Skip to content

Commit 0e94e92

Browse files
dragon-ai-agentdragon-ai-agent
authored
Merge pull request #45 from linkml/genesis-mission-docs
Add DOE Genesis Mission overview page
2 parents cbcb9d9 + 7acfd8c commit 0e94e92

File tree

2 files changed

+236
-0
lines changed

2 files changed

+236
-0
lines changed

‎docs/subsets/genesis-mission.md‎

Lines changed: 234 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,234 @@
1+
# DOE Genesis Mission Value Sets
2+
3+
The U.S. Department of Energy's [Genesis Mission](https://www.energy.gov/genesis) defines
4+
26 national science and technology challenges spanning clean energy, advanced computing,
5+
manufacturing, earth systems, and national security. This project provides standardized
6+
value sets (enums with ontology mappings) that support data interoperability across
7+
these challenge areas.
8+
9+
The 19 schema modules below cover topics from grid modernization and fusion energy to
10+
quantum computing and autonomous laboratories. Each enum is mapped to established
11+
ontologies wherever possible, enabling integration with broader scientific data ecosystems.
12+
13+
## Coverage Summary
14+
15+
| Domain | Schema | Enums | Ontologies |
16+
|--------|--------|------:|------------|
17+
| [Energy and Grid](#energy-and-grid) | grid, subsurface_energy | 6 | OEO, ENVO, CHEBI |
18+
| [Nuclear](#nuclear) | fusion, nuclear_cleanup, nuclear_forensics | 8 | CHEBI, NCIT, CHMO, ENVO |
19+
| [Earth Science](#earth-science) | subsurface, hydrogeology, remote_sensing, water_resources | 12 | ENVO, PATO, CHEBI, OBI |
20+
| [Computing](#computing) | data_centers, microelectronics, quantum | 6 | Brick, CHEBI, NCIT |
21+
| [Industry](#industry) | manufacturing, construction, unconventional_resources | 7 | OBI, CHMO, ENVO, Brick |
22+
| [Materials and Physics](#materials-and-physics) | computational_materials, particle_physics | 5 | NCIT, CHEBI, PATO, SWO |
23+
| [Bioprocessing and Labs](#bioprocessing-and-labs) | biomanufacturing, autonomous_labs | 6 | OBI, CHEBI, NCIT, BAO |
24+
25+
---
26+
27+
## Energy and Grid
28+
29+
Grid modernization and subsurface energy are central to the Genesis challenges on
30+
decarbonization and energy security. These value sets standardize terminology for
31+
grid components, storage technologies, and subsurface resources.
32+
33+
### Enums
34+
35+
- [GridComponentType](../elements/GridComponentType.md) -- transmission lines, transformers, substations, inverters
36+
- [GridEnergyStorageType](../elements/GridEnergyStorageType.md) -- battery chemistries, pumped hydro, hydrogen storage
37+
- [GridManagementStrategyType](../elements/GridManagementStrategyType.md) -- demand response, load balancing, virtual power plants
38+
- [SubsurfaceEnergyResourceType](../elements/SubsurfaceEnergyResourceType.md) -- geothermal, oil, gas hydrate reservoirs
39+
- [SubsurfaceStorageType](../elements/SubsurfaceStorageType.md) -- CCS, underground hydrogen, compressed air
40+
- [ReservoirCharacterizationMethodType](../elements/ReservoirCharacterizationMethodType.md) -- well tests, seismic, core analysis
41+
42+
### Example Mappings
43+
44+
| Permissible Value | Enum | Ontology Mapping |
45+
|-------------------|------|------------------|
46+
| LITHIUM_ION_BATTERY | GridEnergyStorageType | OEO:00000248 |
47+
| GEOTHERMAL_RESERVOIR | SubsurfaceEnergyResourceType | ENVO:2000034 |
48+
| CARBON_CAPTURE_AND_STORAGE | SubsurfaceStorageType | OEO:00010141 |
49+
| TRANSFORMER | GridComponentType | OEO:00000420 |
