhenopacketValidator} to validate annotation of organ systems in a {@link Cohort} - * using provided {@link Ontology} and a collection of organ system {@link TermId}s. + * using provided {@link MinimalOntology} and a collection of organ system {@link TermId}s. *

- * NOTE: the organ system {@link TermId} that is absent from the {@link Ontology} is disregarded + * NOTE: the organ system {@link TermId} that is absent from the {@link MinimalOntology} is disregarded * and not used for validation. * * @param hpo HPO ontology * @param organSystemTermIds a collection of HPO {@link TermId}s corresponding to organ systems. */ - public static PhenopacketValidator cohortHpoOrganSystemValidator(Ontology hpo, + public static PhenopacketValidator cohortHpoOrganSystemValidator(MinimalOntology hpo, Collection organSystemTermIds) { return new CohortHpoOrganSystemValidator(hpo, organSystemTermIds); } } + /** + * A static factory class for providing {@link org.phenopackets.phenopackettools.validator.core.PhenopacketValidator}s + * that check if HPO terms of the Phenopacket schema elements are unique - specified only once. + */ + public static class Unique { + private Unique() { + } + + /** + * Get {@link PhenopacketValidator} to validate {@link Phenopacket} using provided ontology. + * + * @param hpo HPO ontology + */ + public static PhenopacketValidator phenopacketValidator(MinimalOntology hpo) { + return HpoUniqueValidator.phenopacketValidator(hpo); + } + + /** + * Get {@link PhenopacketValidator} to validate {@link Cohort} using provided ontology. + * + * @param hpo HPO ontology + */ + public static PhenopacketValidator cohortValidator(MinimalOntology hpo) { + return HpoUniqueValidator.cohortValidator(hpo); + } + + /** + * Get {@link PhenopacketValidator} to validate {@link Family} using provided ontology. + * + * @param hpo HPO ontology + */ + public static PhenopacketValidator familyValidator(MinimalOntology hpo) { + return HpoUniqueValidator.familyValidator(hpo); + } + } + } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/AbstractHpoAncestryValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/AbstractHpoAncestryValidator.java index 4da56932e..a074a2e40 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/AbstractHpoAncestryValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/AbstractHpoAncestryValidator.java @@ -1,8 +1,7 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.ancestry; import com.google.protobuf.MessageOrBuilder; -import org.monarchinitiative.phenol.ontology.algo.OntologyAlgorithm; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.monarchinitiative.phenol.ontology.data.Term; import org.monarchinitiative.phenol.ontology.data.TermId; import org.phenopackets.phenopackettools.validator.core.ValidationResult; @@ -16,6 +15,7 @@ import org.slf4j.LoggerFactory; import java.util.*; +import java.util.stream.Collectors; import java.util.stream.Stream; /** @@ -39,10 +39,13 @@ public abstract class AbstractHpoAncestryValidator e "HPO ancestry phenotypic feature validator", "Validate that phenopacket does not contain an HPO term and its ancestor based on the provided HPO"); private static final String APR_VIOLATION = "Violation of the annotation propagation rule"; - private static final String UNKNOWN = "UNKNOWN_NAME"; - AbstractHpoAncestryValidator(Ontology hpo) { + private final Set obsoleteTermIds; + + AbstractHpoAncestryValidator(MinimalOntology hpo) { super(hpo); + this.obsoleteTermIds = hpo.obsoleteTermIdsStream() + .collect(Collectors.toSet()); } @Override @@ -67,12 +70,12 @@ private Stream validatePhenopacketPhenotypicFeatures(String id // Check that the component does not contain both observed term and its ancestor. for (TermId observed : featuresByExclusion.observedPhenotypicFeatures()) { - if (isObsoleteTermId(observed)) { + if (obsoleteTermIds.contains(observed)) { LOGGER.debug("Ignoring unknown/obsolete term ID {}", observed.getValue()); continue; } - for (TermId ancestor : OntologyAlgorithm.getAncestorTerms(hpo, observed, false)) { + for (TermId ancestor : hpo.graph().getAncestors(observed, false)) { if (featuresByExclusion.observedPhenotypicFeatures().contains(ancestor)) results.add(constructResultForAnObservedTerm(id, observed, ancestor, false)); if (featuresByExclusion.excludedPhenotypicFeatures().contains(ancestor)) @@ -82,15 +85,12 @@ private Stream validatePhenopacketPhenotypicFeatures(String id // Check that the component does not have negated descendant for (TermId excluded : featuresByExclusion.excludedPhenotypicFeatures()) { - if (isObsoleteTermId(excluded)) { + if (obsoleteTermIds.contains(excluded)) { LOGGER.debug("Ignoring unknown/obsolete term ID {}", excluded.getValue()); continue; } - for (TermId child : OntologyAlgorithm.getDescendents(hpo, excluded)) { - if (child.equals(excluded)) - // skip the parent term - continue; + for (TermId child : hpo.graph().getDescendants(excluded, false)) { if (featuresByExclusion.excludedPhenotypicFeatures().contains(child)) results.add(constructResultForAnExcludedTerm(id, excluded, child)); } @@ -99,15 +99,13 @@ private Stream validatePhenopacketPhenotypicFeatures(String id return results.build(); } - private boolean isObsoleteTermId(TermId termId) { - return hpo.getObsoleteTermIds().contains(termId); - } - private ValidationResult constructResultForAnObservedTerm(String id, TermId observedId, TermId ancestorId, boolean ancestorIsExcluded) { - Term observedTerm = hpo.getTermMap().get(observedId); - String observedTermName = observedTerm == null ? UNKNOWN : observedTerm.getName(); - Term ancestorTerm = hpo.getTermMap().get(ancestorId); - String ancestorTermName = ancestorTerm == null ? UNKNOWN : ancestorTerm.getName(); + String observedTermName = hpo.termForTermId(observedId) + .map(Term::getName) + .orElse(UNKNOWN); + String ancestorTermName = hpo.termForTermId(ancestorId) + .map(Term::getName) + .orElse(UNKNOWN); String message; if (ancestorIsExcluded) message = "Phenotypic features of %s must not contain both an observed term (%s, %s) and an excluded ancestor (%s, %s)".formatted( @@ -120,10 +118,12 @@ private ValidationResult constructResultForAnObservedTerm(String id, TermId obse } private ValidationResult constructResultForAnExcludedTerm(String id, TermId excluded, TermId child) { - Term excludedTerm = hpo.getTermMap().get(excluded); - String excludedTermName = excludedTerm == null ? UNKNOWN : excludedTerm.getName(); - Term childTerm = hpo.getTermMap().get(child); - String childTermName = childTerm == null ? UNKNOWN : childTerm.getName(); + String excludedTermName = hpo.termForTermId(excluded) + .map(Term::getName) + .orElse(UNKNOWN); + String childTermName = hpo.termForTermId(child) + .map(Term::getName) + .orElse(UNKNOWN); String message = "Phenotypic features of %s must not contain both an excluded term (%s, %s) and an excluded child (%s, %s)".formatted( id, excludedTermName, excluded.getValue(), childTermName, child.getValue()); diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/CohortHpoAncestryValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/CohortHpoAncestryValidator.java index c68a35175..1f1d9bbc8 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/CohortHpoAncestryValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/CohortHpoAncestryValidator.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.ancestry; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.schema.v2.CohortOrBuilder; import org.phenopackets.schema.v2.PhenopacketOrBuilder; @@ -8,7 +8,7 @@ public class CohortHpoAncestryValidator extends AbstractHpoAncestryValidator { - public CohortHpoAncestryValidator(Ontology hpo) { + public CohortHpoAncestryValidator(MinimalOntology hpo) { super(hpo); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/FamilyHpoAncestryValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/FamilyHpoAncestryValidator.java index 66ba7e88b..57a9d3848 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/FamilyHpoAncestryValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/FamilyHpoAncestryValidator.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.ancestry; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.schema.v2.FamilyOrBuilder; import org.phenopackets.schema.v2.Phenopacket; import org.phenopackets.schema.v2.PhenopacketOrBuilder; @@ -9,7 +9,7 @@ public class FamilyHpoAncestryValidator extends AbstractHpoAncestryValidator { - public FamilyHpoAncestryValidator(Ontology hpo) { + public FamilyHpoAncestryValidator(MinimalOntology hpo) { super(hpo); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/PhenopacketHpoAncestryValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/PhenopacketHpoAncestryValidator.java index b23ca49a9..3e87d72a1 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/PhenopacketHpoAncestryValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/ancestry/PhenopacketHpoAncestryValidator.java @@ -1,13 +1,13 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.ancestry; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.schema.v2.PhenopacketOrBuilder; import java.util.stream.Stream; public class PhenopacketHpoAncestryValidator extends AbstractHpoAncestryValidator { - public PhenopacketHpoAncestryValidator(Ontology hpo) { + public PhenopacketHpoAncestryValidator(MinimalOntology hpo) { super(hpo); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/base/BaseHpoValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/base/BaseHpoValidator.java index 529569f4e..321df50a8 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/base/BaseHpoValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/base/BaseHpoValidator.java @@ -1,7 +1,7 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.base; import com.google.protobuf.MessageOrBuilder; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator; import org.phenopackets.schema.v2.PhenopacketOrBuilder; @@ -9,10 +9,12 @@ public abstract class BaseHpoValidator implements PhenopacketValidator { - protected final Ontology hpo; + protected static final String UNKNOWN = "UNKNOWN_NAME"; + + protected final MinimalOntology hpo; protected final String hpoVersion; - protected BaseHpoValidator(Ontology hpo) { + protected BaseHpoValidator(MinimalOntology hpo) { this.hpo = Objects.requireNonNull(hpo); this.hpoVersion = hpo.version().orElse("UNKNOWN"); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/AbstractOrganSystemValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/AbstractOrganSystemValidator.java index 2c1fff7c9..020fa6bfb 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/AbstractOrganSystemValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/AbstractOrganSystemValidator.java @@ -1,8 +1,7 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.orgsys; import com.google.protobuf.MessageOrBuilder; -import org.monarchinitiative.phenol.ontology.algo.OntologyAlgorithm; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.monarchinitiative.phenol.ontology.data.Term; import org.monarchinitiative.phenol.ontology.data.TermId; import org.phenopackets.phenopackettools.validator.core.ValidationResult; @@ -41,7 +40,7 @@ public abstract class AbstractOrganSystemValidator e protected final List organSystemTermIds; - protected AbstractOrganSystemValidator(Ontology hpo, + protected AbstractOrganSystemValidator(MinimalOntology hpo, Collection organSystemTermIds) { super(hpo); this.organSystemTermIds = Objects.requireNonNull(organSystemTermIds).stream() @@ -51,9 +50,9 @@ protected AbstractOrganSystemValidator(Ontology hpo, .toList(); } - private static Predicate organSystemTermIdIsInOntology(Ontology hpo) { + private static Predicate organSystemTermIdIsInOntology(MinimalOntology hpo) { return organSystemTermId -> { - if (hpo.containsTerm(organSystemTermId)) { + if (hpo.termForTermId(organSystemTermId).isPresent()) { return true; } else { LOGGER.warn("{} is not present in the ontology", organSystemTermId.getValue()); @@ -90,13 +89,16 @@ private Stream checkPhenotypicFeatures(PhenopacketOrBuilder ph // Check if we have at least one observed annotation for the organ system. for (TermId pf : featuresByExclusion.observedPhenotypicFeatures()) { - if (OntologyAlgorithm.existsPath(hpo, pf, organSystemId)) { + if (hpo.graph().existsPath(pf, organSystemId)) continue organSystemLoop; // It only takes one termId to annotate an organ system. - } } + // We know that the organSystemId is in the HPO because we check the organ system ID presence + // in the constructor. + //noinspection OptionalGetWithoutIsPresent + Term organSystem = hpo.termForTermId(organSystemId).get(); + // The organSystemId is neither annotated nor excluded. We report a validation error. - Term organSystem = hpo.getTermMap().get(organSystemId); ValidationResult result = ValidationResult.error(VALIDATOR_INFO, MISSING_ORGAN_SYSTEM_CATEGORY, "Missing annotation for %s [%s]%s" diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/CohortHpoOrganSystemValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/CohortHpoOrganSystemValidator.java index 96bea28ba..8eabd7bfb 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/CohortHpoOrganSystemValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/CohortHpoOrganSystemValidator.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.orgsys; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.monarchinitiative.phenol.ontology.data.TermId; import org.phenopackets.schema.v2.CohortOrBuilder; import org.phenopackets.schema.v2.PhenopacketOrBuilder; @@ -10,7 +10,7 @@ public class CohortHpoOrganSystemValidator extends AbstractOrganSystemValidator { - public CohortHpoOrganSystemValidator(Ontology hpo, Collection organSystemTermIds) { + public CohortHpoOrganSystemValidator(MinimalOntology hpo, Collection organSystemTermIds) { super(hpo, organSystemTermIds); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/FamilyHpoOrganSystemValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/FamilyHpoOrganSystemValidator.java index 7edf20dfc..dddae345c 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/FamilyHpoOrganSystemValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/FamilyHpoOrganSystemValidator.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.orgsys; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.monarchinitiative.phenol.ontology.data.TermId; import org.phenopackets.schema.v2.FamilyOrBuilder; import org.phenopackets.schema.v2.PhenopacketOrBuilder; @@ -10,7 +10,7 @@ public class FamilyHpoOrganSystemValidator extends AbstractOrganSystemValidator { - public FamilyHpoOrganSystemValidator(Ontology hpo, Collection organSystemTermIds) { + public FamilyHpoOrganSystemValidator(MinimalOntology hpo, Collection organSystemTermIds) { super(hpo, organSystemTermIds); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/PhenopacketHpoOrganSystemValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/PhenopacketHpoOrganSystemValidator.java index d4db9e81d..67ae16ca3 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/PhenopacketHpoOrganSystemValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/orgsys/PhenopacketHpoOrganSystemValidator.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.orgsys; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.monarchinitiative.phenol.ontology.data.TermId; import org.phenopackets.schema.v2.PhenopacketOrBuilder; @@ -9,7 +9,7 @@ public class PhenopacketHpoOrganSystemValidator extends AbstractOrganSystemValidator { - public PhenopacketHpoOrganSystemValidator(Ontology hpo, + public PhenopacketHpoOrganSystemValidator(MinimalOntology hpo, Collection organSystemTerms) { super(hpo, organSystemTerms); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/AbstractHpoPhenotypeValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/AbstractHpoPhenotypeValidator.java index d75cfc7fb..95ce0f39a 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/AbstractHpoPhenotypeValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/AbstractHpoPhenotypeValidator.java @@ -2,13 +2,15 @@ import com.google.protobuf.MessageOrBuilder; import org.monarchinitiative.phenol.base.PhenolRuntimeException; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; +import org.monarchinitiative.phenol.ontology.data.Term; import org.monarchinitiative.phenol.ontology.data.TermId; import org.phenopackets.phenopackettools.validator.core.*; import org.phenopackets.phenopackettools.validator.core.phenotype.base.BaseHpoValidator; import org.phenopackets.schema.v2.PhenopacketOrBuilder; import org.phenopackets.schema.v2.core.PhenotypicFeature; +import java.util.Optional; import java.util.stream.Stream; public abstract class AbstractHpoPhenotypeValidator extends BaseHpoValidator { @@ -20,7 +22,7 @@ public abstract class AbstractHpoPhenotypeValidator private static final String INVALID_TERM_ID = "Invalid TermId"; private static final String OBSOLETED_TERM_ID = "Obsoleted TermId"; - public AbstractHpoPhenotypeValidator(Ontology hpo) { + public AbstractHpoPhenotypeValidator(MinimalOntology hpo) { super(hpo); } @@ -43,7 +45,8 @@ protected Stream checkPhenotypeFeature(PhenopacketOr } if (termId.getPrefix().equals("HP")) { // Check if the HPO contains the term. - if (!hpo.containsTerm(termId)) { + Optional term = hpo.termForTermId(termId); + if (term.isEmpty()) { String idSummary = summarizePhenopacketAndIndividualId(phenopacket); String msg = "%s%s not found in %s".formatted(termId.getValue(), idSummary, hpoVersion); return Stream.of( @@ -52,7 +55,7 @@ protected Stream checkPhenotypeFeature(PhenopacketOr } // Check if the `termId` is a primary ID. // If not, this is a warning. - TermId primaryId = hpo.getPrimaryTermId(termId); + TermId primaryId = term.get().id(); if (!primaryId.equals(termId)) { String idSummary = summarizePhenopacketAndIndividualId(phenopacket); String msg = "Using obsolete id (%s) instead of current primary id (%s)%s".formatted( diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/CohortHpoPhenotypeValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/CohortHpoPhenotypeValidator.java index 0642f21e2..b7beff122 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/CohortHpoPhenotypeValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/CohortHpoPhenotypeValidator.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.primary; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.phenopackettools.validator.core.ValidationResult; import org.phenopackets.schema.v2.CohortOrBuilder; import org.phenopackets.schema.v2.Phenopacket; @@ -11,7 +11,7 @@ public class CohortHpoPhenotypeValidator extends AbstractHpoPhenotypeValidator { - public CohortHpoPhenotypeValidator(Ontology hpo) { + public CohortHpoPhenotypeValidator(MinimalOntology hpo) { super(hpo); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/FamilyHpoPhenotypeValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/FamilyHpoPhenotypeValidator.java index 65beef4e4..179754fba 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/FamilyHpoPhenotypeValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/FamilyHpoPhenotypeValidator.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.primary; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.phenopackettools.validator.core.ValidationResult; import org.phenopackets.schema.v2.FamilyOrBuilder; import org.phenopackets.schema.v2.Phenopacket; @@ -11,7 +11,7 @@ public class FamilyHpoPhenotypeValidator extends AbstractHpoPhenotypeValidator { - public FamilyHpoPhenotypeValidator(Ontology hpo) { + public FamilyHpoPhenotypeValidator(MinimalOntology hpo) { super(hpo); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/PhenopacketHpoPhenotypeValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/PhenopacketHpoPhenotypeValidator.java index 7b43a10e7..dcd60bf63 100644 --- a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/PhenopacketHpoPhenotypeValidator.java +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/primary/PhenopacketHpoPhenotypeValidator.java @@ -1,6 +1,6 @@ package org.phenopackets.phenopackettools.validator.core.phenotype.primary; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.phenopackettools.validator.core.ValidationResult; import org.phenopackets.schema.v2.PhenopacketOrBuilder; import org.phenopackets.schema.v2.core.PhenotypicFeature; @@ -10,7 +10,7 @@ public class PhenopacketHpoPhenotypeValidator extends AbstractHpoPhenotypeValidator { - public PhenopacketHpoPhenotypeValidator(Ontology hpo) { + public PhenopacketHpoPhenotypeValidator(MinimalOntology hpo) { super(hpo); } diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/uniq/HpoUniqueValidator.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/uniq/HpoUniqueValidator.java new file mode 100644 index 000000000..895ec1b39 --- /dev/null +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/uniq/HpoUniqueValidator.java @@ -0,0 +1,159 @@ +package org.phenopackets.phenopackettools.validator.core.phenotype.uniq; + +import com.google.protobuf.MessageOrBuilder; +import org.monarchinitiative.phenol.base.PhenolRuntimeException; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; +import org.monarchinitiative.phenol.ontology.data.Term; +import org.monarchinitiative.phenol.ontology.data.TermId; +import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator; +import org.phenopackets.phenopackettools.validator.core.ValidationResult; +import org.phenopackets.phenopackettools.validator.core.ValidatorInfo; +import org.phenopackets.phenopackettools.validator.core.phenotype.base.BaseHpoValidator; +import org.phenopackets.schema.v2.CohortOrBuilder; +import org.phenopackets.schema.v2.FamilyOrBuilder; +import org.phenopackets.schema.v2.Phenopacket; +import org.phenopackets.schema.v2.PhenopacketOrBuilder; +import org.phenopackets.schema.v2.core.PhenotypicFeature; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.stream.Stream; + +/** + * Check that phenotypic features of a phenopacket are present at most once. + *

+ * The validator groups the phenotypic features by the observation status + * and tests that the phenotypic features are present at most once. + */ +public abstract class HpoUniqueValidator extends BaseHpoValidator { + + private static final Logger LOGGER = LoggerFactory.getLogger(HpoUniqueValidator.class); + + private static final ValidatorInfo VALIDATOR_INFO = ValidatorInfo.of( + "HpoUniqueValidator", + "HPO unique phenotypic feature validator", + "Validate that phenopacket does not contain an HPO term more than once"); + private static final String CATEGORY = "Non-unique phenotypic feature"; + + public static PhenopacketValidator phenopacketValidator(MinimalOntology hpo) { + return new PhenopacketHpoUniqueValidator(hpo); + } + + public static PhenopacketValidator cohortValidator(MinimalOntology hpo) { + return new CohortHpoUniqueValidator(hpo); + } + + public static PhenopacketValidator familyValidator(MinimalOntology hpo) { + return new FamilyHpoUniqueValidator(hpo); + } + + private HpoUniqueValidator(MinimalOntology hpo) { + super(hpo); + } + + @Override + public ValidatorInfo validatorInfo() { + return VALIDATOR_INFO; + } + + @Override + public List validate(T component) { + return extractPhenopackets(component) + .flatMap(pp -> validatePhenotypicFeatures(pp.getId(), pp.getPhenotypicFeaturesList())) + .toList(); + } + + protected abstract Stream extractPhenopackets(T message); + + private Stream validatePhenotypicFeatures(String id, Iterable phenotypicFeatures) { + // Count feature occurrences + Map> counter = new HashMap<>(); + for (PhenotypicFeature pf : phenotypicFeatures) { + counter.computeIfAbsent(pf.getExcluded(), s -> new HashMap<>()) + .merge(pf.getType().getId(), 1, Integer::sum); + } + + // Build results, first for the present features then for the excluded. + Stream.Builder results = Stream.builder(); + for (Map.Entry e : counter.getOrDefault(false, Map.of()).entrySet()) { + if (e.getValue() > 1) { + String termName = extractTermName(e.getKey()); + String msg = """ + Phenotypic features of %s must not contain the same observed feature %s (%s) + more than once but the feature was present %d times""".formatted(id, + termName, e.getKey(), e.getValue()); + results.add(ValidationResult.error(VALIDATOR_INFO, CATEGORY, msg)); + } + } + + for (Map.Entry e : counter.getOrDefault(true, Map.of()).entrySet()) { + if (e.getValue() > 1) { + String termName = extractTermName(e.getKey()); + String msg = """ + Phenotypic features of %s must not contain the same excluded feature %s (%s) + more than once but the feature was present %d times""".formatted(id, + termName, e.getKey(), e.getValue()); + results.add(ValidationResult.error(VALIDATOR_INFO, CATEGORY, msg)); + } + + } + + return results.build(); + } + + private String extractTermName(String curie) { + try { + return hpo.termForTermId(TermId.of(curie)) + .map(Term::getName) + .orElse(UNKNOWN); + } catch (PhenolRuntimeException ex) { + LOGGER.debug("Invalid term ID {}", curie, ex); + return UNKNOWN; + } + } + + private static class PhenopacketHpoUniqueValidator extends HpoUniqueValidator { + + private PhenopacketHpoUniqueValidator(MinimalOntology hpo) { + super(hpo); + } + + @Override + protected Stream extractPhenopackets(PhenopacketOrBuilder message) { + return Stream.of(message); + } + } + + private static class CohortHpoUniqueValidator extends HpoUniqueValidator { + + public CohortHpoUniqueValidator(MinimalOntology hpo) { + super(hpo); + } + + @Override + protected Stream extractPhenopackets(CohortOrBuilder message) { + return message.getMembersList().stream(); + } + } + + private static class FamilyHpoUniqueValidator extends HpoUniqueValidator { + + public FamilyHpoUniqueValidator(MinimalOntology hpo) { + super(hpo); + } + + @Override + protected Stream extractPhenopackets(FamilyOrBuilder message) { + Stream.Builder builder = Stream.builder(); + builder.accept(message.getProband()); + + for (Phenopacket relative : message.getRelativesList()) + builder.add(relative); + + return builder.build(); + } + } +} diff --git a/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/uniq/package-info.java b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/uniq/package-info.java new file mode 100644 index 000000000..546f6aa87 --- /dev/null +++ b/phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/uniq/package-info.java @@ -0,0 +1,10 @@ +/** + * The {@code uniq} package checks uniqueness of the phenotypic features - each feature must be specified exactly once. + *

+ * Currently, the validators only perform naive check, largely ignoring the phenotypic feature + * modifiers, except of the {@linkplain org.phenopackets.schema.v2.core.PhenotypicFeature#getExcluded()} field. + * A phenotypic feature can only be present once within the present or excluded features. + * Note, however, that other validators must check the extreme case of a feature being present and excluded + * at the same time. + */ +package org.phenopackets.phenopackettools.validator.core.phenotype.uniq; \ No newline at end of file diff --git a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/TestData.java b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/TestData.java index f26901d32..65129891a 100644 --- a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/TestData.java +++ b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/TestData.java @@ -1,15 +1,16 @@ package org.phenopackets.phenopackettools.validator.core; -import org.monarchinitiative.phenol.io.OntologyLoader; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.io.MinimalOntologyLoader; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; -import java.nio.file.Path; +import java.io.File; +import java.net.URL; +import java.util.Objects; -public class TestData { - public static final Path TEST_BASE_DIR = Path.of("src/test/resources/org/phenopackets/phenopackettools/validator/core"); - private static final Path HPO_MODULE_PATH = TEST_BASE_DIR.resolve("hp.module.json"); +public class TestData { - public static final Ontology HPO = OntologyLoader.loadOntology(HPO_MODULE_PATH.toFile()); + private static final URL HP_MODULE_URL = TestData.class.getResource("hp.module.json"); + public static final MinimalOntology HPO = MinimalOntologyLoader.loadOntology(new File(Objects.requireNonNull(HP_MODULE_URL.getPath()))); } diff --git a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/ValidationResultTest.java b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/ValidationResultTest.java new file mode 100644 index 000000000..59ebd75e3 --- /dev/null +++ b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/ValidationResultTest.java @@ -0,0 +1,34 @@ +package org.phenopackets.phenopackettools.validator.core; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.SerializationFeature; +import org.junit.jupiter.api.Test; + +import static org.hamcrest.MatcherAssert.*; +import static org.hamcrest.Matchers.*; + +public class ValidationResultTest { + + @Test + public void serialize() throws Exception { + ObjectMapper mapper = new ObjectMapper(); + mapper.enable(SerializationFeature.INDENT_OUTPUT); + + ValidatorInfo info = ValidatorInfo.of("ID", "NAME", "DESCRIPTION"); + ValidationResult result = ValidationResult.of(info, ValidationLevel.ERROR, "CATEGORY", "MESSAGE"); + + assertThat(mapper.writeValueAsString(result), + equalTo(""" + { + "validatorInfo" : { + "validatorId" : "ID", + "validatorName" : "NAME", + "description" : "DESCRIPTION" + }, + "level" : "ERROR", + "category" : "CATEGORY", + "message" : "MESSAGE" + }""".replaceAll("\n", System.lineSeparator())) + ); + } +} \ No newline at end of file diff --git a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/ValidationResultsTest.java b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/ValidationResultsTest.java new file mode 100644 index 000000000..939836385 --- /dev/null +++ b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/ValidationResultsTest.java @@ -0,0 +1,61 @@ +package org.phenopackets.phenopackettools.validator.core; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.SerializationFeature; +import org.junit.jupiter.api.Test; + +import java.util.List; + +import static org.hamcrest.MatcherAssert.*; +import static org.hamcrest.Matchers.