diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 0000000..36d3a43 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,7 @@ +[codespell] +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +skip = .git*,.codespellrc,MRIO-full.*,MRIO-base.*,MRIO-reasoned_hermit.owl,MRIO-oldedit.*,*.obo,MRIO.owl,imports,mirror,tmp,reports,uberon_filtered.owl +check-hidden = true +# case sensitive etc +ignore-regex = created_by: .*|\b(AER|CNA|TE|ND|Chromum)\b +ignore-words-list = ser,cyclin,als,transferrin,mater,te diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 0000000..c59e047 --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,25 @@ +# Codespell configuration is within .codespellrc +--- +name: Codespell + +on: + push: + branches: [main] + pull_request: + branches: [main] + +permissions: + contents: read + +jobs: + codespell: + name: Check for spelling errors + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Annotate locations with typos + uses: codespell-project/codespell-problem-matcher@v1 + - name: Codespell + uses: codespell-project/actions-codespell@v2 diff --git a/README.md b/README.md index be336b3..1b5d7bf 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ An ontology for the representation of MRI acquisition and analysis. MRIO builds on the Ontology for Biomedical Investigations (OBI) to flesh out -the process of acquiring MR images, analyzing these images, and interpretting +the process of acquiring MR images, analyzing these images, and interpreting the results of these analyses. A select set of terms from Uberon are imported to relate MRI analyses to the specific brain regions. @@ -88,7 +88,7 @@ and alignment with other neuroimaging and OBO ontologies (e.g. [NIDM](https://github.com/incf-nidash/nidm-terms)). The MRIO team meets biweekly via Zoom on Thursdays at 2:00pm EST to discuss ongoing development. -External contributers are more than welcome to join these meetings to discuss new terms +External contributors are more than welcome to join these meetings to discuss new terms or anything related to the ontology. To obtain a link to the biweekly MRIO discussion, please contact Alexander Bartnik at adbartni@buffalo.edu. diff --git a/src/ontology/MRIO-edit.owl b/src/ontology/MRIO-edit.owl index e6fc764..40d6ec1 100644 --- a/src/ontology/MRIO-edit.owl +++ b/src/ontology/MRIO-edit.owl @@ -172,7 +172,7 @@ - A relation between some part of the MRI acquisition sequence and the setttings of an MRI machine set by a technician. + A relation between some part of the MRI acquisition sequence and the settings of an MRI machine set by a technician. has MRI acquisition parameter @@ -402,7 +402,7 @@ - A T1 weighted image data set where gadolidium contrast agent has been administered to the participant before image acquistion. + A T1 weighted image data set where gadolidium contrast agent has been administered to the participant before image acquisition. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" @@ -480,7 +480,7 @@ - An magnetic resonance image data set in which the contrast emphasizes density of protons, supressing T1 and T2 effects + An magnetic resonance image data set in which the contrast emphasizes density of protons, suppressing T1 and T2 effects https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" @@ -1103,7 +1103,7 @@ - An MRI acquisition sequence that acheives T1 weighting using gradient echo instead of spin echo. + An MRI acquisition sequence that achieves T1 weighting using gradient echo instead of spin echo. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" T1 GRE sequence @@ -1175,7 +1175,7 @@ - An MRI acquisition sequence that acheives T2 weighting using gradient echo instead of spin echo. + An MRI acquisition sequence that achieves T2 weighting using gradient echo instead of spin echo. Needs GRE sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" @@ -2125,7 +2125,7 @@ The values often belong to a group of pixels or voxels that share the same chara - A structural connectivity matrix where each element respresents the number of white matter streamlines still connecting two brain regions when accounting for focal lesion damage, normalized for the NeMo healthy control tractogram set. + A structural connectivity matrix where each element represents the number of white matter streamlines still connecting two brain regions when accounting for focal lesion damage, normalized for the NeMo healthy control tractogram set. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" nConMat matrix @@ -2466,7 +2466,7 @@ The values often belong to a group of pixels or voxels that share the same chara - A type of magnetic resonance image data set collected using at least three diffusion gradients of some factor "b," which is a function of the amplitude, duration, and interval of the gradiants. + A type of magnetic resonance image data set collected using at least three diffusion gradients of some factor "b," which is a function of the amplitude, duration, and interval of the gradients. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" @@ -2640,7 +2640,7 @@ The values often belong to a group of pixels or voxels that share the same chara - A brain atlas consisting of weighted values that respresent the probability that a voxel X is part of some brain component Y, typically derived from multiple image data sets. + A brain atlas consisting of weighted values that represent the probability that a voxel X is part of some brain component Y, typically derived from multiple image data sets. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" @@ -2965,7 +2965,7 @@ The values often belong to a group of pixels or voxels that share the same chara - A funtional MRI data set analysis software suite of preconfigured pipelines for analysis fMRI data and estimating functional connectomics. + A functional MRI data set analysis software suite of preconfigured pipelines for analysis fMRI data and estimating functional connectomics. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://doi.org/10.3389/conf.fninf.2013.09.00042 The Configurable Pipeline for the Analysis of Connectomes (C-PAC) is a configurable, open-source, Nipype-based, automated processing pipeline for resting state functional MRI (R-fMRI) data, for use by both novice and expert users. @@ -3111,7 +3111,7 @@ The values often belong to a group of pixels or voxels that share the same chara - FreeSurfer stream to derive surface labels and volumes from an invidual at only one timepoint. + FreeSurfer stream to derive surface labels and volumes from an individual at only one timepoint. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" FreeSurfer cross-sectional analysis @@ -3201,7 +3201,7 @@ The values often belong to a group of pixels or voxels that share the same chara A brain volumetric analysis tool that estimates the percent brain volume change in an individual between two timepoints using baseline and follow-up T1w MRI. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" Smith, Stephen M.; De Stefano, Nicola; Jenkinson, Mark; Matthews, Paul M. Normalized Accurate Measurement of Longitudinal Brain Change, Journal of Computer Assisted Tomography: May 2001 - Volume 25 - Issue 3 - p 466-475 - Siena estimates percentage brain volume change (PBVC) betweem two input images, taken of the same subject, at different points in time. It calls a series of FSL programs to strip the non-brain tissue from the two images, register the two brains (under the constraint that the skulls are used to hold the scaling constant during the registration) and analyse the brain change between the two time points. It is also possible to project the voxelwise atrophy measures into standard space in a way that allows for multi-subject voxelwise statistical testing. + Siena estimates percentage brain volume change (PBVC) between two input images, taken of the same subject, at different points in time. It calls a series of FSL programs to strip the non-brain tissue from the two images, register the two brains (under the constraint that the skulls are used to hold the scaling constant during the registration) and analyse the brain change between the two time points. It is also possible to project the voxelwise atrophy measures into standard space in a way that allows for multi-subject voxelwise statistical testing. SIENA analysis @@ -3482,7 +3482,7 @@ The values often belong to a group of pixels or voxels that share the same chara An MRI acquisition sequence that uses diffusion gradients to create contrast in the image corresponding to the Brownian motion of the tissue in the examined voxel. - Add difussion gradient as parameter. + Add diffusion gradient as parameter. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" NCIT:C111116 @@ -5487,7 +5487,7 @@ The values often belong to a group of pixels or voxels that share the same chara - A type of functional magnetic resonance imaging (fMRI) sequence protocol in which the participant is given specific tasks or stimuli that alternate between structured blocks and randomized or semi-randomized order seperated by rest periods during the imaging acquisition. + A type of functional magnetic resonance imaging (fMRI) sequence protocol in which the participant is given specific tasks or stimuli that alternate between structured blocks and randomized or semi-randomized order separated by rest periods during the imaging acquisition. 2024-07-31T21:38:59Z mixed event-related/block design fMRI sequence protocol diff --git a/src/ontology/Makefile b/src/ontology/Makefile index b5844c3..c631459 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -450,7 +450,7 @@ $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) else # MIR=false $(MIRRORDIR)/%.owl: - @echo "Not refreshing $@ because the mirrorring pipeline is disabled (MIR=$(MIR))." + @echo "Not refreshing $@ because the mirroring pipeline is disabled (MIR=$(MIR))." endif diff --git a/src/ontology/mrio-template.tsv b/src/ontology/mrio-template.tsv index 1a44035..9486df4 100644 --- a/src/ontology/mrio-template.tsv +++ b/src/ontology/mrio-template.tsv @@ -226,7 +226,7 @@ raw image data set image data set reagent reconstructed MR image data set regional functional connectome analysis functional connectome analysis -repitition time MRI machine parameter +repetition time MRI machine parameter right auditory cortex right dorsal thalamic volume measurement datum 'is about' some 'right dorsal thalamus'|dorsal thalamic volume measurement datum right dorsal thalamus diff --git a/src/ontology/target/MRIO/CONTRIBUTING.md b/src/ontology/target/MRIO/CONTRIBUTING.md index d201355..22c05ed 100644 --- a/src/ontology/target/MRIO/CONTRIBUTING.md +++ b/src/ontology/target/MRIO/CONTRIBUTING.md @@ -68,11 +68,11 @@ For how to write a good