50+
51+
---
52+
53+
## Nuclear
54+
55+
Fusion energy, environmental cleanup of legacy nuclear sites, and nuclear forensics
56+
each present distinct vocabulary needs. These enums cover confinement approaches,
57+
plasma parameters, remediation techniques, and analytical methods.
58+
59+
### Enums
60+
61+
- [FusionConfinementType](../elements/FusionConfinementType.md) -- tokamak, stellarator, inertial confinement
62+
- [FusionFuelType](../elements/FusionFuelType.md) -- D-T, D-D, D-He3, p-B11 fuel cycles
63+
- [FusionPlasmaParameterType](../elements/FusionPlasmaParameterType.md) -- temperature, density, beta value
64+
- [NuclearRemediationType](../elements/NuclearRemediationType.md) -- soil excavation, vitrification, phytoremediation
65+
- [DecommissioningPhaseType](../elements/DecommissioningPhaseType.md) -- characterization through long-term monitoring
66+
- [RadioactiveContaminantType](../elements/RadioactiveContaminantType.md) -- Cs-137, Sr-90, Tc-99, Pu, U
67+
- [NuclearForensicsMethodType](../elements/NuclearForensicsMethodType.md) -- isotope ratios, mass spec, gamma spectroscopy
68+
- [NuclearThreatCategoryType](../elements/NuclearThreatCategoryType.md) -- IND, RDD, material theft scenarios
69+
70+
### Example Mappings
71+
72+
| Permissible Value | Enum | Ontology Mapping |
73+
|-------------------|------|------------------|
74+
| CESIUM_137 | RadioactiveContaminantType | CHEBI:196959 |
75+
| ISOTOPE_RATIO_ANALYSIS | NuclearForensicsMethodType | CHMO:0000506 |
76+
| DECONTAMINATION | DecommissioningPhaseType | NCIT:C68769 |
77+
| PLASMA_TEMPERATURE | FusionPlasmaParameterType | PATO:0000146 |
78+
79+
---
80+
81+
## Earth Science
82+
83+
Subsurface characterization, hydrogeology, remote sensing, and water resources span
84+
multiple Genesis challenges related to environmental stewardship, critical minerals,
85+
and climate resilience.
86+
87+
### Enums
88+
89+
- [SubsurfaceFormationType](../elements/SubsurfaceFormationType.md) -- aquifers, fault zones, permafrost, shale
90+
- [GeophysicalMethodType](../elements/GeophysicalMethodType.md) -- seismic, GPR, resistivity tomography
91+
- [SubsurfacePropertyType](../elements/SubsurfacePropertyType.md) -- porosity, permeability, geothermal gradient
92+
- [AquiferType](../elements/AquiferType.md) -- unconfined, confined, artesian, karst
93+
- [GroundwaterProcessType](../elements/GroundwaterProcessType.md) -- recharge, discharge, saltwater intrusion
94+
- [HydrogeologyWellType](../elements/HydrogeologyWellType.md) -- monitoring, production, injection wells
95+
- [RemoteSensingPlatformType](../elements/RemoteSensingPlatformType.md) -- satellite, airborne, UAV, ground-based
96+
- [RemoteSensingDataType](../elements/RemoteSensingDataType.md) -- multispectral, hyperspectral, SAR, LiDAR
97+
- [WaterResourceType](../elements/WaterResourceType.md) -- surface water, groundwater, produced water
98+
- [WaterUseCategoryType](../elements/WaterUseCategoryType.md) -- irrigation, industrial cooling, environmental flow
99+
- [WaterQualityParameterType](../elements/WaterQualityParameterType.md) -- pH, dissolved oxygen, turbidity, nitrate
100+
- [WaterContaminantEnum](../elements/WaterContaminantEnum.md) -- water contaminant classification
101+
102+
### Example Mappings
103+
104+
| Permissible Value | Enum | Ontology Mapping |
105+
|-------------------|------|------------------|
106+
| AQUIFER | SubsurfaceFormationType | ENVO:00012408 |
107+
| POROSITY | SubsurfacePropertyType | PATO:0000973 |
108+