*; + +public class ValidationResultsTest { + + @Test + public void serialize() throws Exception { + ObjectMapper mapper = new ObjectMapper(); + mapper.enable(SerializationFeature.INDENT_OUTPUT); + + List validatorInfos = List.of( + ValidatorInfo.of("ID1", "NAME1", "DESCRIPTION1"), + ValidatorInfo.of("ID2", "NAME2", "DESCRIPTION2") + ); + List data = List.of( + ValidationResult.of(validatorInfos.get(0), ValidationLevel.ERROR, "CATEGORY1", "MESSAGE1"), + ValidationResult.of(validatorInfos.get(1), ValidationLevel.WARNING, "CATEGORY2", "MESSAGE2") + ); + ValidationResults results = ValidationResults.of(validatorInfos, data); + + assertThat(mapper.writeValueAsString(results), equalTo(""" + { + "validators" : [ { + "validatorId" : "ID1", + "validatorName" : "NAME1", + "description" : "DESCRIPTION1" + }, { + "validatorId" : "ID2", + "validatorName" : "NAME2", + "description" : "DESCRIPTION2" + } ], + "validationResults" : [ { + "validatorInfo" : { + "validatorId" : "ID1", + "validatorName" : "NAME1", + "description" : "DESCRIPTION1" + }, + "level" : "ERROR", + "category" : "CATEGORY1", + "message" : "MESSAGE1" + }, { + "validatorInfo" : { + "validatorId" : "ID2", + "validatorName" : "NAME2", + "description" : "DESCRIPTION2" + }, + "level" : "WARNING", + "category" : "CATEGORY2", + "message" : "MESSAGE2" + } ] + }""".replaceAll("\n", System.lineSeparator()))); + } +} \ No newline at end of file diff --git a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/ValidatorInfoTest.java b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/ValidatorInfoTest.java new file mode 100644 index 000000000..d1d2d4d69 --- /dev/null +++ b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/ValidatorInfoTest.java @@ -0,0 +1,27 @@ +package org.phenopackets.phenopackettools.validator.core; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.SerializationFeature; +import org.junit.jupiter.api.Test; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; + +public class ValidatorInfoTest { + + @Test + public void serialize() throws Exception { + ObjectMapper mapper = new ObjectMapper(); + mapper.enable(SerializationFeature.INDENT_OUTPUT); + + ValidatorInfo info = ValidatorInfo.of("ID", "NAME", "DESCRIPTION"); + + assertThat(mapper.writeValueAsString(info), equalTo(""" + { + "validatorId" : "ID", + "validatorName" : "NAME", + "description" : "DESCRIPTION" + }""".replaceAll("\n", System.lineSeparator())) + ); + } +} \ No newline at end of file diff --git a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/AncestryHpoValidatorTest.java b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/AncestryHpoValidatorTest.java index aa5467d00..817b52a28 100644 --- a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/AncestryHpoValidatorTest.java +++ b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/AncestryHpoValidatorTest.java @@ -3,7 +3,7 @@ import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Nested; import org.junit.jupiter.api.Test; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator; import org.phenopackets.phenopackettools.validator.core.TestData; import org.phenopackets.phenopackettools.validator.core.ValidationLevel; @@ -19,7 +19,7 @@ public class AncestryHpoValidatorTest { - private static final Ontology HPO = TestData.HPO; + private static final MinimalOntology HPO = TestData.HPO; @Nested public class PhenopacketTest { @@ -36,7 +36,7 @@ public void testValidInput() { // Has some Abnormality of finger but no Arachnodactyly. Phenopacket pp = createPhenopacket( "example-phenopacket", "example-subject", - createPhenotypicFeature("HP:0001167", "Abnormality of finger", false), + createPhenotypicFeature("HP:0001167", "Abnormal finger morphology", false), createPhenotypicFeature("HP:0001166", "Arachnodactyly", true) ).build(); @@ -49,7 +49,7 @@ public void testValidInput() { public void testFailsIfTermAndAncestorIsObserved() { // Has some Abnormality of finger and Arachnodactyly. Only Arachnodactyly should be present. Phenopacket pp = createPhenopacket( - "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormality of finger", false), + "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormal finger morphology", false), createPhenotypicFeature("HP:0001166", "Arachnodactyly", false) ).build(); @@ -60,14 +60,14 @@ public void testFailsIfTermAndAncestorIsObserved() { assertThat(result.validatorInfo(), equalTo(validator.validatorInfo())); assertThat(result.level(), equalTo(ValidationLevel.ERROR)); assertThat(result.category(), equalTo("Violation of the annotation propagation rule")); - assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an observed term (Arachnodactyly, HP:0001166) and an observed ancestor (Abnormality of finger, HP:0001167)")); + assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an observed term (Arachnodactyly, HP:0001166) and an observed ancestor (Abnormal finger morphology, HP:0001167)")); } @Test public void testFailsIfTermAndAncestorIsExcluded() { // Has neither Abnormality of finger nor Arachnodactyly. Only Abnormality of finger should be present. Phenopacket pp = createPhenopacket( - "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormality of finger", true), + "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormal finger morphology", true), createPhenotypicFeature("HP:0001166", "Arachnodactyly", true) ).build(); @@ -77,14 +77,14 @@ public void testFailsIfTermAndAncestorIsExcluded() { ValidationResult result = results.get(0); assertThat(result.level(), equalTo(ValidationLevel.ERROR)); assertThat(result.category(), equalTo("Violation of the annotation propagation rule")); - assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an excluded term (Abnormality of finger, HP:0001167) and an excluded child (Arachnodactyly, HP:0001166)")); + assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an excluded term (Abnormal finger morphology, HP:0001167) and an excluded child (Arachnodactyly, HP:0001166)")); } @Test public void testFailsIfTermIsPresentAndAncestorIsExcluded() { // Has neither Abnormality of finger nor Arachnodactyly. Only Abnormality of finger should be present. Phenopacket pp = createPhenopacket( - "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormality of finger", true), + "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormal finger morphology", true), createPhenotypicFeature("HP:0001166", "Arachnodactyly", false) ).build(); @@ -94,7 +94,7 @@ public void testFailsIfTermIsPresentAndAncestorIsExcluded() { ValidationResult result = results.get(0); assertThat(result.level(), equalTo(ValidationLevel.ERROR)); assertThat(result.category(), equalTo("Violation of the annotation propagation rule")); - assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an observed term (Arachnodactyly, HP:0001166) and an excluded ancestor (Abnormality of finger, HP:0001167)")); + assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an observed term (Arachnodactyly, HP:0001166) and an excluded ancestor (Abnormal finger morphology, HP:0001167)")); } } diff --git a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/HpoUniqueValidatorTest.java b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/HpoUniqueValidatorTest.java new file mode 100644 index 000000000..cad3ce4d7 --- /dev/null +++ b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/HpoUniqueValidatorTest.java @@ -0,0 +1,171 @@ +package org.phenopackets.phenopackettools.validator.core.phenotype; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Nested; +import org.junit.jupiter.api.Test; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; +import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator; +import org.phenopackets.phenopackettools.validator.core.TestData; +import org.phenopackets.phenopackettools.validator.core.ValidationLevel; +import org.phenopackets.phenopackettools.validator.core.ValidationResult; +import org.phenopackets.schema.v2.*; +import org.phenopackets.schema.v2.core.PhenotypicFeature; + +import java.util.List; + +import static org.hamcrest.MatcherAssert.*; +import static org.hamcrest.Matchers.*; +import static org.phenopackets.phenopackettools.validator.core.phenotype.Utils.createPhenopacket; +import static org.phenopackets.phenopackettools.validator.core.phenotype.Utils.createPhenotypicFeature; + +public class HpoUniqueValidatorTest { + + private static final MinimalOntology HPO = TestData.HPO; + + @Nested + public class PhenopacketTest { + + private PhenopacketValidator validator; + + @BeforeEach + public void setUp() { + validator = HpoPhenotypeValidators.Unique.phenopacketValidator(HPO); + } + + @Test + public void testValidInput() { + // Has some Abnormality of finger but no Arachnodactyly. + Phenopacket pp = createPhenopacket( + "example-phenopacket", "example-subject", + createPhenotypicFeature("HP:0001167", "Abnormality of finger", false), + createPhenotypicFeature("HP:0001166", "Arachnodactyly", true) + ).build(); + + List results = validator.validate(pp); + + assertThat(results, is(empty())); + } + + @Test + public void testFailsIfObservedTermIsPresentTwice() { + // Has Arachnodactyly twice. + Phenopacket pp = createPhenopacket( + "example-phenopacket", "example-subject", + createPhenotypicFeature("HP:0001167", "Abnormality of finger", false), + createPhenotypicFeature("HP:0001166", "Arachnodactyly", false), + createPhenotypicFeature("HP:0001166", "Arachnodactyly", false) + ).build(); + + List results = validator.validate(pp); + + assertThat(results, hasSize(1)); + ValidationResult result = results.get(0); + assertThat(result.validatorInfo(), equalTo(validator.validatorInfo())); + assertThat(result.level(), equalTo(ValidationLevel.ERROR)); + assertThat(result.category(), equalTo("Non-unique phenotypic feature")); + assertThat(result.message(), equalTo(""" + Phenotypic features of example-phenopacket must not contain the same observed feature Arachnodactyly (HP:0001166) + more than once but the feature was present 2 times""")); + } + + @Test + public void testFailsIfExcludedTermIsPresentTwice() { + // Has excluded Arachnodactyly twice. + Phenopacket pp = createPhenopacket( + "example-phenopacket", "example-subject", + createPhenotypicFeature("HP:0001167", "Abnormality of finger", true), + createPhenotypicFeature("HP:0001166", "Arachnodactyly", true), + createPhenotypicFeature("HP:0001166", "Arachnodactyly", true) + ).build(); + + List results = validator.validate(pp); + + assertThat(results, hasSize(1)); + ValidationResult result = results.get(0); + assertThat(result.validatorInfo(), equalTo(validator.validatorInfo())); + assertThat(result.level(), equalTo(ValidationLevel.ERROR)); + assertThat(result.category(), equalTo("Non-unique phenotypic feature")); + assertThat(result.message(), equalTo(""" + Phenotypic features of example-phenopacket must not contain the same excluded feature Arachnodactyly (HP:0001166) + more than once but the feature was present 2 times""")); + } + } + + /** + * White-box testing - we know that the {@link PhenotypicFeature} is an attribute of a {@link Phenopacket}, so we + * test the validation logic extensively in {@link HpoUniqueValidatorTest.PhenopacketTest}. + * The {@link HpoUniqueValidatorTest.FamilyTest} test suite ensures there are not errors in valid input. + */ + @Nested + public class FamilyTest { + + private PhenopacketValidator validator; + + @BeforeEach + public void setUp() { + validator = HpoPhenotypeValidators.Unique.familyValidator(HPO); + } + + @Test + public void testValidInput() { + Family family = Family.newBuilder() + .setProband(createPhenopacket("example-phenopacket", "example-subject", + createPhenotypicFeature("HP:0001167", "Abnormality of finger", false), + createPhenotypicFeature("HP:0001166", "Arachnodactyly", true)) + .build()) + .addRelatives(createPhenopacket("dad-phenopacket", "example-dad", + createPhenotypicFeature("HP:0001238", "Slender finger", false), + createPhenotypicFeature("HP:0100807", "Long fingers", false)) + .build()) + .addRelatives(createPhenopacket("mom-phenopacket", "example-mom", + createPhenotypicFeature("HP:0001238", "Slender finger", false), + createPhenotypicFeature("HP:0001166", "Arachnodactyly", true)) + .build()) + .build(); + + List results = validator.validate(family); + + assertThat(results, is(empty())); + } + } + + /** + * White-box testing (same as in {@link HpoUniqueValidatorTest.FamilyTest}) - we know that the {@link PhenotypicFeature} + * is an attribute of a {@link Phenopacket}, so we test the validation logic extensively + * in {@link HpoUniqueValidatorTest.PhenopacketTest}. + * The {@link HpoUniqueValidatorTest.CohortTest} test suite ensures there are not errors in valid input. + */ + @Nested + public class CohortTest { + + private PhenopacketValidator validator; + + @BeforeEach + public void setUp() { + validator = HpoPhenotypeValidators.Ancestry.cohortHpoAncestryValidator(HPO); + } + + @Test + public void testValidInput() { + Cohort cohort = Cohort.newBuilder() + .addMembers(createPhenopacket("joe-phenopacket", "example-subject", + createPhenotypicFeature("HP:0001167", "Abnormality of finger", false), + createPhenotypicFeature("HP:0001166", "Arachnodactyly", true)) + .build()) + .addMembers(createPhenopacket("jim-phenopacket", "example-jim", + createPhenotypicFeature("HP:0001238", "Slender finger", false), + createPhenotypicFeature("HP:0100807", "Long fingers", false)) + .build()) + .addMembers(createPhenopacket("jane-phenopacket", "example-jane", + createPhenotypicFeature("HP:0001238", "Slender finger", false), + createPhenotypicFeature("HP:0001166", "Arachnodactyly", true)) + .build()) + .build(); + + List results = validator.validate(cohort); + + assertThat(results, is(empty())); + } + } + +} \ No newline at end of file diff --git a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/OrganSystemValidatorTest.java b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/OrganSystemValidatorTest.java index 845fdc51d..d3a2e9b0f 100644 --- a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/OrganSystemValidatorTest.java +++ b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/OrganSystemValidatorTest.java @@ -5,7 +5,7 @@ import org.junit.jupiter.api.Test; import org.junit.jupiter.params.ParameterizedTest; import org.junit.jupiter.params.provider.CsvSource; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.monarchinitiative.phenol.ontology.data.TermId; import org.phenopackets.phenopackettools.validator.core.*; import org.phenopackets.schema.v2.*; @@ -20,7 +20,7 @@ public class OrganSystemValidatorTest { - private static final Ontology HPO = TestData.HPO; + private static final MinimalOntology HPO = TestData.HPO; private static final Set ABNORMALITY_OF_LIMBS_ORGAN_SYSTEM = Set.of(TermId.of("HP:0040064")); // Not a real organ system, but for the sake of testing... private static final Set SLENDER_FINGER_ORGAN_SYSTEM = Set.of(TermId.of("HP:0001238")); diff --git a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/PrimaryHpoPhenotypeValidatorTest.java b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/PrimaryHpoPhenotypeValidatorTest.java index 64e4ade80..5265585e1 100644 --- a/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/PrimaryHpoPhenotypeValidatorTest.java +++ b/phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/PrimaryHpoPhenotypeValidatorTest.java @@ -4,7 +4,7 @@ import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Nested; import org.junit.jupiter.api.Test; -import org.monarchinitiative.phenol.ontology.data.Ontology; +import org.monarchinitiative.phenol.ontology.data.MinimalOntology; import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator; import org.phenopackets.phenopackettools.validator.core.TestData; import org.phenopackets.phenopackettools.validator.core.ValidationLevel; @@ -18,7 +18,7 @@ public class PrimaryHpoPhenotypeValidatorTest { - private static final Ontology HPO = TestData.HPO; + private static final MinimalOntology HPO = TestData.HPO; @Nested public class PhenopacketTest { @@ -85,7 +85,7 @@ public void testMissingTermId() throws Exception { ValidationResult result = results.get(0); assertThat(result.level(), equalTo(ValidationLevel.ERROR)); assertThat(result.category(), equalTo("Invalid TermId")); - assertThat(result.message(), equalTo("HP:0001182 in proband A not found in 2021-06-08")); + assertThat(result.message(), equalTo("HP:0001182 in proband A not found in 2026-06-06")); } @Test diff --git a/phenopacket-tools-validator-core/src/test/resources/org/phenopackets/phenopackettools/validator/core/README.md b/phenopacket-tools-validator-core/src/test/resources/org/phenopackets/phenopackettools/validator/core/README.md index e94b3ba52..6964d9724 100644 --- a/phenopacket-tools-validator-core/src/test/resources/org/phenopackets/phenopackettools/validator/core/README.md +++ b/phenopacket-tools-validator-core/src/test/resources/org/phenopackets/phenopackettools/validator/core/README.md @@ -4,5 +4,71 @@ The folder contains test resources. ## HPO The `hp.module.json` contains Human Phenotype Ontology module in Obographs format. For the *Phenotypic abnormality* -subhierarchy, the module contains *Arachnodactyly* (`HP:0001166`) and the ancestors. The module contains all other HPO -subhierarchies. +subhierarchy, the module contains *Arachnodactyly* (`HP:0001166`), *Focal clonic seizure* (`HP:0002266`), +and their ancestors. The module contains all other HPO subhierarchies. + +Run the following to prepare the module: + +```shell +module load robot/1.9.8 + +HPO=https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2026-06-06/hp.obo + +wget $HPO + +# Arachnodactyly HP:0001166 +robot extract --input hp.obo --method BOT --term HP:0001166 \ + convert --output arachnodactyly.hp.obo + +# Focal clonic seizure HP:0002266 +robot extract --input hp.obo --method BOT --term HP:0002266 \ + convert --output fcs.hp.obo + +# We use a kind of a hack to include both +# Clinical modifier HP:0012823 +robot extract --input hp.obo --method BOT --term HP:0012823 \ + convert --output cm.bot.hp.obo +robot extract --input hp.obo --method TOP --term HP:0012823 \ + convert --output cm.top.hp.obo + +# Frequency HP:0040279 +robot extract --input hp.obo --method BOT --term HP:0040279 \ + convert --output freq.bot.hp.obo +robot extract --input hp.obo --method TOP --term HP:0040279 \ + convert --output freq.top.hp.obo + +# Mode of inheritance HP:0000005 +robot extract --input hp.obo --method BOT --term HP:0000005 \ + convert --output moi.bot.hp.obo +robot extract --input hp.obo --method TOP --term HP:0000005 \ + convert --output moi.top.hp.obo + +# Past medical history HP:0032443 +robot extract --input hp.obo --method BOT --term HP:0032443 \ + convert --output pmh.bot.hp.obo +robot extract --input hp.obo --method TOP --term HP:0032443 \ + convert --output pmh.top.hp.obo + +# Blood group HP:0032223 +robot extract --input hp.obo --method BOT --term HP:0032223 \ + convert --output bg.bot.hp.obo +robot extract --input hp.obo --method TOP --term HP:0032223 \ + convert --output bg.top.hp.obo + +# Merge into one file +robot merge --input arachnodactyly.hp.obo \ + --input fcs.hp.obo \ + --input cm.bot.hp.obo \ + --input cm.top.hp.obo \ + --input freq.bot.hp.obo \ + --input freq.top.hp.obo \ + --input moi.bot.hp.obo \ + --input moi.top.hp.obo \ + --input pmh.bot.hp.obo \ + --input pmh.top.hp.obo \ + --input bg.bot.hp.obo \ + --input bg.top.hp.obo \ + --output hp.module.json + +rm *.obo +``` \ No newline at end of file diff --git a/phenopacket-tools-validator-core/src/test/resources/org/phenopackets/phenopackettools/validator/core/hp.module.json b/phenopacket-tools-validator-core/src/test/resources/org/phenopackets/phenopackettools/validator/core/hp.module.json index 2790cd666..763f56646 100644 --- a/phenopacket-tools-validator-core/src/test/resources/org/phenopackets/phenopackettools/validator/core/hp.module.json +++ b/phenopacket-tools-validator-core/src/test/resources/org/phenopackets/phenopackettools/validator/core/hp.module.json @@ -1,10506 +1,19972 @@ { - "graphs": [ - { - "domainRangeAxioms": [], - "edges": [ - { - "obj": "http://purl.obolibrary.org/obo/HP_0000001", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/HP_0000005" - }, - { - "obj": "http://purl.obolibrary.org/obo/HP_0000001", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/HP_0000118" - }, - { - "obj": "http://purl.obolibrary.org/obo/HP_0000001", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/HP_0012823" - }, - { - "obj": "http://purl.obolibrary.org/obo/HP_0000001", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/HP_0032223" - }, - { - "obj": "http://purl.obolibrary.org/obo/HP_0000001", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/HP_0032443" - }, - { - "obj": "http://purl.obolibrary.org/obo/HP_0000001", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/HP_0040279" - }, - { - "obj": "http://purl.obolibrary.org/obo/HP_0000005", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/HP_0000006" - }, - { - 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"synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Infantile death", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Lethal in infancy", - "xrefs": [] - }, - { - "pred": "hasRelatedSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Death in early childhood", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "UMLS:C1844947" - }, - { - "val": "UMLS:C1858430" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0002813", - "lbl": "Abnormality of limb bone morphology", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "definition": { - "val": "Any abnormality of bones of the arms or legs.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - 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}, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "HP:0003631" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "HP:0003667" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "HP:0003672" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "HP:0010573" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "comments": [ - "Onset of signs or symptoms of disease within the first 12 months of life." - ], - "definition": { - "val": "Onset of signs or symptoms of disease between 28 days to one year of life.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Infantile onset", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - 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This is approximately the duration since the woman's last menstrual period began." - ], - "definition": { - "val": "Onset prior to birth but after 8 weeks of embryonic development (corresponding to a gestational age of 10 weeks).", - "xrefs": [ - "DDD:whouwehand" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#uk_spelling", - "val": "Foetal onset", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "UMLS:C4023347" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0011462", - "lbl": "Young adult onset", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-03-25T07:01:15Z" - } - ], - "definition": { - "val": "Onset of disease at the age of between 16 and 40 years.", - "xrefs": [ - "DDD:hfirth" - ] - }, - "xrefs": [ - { - "val": "UMLS:C3554568" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0011463", - "lbl": "Childhood onset", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-03-25T07:16:20Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "HP:0003586" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "HP:0003617" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "comments": [ - "This term refers to ages up to but not including the fifth birthday (see Juvenile onset)." - ], - "definition": { - "val": "Onset of disease at the age of between 1 and 5 years.", - "xrefs": [ - "DDD:hfirth" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Symptoms begin in childhood", - "xrefs": [ - "orcid.org/0000-0002-6548-5200" - ] - } - ], - "xrefs": [ - { - "val": "UMLS:C1837352" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0011842", - "lbl": "Abnormality of skeletal morphology", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-05-07T08:08:37Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "definition": { - "val": "An abnormality of the form, structure, or size of the skeletal system.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Abnormally shaped skeletal", - "xrefs": [ - "ORCID:0000-0001-5208-3432" - ] - } - ], - "xrefs": [ - { - "val": "UMLS:C4023165" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0011844", - "lbl": "Abnormal appendicular skeleton morphology", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-05-07T08:12:26Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "definition": { - "val": "An abnormality of the appendicular skeletal system, consisting of the of the limbs, shoulder and pelvic girdles.", - "xrefs": [ - "HPO:probinson" - ] - }, - "xrefs": [ - { - "val": "UMLS:C4023163" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012274", - "lbl": "Autosomal dominant inheritance with paternal imprinting", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2013-04-07T02:19:07Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "comments": [ - "Since the paternally inherited copy of such genes is silenced normally, only a maternally transmitted mutation leads to disease in this kind of inheritance." - ], - "definition": { - "val": "A type of autosomal dominant inheritance involving a gene that is imprinted with paternal silencing.", - "xrefs": [ - "HPO:probinson", - "PMID:18678320" - ] - }, - "xrefs": [ - { - "val": "UMLS:C4022976" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012275", - "lbl": "Autosomal dominant inheritance with maternal imprinting", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2013-04-07T02:54:09Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "comments": [ - "Since the maternally inherited copy of such genes is silenced normally, only a paternally transmitted mutation leads to disease in this kind of inheritance." - ], - "definition": { - "val": "A type of autosomal dominant inheritance involving a gene that is imprinted with maternal silencing.", - "xrefs": [ - "HPO:probinson" - ] - }, - "xrefs": [ - { - "val": "UMLS:C4022975" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012823", - "lbl": "Clinical modifier", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T06:34:24Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "HP:0000004" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "comments": [ - "Note that some of the terms, such as Intellectual disability, have children terms such as Severe intellectual disability that represent precomposed combinations of modifiers and phenotypic abnormality terms. 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For computational reasoning, the semantics are intended to be the same as if there was a combination of the phenotype term and the clinical modifier term." - ], - "definition": { - "val": "This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Phenotypic modifier", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "UMLS:C4021064" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012824", - "lbl": "Severity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T06:39:22Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "comments": [ - "Synonymous with PATO:0000049, intensity." - ], - "definition": { - "val": "The intensity or degree of a manifestation.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Intensity", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "SNOMEDCT_US:103370009" - }, - { - "val": "UMLS:C0522510" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012825", - "lbl": "Mild", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T06:41:33Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "comments": [ - "PATO:0000394, mild." - ], - "definition": { - "val": "Having a relatively minor degree of severity. 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For quantitative traits, a deviation of between three and four standard deviations from the appropriate population mean.", - "xrefs": [ - "HPO:probinson" - ] - }, - "xrefs": [ - { - "val": "SNOMEDCT_US:446421000124109" - }, - { - "val": "SNOMEDCT_US:6736007" - }, - { - "val": "UMLS:C0205081" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012827", - "lbl": "Borderline", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T06:52:16Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "comments": [ - "PATO:0000394, mild." - ], - "definition": { - "val": "Having a minor degree of severity that is considered to be on the boundary between the normal and the abnormal ranges. For quantitative traits, a deviation of that is less than two standard deviations from the appropriate population mean.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Borderline", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "UMLS:C0205189" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012828", - "lbl": "Severe", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T07:03:17Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "comments": [ - "PATO:0000396, severe." - ], - "definition": { - "val": "Having a high degree of severity. For quantitative traits, a deviation of between four and five standard deviations from the appropriate population mean.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Severe", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "SNOMEDCT_US:24484000" - }, - { - "val": "UMLS:C0205082" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012829", - "lbl": "Profound", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T07:05:46Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "definition": { - "val": "Having an extremely high degree of severity. For quantitative traits, a deviation of more than five standard deviations from the appropriate population mean.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Profound", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "SNOMEDCT_US:795002" - }, - { - "val": "UMLS:C0439808" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012830", - "lbl": "Position", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T07:18:35Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "definition": { - "val": "The anatomical localization of the specified phenotypic abnormality.", - "xrefs": [ - "HPO:probinson" - 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"val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T07:20:42Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "definition": { - "val": "Being present on both sides of the body.", - "xrefs": [ - "HPO:probinson" - ] - }, - "xrefs": [ - { - "val": "SNOMEDCT_US:51440002" - }, - { - "val": "UMLS:C0238767" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012833", - "lbl": "Unilateral", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T07:21:12Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "definition": { - "val": "Being present on only the left or only the right side of the body.", - "xrefs": [ - "HPO:probinson" - ] - }, - "xrefs": [ - { - "val": "SNOMEDCT_US:66459002" - }, - { - "val": "UMLS:C0205092" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012834", - "lbl": "Right", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T07:21:46Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "definition": { - "val": "Being located on the right side of the body.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Right-sided", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "SNOMEDCT_US:264180000" - }, - { - "val": "UMLS:C0444532" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012835", - "lbl": "Left", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T07:23:17Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "definition": { - "val": "Being located on the left side of the body.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Left-sided", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "SNOMEDCT_US:263795004" - }, - { - "val": "UMLS:C0443246" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012836", - "lbl": "Spatial pattern", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T07:25:02Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "definition": { - "val": "The pattern by which a phenotype affects one or more regions of the body.", - "xrefs": [ - "HPO:probinson" - ] - }, - "xrefs": [ - { - "val": "UMLS:C4022711" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012837", - "lbl": "Generalized", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T07:25:58Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "comments": [ - "PATO:0002403." - ], - "definition": { - "val": "Affecting all regions without specificity of distribution.