term request, please read the [best practices carefully] ### How to add a new term -If you have never editted this ontology before, first follow a [general tutorial](https://oboacademy.github.io/obook/lesson/contributing-to-obo-ontologies) +If you have never edited this ontology before, first follow a [general tutorial](https://oboacademy.github.io/obook/lesson/contributing-to-obo-ontologies) **Process**: -1. Clone the repository (In case you are not an offical team member, create a fork first) +1. Clone the repository (In case you are not an official team member, create a fork first) 1. Create new branch in git, for example `git checkout -b issue123` 1. Open src/ontology/MRIO-edit.owl in your favourite editor, i.e. [Protege](https://protege.stanford.edu/). **Careful:** double check you are editing the correct file. There are many ontology files in this repository, but only one _editors file_! 1. Perform your edit and save your changes diff --git a/src/ontology/target/MRIO/src/ontology/Makefile b/src/ontology/target/MRIO/src/ontology/Makefile index 8abe863..a1922c0 100644 --- a/src/ontology/target/MRIO/src/ontology/Makefile +++ b/src/ontology/target/MRIO/src/ontology/Makefile @@ -450,7 +450,7 @@ $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) else # MIR=false $(MIRRORDIR)/%.owl: - @echo "Not refreshing $@ because the mirrorring pipeline is disabled (MIR=$(MIR))." + @echo "Not refreshing $@ because the mirroring pipeline is disabled (MIR=$(MIR))." endif diff --git a/src/ontology/target/MRIO/src/ontology/README-editors.md b/src/ontology/target/MRIO/src/ontology/README-editors.md index 9002fde..40a0083 100644 --- a/src/ontology/target/MRIO/src/ontology/README-editors.md +++ b/src/ontology/target/MRIO/src/ontology/README-editors.md @@ -6,7 +6,7 @@ For more details on ontology management, please see the [OBO Academy Tutorials](https://oboacademy.github.io/obook/), the [OBO tutorial](https://github.com/jamesaoverton/obo-tutorial) or the [Gene Ontology Editors Tutorial](https://go-protege-tutorial.readthedocs.io/en/latest/) -This documentation has been superceded by the ODK automatic documentation, which you can +This documentation has been superseded by the ODK automatic documentation, which you can activate by adding: ``` diff --git a/src/ontology/target/MRIO/src/scripts/update_repo.sh b/src/ontology/target/MRIO/src/scripts/update_repo.sh index 90249c9..f6f0b04 100644 --- a/src/ontology/target/MRIO/src/scripts/update_repo.sh +++ b/src/ontology/target/MRIO/src/scripts/update_repo.sh @@ -1,5 +1,5 @@ echo "This (experimental) update script will create a new repo according to your config file. It will:" -echo "(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries wont be touched) and docker wrapper (run.sh)." +echo "(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries won't be touched) and docker wrapper (run.sh)." echo "(2) and add missing files, if any." set -e diff --git a/src/ontology/target/MRIO/src/sparql/README.md b/src/ontology/target/MRIO/src/sparql/README.md index 4f6e5a8..69e6971 100644 --- a/src/ontology/target/MRIO/src/sparql/README.md +++ b/src/ontology/target/MRIO/src/sparql/README.md @@ -2,7 +2,7 @@ [SPARQL](https://www.w3.org/TR/rdf-sparql-query/) is a W3C standard query language for RDF. This directory contains useful SPARQL queries -for perfoming over the ontology. +for performing over the ontology. SPARQL can be executed on a triplestore or directly on any OWL file. The queries here are all executed on either MRIO-edit.obo or diff --git a/src/scripts/assign_analyses.py b/src/scripts/assign_analyses.py index 78fa2c0..05fe274 100644 --- a/src/scripts/assign_analyses.py +++ b/src/scripts/assign_analyses.py @@ -18,7 +18,7 @@ def find_analyses(seq_labels): #input should be list of strings with identifying #list of image IRIs args = list([]) - #contruction of 1st query, linking sequences to images + #construction of 1st query, linking sequences to images str_a = "PREFIX owl: PREFIX rdf: PREFIX rdfs: PREFIX root: PREFIX output: SELECT DISTINCT ?seq ?seq_label ?image ?image_label WHERE { ?image rdfs:subClassOf* root: . ?image rdfs:label ?image_label . ?seq rdfs:label ?seq_label . ?seq rdfs:subClassOf [ a owl:Restriction; owl:onProperty output:; owl:someValuesFrom ?image ]. " str_c = "} order by ?image" for x in range(len(seq_labels)): diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh index 90249c9..f6f0b04 100644 --- a/src/scripts/update_repo.sh +++ b/src/scripts/update_repo.sh @@ -1,5 +1,5 @@ echo "This (experimental) update script will create a new repo according to your config file. It will:" -echo "(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries wont be touched) and docker wrapper (run.sh)." +echo "(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries won't be touched) and docker wrapper (run.sh)." echo "(2) and add missing files, if any." set -e diff --git a/src/sparql/README.md b/src/sparql/README.md index 4f6e5a8..69e6971 100644 --- a/src/sparql/README.md +++ b/src/sparql/README.md @@ -2,7 +2,7 @@ [SPARQL](https://www.w3.org/TR/rdf-sparql-query/) is a W3C standard query language for RDF. This directory contains useful SPARQL queries -for perfoming over the ontology. +for performing over the ontology. SPARQL can be executed on a triplestore or directly on any OWL file. The queries here are all executed on either MRIO-edit.obo or