| SURFACE_WATER | WaterResourceType | ENVO:00002042 |
109+
| DISSOLVED_OXYGEN | WaterQualityParameterType | CHEBI:15379 |
110+
111+
---
112+
113+
## Computing
114+
115+
Data center infrastructure, semiconductor fabrication, and quantum computing are
116+
addressed by Genesis challenges on advanced computing and microelectronics supply chains.
117+
118+
### Enums
119+
120+
- [DataCenterCoolingType](../elements/DataCenterCoolingType.md) -- air, liquid, immersion, geothermal cooling
121+
- [DataCenterTierLevel](../elements/DataCenterTierLevel.md) -- Tier I through Tier IV reliability
122+
- [SemiconductorMaterialType](../elements/SemiconductorMaterialType.md) -- silicon, GaN, SiC, diamond
123+
- [ChipFabricationNodeType](../elements/ChipFabricationNodeType.md) -- 3 nm through mature node processes
124+
- [QubitType](../elements/QubitType.md) -- superconducting, trapped ion, photonic, topological
125+
- [QuantumAlgorithmCategoryType](../elements/QuantumAlgorithmCategoryType.md) -- optimization, simulation, ML, cryptography
126+
127+
### Example Mappings
128+
129+
| Permissible Value | Enum | Ontology Mapping |
130+
|-------------------|------|------------------|
131+
| SILICON | SemiconductorMaterialType | CHEBI:27573 |
132+
| SILICON_CARBIDE | SemiconductorMaterialType | CHEBI:29390 |
133+
| PHOTONIC | QubitType | CHEBI:30212 |
134+
| SYNCHROTRON | ParticleAcceleratorType | NCIT:C48205 |
135+
136+
---
137+
138+
## Industry
139+
140+
Advanced manufacturing, building energy performance, and unconventional mineral
141+
resources reflect Genesis challenges on industrial competitiveness, infrastructure
142+
resilience, and critical material supply chains.
143+
144+
### Enums
145+
146+
- [ManufacturingProcessType](../elements/ManufacturingProcessType.md) -- additive, subtractive, casting, CVD, PVD
147+
- [SmartManufacturingTechnologyType](../elements/SmartManufacturingTechnologyType.md) -- digital twins, IIoT, predictive maintenance
148+
- [BuildingSystemType](../elements/BuildingSystemType.md) -- HVAC, electrical, structural, fire protection
149+
- [BuildingEnergyPerformanceLevel](../elements/BuildingEnergyPerformanceLevel.md) -- net zero, passive house, LEED tiers
150+
- [UnconventionalMineralResourceType](../elements/UnconventionalMineralResourceType.md) -- mine tailings, red mud, fly ash, geothermal brine
151+
- [BioextractionMethodType](../elements/BioextractionMethodType.md) -- bioleaching, phytomining, biosorption
152+
- [TailingCharacterizationType](../elements/TailingCharacterizationType.md) -- particle size, mineralogy, metal content
153+
154+
### Example Mappings
155+
156+
| Permissible Value | Enum | Ontology Mapping |
157+
|-------------------|------|------------------|
158+
| INJECTION_MOLDING | ManufacturingProcessType | CHMO:0001430 |
159+
| HVAC | BuildingSystemType | brick:HVAC_System |
160+
| MINE_TAILINGS | UnconventionalMineralResourceType | ENVO:00000003 |
161+
| HEAP_BIOLEACHING | BioextractionMethodType | CHMO:0001681 |
162+
163+
---
164+
165+
## Materials and Physics
166+
167+
Computational materials discovery and particle physics instrumentation underpin
168+
Genesis challenges on scientific discovery and next-generation materials.
169+
170+
### Enums
171+
172+
- [MaterialsSimulationType](../elements/MaterialsSimulationType.md) -- DFT, molecular dynamics, Monte Carlo, phase field
173+
- [MaterialPropertyPredictionType](../elements/MaterialPropertyPredictionType.md) -- band gap, elastic modulus, thermal conductivity
174+