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#uk_spelling", - "val": "Generalised", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "SNOMEDCT_US:60132005" - }, - { - "val": "UMLS:C0205246" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012838", - "lbl": "Localized", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T07:27:48Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "comments": [ - "PATO:0000627." - ], - "definition": { - "val": "Being confined or restricted to a particular location.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Localized", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#uk_spelling", - "val": "Localised", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "SNOMEDCT_US:255471002" - }, - { - "val": "UMLS:C0392752" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0012839", - "lbl": "Distal", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-06-06T07:29:38Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "human_phenotype" - } - ], - "definition": { - "val": "Localized away from the central point of the body.", - "xrefs": [ - "HPO:probinson" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Outermost", - "xrefs": [ - "ORCID:0000-0001-6908-9849" - ] - } - ], - "xrefs": [ - { - "val": "SNOMEDCT_US:46053002" - 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}, - { - "val": "UMLS:C0205219" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0020121", - "lbl": "Conception by assisted reproductive technology", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "robinp" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2019-07-02T16:46:09Z" - } - ], - "comments": [ - "Assisted reproductive technology is used primarily for infertility treatments to achieve pregnancy." - ], - "definition": { - "val": "A history of conception by an assisted reproductive technology such as in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), and cryopreservation.", - "xrefs": [ - "PMID:28844405" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0020138", - "lbl": "History of recent animal bite", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - 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"val": "Triggered by cigarette consumption", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Triggered by smoking", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Triggered by tobacco use", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Smoking triggered symptoms", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025224", - "lbl": "Triggered by sodium ingestion", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-10T14:08:50Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by eating or drinking sodium.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#abbreviation", - "val": "Triggered by Na ingestion", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#abbreviation", - "val": "Triggered by Na+ ingestion", - "xrefs": [] - }, - { - "pred": "hasNarrowSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Triggered by salt ingestion", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Sodium ingestion triggered symptoms", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Sodium intake triggered attacks", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Triggered by sodium intake", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025225", - "lbl": "Triggered by sound", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-10T14:09:30Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "comments": [ - "For instance, seizures associated with autosomal dominant partial epilepsy with auditory features may be triggered by certain sounds such as telephone ringing or speech." - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by exposure to sound or noise.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Triggered by sound", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Sound triggered symptoms", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025226", - "lbl": "Triggered by stress", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-10T14:24:37Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by a physical, mental, or emotional factor associated with bodily or mental tension.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Triggered by stress", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Stress triggered symptoms", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025227", - "lbl": "Triggered by excitement", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-10T14:28:21Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by a a state of excitement or by being startled.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Triggered by excitement", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Excitement triggered symptoms", - "xrefs": [] - }, - { - "pred": "hasRelatedSynonym", - "val": "Triggered by startle", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025228", - "lbl": "Triggered by sudden movement", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-10T14:29:50Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by a sudden movement.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Triggered by sudden movement", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Kinesigenic", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Sudden movement triggered symptoms", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025229", - "lbl": "Triggered by vestibular stimulation", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-10T14:30:38Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by vestibular stimulation, including head turning, cold calorics, postural changes, or rotating chair.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Vestibular stimulation triggered attacks", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Vestibular stimulation triggered symptoms", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025254", - "lbl": "Ameliorated by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-17T14:17:46Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "An ameliorating factor is defined as an external factor that leads to a sign or symptom that is already present improving or becoming more bearable", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Improved by", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025255", - "lbl": "Ameliorated by pregnancy", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-17T14:19:29Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is improved or made more bearable by pregnancy in a female.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Pregnancy relieves symptoms", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025256", - "lbl": "Ameliorated by heat", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-17T14:20:45Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is improved or made more bearable by heat (including fever).", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Heat improves condition", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Heat improves symptom", - "xrefs": [] - }, - { - "pred": "hasNarrowSynonym", - "val": "Fever improves condition", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025257", - "lbl": "Ameliorated by carbohydrate ingestion", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-17T14:21:33Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is improved or made more bearable by eating or drinking carbohydrates including glucose (sugar).", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025275", - "lbl": "Lateral", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T14:47:04Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to an abnormality that is located farther from the median plane or midline of the body or of the referenced structure.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025279", - "lbl": "Migratory", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T15:18:09Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025280", - "lbl": "Pain characteristic", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T15:21:51Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "A pain characteristic is defined as a subjective category or type of pain.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025281", - "lbl": "Sharp", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T15:23:03Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applied to pain that is described as sharp, i.e., sudden and severe.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025282", - "lbl": "Dull", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T15:23:43Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applied to pain that is dull, i.e., not severe but that continues over a long period of time.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Dull pain", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025283", - "lbl": "Tender", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T15:25:03Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applied to pain that is tender, i.e., elicited by touching the affected body part.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025284", - "lbl": "Sleep-interrupting", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T15:26:21Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applied to pain that wakes the affecting individual from sleep.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025285", - "lbl": "Aggravated by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T15:29:42Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "An aggravating factor is defined as an external factor that leads to a sign or symptom that is already present getting worse or becoming more severe.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Exacerbated by", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025286", - "lbl": "Aggravated by activity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T15:30:58Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applied to a sign or symptom that is aggravated by activity, exertion, or exercise.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Aggravated by exercise", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Aggravated by exertion", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Worse with activity", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Worsened by activity", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025287", - "lbl": "Axial", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T15:34:25Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to an abnormality that is situated in the central part of the body, in the head and trunk as distinguished from the limbs.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025290", - "lbl": "Upper-body predominance", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T16:11:12Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to an abnormality that affects the arms, trunk, head more than the legs.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025291", - "lbl": "Lower-body predominance", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T16:12:27Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to an abnormality that affects the legs more than the arms, trunk, head.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025292", - "lbl": "Acral", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T16:15:24Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to an abnormality that affects the distal portions of limbs (hand, foot) and head (ears, nose).", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025293", - "lbl": "Distributed along Blaschko lines", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T16:16:24Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to an abnormality whose localization corresponds to the lines of Blaschko, which correspond to the lineage of epithelia cells. Blaschko lines are normally invisible but may become apparent with certain skin diseases and then can be seen to be distributed in lines horizontal to the body.", - "xrefs": [ - "PMID:17061271" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025294", - "lbl": "Dermatomal", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T16:17:51Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "comments": [ - "This distribution can be seen with certain skin findings such as shingles. The term radicular is used to describe a dermatomal distribution of nerve root pain." - ], - "definition": { - "val": "Applies to an abnormality whose localization corresponds to the dermatomes, i.e., the nerve root distribution.", - "xrefs": [ - "PMID:19772560" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Radicular", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025295", - "lbl": "Herpetiform", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T16:19:13Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to an abnormality whose distribution and appearance resembles that of the grouped umbilicated vesicles seen in herpes simplex and herpes zoster infections.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025296", - "lbl": "Morbilliform", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T16:20:14Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to an abnormality whose distribution and appearance resembles that of measles, i.e., maculopapular lesions that are red and roughly 2 to 10 mm in diameter and may be partially confluent.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025297", - "lbl": "Prolonged", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-18T16:26:30Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applied to an abnormality whose duration is extended over a longer period of time than is expected or usual (e.g., prolonged fever lasts longer than one usually sees with an infection).", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025301", - "lbl": "Nocturnal", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-20T12:30:06Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to an abnormality that occurs in or is exacerbated during the night.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025302", - "lbl": "Diurnal", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-20T12:31:12Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign, symptom, or other abnormality that occurs in or is exacerbated in the day time.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025303", - "lbl": "Episodic", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-21T00:51:43Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "comments": [ - "In our definition, episodic is synonymous with intermittent and recurrent. The term does not imply any particular temporal pattern of the recurrence." - ], - "definition": { - "val": "Applied to a sign, symptom, or other manifestation that occurs multiple times at usually irregular intervals. The occurences are separated by an interval in which the sign, symptom, or manifestation is not present.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Now and then", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025304", - "lbl": "Periodic", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-21T00:55:09Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign, symptom, or other manifestation that recurs with a fixed time interval, i.e., the symptom-free periods are always of the same length.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Cyclic", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Cyclical", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025305", - "lbl": "Quotidian", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-21T00:57:17Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign, symptom, or other manifestation that is episodic with a fixed time interval of one day (24 hours).", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025306", - "lbl": "Acute emergence over minutes", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-21T01:00:35Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Acute appearance of disease manifestations in a period of minutes.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025307", - "lbl": "Acute emergence over hours", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-21T01:01:25Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Acute appearance of disease manifestations in a period of hours.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025308", - "lbl": "Acute emergence over days", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-21T01:01:46Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Acute appearance of disease manifestations in a period of days.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025315", - "lbl": "Exacerbated by head trauma", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2016-12-21T02:22:58Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "comments": [ - "Childhood ataxia with central nervous system hypomyelination/vanishing white matter disease is an autosomal recessive disorder characterized by ataxia, spasticity, and variable optic atrophy. Chronic progressive decline can be exacerbated by rapid deterioration during febrile illnesses or following head trauma." - ], - "definition": { - "val": "Applies to a sign or symptom that is worsened, aggravated, or exacerbated by head trauma.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025334", - "lbl": "Triggered by emotion", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2017-02-12T11:38:35Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by a strong spontaneously arising mental state, reaction or feeling (emotion).", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Emotion triggered symptoms", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025352", - "lbl": "Autosomal dominant germline de novo mutation", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2017-02-13T00:19:00Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "definition": { - "val": "Being related to a mutation that gamete that participates in fertilization. All cells of the emerging organism will be affected and the variant canl be passed on to the next generation.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0025377", - "lbl": "Triggered by exertion", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2017-04-08T13:36:52Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:probinson" - } - ], - "comments": [ - "For convenience, several HPO terms exist with the phrase 'Exercise-induced' in their label. This is meant to be logically equvalent to the combination of the basis term and this modifier." - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by exertion or physical exercise.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Exertion triggered symptoms", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Triggered by physical exercise", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0030645", - "lbl": "Central", - "meta": { - "definition": { - "val": "Applies to an abnormality that is located close to the median plane or midline of the body or of the referenced structure.", - "xrefs": [] - }, - "xrefs": [ - { - "val": "SNOMEDCT_US:26216008" - }, - { - "val": "UMLS:C0205099" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0030646", - "lbl": "Peripheral", - "meta": { - "xrefs": [ - { - "val": "SNOMEDCT_US:14414005" - }, - { - "val": "UMLS:C0205100" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0030647", - "lbl": "Paracentral", - "meta": { - "xrefs": [ - { - "val": "UMLS:C4073110" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0030648", - "lbl": "Midperipheral", - "meta": { - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Mid-peripheral", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "UMLS:C4073111" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0030649", - "lbl": "Pericentral", - "meta": { - "xrefs": [ - { - "val": "UMLS:C4073112" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0030650", - "lbl": "Focal", - "meta": { - "xrefs": [ - { - "val": "SNOMEDCT_US:87017008" - }, - { - "val": "UMLS:C0205234" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0030651", - "lbl": "Multifocal", - "meta": { - "xrefs": [ - { - "val": "SNOMEDCT_US:524008" - }, - { - "val": "UMLS:C0205292" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0030674", - "lbl": "Antenatal onset", - "meta": { - "definition": { - "val": "Onset prior to birth.", - "xrefs": [ - "HPO:probinson" - ] - }, - "xrefs": [ - { - "val": "UMLS:C2673646" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0031135", - "lbl": "Triggered by physical trauma", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2017-06-10T13:29:55Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by exposure to a trauma (injury to tissue).", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Physical trauma triggered symptoms", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0031167", - "lbl": "Triggered by ingestion of potassium-rich food", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2017-06-18T19:18:01Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "In contrast to paramyotonia congenita or hyperkalaemic periodic paralysis, potassium-aggravated myotonias (PAM) patients show no muscle weakness and hardly any cold sensitivity. However, they show an aggravation of their myotonia after ingestion of potassium, which distinguishes them from patients with chloride channelopathies." - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by eating or drinking foods rich in potassium.", - "xrefs": [ - "PMID:19472919" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#abbreviation", - "val": "Triggered by ingestion of K-rich food", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Potassium-rich food triggered symptoms", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0031362", - "lbl": "Sex-limited autosomal recessive inheritance", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2017-08-29T11:43:01Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes in a sex-specific manner (i.e. only in males or only in females).", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0031375", - "lbl": "Refractory", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2017-09-02T01:54:32Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is difficult to treat or cure.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0031450", - "lbl": "Polycyclic", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2017-09-17T15:00:02Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "A distribution of skin lesions resembling multiple merged circles. For instance, this can be seen with multiple urticarial wheals as the individual, circular wheals resolve and merge.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0031796", - "lbl": "Recurrent", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2018-02-25T14:40:47Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to a sign, symptom or manifestation that occurs multiple times separated by intervals in which the sign, symptom, or manifestation is not present.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Intermittent", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0031797", - "lbl": "Clinical course", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2018-02-25T14:55:46Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasRelatedSynonym", - "val": "Natural history of disease", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0031914", - "lbl": "Fluctuating", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2018-07-01T21:29:25Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Varying irregularly over time in severity, amount, or amplitude.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0031915", - "lbl": "Stable", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2018-07-01T21:31:19Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "This modifier can be applied to a phenotypic feature that does not vary in severity or amount over time.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032113", - "lbl": "Semidominant mode of inheritance", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2018-11-17T14:33:51Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "Familial hypercholesterolemia is an example of a disease with this inheritance pattern." - ], - "definition": { - "val": "A mode of inheritance that is observed for traits related to a gene encoded on chromosomes in which a trait can manifest in the heterozygotes and homozygotes, with differing phenotype severity present dependent on the number of alleles affected.", - "xrefs": [ - "ClinGen:courtneythaxton", - "ClinGen:erinriggs", - "ClinGen:jennygoldstein", - "ClinGen:jimmyzqhen", - "ClinGen:marinadistefano", - "ClinGen:mattwright", - "ClinGen:scottgoehringer", - "ClinGen:tristannelson" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032223", - "lbl": "Blood group", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-01-24T11:33:51Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "At present, there are 34 blood group systems recognized by the International Society for Blood Transfusion." - ], - "definition": { - "val": "Any of the various types of human blood whose antigen characteristics determine compatibility in transfusion. While the ABO and Rhesus sytems are the most well known, there are in total about 300 different blood type antigens distributed across 34 different blood type systems.", - "xrefs": [ - "PMID:26085552" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032224", - "lbl": "ABO blood group", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-01-24T11:40:47Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "The ABO histo-blood group consists of two antigens (A and B antigens) and four blood types (types A, B, AB, and O). The A and B antigens are the product of the ABO gene and are autosomal codominant. The group O phenotype is an autosomal-recessive phenotype due to the homozygous inheritance of two null ABO alleles. Group O individuals express the H antigen, the biosynthetic precursor to A and B antigens. ABO, therefore, is the blood type, whereas A, B, and H refer to the antigens." - ], - "definition": { - "val": "The ABO system consists of A and B antigens and antibodies against these antigens.", - "xrefs": [ - "PMID:15373665", - "PMID:26085552" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032316", - "lbl": "Family history", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-14T11:40:50Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "This subontology is intended to help record summary information about family members if only a limited amount of information is available or required." - ], - "definition": { - "val": "Information about close relatives of an individual who is the proband of a study or who is being investigated with the goal of identifying a medical diagnosis. Usually, the family history includes information from three generations of relatives, including children, brothers and sisters, parents, aunts and uncles, nieces and nephews, grandparents, and cousins.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032317", - "lbl": "Family history of cancer", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-14T11:43:34Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "A close blood relative had cancer.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032318", - "lbl": "Family history of heart disease", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-14T11:45:48Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "A close blood relative had heart disease.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032319", - "lbl": "Health status", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-14T11:46:18Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Health status of a family member with respect to the disease being investigated in a proband.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032320", - "lbl": "Affected", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-14T11:47:51Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "This term applies to a family member who is diagnosed with the same condition as the individual who is the primary focus of investigation (the proband).", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032321", - "lbl": "Unaffected", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-14T11:48:40Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "This term applies to a family member in whom the diagnosis that is the primary focus of investigation is excluded.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032322", - "lbl": "Healthy", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-14T11:49:52Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "No history of any serious disease, including the disease being investigated in the proband.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032365", - "lbl": "Exacerbated by aspirin ingestion", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-23T17:36:45Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applied to a sign or symptom that is worsened by ingestion of aspirin.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032370", - "lbl": "Blood group A", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-23T18:59:31Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "ABO phenotype A, corresponding to the genotype AO or AA.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032373", - "lbl": "Duffy blood group", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-24T13:37:17Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "FY has two major codominant alleles, FYA and FYB, which result from a SNP (125G>A), and the corresponding Fya and Fyb antigens differ by a single amino acid (G42D). Individuals who are homozygous for a -33T>C SNP in the erythroid promoter region of the FYB allele have the phenotype Fy(a-b-) and do not express Duffy antigens on their RBCs." - ], - "definition": { - "val": "The Duffy blood group system is based on the presence of a glycoprotein termed Fy that is on the surface of erythrocytes and some other cells. There are two Duffy antigens named Fya and Fyb, and thus there are four Duffy phenotypes: a+b+, a+b-, a-b+,a-b-.", - "xrefs": [ - "PMID:19480920" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032374", - "lbl": "Duffy Fya positivity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-24T13:40:29Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Presence of the Duffy Fya antigen.", - "xrefs": [ - "PMID:19480920" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032375", - "lbl": "Duffy Fyb positivity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-24T13:42:55Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Presence of the Duffy Fyb antigen.", - "xrefs": [ - "PMID:19480920" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032382", - "lbl": "Uniparental disomy", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-24T14:58:52Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "UPD may comprise the whole chromosome, or just part of it (segmental UPD). Isodisomy is presented as 2 copies from the same chromosome of a parent, and heterodisomy is presented as 1 copy of each of the 2 homologues from the same parent. UPD is related to abnormalities formed during meiosis, fertilization, and mitosis. There are 5 different mechanisms that explain the etiology of UPD, including Trisomic rescue; Nullisomic gamete complementation; Monosomic rescue; Mitotic aberrations; and Structural chromosome aberrations. If prenatal genetic analysis reveals a homologous robertsonian translocation, the risk of fetal UPD is very high, and a marker chromosome or chromosome aneuploidy can be associated with UPD." - ], - "definition": { - "val": "Inheritance of both homologues of a chromosome pair from the same parent.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032383", - "lbl": "Uniparental heterodisomy", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-24T15:04:03Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "A type of uniparental disomy in which the two different chromosomes (or chromosome segments) of the same parent are transmitted.", - "xrefs": [ - "PMID:25547535" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032384", - "lbl": "Uniparental isodisomy", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-02-24T15:05:18Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "A type of uniparental disomy in which the two identical chromosomes (or chromosome segments) of the same parent are transmitted.", - "xrefs": [ - "PMID:25547535" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032440", - "lbl": "Blood group B", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-03-03T16:34:03Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "ABO phenotype B, corresponding to the genotype BO or BB.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032441", - "lbl": "Blood group AB", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-03-03T16:37:30Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "ABO phenotype AB, corresponding to the genotype AB.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032442", - "lbl": "Blood group O", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-03-03T16:37:48Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "ABO phenotype O, corresponding to the genotype OO.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032443", - "lbl": "Past medical history", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-03-03T16:39:26Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "This subontology of the HPO is not intended to provide all needed terms to describe the past medical history, but rather to be combined with other ontologies such as MONDO in order to capture information that is often needed to properly assess phenotypic findings related to a presenting medical problem." - ], - "definition": { - "val": "In a medical encounter, the physician generally will interview the patient about his or her current problem, and may perform additional testing. The past medical history (PMH) in contrast records information about the patient's medical, personal and family history that might be relevant to the presenting illness or to provide optimal clinical management. The PMH generally includes (if relevant) other major illnesses, hospitalizations, surgeries, injuries, allergies, gynecologic and obstetric history, family history, personal history including occupational history, alcohol and drug use, etc.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032444", - "lbl": "Status post organ transplantation", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-03-03T16:49:25Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "The affected individual has received an organ transplant previous to the current medical encounter.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "s/p organ transplantation", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032467", - "lbl": "Past obstetric history", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-04-04T09:46:23Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Information about past pregnancies including gravidity (number of times a woman has been pregnant, regardless of the outcome), parity (total number of births), gestational age of births, and medical conditions related to past pregnancies.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Maternal medical history", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032468", - "lbl": "History of stillbirth", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-04-04T09:53:23Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "One or more previous pregnancies resulted in stillbirth, defined as death of a fetus in the later stages of pregnancy (definitions in the literature vary, with cut-offs ranging from 20 to 28 weeks gestation).", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032500", - "lbl": "Exacerbated by tobacco use", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-23T22:51:26Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applied to a sign or symptom that is worsened by smoking tobacco products.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Aggravated by tobacco use", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Exacerbated by smoking", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Smoking or tobacco use exacerbates symptoms", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032501", - "lbl": "Exacerbated by contraceptive medication", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-23T22:53:32Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applied to a sign or symptom that is worsened by taking contraceptive medication.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Contraceptive pills aggravate symptoms", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032502", - "lbl": "Exacerbated by barbiturate medication", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-23T22:55:06Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applied to a sign or symptom that is worsened by taking barbituates.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Barbiturates produce worsening", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032503", - "lbl": "Ameliorated by ethanol ingestion", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-23T22:56:25Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is improved or made more bearable by drinking alcohol (ethanol).", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Ethanol reduces manifestations", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032522", - "lbl": "Ameliorated by immunosuppresion", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-26T11:24:41Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is improved or made more bearable by treatment with immunosuppresive medication.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Immunosupressive therapy improves condition", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032525", - "lbl": "Aggravated by acetylcholinesterase inhibitor", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-26T11:44:24Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applied to a sign or symptom that is worsened by treatment with an acetylcholinesterase inhibitor such as tensilon (edrophonium) or pyridostigmine (Mestinon).", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032526", - "lbl": "Ameliorated by acetylcholinesterase inhibitor", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-26T11:47:48Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is improved or made more bearable by an acetylcholinesterase inhibitor such as mestinon or tensilon.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032534", - "lbl": "Exacerbated by methylxanthine ingestion", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-27T13:08:24Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applied to a sign or symptom that is worsened by ingestion of food containing a methylxanthine compound (for instance, coffee, caffeine, chocolate).", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Methylxanthines produce worsening", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032535", - "lbl": "Cervical (neck)", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-27T13:12:21Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to an abnormality that is situated in the neck.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032539", - "lbl": "Joint extensor surface localization", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-27T13:48:37Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to an abnormality that is situated in extensor surface of the joint. The extensor surface refers to the skin on the opposite side of a joint.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032540", - "lbl": "Joint flexor surface localization", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-27T13:51:06Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to an abnormality that is situated in flexor surface of the joint. The flexor surface refers to the skin that touches when a joint is bent (flexed).", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032542", - "lbl": "Exacerbated by pregnancy", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-05-27T15:16:46Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applied to a sign or symptom that is worsened by being pregnant.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032544", - "lbl": "Predominant small joint localization", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-06-12T10:19:53Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to an abnormality that mainly affects the small joints, including fingers, toes, interphalangeal, metacarpophalangeal, metatarsophalangeal, wrists, ankles, vertebrae, and neck.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0032557", - "lbl": "History of bone marrow transplant", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2019-06-14T11:13:53Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "A past medical history of hematopoietic stem cell transplantation involving myeloablative chemoradiotherapy followed by stem cell rescue with autologous or human leukocyte antigen (HLA)-matched stem cells derived from a donor.", - "xrefs": [ - "PMID:24198516" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#uk_spelling", - "val": "Status post haematopoietic stem cell transplantation", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Status post hematopoietic stem cell transplantation", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033032", - "lbl": "Triggered by an abusive adult", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "Munchausen syndrome by proxy is not a pediatric condition, but the outward manifestation of an adult psychiatric disorder." - ], - "definition": { - "val": "Applies to a sign or symptom that is induced by an abusive adult (usually a parent).", - "xrefs": [ - "LMU:chrapp", - "PMID:29938745" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Munchausen syndrome by proxy", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033127", - "lbl": "Abnormality of the musculoskeletal system", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2020-09-05T13:35:03Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "An anomaly of the musculoskeletal system, which consists of the bones of the skeleton, muscles, cartilage, tendons, ligaments, joints, and other connective tissue. The musculoskeletal system supports the weight of the body, maintains body position and produces movements of the body or of parts of the body.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033184", - "lbl": "Triggered by infection", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2020-10-04T11:47:16Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "Applies to a sign or symptom that is provoked or brought about by an infection, that is by invasion and multiplication of microorganisms such as bacteria, viruses, and parasites that are not normally present within the body." - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033185", - "lbl": "Triggered by EBV infection", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2020-10-04T11:48:39Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by infection by the Epstein-Barr virus.", - "xrefs": [ - "PMID:19425169" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Triggered by Epstein Barr virus infection", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033198", - "lbl": "Triggered by viral infection", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2020-10-11T12:16:45Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by infection by a virus.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033349", - "lbl": "Seizure cluster", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2020-11-30T22:08:36Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "This term should be used with an HPO term for the appropriate type of seizure to denote clustered occurence of seizures. There is no consensus within the medical community regarding the definition of a seizure cluster, where limitations of current clinical definitions include poor sensitivity and specificity. The proposed definition is meant to serve as a placeholder until a more robust definition, likely facilitated by technological advances in seizure tracking devices and personalised cluster identification is agreed upon." - ], - "definition": { - "val": "A fourfold or greater increase of usual seizure frequency within a 3-day period, where the patient demonstrates full recovery between seizure events within the cluster. The seizure cluster should be recognisable by the primary clinician, carer or patient.", - "xrefs": [ - "PMID:29871784", - "PMID:32305858" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Acute repetitive seizures", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Crescendo seizures", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Cyclical seizures", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Recurrent seizures", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Seizure flurries", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Serial seizures", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033623", - "lbl": "Birth history", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-01-30T23:06:26Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Information about the delivery and health status at birth typically elicited as a part of the past medical history.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033624", - "lbl": "History of congenital CMV infection", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-01-30T23:08:18Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "A congenital cytomegalovirus (CMV) infection of the newborn can follow either a primary or recurrent maternal infection. Jaundice, petechiae, and hepatosplenomegaly are the most frequently noted clinical triad in symptomatic infants. Affected infants may develop permanent disabilities such as hearing loss, vision loss, motor and cognitive deficits.", - "xrefs": [ - "PMID:29503048" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "History of congenital cytomegalovirus infection", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033763", - "lbl": "Death in adulthood", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-04-30T11:20:03Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Cessation of life at the age of 16 years or later.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033764", - "lbl": "Death in middle age", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-04-30T11:20:49Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Death between the age of 40 and 60 years.", - "xrefs": [ - "ORCID:0000-0002-6410-0882" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033765", - "lbl": "Death in late adulthood", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-04-30T11:21:09Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Death at an age of at least 60 years.", - "xrefs": [ - "ORCID:0000-0002-6410-0882" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033789", - "lbl": "Triggered by cheese ingestion", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-05-07T11:11:07Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "comments": [ - "Cheese contains tyramine, which is thought to be responsible for tachycardia and hypertension that can be tirggered by eating cheese in persons with Trimethylaminuria." - ], - "definition": { - "val": "Applies to a sign or symptom that is provoked or brought about by eating cheese.", - "xrefs": [ - "PMID:9398858" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033793", - "lbl": "Triggered by food ingestion", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-05-07T17:28:49Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Applies to a sign or symptom that is provoked or brought about by eating a certain food.", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033813", - "lbl": "Perilobular", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-05-09T12:03:28Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Situated or occurring around a lobe of an organ.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033814", - "lbl": "Paraseptal", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-05-09T12:08:03Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Characterized by predominant involvement of the distal alveoli and their ducts and sacs. It is characteristically bounded by any pleural surface and the interlobular septa.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033815", - "lbl": "Bronchocentric", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-05-09T12:11:30Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Centered in bronchi or bronchioles.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033816", - "lbl": "Centrilobular", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-05-09T12:12:13Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Located in the center of the secondary pulmonary lobules, which are the functional units of the lungs.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033817", - "lbl": "Miliary", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-05-09T12:13:42Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Characterized by numerous small lesions said to resemble millet seed.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033818", - "lbl": "Reticular", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-05-09T12:18:27Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to an abnormality whose distribution and appearance resembles a net or network-like structure.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033819", - "lbl": "Perilymphatic", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-05-09T12:19:16Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to an abnormality whose distribution and appearance are located at or near lymphatic structures (node or vessel).", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0033820", - "lbl": "Apical", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/date", - "val": "2021-05-09T12:20:29Z" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "peter" - } - ], - "definition": { - "val": "Applies to an abnormality whose distribution and appearance are located at the apex of an organ. For instance, apical refers to the superior portion of the lung.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0040006", - "lbl": "Mortality/Aging", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:skoehler" - } - ], - "xrefs": [ - { - "val": "UMLS:C4022499" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0040064", - "lbl": "Abnormality of limbs", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:skoehler" - } - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Abnormal limbs", - "xrefs": [ - "HPO:skoehler" - ] - }, - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Abnormality of limbs", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "Limb anomaly", - "xrefs": [ - "https://orcid.org/0000-0001-5208-3432" - ] - }, - { - "pred": "hasRelatedSynonym", - "val": "Dysmelia", - "xrefs": [ - "HPO:probinson" - ] - } - ], - "xrefs": [ - { - "val": "SNOMEDCT_US:445144002" - }, - { - "val": "UMLS:C0239337" - }, - { - "val": "UMLS:C4073131" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0040068", - "lbl": "Abnormality of limb bone", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "HPO:skoehler" - } - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/hp#layperson", - "val": "Abnormality of limb bone", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "UMLS:C4022456" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0040279", - "lbl": "Frequency", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "ORCID:0000-0002-5316-1399" - } - ], - "comments": [ - "Aligned with Orphanet" - ], - "definition": { - "val": "Class to represent frequency of phenotypic abnormalities within a patient cohort.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0040280", - "lbl": "Obligate", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "ORCID:0000-0002-5316-1399" - } - ], - "definition": { - "val": "Always present, i.e. in 100% of the cases.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Obligate (100%)", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "ORPHA:453310" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0040281", - "lbl": "Very frequent", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "ORCID:0000-0002-5316-1399" - } - ], - "definition": { - "val": "Present in 80% to 99% of the cases.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Very frequent (99-80%)", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "ORPHA:453311" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0040282", - "lbl": "Frequent", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "ORCID:0000-0002-5316-1399" - } - ], - "definition": { - "val": "Present in 30% to 79% of the cases.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "Frequent (79-30%)", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "ORPHA:453312" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/HP_0040283", - "lbl": "Occasional", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "ORCID:0000-0002-5316-1399" - } - ], - "definition": { - 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Depending on the muscle groups involved and the way they are affected, the movement features of a motor onset seizure may be simple or more complex." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#plural_form", + "pred" : "hasExactSynonym", + "val" : "Focal motor seizures" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Localised motor seizure" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Localised motor seizures" + }, { + "pred" : "hasExactSynonym", + "val" : "Localized motor seizure" + }, { + "pred" : "hasExactSynonym", + "val" : "Localized motor seizures", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Partial motor seizure" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#plural_form", + "pred" : "hasExactSynonym", + "val" : "Partial motor seizures", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Segmental motor seizure" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:128612007" + }, { + "val" : "SNOMEDCT_US:82401000" + }, { + "val" : "UMLS:C0016399" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2011-10-18T02:33:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011297", + "lbl" : "Abnormal digit morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A morphological abnormality of a digit, i.e., of a finger or toe.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp.obo#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of digit" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of fingers or toes" + }, { + "pred" : "hasExactSynonym", + "val" : "Digital anomalies" + } ], + "xrefs" : [ { + "val" : "UMLS:C3550704" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2012-02-11T07:16:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011420", + "lbl" : "Age of death", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The age group when the cessation of life happens.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C1546180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011421", + "lbl" : "Death in adolescence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Death during adolescence, the period between childhood and adulthood (roughly between the ages of 10 and 16 years).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#layperson", + "pred" : "hasExactSynonym", + "val" : "Death in adolescence" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023368" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2012-03-16T06:38:44Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011432", + "lbl" : "Elevated maternal circulating alpha-fetoprotein concentration", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Increase in the levels of maternal serum alpha-fetoprotein levels during pregnancy.", + "xrefs" : [ "PMID:32039804" ] + }, + "comments" : [ "Increased levels of maternal serum alpha-fetoprotein is often part of the triple (AFP, Estriol, and human chorionic gonadotropin) or quadruple screening tests (AFP, estriol, human chorionic gonadotropin and Inhibin A) for congenital birth defects. It can be seen in fetal neural tube defects (NTD), abdominal wall defects, congenital renal disease, esophageal atresia, other fetal distress situations (eg, threatened abortion and fetal demise), multiple pregnancy, placental chorioangioma and placental lakes and other fetal and maternal conditions. Association with various adverse pregnancy outcomes reported. Usually assessed in second trimester and values above 2.5 MoM considered as significantly increased. For NTD, a screen-negative result indicates that the calculated alpha-fetoprotein (AFP) multiple of the median (MoM) falls below the established cutoff of 2.50 MoM. A negative screen does not guarantee the absence of neural tube defects. A screen-positive result indicates that the calculated AFP MoM is 2.50 or greater and may indicate an increased risk for open NTD. The actual risk depends on the level of AFP and the individual's pretest risk of having a child with NTD based on family history, geographical location, maternal conditions such as diabetes and epilepsy, and use of folate prior to conception. A screen-positive result does not infer a definitive diagnosis of a NTD but indicates that further evaluation should be considered. Reduced levels of alpha-fetoprotein can be seen in some fetal disorders such as Down syndrome." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Elevated maternal serum alpha-fetoprotein" + }, { + "pred" : "hasExactSynonym", + "val" : "High MSAFP MoM" + }, { + "pred" : "hasExactSynonym", + "val" : "High maternal circulating alpha-fetoprotein concentration" + }, { + "pred" : "hasExactSynonym", + "val" : "High maternal serum alpha-fetoprotein" + }, { + "pred" : "hasExactSynonym", + "val" : "High maternal serum alpha-fetoprotein MoM" + }, { + "pred" : "hasExactSynonym", + "val" : "Increased maternal serum alpha-fetoprotein level" + }, { + "pred" : "hasExactSynonym", + "val" : "MSAFP MoM>2.5" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023361" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2012-03-17T07:45:07Z" + }, { + "pred" : 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} ], + "xrefs" : [ { + "val" : "UMLS:C4021149" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2012-03-17T07:48:26Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011435", + "lbl" : "Low maternal circulating PAPP-A concentration", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormally low concentration of serum PAPP-A (pregnancy associated plasma protein A), as compared to normal values for gestational-age.", + "xrefs" : [ "PMID:19038077", "https://orcid.org/0000-0002-6410-0882" ] + }, + "comments" : [ "Reduced levels of alpha-fetoprotein can be seen in some fetal disorders such as Down syndrome." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Low maternal serum PAPP-A" + } ], + 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In human obstetrics, gestational age refers to the fertilization age plus two weeks. This is approximately the duration since the woman's last menstrual period began." ], + "xrefs" : [ { + "val" : "UMLS:C4023348" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2012-03-25T06:57:48Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011461", + "lbl" : "Fetal onset", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Onset prior to birth but after 8 weeks of embryonic development (corresponding to a gestational age of 10 weeks).", + "xrefs" : [ "https://orcid.org/0000-0002-7744-1790" ] + }, + "comments" : [ "The time interval of a gestation is called the gestation period. In human obstetrics, gestational age refers to the fertilization age plus two weeks. This is approximately the duration since the woman's last menstrual period began." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Foetal onset" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023347" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2012-03-25T06:58:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011462", + "lbl" : "Young adult onset", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Onset of disease at the age of between 16 and 40 years.", + "xrefs" : [ "https://orcid.org/0000-0002-6410-0882" ] + }, + "xrefs" : [ { + "val" : "UMLS:C3554568" + } ], + "basicPropertyValues" : [ { + "pred" : 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"id" : "http://purl.obolibrary.org/obo/HP_0012274", + "lbl" : "Autosomal dominant inheritance with paternal imprinting", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of autosomal dominant inheritance involving a gene that is imprinted with paternal silencing.", + "xrefs" : [ "PMID:18678320", "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Since the paternally inherited copy of such genes is silenced normally, only a maternally transmitted mutation leads to disease in this kind of inheritance." ], + "xrefs" : [ { + "val" : "UMLS:C4022976" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2013-04-07T02:19:07Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012275", + "lbl" : "Autosomal dominant inheritance with maternal imprinting", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of autosomal dominant inheritance involving a gene that is imprinted with maternal silencing.