- [ParticleAcceleratorType](../elements/ParticleAcceleratorType.md) -- linac, synchrotron, cyclotron, FEL
175+
- [FundamentalParticleType](../elements/FundamentalParticleType.md) -- Standard Model particles (quarks, leptons, bosons)
176+
- [DetectorType](../elements/DetectorType.md) -- calorimeters, tracking, Cherenkov, muon spectrometers
177+
178+
### Example Mappings
179+
180+
| Permissible Value | Enum | Ontology Mapping |
181+
|-------------------|------|------------------|
182+
| MOLECULAR_DYNAMICS | MaterialsSimulationType | NCIT:C18097 |
183+
| ELASTIC_MODULUS | MaterialPropertyPredictionType | PATO:0001031 |
184+
| ELECTRON | FundamentalParticleType | CHEBI:10545 |
185+
| HIGGS_BOSON | FundamentalParticleType | CHEBI:146278 |
186+
187+
---
188+
189+
## Bioprocessing and Labs
190+
191+
Biomanufacturing scale-up and autonomous/self-driving laboratories address Genesis
192+
challenges on the bioeconomy and accelerated scientific discovery.
193+
194+
### Enums
195+
196+
- [BiomanufacturingScaleType](../elements/BiomanufacturingScaleType.md) -- micro through commercial scale
197+
- [BioproductCategoryType](../elements/BioproductCategoryType.md) -- biofuels, biochemicals, enzymes, biopharmaceuticals
198+
- [BioprocessOptimizationType](../elements/BioprocessOptimizationType.md) -- media optimization, strain engineering, PAT
199+
- [AutonomousLabComponentType](../elements/AutonomousLabComponentType.md) -- robotic handlers, synthesizers, HTS platforms
200+
- [ExperimentalDesignMethodType](../elements/ExperimentalDesignMethodType.md) -- Bayesian optimization, active learning, DOE
201+
- [LabAutomationWorkflowType](../elements/LabAutomationWorkflowType.md) -- closed-loop optimization, self-driving experimentation
202+
203+
### Example Mappings
204+
205+
| Permissible Value | Enum | Ontology Mapping |
206+
|-------------------|------|------------------|
207+
| BIOFUEL | BioproductCategoryType | CHEBI:33292 |
208+
| ROBOTIC_SAMPLE_HANDLER | AutonomousLabComponentType | OBI:0400112 |
209+
| HIGH_THROUGHPUT_SCREENING | LabAutomationWorkflowType | BAO:0010074 |
210+
| DOWNSTREAM_PURIFICATION | BioprocessOptimizationType | OBI:0001505 |
211+
212+
---
213+
214+
## Ontology Coverage
215+
216+
The Genesis value sets draw on 15 ontologies:
217+
218+
| Ontology | Full Name | Used In |
219+
|----------|-----------|---------|
220+
| CHEBI | Chemical Entities of Biological Interest | 9 modules |
221+
| ENVO | Environment Ontology | 8 modules |
222+
| NCIT | NCI Thesaurus | 8 modules |
223+
| PATO | Phenotype and Trait Ontology | 6 modules |
224+
| OBI | Ontology for Biomedical Investigations | 4 modules |
225+
| CHMO | Chemical Methods Ontology | 4 modules |
226+
| OEO | Open Energy Ontology | 3 modules |
227+
| Brick | Brick Schema for Buildings | 2 modules |
228+
| MS | Mass Spectrometry Ontology | 1 module |
229+
| SWO | Software Ontology | 1 module |
230+
| AGRO | Agronomy Ontology | 1 module |
231+
| FOODON | Food Ontology | 1 module |
232+
| PROCO | Process Chemistry Ontology | 1 module |
233+
| BAO | BioAssay Ontology | 1 module |
234+
| STATO | Statistics Ontology | 1 module |

‎mkdocs.yml‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -33,6 +33,8 @@ nav:
3333
- how-to-guides/dynamic-valuesets-validation.md
3434
- how-to-guides/sync-uniprot-species.md
3535
- Slot Generation: slot-generation.md
36+
- Subsets:
37+
- DOE Genesis Mission: subsets/genesis-mission.md
3638
- Slides: slides/index.md
3739
- About: about.md
3840

0 commit comments

Comments
 (0)