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Since the maternally inherited copy of such genes is silenced normally, only a paternally transmitted mutation leads to disease in this kind of inheritance." ], + "xrefs" : [ { + "val" : "UMLS:C4022975" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2013-04-07T02:54:09Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012536", + "lbl" : "Maternal anticardiolipin antibody positive", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The presence of circulating autoantibodies to anticardiolipin in the mother.", + "xrefs" : [ "PMID:1495720", "PMID:9722063", "https://orcid.org/0000-0001-5208-3432" ] + }, + "comments" : [ "There have been reports of cerebral infarction in a newborns in association with elevated maternal anticardiolipin antibodies." ], + "xrefs" : [ { + "val" : "UMLS:C4022860" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2013-12-15T10:20:51Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012546", + "lbl" : "Skewed maternal X inactivation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A deviation from equal (50%) inactivation of each parental X chromosome in maternal cells.", + "xrefs" : [ "PMID:18097476", "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "X chromosome inactivation (XCI) is the process by which one of the two copies of the X chromosome present in females is inactivated in order to achieves dosage equivalency for X-linked genes between XY males and XX females. An individual cell's decision to inactivate either the paternal or maternal X is made early in development, at approximately the time of implantation, such that normally there is a roughly equal distribution of either X being active. A deviation from equality is known as skewing, with common criteria for \"skewed\" inactivation being arbitrarily defined as the observation of inactivation of the same allele in 75% or 80% of cells (and very skewed inactivation resulting in 90% or 95% of cells with the same allele inactive). For some X-linked diseases there is strong selection in the heterozygous carrier in favor of cells bearing the mutation on the silenced inactive X, and thus, assessment of XCI skewing in female family members can be suggestive of carrier status." ], + "xrefs" : [ { + "val" : "UMLS:C4022856" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2013-12-21T09:22:57Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012638", + "lbl" : "Abnormal nervous system physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A functional anomaly of the nervous system.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of nervous system physiology" + } ], + "xrefs" : [ { + "val" : "UMLS:C4022811" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-01-19T08:02:46Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012823", + "lbl" : "Clinical modifier", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Note that some of the terms, such as Intellectual disability, have children terms such as Severe intellectual disability that represent precomposed combinations of modifiers and phenotypic abnormality terms. This done where the medical community commonly uses these terms with a fixed meaning (for instance, the Intellectual disability terms are used with specific IQ ranges). For computational reasoning, the semantics are intended to be the same as if there was a combination of the phenotype term and the clinical modifier term." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Phenotypic modifier" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021064" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T06:34:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012824", + "lbl" : "Severity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The intensity or degree of a manifestation.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Synonymous with PATO:0000049, intensity." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Intensity" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:103370009" + }, { + "val" : "UMLS:C0522510" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T06:39:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012825", + "lbl" : "Mild", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Having a relatively minor degree of severity. For quantitative traits, a deviation of between two and three standard deviations from the appropriate population mean.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "PATO:0000394, mild." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#layperson", + "pred" : "hasExactSynonym", + "val" : "Mild" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:446411000124101" + }, { + "val" : "UMLS:C1513302" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T06:41:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012826", + "lbl" : "Moderate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Having a medium degree of severity. For quantitative traits, a deviation of between three and four standard deviations from the appropriate population mean.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "PATO:0000395, moderate." ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:446421000124109" + }, { + "val" : "SNOMEDCT_US:6736007" + }, { + "val" : "UMLS:C0205081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T06:48:12Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012827", + "lbl" : "Borderline", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Having a minor degree of severity that is considered to be on the boundary between the normal and the abnormal ranges. For quantitative traits, a deviation of that is less than two standard deviations from the appropriate population mean.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "PATO:0000394, mild." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#layperson", + "pred" : "hasExactSynonym", + "val" : "Borderline" + } ], + "xrefs" : [ { + "val" : "UMLS:C0205189" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T06:52:16Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012828", + "lbl" : "Severe", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Having a high degree of severity. For quantitative traits, a deviation of between four and five standard deviations from the appropriate population mean.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "PATO:0000396, severe." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#layperson", + "pred" : "hasExactSynonym", + "val" : "Severe" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:24484000" + }, { + "val" : "UMLS:C0205082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T07:03:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012829", + "lbl" : "Profound", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Having an extremely high degree of severity. For quantitative traits, a deviation of more than five standard deviations from the appropriate population mean.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#layperson", + "pred" : "hasExactSynonym", + "val" : "Profound" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:795002" + }, { + "val" : "UMLS:C0439808" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T07:05:46Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012830", + "lbl" : "Position", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The anatomical localization of the specified phenotypic abnormality.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4019252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T07:18:35Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012831", + "lbl" : "Laterality", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The localization with respect to the side of the body of the specified phenotypic abnormality.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "SNOMEDCT_US:272741003" + }, { + "val" : "UMLS:C0332304" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T07:19:19Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012832", + "lbl" : "Bilateral", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Being present on both sides of the body.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "SNOMEDCT_US:51440002" + }, { + "val" : "UMLS:C0238767" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T07:20:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012833", + "lbl" : "Unilateral", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Being present on only the left or only the right side of the body.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "SNOMEDCT_US:66459002" + }, { + "val" : "UMLS:C0205092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T07:21:12Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012834", + "lbl" : "Right", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Being located on the right side of the body.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Right-sided" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:264180000" + }, { + "val" : "UMLS:C0444532" + } ], + "basicPropertyValues" : [ { + "pred" : 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+ "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012836", + "lbl" : "Spatial pattern", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The pattern by which a phenotype affects one or more regions of the body.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4022711" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T07:25:02Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012837", + "lbl" : "Generalized", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Affecting all regions without specificity of distribution.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "PATO:0002403." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Generalised" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:60132005" + }, { + "val" : "UMLS:C0205246" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2014-06-06T07:25:58Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012838", + "lbl" : "Localized", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Being confined or restricted to a particular location.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "PATO:0000627." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#uk_spelling", + "pred" : 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+ "meta" : { + "definition" : { + "val" : "Applies to a lesion that is localized on the arm or leg." + }, + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "Skin lesions on limbs" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-10-26T12:26:31Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0020070", + "lbl" : "Exposure to humid conditions", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A history of living in an environment characterized by excess moisture and heat, tropical conditions, or muggy weather." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-10-26T12:28:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0020121", + "lbl" : "Conception by assisted reproductive technology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A history of conception by an assisted reproductive technology such as in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), and cryopreservation.", + "xrefs" : [ "PMID:28844405" ] + }, + "comments" : [ "Assisted reproductive technology is used primarily for infertility treatments to achieve pregnancy." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-07-02T16:46:09Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0020138", + "lbl" : "History of recent animal bite", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Medical history of a recent bite injury due to an animal.", + "xrefs" : [ "PMID:26179017" ] + }, + "comments" : [ "The spectrum of injury is broad and infectious complications, generally due to unusual pathogens, are common." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-07-05T17:44:09Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0020139", + "lbl" : "History of recent insect bite", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Medical history of a recent bite injury due to an insect.", + "xrefs" : [ "PMID:24364549" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-07-05T17:46:38Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0020140", + "lbl" : "History of recent tick bite", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Medical history of a recent bite injury due to a tick.", + "xrefs" : [ "PMID:24364549" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-07-05T17:48:14Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0020219", + "lbl" : "Motor 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"Triggered by ethanol ingestion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by drinking or otherwise ingesting ethanol." + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#layperson", + "pred" : "hasBroadSynonym", + "val" : "Triggered by alcohol ingestion" + }, { + "pred" : "hasExactSynonym", + "val" : "Ethanol ingestion triggered symptoms" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-10T13:50:14Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025212", + "lbl" : "Triggered by fasting", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked 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"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025256", + "lbl" : "Ameliorated by heat", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by heat (including fever)." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Heat improves condition" + }, { + "pred" : "hasExactSynonym", + "val" : "Heat improves symptom" + }, { + "pred" : "hasNarrowSynonym", + "val" : "Fever improves condition" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-17T14:20:45Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025257", + "lbl" : "Ameliorated by carbohydrate ingestion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by eating or drinking carbohydrates including glucose (sugar)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-17T14:21:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025275", + "lbl" : "Lateral", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that is located farther from the median plane or midline of the body or of the referenced structure." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T14:47:04Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025279", + "lbl" : "Migratory", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T15:18:09Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025280", + "lbl" : "Pain characteristic", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A pain characteristic is defined as a subjective category or type of pain." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T15:21:51Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025281", + "lbl" : "Sharp", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to pain that is described as sharp, i.e., sudden and severe." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Stabbing pain" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T15:23:03Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025282", + "lbl" : "Dull", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to pain that is dull, i.e., not severe but that continues over a long period of time." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Dull pain" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T15:23:43Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025283", + "lbl" : "Tender", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to pain that is tender, i.e., elicited by touching the affected body part." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T15:25:03Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025284", + "lbl" : "Sleep-interrupting", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to pain that wakes the affecting individual from sleep." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T15:26:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025285", + "lbl" : "Aggravated by", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An aggravating factor is defined as an external factor that leads to a sign or symptom that is already present getting worse or becoming more severe." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Exacerbated by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T15:29:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025286", + "lbl" : "Aggravated by activity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to a sign or symptom that is aggravated by activity, exertion, or exercise." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Aggravated by exercise" + }, { + "pred" : "hasExactSynonym", + "val" : "Aggravated by exertion" + }, { + "pred" : "hasExactSynonym", + "val" : "Worse with activity" + }, { + "pred" : "hasExactSynonym", + "val" : "Worsened by activity" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T15:30:58Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025287", + "lbl" : "Axial", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that is situated in the central part of the body, in the head and trunk as distinguished from the limbs." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T15:34:25Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025290", + "lbl" : "Upper-body predominance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that affects the arms, trunk, head more than the legs." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T16:11:12Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025291", + "lbl" : "Lower-body predominance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that affects the legs more than the arms, trunk, head." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T16:12:27Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025292", + "lbl" : "Acral", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that affects the distal portions of limbs (hand, foot) and head (ears, nose)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T16:15:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025293", + "lbl" : "Distributed along Blaschko lines", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality whose localization corresponds to the lines of Blaschko, which correspond to the lineage of epithelia cells. Blaschko lines are normally invisible but may become apparent with certain skin diseases and then can be seen to be distributed in lines horizontal to the body.", + "xrefs" : [ "PMID:17061271" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T16:16:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025294", + "lbl" : "Dermatomal", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality whose localization corresponds to the dermatomes, i.e., the nerve root distribution.", + "xrefs" : [ "PMID:19772560" ] + }, + "comments" : [ "This distribution can be seen with certain skin findings such as shingles. The term radicular is used to describe a dermatomal distribution of nerve root pain." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Radicular" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T16:17:51Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025295", + "lbl" : "Herpetiform", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality whose distribution and appearance resembles that of the grouped umbilicated vesicles seen in herpes simplex and herpes zoster infections." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T16:19:13Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025296", + "lbl" : "Morbilliform", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality whose distribution and appearance resembles that of measles, i.e., maculopapular lesions that are red and roughly 2 to 10 mm in diameter and may be partially confluent." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T16:20:14Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025297", + "lbl" : "Prolonged", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to an abnormality whose duration is extended over a longer period of time than is expected or usual (e.g., prolonged fever lasts longer than one usually sees with an infection)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-18T16:26:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025301", + "lbl" : "Nocturnal", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that occurs in or is exacerbated during the night." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-20T12:30:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025302", + "lbl" : "Diurnal", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign, symptom, or other abnormality that occurs in or is exacerbated in the day time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-20T12:31:12Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025303", + "lbl" : "Episodic", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to a sign, symptom, or other manifestation that occurs multiple times at usually irregular intervals. The occurrences are separated by an interval in which the sign, symptom, or manifestation is not present." + }, + "comments" : [ "In our definition, episodic is synonymous with intermittent and recurrent. The term does not imply any particular temporal pattern of the recurrence." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#layperson", + "pred" : "hasExactSynonym", + "val" : "Now and then" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-21T00:51:43Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025304", + "lbl" : "Periodic", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign, symptom, or other manifestation that recurs with a fixed time interval, i.e., the symptom-free periods are always of the same length." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Cyclic" + }, { + "pred" : "hasExactSynonym", + "val" : "Cyclical" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-21T00:55:09Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025305", + "lbl" : "Quotidian", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign, symptom, or other manifestation that is episodic with a fixed time interval of one day (24 hours)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-21T00:57:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025306", + "lbl" : "Acute emergence over minutes", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Acute appearance of disease manifestations in a period of minutes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-21T01:00:35Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025307", + "lbl" : "Acute emergence over hours", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Acute appearance of disease manifestations in a period of hours." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-21T01:01:25Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025308", + "lbl" : "Acute emergence over days", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Acute appearance of disease manifestations in a period of days." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-21T01:01:46Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025315", + "lbl" : "Exacerbated by head trauma", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is worsened, aggravated, or exacerbated by head trauma." + }, + "comments" : [ "Childhood ataxia with central nervous system hypomyelination/vanishing white matter disease is an autosomal recessive disorder characterized by ataxia, spasticity, and variable optic atrophy. Chronic progressive decline can be exacerbated by rapid deterioration during febrile illnesses or following head trauma." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-21T02:22:58Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025334", + "lbl" : "Triggered by emotion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by a strong spontaneously arising mental state, reaction or feeling (emotion)." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Emotion triggered symptoms" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2017-02-12T11:38:35Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025352", + "lbl" : "Typically de novo", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Description of conditions that are exclusively or predominantly observed to display de novo variants. In some cases, this may be due to the limited reproductive fitness of affected individuals.", + "xrefs" : [ "PMID:22805709" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Autosomal dominant germline de novo mutation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2017-02-13T00:19:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025377", + "lbl" : "Triggered by exertion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by exertion or physical exercise." + }, + "comments" : [ "For convenience, several HPO terms exist with the phrase 'Exercise-induced' in their label. This is meant to be logically equivalent to the combination of the basis term and this modifier." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Exertion triggered symptoms" + }, { + "pred" : "hasExactSynonym", + "val" : "Triggered by physical exercise" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2017-04-08T13:36:52Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025708", + "lbl" : "Early young adult onset", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Onset of disease at an age of greater than or equal to 16 to under 19 years." + }, + "comments" : [ "This term includes the full 16th year of age up to the completed 18th year of age (i.e., less than the 19th birthday)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-01-31T14:14:12Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025709", + "lbl" : "Intermediate young adult onset", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Onset of disease at an age of greater than or equal to 19 to under 25 years." + }, + "comments" : [ "This term includes the full 19th year of age up to the completed 25th year of age (i.e., less than the 25th birthday)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-01-31T14:14:12Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025710", + "lbl" : "Late young adult onset", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Onset of disease at an age of greater than or equal to 25 to under 40 years." + }, + "comments" : [ "This term includes the full 25th year of age up to the completed 40th year of age (i.e., less than the 40th birthday)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-01-31T14:14:12Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025758", + "lbl" : "Characteristic of mass", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A mass is a general term for a lump or growth that may be caused by the abnormal growth of cells, a cyst, hormonal changes, or an immune reaction. This term refers to a property (characteristic) of a mass." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-07-20T09:44:55Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025759", + "lbl" : "Mobile lump", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This modifier is applied to a palpable mass or swelling in the body that can be moved or shifted under the skin when pressed or manipulated." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Mobile mass" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-07-20T09:46:13Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025760", + "lbl" : "Immobile lump", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This modifier is applied to a palpable mass or swelling in the body that cannot be moved or shifted under the skin when pressed or manipulated." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Immobile mass" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-07-20T09:47:48Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025761", + "lbl" : "Painless mass", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This modifier is applied to a palpable mass or swelling in the body that does not elicit pain upon palpation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-07-20T09:49:39Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025765", + "lbl" : "Rubber-like lump", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This modifier is applied to a palpable mass or swelling in the body that has a rubber-like consistency, that is, it is soft and somewhat compressible." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Rubber-like mass" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-07-21T11:55:49Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025788", + "lbl" : "Radiographic modifier", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A characteristic of a lesion on radiography." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Radiographic quality" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-08-06T06:13:18Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025789", + "lbl" : "Radiolucent", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a lesion that allows x-rays to penetrate through them and expose the receptor (radiolucency). Soft tissues appear black or dark on the processed radiograph and are called radiolucent." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Radiolucent appearance" + }, { + "pred" : "hasExactSynonym", + "val" : "Radiolucent character" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-08-06T06:15:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025790", + "lbl" : "Radiodense", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a lesion that attenuates X-rays and appears radiodense (white) on a radiograph." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-08-06T06:19:10Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025803", + "lbl" : "Mucocutaneous lesion painful", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to pain that colocalizes with lesions in the skin or mucous membranes." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Skin or mucosal lesions painful" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-03-01T12:27:12Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025804", + "lbl" : "Painful lymphadenopathy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to pain that is localizes to a swollen lymph node." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Lymph node pain" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-03-01T12:34:52Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025820", + "lbl" : "Offspring of consanguineous relationship", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The parents of the index patient are related as second cousins or closer." + }, + "comments" : [ "Consanguinity has a major role in congenital and genetic diseases." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Consanguineous" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-04-24T16:26:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025849", + "lbl" : "Localized along nerve distribution", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Refers to findings sich as paresthesias or weakness that are distributed according to the anatomical location of a periperipheral nerve." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-04T13:10:27Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030244", + "lbl" : "Maternal fever in pregnancy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The occurrence of an elevated body temperature of the mother during pregnancy.", + "xrefs" : [ "PMID:24567014", "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "There is evidence to suugest that maternal fever during pregnancy may negatively affect offspring healthneural tube defects, congenital heart defects, and oral clefts, in which meta-analyses suggested between a 1.5- and nearly 3-fold increased risk with fever exposure in the first trimester." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Maternal fever during pregnancy" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021041" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030245", + "lbl" : "Intrapartum fever", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The occurrence of maternal fever during labor.", + "xrefs" : [ "PMID:11430951", "PMID:8135133", "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Intrapartum fever may indicate chorioamnionitis. Intrapartum fever is an important predictor of neonatal morbidity and infection-related mortality." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#layperson", + "pred" : "hasExactSynonym", + "val" : "Maternal fever during labor", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Maternal fever during labour" + } ], + "xrefs" : [ { + "val" : "UMLS:C3829514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030246", + "lbl" : "Maternal first trimester fever", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The occurrence of fever in a mother during the first trimester of pregnancy.", + "xrefs" : [ "PMID:24917213", "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4022561" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030645", + "lbl" : "Central", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that is located close to the median plane or midline of the body or of the referenced structure." + }, + "xrefs" : [ { + "val" : "SNOMEDCT_US:26216008" + }, { + "val" : "UMLS:C0205099" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030646", + "lbl" : "Peripheral", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "SNOMEDCT_US:14414005" + }, { + "val" : "UMLS:C0205100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030647", + "lbl" : "Paracentral", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "UMLS:C4073110" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030648", + "lbl" : "Midperipheral", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Mid-peripheral" + } ], + "xrefs" : [ { + "val" : "UMLS:C4073111" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030649", + "lbl" : "Pericentral", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "UMLS:C4073112" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030650", + "lbl" : "Focal", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "SNOMEDCT_US:87017008" + }, { + "val" : "UMLS:C0205234" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030651", + "lbl" : "Multifocal", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "SNOMEDCT_US:524008" + }, { + "val" : "UMLS:C0205292" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030674", + "lbl" : "Antenatal onset", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Onset prior to birth.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Intrauterine onset" + }, { + "pred" : "hasExactSynonym", + "val" : "Onset in utero" + }, { + "pred" : "hasExactSynonym", + "val" : "Prenatal onset" + } ], + "xrefs" : [ { + "val" : "UMLS:C2673646" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2015-12-23T15:25:45Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031135", + "lbl" : "Triggered by physical trauma", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by exposure to a trauma (injury to tissue)." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Physical trauma triggered symptoms" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2017-06-10T13:29:55Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031167", + "lbl" : "Triggered by ingestion of potassium-rich food", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by eating or drinking foods rich in potassium.", + "xrefs" : [ "PMID:19472919" ] + }, + "comments" : [ "In contrast to paramyotonia congenita or hyperkalaemic periodic paralysis, potassium-aggravated myotonias (PAM) patients show no muscle weakness and hardly any cold sensitivity. However, they show an aggravation of their myotonia after ingestion of potassium, which distinguishes them from patients with chloride channelopathies." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Potassium-rich food triggered symptoms" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#abbreviation", + "pred" : "hasExactSynonym", + "val" : "Triggered by ingestion of K-rich food" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2017-06-18T19:18:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031362", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "http://purl.obolibrary.org/obo/IAO_0000227" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/HP_0000007" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031375", + "lbl" : "Refractory", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is difficult to treat or cure." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2017-09-02T01:54:32Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031437", + "lbl" : "Pregnancy exposure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Exposure of pregnant women to toxins from any source, such as environmental toxins or chemicals, that may potentially cause problems such as miscarriage, preterm delivery, low birth weight, and, in some cases, developmental delays in infants.", + "xrefs" : [ "https://orcid.org/0000-0002-6387-4317" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Exposure during pregnancy" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2017-09-16T13:01:58Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031450", + "lbl" : "Polycyclic", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A distribution of skin lesions resembling multiple merged circles. For instance, this can be seen with multiple urticarial wheals as the individual, circular wheals resolve and merge." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2017-09-17T15:00:02Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031456", + "lbl" : "Ectopic pregnancy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A pregnancy in which the fertilized egg inserts in a location outside of the main cavity of the uterus (usually in the Fallopian tube)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2017-09-17T15:55:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031796", + "lbl" : "Recurrent", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign, symptom or manifestation that occurs multiple times separated by intervals in which the sign, symptom, or manifestation is not present." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Intermittent" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2018-02-25T14:40:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031797", + "lbl" : "Clinical course", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "Natural history of disease" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2018-02-25T14:55:46Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031914", + "lbl" : "Fluctuating", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Varying irregularly over time in severity, amount, or amplitude." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2018-07-01T21:29:25Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031915", + "lbl" : "Stable", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This modifier can be applied to a phenotypic feature that does not vary in severity or amount over time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2018-07-01T21:31:19Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032113", + "lbl" : "Semidominant inheritance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A mode of inheritance that is observed for traits related to a gene encoded on chromosomes in which a trait can manifest in a monoallelic (e.g. heterozygotes) and biallelic (e.g. homozygotes, compound heterozygotes) state, with similar or differing phenotype severity present dependent on the number of alleles affected.", + "xrefs" : [ "https://orcid.org/0000-0001-5243-225X", "https://orcid.org/0000-0001-5298-0168", "https://orcid.org/0000-0002-2650-2426", "https://orcid.org/0000-0002-5655-9589", "https://orcid.org/0000-0002-6647-5493", "https://orcid.org/0000-0002-6733-369X", "https://orcid.org/0000-0002-8016-0076", "https://orcid.org/0000-0002-8218-5111" ] + }, + "comments" : [ "Familial hypercholesterolemia is an example of a disease with this inheritance pattern." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Semidominant mode of inheritance" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2018-11-17T14:33:51Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032223", + "lbl" : "Blood group", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any of the various types of human blood whose antigen characteristics determine compatibility in transfusion. While the ABO and Rhesus systems are the most well known, there are in total about 300 different blood type antigens distributed across 34 different blood type systems.", + "xrefs" : [ "PMID:26085552" ] + }, + "comments" : [ "At present, there are 34 blood group systems recognized by the International Society for Blood Transfusion." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-01-24T11:33:51Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032224", + "lbl" : "ABO blood group", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The ABO system consists of A and B antigens and antibodies against these antigens.", + "xrefs" : [ "PMID:15373665", "PMID:26085552" ] + }, + "comments" : [ "The ABO histo-blood group consists of two antigens (A and B antigens) and four blood types (types A, B, AB, and O). The A and B antigens are the product of the ABO gene and are autosomal codominant. The group O phenotype is an autosomal-recessive phenotype due to the homozygous inheritance of two null ABO alleles. Group O individuals express the H antigen, the biosynthetic precursor to A and B antigens. ABO, therefore, is the blood type, whereas A, B, and H refer to the antigens." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-01-24T11:40:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032316", + "lbl" : "Family history", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Information about close relatives of an individual who is the proband of a study or who is being investigated with the goal of identifying a medical diagnosis. Usually, the family history includes information from three generations of relatives, including children, brothers and sisters, parents, aunts and uncles, nieces and nephews, grandparents, and cousins." + }, + "comments" : [ "This subontology is intended to help record summary information about family members if only a limited amount of information is available or required." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-14T11:40:50Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032317", + "lbl" : "Family history of cancer", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A close blood relative had cancer." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-14T11:43:34Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032318", + "lbl" : "Family history of heart disease", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A close blood relative had heart disease." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-14T11:45:48Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032319", + "lbl" : "Health status", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Health status of a family member with respect to the disease being investigated in a proband." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-14T11:46:18Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032320", + "lbl" : "Affected", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This term applies to a family member who is diagnosed with the same condition as the individual who is the primary focus of investigation (the proband)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-14T11:47:51Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032321", + "lbl" : "Unaffected", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This term applies to a family member in whom the diagnosis that is the primary focus of investigation is excluded." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-14T11:48:40Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032322", + "lbl" : "Healthy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "No history of any serious disease, including the disease being investigated in the proband." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-14T11:49:52Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032365", + "lbl" : "Exacerbated by aspirin exposure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to a sign or symptom that is worsened by ingestion of aspirin." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-23T17:36:45Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032370", + "lbl" : "Blood group A", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "ABO phenotype A, corresponding to the genotype AO or AA." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-23T18:59:31Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032373", + "lbl" : "Duffy blood group", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The Duffy blood group system is based on the presence of a glycoprotein termed Fy that is on the surface of erythrocytes and some other cells. There are two Duffy antigens named Fya and Fyb, and thus there are four Duffy phenotypes: a+b+, a+b-, a-b+,a-b-.", + "xrefs" : [ "PMID:19480920" ] + }, + "comments" : [ "FY has two major codominant alleles, FYA and FYB, which result from a SNP (125G>A), and the corresponding Fya and Fyb antigens differ by a single amino acid (G42D). Individuals who are homozygous for a -33T>C SNP in the erythroid promoter region of the FYB allele have the phenotype Fy(a-b-) and do not express Duffy antigens on their RBCs." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-24T13:37:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032374", + "lbl" : "Duffy Fya positivity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Presence of the Duffy Fya antigen.", + "xrefs" : [ "PMID:19480920" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-24T13:40:29Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032375", + "lbl" : "Duffy Fyb positivity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Presence of the Duffy Fyb antigen.", + "xrefs" : [ "PMID:19480920" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-24T13:42:55Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032382", + "lbl" : "Uniparental disomy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Inheritance of both homologues of a chromosome pair from the same parent." + }, + "comments" : [ "UPD may comprise the whole chromosome, or just part of it (segmental UPD). Isodisomy is presented as 2 copies from the same chromosome of a parent, and heterodisomy is presented as 1 copy of each of the 2 homologues from the same parent. UPD is related to abnormalities formed during meiosis, fertilization, and mitosis. There are 5 different mechanisms that explain the etiology of UPD, including Trisomic rescue; Nullisomic gamete complementation; Monosomic rescue; Mitotic aberrations; and Structural chromosome aberrations. If prenatal genetic analysis reveals a homologous robertsonian translocation, the risk of fetal UPD is very high, and a marker chromosome or chromosome aneuploidy can be associated with UPD." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#abbreviation", + "pred" : "hasExactSynonym", + "val" : "UPD" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-24T14:58:52Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032383", + "lbl" : "Uniparental heterodisomy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of uniparental disomy in which the two different chromosomes (or chromosome segments) of the same parent are transmitted.", + "xrefs" : [ "PMID:25547535" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-24T15:04:03Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032384", + "lbl" : "Uniparental isodisomy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of uniparental disomy in which the two identical chromosomes (or chromosome segments) of the same parent are transmitted.", + "xrefs" : [ "PMID:25547535" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-02-24T15:05:18Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032440", + "lbl" : "Blood group B", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "ABO phenotype B, corresponding to the genotype BO or BB." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-03-03T16:34:03Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032441", + "lbl" : "Blood group AB", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "ABO phenotype AB, corresponding to the genotype AB." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-03-03T16:37:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032442", + "lbl" : "Blood group O", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "ABO phenotype O, corresponding to the genotype OO." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-03-03T16:37:48Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032443", + "lbl" : "Past medical history", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "In a medical encounter, the physician generally will interview the patient about his or her current problem, and may perform additional testing. The past medical history (PMH) in contrast records information about the patient's medical, personal and family history that might be relevant to the presenting illness or to provide optimal clinical management. The PMH generally includes (if relevant) other major illnesses, hospitalizations, surgeries, injuries, allergies, gynecologic and obstetric history, family history, personal history including occupational history, alcohol and drug use, etc." + }, + "comments" : [ "This subontology of the HPO is not intended to provide all needed terms to describe the past medical history, but rather to be combined with other ontologies such as MONDO in order to capture information that is often needed to properly assess phenotypic findings related to a presenting medical problem." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-03-03T16:39:26Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032444", + "lbl" : "Status post organ transplantation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The affected individual has received an organ transplant previous to the current medical encounter." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "s/p organ transplantation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-03-03T16:49:25Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032467", + "lbl" : "Past obstetric history", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Information about past pregnancies including gravidity (number of times a woman has been pregnant, regardless of the outcome), parity (total number of births), gestational age of births, and medical conditions related to past pregnancies." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Maternal medical history" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-04-04T09:46:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032468", + "lbl" : "History of stillbirth", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "One or more previous pregnancies resulted in stillbirth, defined as death of a fetus in the later stages of pregnancy (definitions in the literature vary, with cut-offs ranging from 20 to 28 weeks gestation)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-04-04T09:53:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032500", + "lbl" : "Exacerbated by tobacco use", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to a sign or symptom that is worsened by smoking tobacco products." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Aggravated by tobacco use" + }, { + "pred" : "hasExactSynonym", + "val" : "Exacerbated by smoking" + }, { + "pred" : "hasExactSynonym", + "val" : "Smoking or tobacco use exacerbates symptoms" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-23T22:51:26Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032501", + "lbl" : "Exacerbated by contraceptive medication exposure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to a sign or symptom that is worsened by taking contraceptive medication." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Contraceptive pills aggravate symptoms" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-23T22:53:32Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032502", + "lbl" : "Exacerbated by barbiturate exposure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to a sign or symptom that is worsened by taking barbituates." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Barbiturates produce worsening" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-23T22:55:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032503", + "lbl" : "Ameliorated by ethanol ingestion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by drinking alcohol (ethanol)." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Ethanol reduces manifestations" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-23T22:56:25Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032522", + "lbl" : "Ameliorated by immunosuppresion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by treatment with immunosuppresive medication." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Immunosupressive therapy improves condition" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-26T11:24:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032525", + "lbl" : "Exacerbated by acetylcholinesterase inhibitor exposure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to a sign or symptom that is worsened by treatment with an acetylcholinesterase inhibitor such as tensilon (edrophonium) or pyridostigmine (Mestinon)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-26T11:44:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032526", + "lbl" : "Ameliorated by acetylcholinesterase inhibitor", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by an acetylcholinesterase inhibitor such as mestinon or tensilon." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-26T11:47:48Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032534", + "lbl" : "Exacerbated by methylxanthine ingestion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to a sign or symptom that is worsened by ingestion of food containing a methylxanthine compound (for instance, coffee, caffeine, chocolate)." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Methylxanthines produce worsening" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-27T13:08:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032535", + "lbl" : "Cervical (neck)", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that is situated in the neck." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-27T13:12:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032539", + "lbl" : "Joint extensor surface localization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that is situated in extensor surface of the joint. The extensor surface refers to the skin on the opposite side of a joint." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-27T13:48:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032540", + "lbl" : "Joint flexor surface localization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that is situated in flexor surface of the joint. The flexor surface refers to the skin that touches when a joint is bent (flexed)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-27T13:51:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032542", + "lbl" : "Exacerbated by pregnancy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to a sign or symptom that is worsened by being pregnant." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-05-27T15:16:46Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032544", + "lbl" : "Predominant small joint localization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that mainly affects the small joints, including fingers, toes, interphalangeal, metacarpophalangeal, metatarsophalangeal, wrists, ankles, vertebrae, and neck." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-06-12T10:19:53Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032557", + "lbl" : "History of bone marrow transplant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A past medical history of hematopoietic stem cell transplantation involving myeloablative chemoradiotherapy followed by stem cell rescue with autologous or human leukocyte antigen (HLA)-matched stem cells derived from a donor.", + "xrefs" : [ "PMID:24198516" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Status post haematopoietic stem cell transplantation" + }, { + "pred" : "hasExactSynonym", + "val" : "Status post hematopoietic stem cell transplantation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-06-14T11:13:53Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033032", + "lbl" : "Triggered by an abusive adult", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is induced by an abusive adult (usually a parent).", + "xrefs" : [ "PMID:29938745", "https://orcid.org/0000-0002-7371-8158" ] + }, + "comments" : [ "Munchausen syndrome by proxy is not a pediatric condition, but the outward manifestation of an adult psychiatric disorder." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Munchausen syndrome by proxy" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2020-06-13T11:41:12Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033127", + "lbl" : "Abnormality of the musculoskeletal system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anomaly of the musculoskeletal system, which consists of the bones of the skeleton, muscles, cartilage, tendons, ligaments, joints, and other connective tissue. The musculoskeletal system supports the weight of the body, maintains body position and produces movements of the body or of parts of the body." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2020-09-05T13:35:03Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033184", + "lbl" : "Triggered by infection", + "type" : "CLASS", + "meta" : { + "comments" : [ "Applies to a sign or symptom that is provoked or brought about by an infection, that is by invasion and multiplication of microorganisms such as bacteria, viruses, and parasites that are not normally present within the body." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2020-10-04T11:47:16Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033185", + "lbl" : "Triggered by EBV infection", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by infection by the Epstein-Barr virus.", + "xrefs" : [ "PMID:19425169" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Triggered by Epstein Barr virus infection" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2020-10-04T11:48:39Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033198", + "lbl" : "Triggered by viral infection", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by infection by a virus." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2020-10-11T12:16:45Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033349", + "lbl" : "Seizure cluster", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A fourfold or greater increase of usual seizure frequency within a 3-day period, where the patient demonstrates full recovery between seizure events within the cluster. The seizure cluster should be recognizable by the primary clinician, carer or patient.", + "xrefs" : [ "PMID:29871784", "PMID:32305858" ] + }, + "comments" : [ "This term should be used with an HPO term for the appropriate type of seizure to denote clustered occurrence of seizures. There is no consensus within the medical community regarding the definition of a seizure cluster, where limitations of current clinical definitions include poor sensitivity and specificity. The proposed definition is meant to serve as a placeholder until a more robust definition, likely facilitated by technological advances in seizure tracking devices and personalized cluster identification is agreed upon." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Acute repetitive seizures" + }, { + "pred" : "hasExactSynonym", + "val" : "Crescendo seizures" + }, { + "pred" : "hasExactSynonym", + "val" : "Cyclical seizures" + }, { + "pred" : "hasExactSynonym", + "val" : "Recurrent seizures" + }, { + "pred" : "hasExactSynonym", + "val" : "Seizure flurries" + }, { + "pred" : "hasExactSynonym", + "val" : "Serial seizures" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2020-11-30T22:08:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033623", + "lbl" : "Birth history", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Information about the delivery and health status at birth typically elicited as a part of the past medical history." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-01-30T23:06:26Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033624", + "lbl" : "History of congenital CMV infection", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A congenital cytomegalovirus (CMV) infection of the newborn can follow either a primary or recurrent maternal infection. Jaundice, petechiae, and hepatosplenomegaly are the most frequently noted clinical triad in symptomatic infants. Affected infants may develop permanent disabilities such as hearing loss, vision loss, motor and cognitive deficits.", + "xrefs" : [ "PMID:29503048" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "History of congenital cytomegalovirus infection" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-01-30T23:08:18Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033763", + "lbl" : "Death in adulthood", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Cessation of life at the age of 16 years or later." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-04-30T11:20:03Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033764", + "lbl" : "Death in middle age", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Death between the age of 40 and 60 years.", + "xrefs" : [ "https://orcid.org/0000-0002-6410-0882" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-04-30T11:20:49Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033765", + "lbl" : "Death in late adulthood", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Death at an age of at least 60 years.", + "xrefs" : [ "https://orcid.org/0000-0002-6410-0882" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-04-30T11:21:09Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033789", + "lbl" : "Triggered by cheese ingestion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by eating cheese.", + "xrefs" : [ "PMID:9398858" ] + }, + "comments" : [ "Cheese contains tyramine, which is thought to be responsible for tachycardia and hypertension that can be tirggered by eating cheese in persons with Trimethylaminuria." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-05-07T11:11:07Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033793", + "lbl" : "Triggered by food ingestion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by eating a certain food." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-05-07T17:28:49Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033813", + "lbl" : "Perilobular", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Situated or occurring around a lobe of an organ." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-05-09T12:03:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033814", + "lbl" : "Paraseptal", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Characterized by predominant involvement of the distal alveoli and their ducts and sacs. It is characteristically bounded by any pleural surface and the interlobular septa." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-05-09T12:08:03Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033815", + "lbl" : "Bronchocentric", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Centered in bronchi or bronchioles." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-05-09T12:11:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033816", + "lbl" : "Centrilobular", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Located in the center of the secondary pulmonary lobules, which are the functional units of the lungs." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-05-09T12:12:13Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033817", + "lbl" : "Miliary", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Characterized by numerous small lesions said to resemble millet seed." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-05-09T12:13:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033818", + "lbl" : "Reticular", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality whose distribution and appearance resembles a net or network-like structure." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-05-09T12:18:27Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033819", + "lbl" : "Perilymphatic", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality whose distribution and appearance are located at or near lymphatic structures (node or vessel)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-05-09T12:19:16Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033820", + "lbl" : "Apical", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality whose distribution and appearance are located at the apex of an organ. For instance, apical refers to the superior portion of the lung." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-05-09T12:20:29Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034060", + "lbl" : "Triggered by fava bean ingestion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by eating fava beans.", + "xrefs" : [ "PMID:29298156" ] + }, + "comments" : [ "The fava bean plant (Vicia faba) was probably one of the first plants to be domesticated, V. faba contains high concentrations of two beta-glucosides (up to 2% in dry weight): vicine and convicine. On ingestion of fava beans, vicine and convicine undergo hydrolysis by glucosidases present both in the beans and in the gastrointestinal tract, releasing the respective aglycones: divicine (2,6-diamino-4,5-dihydroxypyrimidine) and isouramil (6-amino-2,4,5-trihydroxypyrimidine). These highly reactive redox compounds have antifungal and pesticide activity, which probably helps prevent fava beans from rotting, but the compounds are also capable of triggering a favism attack in persons with glucose-6-phosphate dehydrogenase (G6PD) deficiency." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-11-27T19:36:52Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034195", + "lbl" : "Triggered by muscle relaxant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by exposure to a muscle relaxant such as suxamethonium and mivacurium." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-04-07T13:21:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034197", + "lbl" : "Third trimester onset", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This term refers to a phenotypic feature that was first observed prior to birth during the third trimester, which is defined as 28 weeks and zero days (28+0) of gestation and beyond." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-04-07T15:49:34Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034198", + "lbl" : "Second trimester onset", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This term refers to a phenotypic feature that was first observed prior to birth during the second trimester, which comprises the range of gestational ages from 14 0/7 weeks to 27 6/7 (inclusive)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-04-07T16:11:04Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034199", + "lbl" : "Late first trimester onset", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This term refers to a phenotypic feature that was first observed prior to birth in the first trimester during the early fetal period, which is defined as 11 0/7 to 13 6/7 weeks of gestation (inclusive)." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Early fetal onset" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Early foetal onset" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-04-07T16:13:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034241", + "lbl" : "Prenatal death", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Death of a fetus in the uterus." + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#layperson", + "pred" : "hasExactSynonym", + "val" : "Death before birth" + }, { + "pred" : "hasExactSynonym", + "val" : "Intrauterine death" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-04-10T17:51:32Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034335", + "lbl" : "Inheritance qualifier", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The terms in this hierarchy can be used to specify the context in which inheritance of a disease is typically observed." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Inheritance modifier" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-09-04T11:54:50Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034338", + "lbl" : "Imprinted", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Requires that the abnormal allele be paternal or maternal in origin, depending on the disease-gene relationship. Imprinting refers to a normal developmental process in which either the paternal or maternal allele is inactivated, depending on the specific locus, thus leading to expression from only one copy of the gene. Disease typically manifests when a deleterious variant is inherited from a parent whose copy of the gene would normally be expressed, but not when a deleterious variant is inherited from a parent whose copy of the gene would normally be inactivated." + }, + "comments" : [ "Imprinting disorders can be caused by a variety of mutational mechanisms (including copy number variants, nucleotide variants, and abnormal imprinting patterns) thus requiring some care when designing analytic pipelines." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-09-04T13:13:25Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034339", + "lbl" : "Pseudoautosomal inheritance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A pattern of inheritance observed for alleles in the X-Y identical regions is referred to as pseudoautosomal inheritance, because it resembles the pattern seen for alleles located on autosomes.", + "xrefs" : [ "PMID:18660847" ] + }, + "comments" : [ "The pseudoautosomal regions (PAR1 and PAR2) are short regions of homology between the mammalian X and Y chromosomes. The PAR behave like an autosome and recombine during meiosis. Thus genes in this region are inherited in an autosomal rather than a strictly sex-linked fashion." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Pseudoautosomal region inheritance" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-09-04T13:22:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034340", + "lbl" : "Pseudoautosomal dominant inheritance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of pseudoautosomal inheritance that is dominant and in which heterozygous males and females both manifest a disease phenotype." + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#allelic_requirement", + "pred" : "hasExactSynonym", + "val" : "monoallelic_PAR" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-09-04T13:30:31Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034341", + "lbl" : "Pseudoautosomal recessive inheritance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of pseudoautosomal inheritance that is recessive and in which biallelic males and females both manifest a disease phenotype." + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp.obo#allelic_requirement", + "pred" : "hasExactSynonym", + "val" : "biallelic_PAR" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-09-04T13:36:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034343", + "lbl" : "Requires heterozygosity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A rarely encountered phenomenon in which condition is most severe in the heterozygous state. Such disorders are rare and currently all are X-linked. Most X-linked recessive conditions manifest if hemizygous in males, or biallelic in females, though may have a mild phenotype in the heterozygous state in females." + }, + "comments" : [ "Craniofrontonasal dysplasia due to EFNB1 and PCDH19-related epilepsy are both X-linked recessive and paradoxically more severe in females. Hemizygous males may be mildly affected but seldom manifest the full phenotype. Importantly the mutant allele can be inherited from a normal or very mildly affected father. The mechanism is currently accepted to be due to cellular interference whereby the two distinct cell populations (those with and without the variant) exhibit abnormal cellular interactions in the mosaic state - in women, who are functionally mosaic due to random X inactivation, or mosaic males. The same mechanism could theoretically be applicable to autosomal genes with a mosaic variant." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-09-04T13:51:05Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034344", + "lbl" : "Female-limited expression", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Used to refer to a monogenic trait linked to an autosomal locus in which the phenotypic effects of allelic differences are expressed only in the female sex." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-09-04T14:10:48Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034345", + "lbl" : "Mendelian inheritance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A mode of inheritance of diseases whose pathophysiology can be traced back to deleterious variants in a single gene. The inheritance patterns of these single-gene (monogenic) diseases are often referred to as Mendelian in honor of Gregor Mendel." + }, + "comments" : [ "Mendelian, or monogenic, inheritance of human diseases refers to patterns of transmission of recognizable disease entities. In many cases variability of clinical manifestations is observed and may be related to variation in other genes, environmental factors, or other unknown causes." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-09-04T14:25:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034382", + "lbl" : "Disease remission", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A decrease in or disappearance of signs and symptoms typically associated with a disease course.", + "xrefs" : [ "https://orcid.org/0000-0001-8314-2140" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-09-05T14:19:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034420", + "lbl" : "History of cardiovascular procedure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Indicates that a cardiovascular procedure such as stenting, bypass, catherization was performed on a patient." + }, + "xrefs" : [ { + "val" : "UMLS:0189573" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-11-12T12:05:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034423", + "lbl" : "Triggered by allergens", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by exposure to allergens." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-11-12T12:27:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034432", + "lbl" : "Intertriginous distribution", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to the localization of a skin lesion involving any area of the body where two opposing skin surfaces can touch and rub or chaff.", + "xrefs" : [ "PMID:21396557" ] + }, + "comments" : [ "The word intertrigo comes from the Latin inter (between) and terere (to rub) and reflects the rubbing together of skin against skin to create maceration and irritation, hence, friction dermatitis or chaffing." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Intertriginous distribution of skin lesions" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-11-26T13:08:34Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034433", + "lbl" : "Distributed along skin tension lines", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to the localization of a skin lesion that correspond to skin tension lines, which are linear clefts in the skin that indicate the direction of orientation of the underlying collagen fibers. Skin tension lines are also known as Langer's lines or lines of cleavage." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Distributed along Langer's lines" + }, { + "pred" : "hasExactSynonym", + "val" : "Lesions follow lines of cleavage" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-11-26T13:11:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034439", + "lbl" : "Instep location", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that is situated in the arched middle portion of the foot in front of the ankle joint (i.e., instep)." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Instep localization to skin abnormality" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-11-26T13:40:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034440", + "lbl" : "Ameliorated by ultraviolet light exposure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a skin lesion that is improved or made more bearable by exposure to ultraviolet light (sunshine or phototherapy)." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Ultraviolet exposure improves condition" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-11-26T13:42:56Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034459", + "lbl" : "Ameliorated by lumbar puncture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by lumbar puncture." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Lumbar puncture relieves symptoms" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-12-03T23:21:49Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034516", + "lbl" : "Ameliorated by ketogenic diet", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by following a ketogenic diet." + }, + "comments" : [ "The ketogenic diet is a method of nutrition leading to the increased production of ketone bodies (beta-hydroxybutyrate, acetoacetate and acetone) in the organism and, thus, to a condition of ketosis. This effect comes about by obtaining the greatest energy share from fats and minimizing the consumption of carbohydrates." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Ketogenic diet improves symptoms" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-12-14T13:53:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034533", + "lbl" : "Triggered by monoamine oxidase inhibitor", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by exposure to a monoamine oxidase inhibitor.", + "xrefs" : [ "PMID:30969670" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "MAO inhibitors trigger attacks" + }, { + "pred" : "hasExactSynonym", + "val" : "Triggered by MAO inhibitor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-02-10T13:43:12Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034534", + "lbl" : "Triggered by serotonin reuptake inhibitor", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by exposure to a serotonin reuptake inhibitor.", + "xrefs" : [ "PMID:32119293" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Serotonin uptake inhibitors trigger attacks" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-02-10T13:45:39Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034535", + "lbl" : "Ameliorated by acetazolamide", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by treatment with acetazolamide." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Acetazolamide relieves attacks" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-02-10T13:47:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034536", + "lbl" : "Ameliorated by exposure to medication", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by treatment with a medication. Terms in this subhierarchy are intended to be used for cases in which the fact that a manifestation of a disease responds to a specific treatment can be used in the differential diagnosis." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-02-10T13:49:13Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034537", + "lbl" : "Ameliorated by vitamin B12", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by treatment with vitamin B12." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Vitamin B12 treatment produces improvement" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : 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thrombosis in the mother during a pregnancy.", + "xrefs" : [ "PMID:25401392", "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Maternal thrombophilia has been linked to an increased incidence of placental abruption, as well as other adverse pregnancy outcomes. It is believed that the increased obstetrical risk is mediated through placental vascular dysfunction. Placental thrombosis can then result in subsequent ischemic complications, such as fetal loss, preeclampsia, and fetal growth restriction. Placental abruption has been identified as being part of the spectrum of ischemic placental disease and is postulated to be a chronic disease process (PMID:25401392)." ], + "xrefs" : [ { + "val" : "UMLS:C4280721" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-01-21T16:03:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0040279", + "lbl" : "Frequency", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Class to represent frequency of phenotypic abnormalities within a patient cohort." + }, + "comments" : [ "Aligned with Orphanet" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-5316-1399" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-01T11:44:56Z" + }, { + "pred" : 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"hasExactSynonym", + "val" : "Very frequent (99-80%)" + } ], + "xrefs" : [ { + "val" : "ORPHA:453311" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-5316-1399" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-01T11:44:56Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0040282", + "lbl" : "Frequent", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Present in 30% to 79% of the cases." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Frequent (79-30%)" + } ], + "xrefs" : [ { + "val" : "ORPHA:453312" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-5316-1399" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-01T11:44:56Z" + }, { + "pred" : 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: "Very rare (<4-1%)" + }, { + "pred" : "hasExactSynonym", + "val" : "Very rare (<4-1%)" + } ], + "xrefs" : [ { + "val" : "ORPHA:453314" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-5316-1399" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-01T11:44:56Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0040285", + "lbl" : "Excluded", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Present in 0% of the cases." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Excluded (0%)" + } ], + "xrefs" : [ { + "val" : "ORPHA:453315" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-5316-1399" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2016-12-01T11:44:56Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0040402", + "lbl" : "Nipple localization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is distributed around the nipples or located in the nipples." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-01-02T10:21:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0040406", + "lbl" : "Perimenopausal", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Perimenopause, or the menopausal transition, encompasses that period of time during which physiologic changes mark progression toward a woman's final menstrual period. This phase begins with the onset of menstrual irregularities and continues until a woman reaches menopause, or one year after amenorrhea has occurred. Perimenopause can last for a variable amount of time, the median of which is four years.", + "xrefs" : [ "PMID:29952797" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-01-02T13:17:13Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0040408", + "lbl" : "Ameliorated by menopause", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by menopause." + }, + "comments" : [ "This term may apply to breast fibroadenoma and premenstrual dysphoric disorder." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-01-02T13:51:38Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0040409", + "lbl" : "Fluctuance on palpation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Yielding to alternate pressure by palpating fingers so as to suggest that the area being felt contains fluid." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-01-02T13:53:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0040410", + "lbl" : "History of vasectomy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A medical history of having undergone a vasectomy prior to the current presentation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-01-02T13:55:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0041090", + "lbl" : "Pelvic avulsion fracture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An avulsion fracture (i.e., a type of fracture in which a piece of bone tears away from the site where the muscle attaches to the bone) of a bone of the pelvis.", + "xrefs" : [ "PMID:32106326" ] + }, + "comments" : [ "Pelvic avulsion injuries can occur in both adolescents and adults when either the apophysis is not yet completely fused or the enthesis, i. e. the site of attachment of a tendon or ligament, cannot withstand the tractional force encountered. Anatomically, the enthesis refers to the site of insertion of a tendon or ligament and the adjacent tissues which are functionally related." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Avulsion fractured pelvic region of trunk" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0001-5208-3432" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2020-07-28T16:21:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0045088", + "lbl" : "Clinical relevance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Subontology for annotating phenotypic features as distinctive or minor findings in patients. The subontology is intended to be used to annotate subjective clinical impressions of whether a certain finding is important for the differential diagnosis." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-5316-1399" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-07-09T12:04:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0045089", + "lbl" : "Distinctive finding", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "In clinical parlance, findings are occasionally interpreted as being distinctive or minor, reflecting a subjective clinical impression of the importance of a feature for the differential diagnosis. A minor finding is taken to be one that is likely to have high utility in distinguishing the correct diagnosis from other candidates in the differential." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-5316-1399" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-07-09T12:04:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0045090", + "lbl" : "Minor finding", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "In clinical parlance, findings are occasionally interpreted as being distinctive or minor, reflecting a subjective clinical impression of the importance of a feature for the differential diagnosis. A minor finding is taken to be one that is unlikely to help distinguish the correct diagnosis from other candidates in the differential." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-5316-1399" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2019-07-09T12:04:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100601", + "lbl" : "Eclampsia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An acute and life-threatening complication of pregnancy, which is characterized by the appearance of tonic-clonic seizures, usually in a patient who had developed pre-eclampsia. Eclampsia includes seizures and coma that happen during pregnancy but are not due to preexisting or organic brain disorders.", + "xrefs" : [ "https://orcid.org/0009-0006-4530-3154" ] + }, + "xrefs" : [ { + "val" : "SNOMEDCT_US:15938005" + }, { + "val" : "UMLS:C0013537" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2010-12-27T05:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100602", + "lbl" : "Preeclampsia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Pregnancy-induced hypertension in association with significant amounts of protein in the urine.", + "xrefs" : [ "https://orcid.org/0009-0006-4530-3154" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Pre-eclampsia" + } ], + 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"pred" : "hasExactSynonym", + "val" : "Toxaemia of pregnancy" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:15394000" + }, { + "val" : "SNOMEDCT_US:398254007" + }, { + "val" : "UMLS:C0032914" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2010-12-27T05:27:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100610", + "lbl" : "Maternal hyperphenylalaninemia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A medical history of exposure during the fetal period to hyperphenylalaninemia because the mother had phenylketonuria with inadequate control during pregnancy.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : 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"http://purl.obolibrary.org/obo/HP_4000102", + "lbl" : "Triggered by allopurinol", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is provoked or brought about by exposure to allopurinol." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Allopurinol exposure" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-16T09:11:45Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_4000103", + "lbl" : "Ameliorated by oral zinc supplementation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to a sign or symptom that is improved or made more bearable by oral zinc supplementation." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Zinc oral supplementation produces improvement" + } ], + "basicPropertyValues" : [ { + "pred" : 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by exposure (cutaneous contact) to poison ivy, poison oak, and poison sumac. 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"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000054", + "lbl" : "Multiparity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "History of multiple previous births." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-12-28T15:12:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000055", + "lbl" : "Exposure to aquatic animals", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "History of exposure to aquatic animals.", + "xrefs" : [ "PMID:29493404" ] + }, + "comments" : [ "Mycobacterium marinum is an opportunistic pathogen inducing infection in fresh and marine water fish. Human infections with Mycobacterium marinum have been associated with the exposure of damaged skin to polluted water from fish pools or contacting objects contaminated with infected fish. Fish mycobacteriosis is clinically manifested and characterized in man by purple painless nodules, liable to develop into superficial crusting ulceration with scar formation." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10000" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-12-30T09:25:04Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000058", + "lbl" : "Exacerbation of eyelid lesion by crying", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an eyelid lesion such as hemangiomas or varices that swells upon crying." + }, + "basicPropertyValues" : [ { + "pred" : 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"type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applied to a sign or symptom that is present during pregnancy and becomes worse following birth." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Symptoms worsen in post-partum state" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/9990" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-12-31T08:27:55Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000092", + "lbl" : "Retinoid exposure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "History of having taken retinoids." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Exposure to retinoids" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/9991" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-12-31T08:27:55Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000093", + "lbl" : "Propylthiouracil exposure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "History of having been treated with propylthiouracil." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Exposure to propylthiouracil" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : 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"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000098", + "lbl" : "Contact lens wearer", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A past medical history of wearing contact lenses.", + "xrefs" : [ "PMID:26292204" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/7998" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-12-31T10:32:04Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000103", + "lbl" : "Precipitous labor", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Precipitous labor 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: [ "PMID:33622004" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/7959" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-01-03T21:46:25Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000110", + "lbl" : "Large joint predominance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Refers to a phenotypic abnormality that mainly affect large joints." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/7968" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : 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"http://purl.obolibrary.org/obo/HP_6000136", + "lbl" : "Elbow localization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that is situated in (or predominant in) the elbow." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/7973" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-01-07T09:41:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000138", + "lbl" : "Heel localization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that is situated in (or predominant in) the heel." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Heel predominance" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/7976" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-01-07T09:41:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000162", + "lbl" : "Excessive licorice consumption", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Ingestion of large amounts of licorice.", + "xrefs" : [ "PMID:23185686", "PMID:35321787" ] + }, + "comments" : [ "Licorice is a popular sweetener found in many soft drinks, food products, snacks and herbal medicines. Licorice toxicity is characterized by the symptom triad of hypertension, hypokalemia, and metabolic alkalosis, so-called pseudohyperaldosteronism. The active ingredient in licorice is glycyrrhizin, which is converted to 3beta-monoglucuronyl-18beta-glycyrrhetinic acid (3MGA) and 18beta-glycyrrhetinic acid (GA) in the gut. These active metabolites inhibit the 11beta-hydroxysteroid dehydrogenase type II enzyme and prevent the conversion of cortisol to cortisone. Unlike cortisone, cortisol binds to the mineralocorticoid receptor. This cortisol excess leads to increased potassium and proton excretion as well as to sodium and water retention, with increased systemic resistance. The triad of symptoms typical of classic hyperaldosteronism (Conn syndrome) results from the aldosterone-like effect: hypokalemia, hypertension, and metabolic alkalosis." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/7834" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-01-16T08:09:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000163", + "lbl" : "Shoulder localization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that is situated in (or predominant in) the shoulder." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/7841" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-01-16T08:09:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6000164", + "lbl" : "Pregnancy conceived despite intrauterine device", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Intrauterine devices (IUDs) are used for contraception. 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High spinal injuries often impair cardiorespiratory function, requiring emergent interventions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10804" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-12-03T17:26:54Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001136", + "lbl" : "Femoral nerve distribution", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Paresthesias in anterior/medial aspect of the thigh (anterior and medial cutaneous nerves of the thigh) and/or medial aspect of the lower leg and foot (saphenous distribution). 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Patients also may report visual symptoms, which classically present as a yellow-green discoloration, and cardiovascular symptoms, such as palpitations, dyspnea, and syncope." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Digitalis exposure" + }, { + "pred" : "hasExactSynonym", + "val" : "Lanoxin exposure" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10675" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-12-06T08:59:20Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001148", + "lbl" : "Pain exacerbated by passive flexion at joint", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Pain 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increase risk of prepatellar bursitis and knee osteoarthritis." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "History of frequent kneeling" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10823" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-01-07T09:05:02Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001169", + "lbl" : "Supraclavicular nerve distribution", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Localization of symptoms such as numbness or paresthesias on the skin over the upper chest, specifically above the clavicle and over the lateral aspect of the neck, corresponding to the distribution of the supraclavicular nerve." + }, + "comments" : [ "May be observed with clavicle shaft fracture." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10942" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-01-31T09:45:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001176", + "lbl" : "Radial nerve distribution", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to the localization of findings corresponding to the distribution of the radial nevrve, such as (i)paresthesias on the dorsoradial aspect of the hand and wrist, including the dorsal thumb, index finger and middle finger and (ii) Weakness in elbow extension, wrist extension, finger extension, thumb extension and/or supination of the forearm." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10792" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-02-22T15:17:09Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001195", + "lbl" : "Occupational exposure to frequent hand trauma", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A history of exposure to repeated hand trauma as observed with occupations in which use of hands is frequent such as construction, food preparation and serving related occupations, and transportation and material moving occupations." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10699" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-03-01T12:03:43Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001199", + "lbl" : "FInger pulp localization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality whose distribution is limited to or predominantly affects the fleshy mass on the volar (palmar) aspect of the digit, distal to the distal interphalangeal (DIP) joint (known as the pulp of the finger)." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Symptoms localized to pulp of the finger" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10717" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-03-01T12:03:43Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001203", + "lbl" : "Snapping sensation at time of injury", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A popping or snapping sensation (noise or feeling) at the time of an injury." + }, + "comments" : [ "Sudden snapping or popping at the time of an injury can be a sign of significant damage to muscles, tendons, ligaments, or bones." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + 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nevi, de novo epithelioid melanocytic dysplasia, and melanoma. Pagetoid melanocytosis may also be a common feature of acral nevi, traumatized nevi, or in nevi after acute sun exposure." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/9951" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-03-08T14:14:35Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001205", + "lbl" : "Central scarring", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Central scarring of skin lesions.", + "xrefs" : [ "PMID:29261968", "PMID:36911588" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/9962" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-03-08T14:14:35Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001213", + "lbl" : "History of thumb sucking past the age of four years", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Thumb sucking is a behavior that ceases spontaneously in most children between 2 and 4 years of age. If thumb sucking continues, negative consequences can occur, such as a deformity of the nail or paronychia. This term refers to a history of habitual thumb sucking past the age of 4 years of life.", + "xrefs" : [ "PMID:32310572" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10673" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-03-09T11:22:14Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001243", + "lbl" : "Physeal fracture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Salter-Harris fractures (physeal fractures) refer to fractures through a growth plate (physis) and are, therefore, specifically applied to bone fractures in children.", + "xrefs" : [ "PMID:28613461" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10707" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-03T09:32:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001244", + "lbl" : "Salter I fracture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of physeal (Salter-Harris) fracture in which the fracture line extends through the physis or within the growth plate. Type I fractures are due to the longitudinal force applied through the physis, which splits the epiphysis from the metaphysis.", + "xrefs" : [ "PMID:28613461" ] + }, + "comments" : [ "Beware that a normal radiograph cannot exclude a physis injury in a symptomatic pediatric patient. A radiograph may be normal due to lack of bony involvement, and mild to moderate soft tissue swelling may be noted. Look for the widening of the physis or displacement of the epiphysis, which may suggest a fracture. Diagnosis is based on clinical findings, such as the presence of focal tenderness or swelling surrounding the growth plate." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Slipped physeal fracture" + }, { + "pred" : "hasExactSynonym", + "val" : "Type I Salter-Harris fracture" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10707" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-03T09:32:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001245", + "lbl" : "Salter II fracture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of physeal (Salter-Harris) fracture in which the fracture extends through both the physis and metaphysis. These are most common and occur away from the joint space. When the small corner of the metaphysis is visible, this is known as a corner sign or Thurston-Holland fragment.", + "xrefs" : [ "PMID:28613461" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Type II Salter-Harris fracture" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10707" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-03T09:32:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001246", + "lbl" : "Salter III fracture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of physeal (Salter-Harris) fracture in which the fracture is intra-articular and extends from the physis into the epiphysis.", + "xrefs" : [ "PMID:28613461" ] + }, + "comments" : [ "If the fracture extends the complete length of the physis, this type of fracture may form two epiphyseal segments. Since the epiphysis is involved, damage to the articular cartilage may occur. One example is a Tillaux fracture of the ankle, which is a fracture of the anterolateral aspect of the growth plate and epiphysis." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Type III Salter-Harris fracture" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10707" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-03T09:32:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001247", + "lbl" : "Salter IV fracture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of physeal (Salter-Harris) fracture in which the fracture is intra-articular and passes through the epiphysis, physis, and metaphysis.", + "xrefs" : [ "PMID:28613461" ] + }, + "comments" : [ "As this fracture involves the epiphysis, the articular cartilage may be damaged. Types III and IV fractures each carry a risk for growth retardation, altered joint mechanics, and functional impairment. Therefore, both require urgent orthopedic evaluation." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Type IV Salter-Harris fracture" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10707" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-03T09:32:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001248", + "lbl" : "Salter V fracture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of physeal (Salter-Harris) fracture that is due to a crush or compression injury of the growth plate. In type V, the force is transmitted through the epiphysis and physis, potentially disrupting the germinal matrix, hypertrophic region, and vascular supply.", + "xrefs" : [ "PMID:28613461" ] + }, + "comments" : [ "Though Harris-Salter V fractures are very rare, they may be seen in electric shock, frostbite, and irradiation cases. As this fracture pattern tends to result from severe injury, these typically have a poor prognosis leading to bone growth arrest." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Type V Salter-Harris fracture" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10707" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-03T09:32:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001250", + "lbl" : "History of distal radius fracture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Recent or remote history of distal radius fracture of the symptomatic arm." + }, + "comments" : [ "This finding refers to a medical history of distal radius fracture in the arm that is the focus of current medical attention. This finding may relate to scapholunate advanced collapse, distal radioulnar joint arthritis, and scapholunate ligament injury." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10720" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-03T09:32:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001251", + "lbl" : "History of triangular fibrocartilage complex tear", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Recent or remote history of a tear in the triangular fibrocartilage complex (TFCC). The TFCC is a load-bearing structure between the lunate, triquetrum, and ulnar head. The function of the TFCC is to act as a stabilizer for the ulnar aspect of the wrist. The TFCC is at risk for either acute or chronic degenerative injury.", + "xrefs" : [ "PMID:30725740" ] + }, + "comments" : [ "Such a history is important for the diagnosis of Distal radioulnar joint (DRUJ) arthritis." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "History of TFCC tear" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/10721" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-03T09:32:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001265", + "lbl" : "Localized to lower eyelid", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A descriptor indicating that a condition, lesion, or abnormality is confined to the lower eyelid. This localization may be relevant for various ocular conditions, including infections, structural abnormalities, or dermatological diseases affecting the lower eyelid region.", + "xrefs" : [ "PMID:30616908", "PMID:37777491" ] + }, + "comments" : [ "An anatomical spatial pattern or localization referring to the lower eyelid, the smaller, less mobile fold of skin and tissue positioned below the eye." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Inferior palpebral location" + }, { + "pred" : "hasExactSynonym", + "val" : "Lower lid location" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/11046" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9042-0508" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-04T15:27:15Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001266", + "lbl" : "Localized to eyelid", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Applies to an abnormality that is situated in an eyelid." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/11046" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-04T15:27:15Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001270", + "lbl" : "Axillary nerve distribution", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Paresthesias on the lateral aspect of the shoulder and upper arm. Weakness in shoulder abduction (deltoid) and shoulder external rotation (teres minor)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/human-phenotype-ontology/issues/11071" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2025-05-04T15:27:15Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "human_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_6001273", + "lbl" : "Pain exacerbated by weight bearing", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Refers to pain that is worse when the individual bears weight with the affected body part." + }, + "comments" : [ "This feature may be observed in conditions such as hip fracture, tibial shaft fracture, calcaneus fracture, and ankle sprain." ], + 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"sub" : "http://purl.obolibrary.org/obo/HP_6001089", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0032443" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001092", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000110" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001093", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000110" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001094", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000110" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001106", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000110" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001109", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0012838" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001116", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0032443" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001118", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000144" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001120", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0035010" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001121", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0012836" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001122", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0012836" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001123", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0025280" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001128", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000144" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001129", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000110" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001135", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000110" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001136", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0025849" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001138", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000112" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001148", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0025280" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001152", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0025280" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001157", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0035010" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001169", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0025849" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001176", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0025849" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001195", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0035010" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001199", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0012838" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001203", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0025280" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001204", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0012836" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001205", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0012836" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001213", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0032443" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001243", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000042" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001244", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_6001243" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001245", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_6001243" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001246", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_6001243" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001247", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_6001243" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001248", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_6001243" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001250", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0032443" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001251", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0032443" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001265", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_6001266" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001266", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0012838" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001270", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0025849" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001273", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0025285" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001292", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000176" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001293", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0025285" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001319", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000110" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001324", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000176" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001335", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0012838" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001413", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000176" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001414", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_4000110" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001419", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_6001152" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001420", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_6001152" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001424", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0025758" + }, { + "sub" : "http://purl.obolibrary.org/obo/HP_6001448", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/HP_0430103" + } ] + } ] +} \ No newline at end of file diff --git a/phenopacket-tools-validator-jsonschema/pom.xml b/phenopacket-tools-validator-jsonschema/pom.xml index 89295ca12..ed130fd96 100644 --- a/phenopacket-tools-validator-jsonschema/pom.xml +++ b/phenopacket-tools-validator-jsonschema/pom.xml @@ -7,7 +7,7 @@ org.phenopackets.phenopackettools phenopacket-tools - 1.0.0-RC3 + 1.0.0 phenopacket-tools-validator-jsonschema diff --git a/phenopacket-tools-validator-jsonschema/src/main/java/module-info.java b/phenopacket-tools-validator-jsonschema/src/main/java/module-info.java index 9d2de689e..09b55e53d 100644 --- a/phenopacket-tools-validator-jsonschema/src/main/java/module-info.java +++ b/phenopacket-tools-validator-jsonschema/src/main/java/module-info.java @@ -11,7 +11,8 @@ module org.phenopackets.phenopackettools.validator.jsonschema { requires org.phenopackets.phenopackettools.util; requires transitive org.phenopackets.phenopackettools.validator.core; - requires org.phenopackets.schema; + // Transitive due to export of Phenopacket, Cohort, Family in JsonSchemaValidationWorkflowRunner. + requires transitive org.phenopackets.schema; requires com.fasterxml.jackson.databind; requires json.schema.validator; requires org.slf4j; diff --git a/phenopacket-tools-validator-jsonschema/src/main/resources/org/phenopackets/phenopackettools/validator/jsonschema/v2/base.json b/phenopacket-tools-validator-jsonschema/src/main/resources/org/phenopackets/phenopackettools/validator/jsonschema/v2/base.json index f18df1331..21bc2041f 100644 --- a/phenopacket-tools-validator-jsonschema/src/main/resources/org/phenopackets/phenopackettools/validator/jsonschema/v2/base.json +++ b/phenopacket-tools-validator-jsonschema/src/main/resources/org/phenopackets/phenopackettools/validator/jsonschema/v2/base.json @@ -94,7 +94,8 @@ "properties": { "iso8601duration": { "description": "An ISO8601 string representing age.", - "type": "string" + "type": "string", + "pattern": "^P(?!$)(\\d+Y)?(\\d+M)?(\\d+W)?(\\d+D)?(T(?=\\d+[HMS])(\\d+H)?(\\d+M)?(\\d+S)?)?$" } }, "required": ["iso8601duration"], diff --git a/phenopacket-tools-validator-jsonschema/src/test/java/org/phenopackets/phenopackettools/validator/jsonschema/JsonSchemaValidationWorkflowRunnerTest.java b/phenopacket-tools-validator-jsonschema/src/test/java/org/phenopackets/phenopackettools/validator/jsonschema/JsonSchemaValidationWorkflowRunnerTest.java index b6e45e088..4d219f1c0 100644 --- a/phenopacket-tools-validator-jsonschema/src/test/java/org/phenopackets/phenopackettools/validator/jsonschema/JsonSchemaValidationWorkflowRunnerTest.java +++ b/phenopacket-tools-validator-jsonschema/src/test/java/org/phenopackets/phenopackettools/validator/jsonschema/JsonSchemaValidationWorkflowRunnerTest.java @@ -148,7 +148,6 @@ public void checkPhenotypicFeatureConstraints(String path, String action, String "/phenotypicFeatures[0]/onset/gestationalAge/weeks, SET[-1], 'phenotypicFeatures[0].onset.gestationalAge.weeks' must have a minimum value of 0", "/phenotypicFeatures[0]/onset/gestationalAge/days, SET[-1], 'phenotypicFeatures[0].onset.gestationalAge.days' must have a minimum value of 0", "/phenotypicFeatures[1]/onset/age/iso8601duration, DELETE, 'phenotypicFeatures[1].onset.age.iso8601duration' is missing but it is required", - // TODO - add test for ensuring that the duration is in an ISO8601 pattern "/phenotypicFeatures[2]/onset/ageRange/start, DELETE, 'phenotypicFeatures[2].onset.ageRange.start' is missing but it is required", "/phenotypicFeatures[2]/onset/ageRange/end, DELETE, 'phenotypicFeatures[2].onset.ageRange.end' is missing but it is required", // TODO - require end being at or after start @@ -160,6 +159,47 @@ public void checkTimeElementConstraints(String path, String action, String expec testErrors(runner, readBethlemPhenopacketNode(), path, action, expected, true); } + /** + * Check that error in the ISO8601 period leads to the appropriate + * {@link org.phenopackets.phenopackettools.validator.core.ValidationLevel#ERROR}. + */ + @ParameterizedTest + @CsvSource({ + // Age + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[P1H], 'phenotypicFeatures[1].onset.age.iso8601duration' does not match the regex pattern ^P(?!$)(\\d+Y)?(\\d+M)?(\\d+W)?(\\d+D)?(T(?=\\d+[HMS])(\\d+H)?(\\d+M)?(\\d+S)?)?$", + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[PT1D], 'phenotypicFeatures[1].onset.age.iso8601duration' does not match the regex pattern ^P(?!$)(\\d+Y)?(\\d+M)?(\\d+W)?(\\d+D)?(T(?=\\d+[HMS])(\\d+H)?(\\d+M)?(\\d+S)?)?$", + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[P], 'phenotypicFeatures[1].onset.age.iso8601duration' does not match the regex pattern ^P(?!$)(\\d+Y)?(\\d+M)?(\\d+W)?(\\d+D)?(T(?=\\d+[HMS])(\\d+H)?(\\d+M)?(\\d+S)?)?$", + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[PT], 'phenotypicFeatures[1].onset.age.iso8601duration' does not match the regex pattern ^P(?!$)(\\d+Y)?(\\d+M)?(\\d+W)?(\\d+D)?(T(?=\\d+[HMS])(\\d+H)?(\\d+M)?(\\d+S)?)?$", + // Wrong token order. + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[P10M4Y], 'phenotypicFeatures[1].onset.age.iso8601duration' does not match the regex pattern ^P(?!$)(\\d+Y)?(\\d+M)?(\\d+W)?(\\d+D)?(T(?=\\d+[HMS])(\\d+H)?(\\d+M)?(\\d+S)?)?$", + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[P1YT4M12H], 'phenotypicFeatures[1].onset.age.iso8601duration' does not match the regex pattern ^P(?!$)(\\d+Y)?(\\d+M)?(\\d+W)?(\\d+D)?(T(?=\\d+[HMS])(\\d+H)?(\\d+M)?(\\d+S)?)?$", + }) + public void checkTimeElementConstraints_ISO8601_errors(String path, String action, String expected) { + testErrors(runner, readBethlemPhenopacketNode(), path, action, expected, true); + } + + /** + * Check that correct ISO8601 period yields no + * {@link org.phenopackets.phenopackettools.validator.core.ValidationLevel#ERROR}s. + */ + @ParameterizedTest + @CsvSource({ + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[P1Y4M3W2DT1H23M44S]", + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[P1Y]", + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[P4M]", + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[P3W]", + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[P2D]", + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[PT1H]", + "/phenotypicFeatures[1]/onset/age/iso8601duration, SET[PT1H2M]", + }) + public void checkTimeElementConstraints_ISO8601_OK(String path, String action) { + JsonNode tampered = TAMPERER.tamper(readBethlemPhenopacketNode(), path, Action.valueOf(action)); + + ValidationResults results = runner.validate(tampered.toPrettyString()); + + assertThat(results.isValid(), equalTo(true)); + } + /** * Absence of phenotypic feature id leads to an {@link org.phenopackets.phenopackettools.validator.core.ValidationLevel#ERROR}. */ @@ -683,10 +723,6 @@ private static void testErrors(ValidationWorkflowRu JsonNode tampered = TAMPERER.tamper(node, path, Action.valueOf(action)); ValidationResults results = runner.validate(tampered.toPrettyString()); - // TODO - remove after the tests are completed -// results.validationResults().stream() -// .map(ValidationResult::message) -// .forEach(System.err::println); Collection tokens = Arrays.asList(errors.split("\\|")); if (validateCount) { diff --git a/pom.xml b/pom.xml index dd2a2a31a..f5ffad1cc 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.phenopackets.phenopackettools phenopacket-tools - 1.0.0-RC3 + 1.0.0 Phenopacket-tools An app and library for building, conversion and validation of GA4GH Phenopackets @@ -15,7 +15,7 @@ https://phenopackets.org/phenopacket-tools - 3.6.0 + 3.6.3 @@ -37,8 +37,6 @@ - - The 3-Clause BSD License @@ -50,15 +48,15 @@ Peter Robinson - peter.robinson@jax.org - The Jackson Laboratory - https://www.jax.org/ + peter.robinson@bih-charite.de + Berlin Institute of Health at Charité + https://www.bihealth.org/ Daniel Danis - daniel.danis@jax.org - The Jackson Laboratory - https://www.jax.org/ + daniel.danis@bih-charite.de + Berlin Institute of Health at Charité + https://www.bihealth.org/ Jules Jacobsen @@ -75,32 +73,27 @@ v${project.version} - - - ossrh - https://oss.sonatype.org/service/local/staging/deploy/maven2/ - - - ossrh - https://oss.sonatype.org/content/repositories/snapshots - - - UTF-8 UTF-8 17 - 3.21.7 + [4.28.2,) 2.0.2 - 2.0.0 + 2.1.4 2.14.2 1.0.79 - 2.0 - 1.10.0 - 4.7.1 - 5.9.2 + [2.0,3.0) + 1.14.1 + 4.7.7 + + + central + https://ossrh-staging-api.central.sonatype.com/service/local/staging/deploy/maven2/ + + + @@ -230,9 +223,6 @@ - - - release @@ -276,10 +266,9 @@ 3.0.0-M5 - org.apache.maven.plugins maven-gpg-plugin - 1.6 + 3.2.8 sign-artifacts @@ -290,6 +279,17 @@ + + org.sonatype.central + central-publishing-maven-plugin + 0.9.0 + true + + central + true + published + + org.apache.maven.plugins maven-deploy-plugin @@ -310,6 +310,10 @@ org.apache.maven.plugins maven-javadoc-plugin + + org.sonatype.central + central-publishing-maven-plugin +