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Merged
cmungall merged 2 commits into from
Feb 22, 2026
Merged

Expand assay value sets and add BioPortal links #53

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f8631c4
Expand assay value sets and add BioPortal links to enum docs
dragon-ai-agent Feb 22, 2026
444c68b
Add view docs, design plan, update ontology caches
dragon-ai-agent Feb 22, 2026
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15 changes: 15 additions & 0 deletions cache/chebi/terms.csv
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Expand Up @@ -238,3 +238,18 @@ CHEBI:29238,tritium atom,2025-12-14T23:20:37.648492
CHEBI:36927,carbon-14 atom,2025-12-14T23:20:37.649036
CHEBI:37340,polonium-210 atom,2025-12-14T23:20:37.649555
CHEBI:26188,polyketide,2025-12-14T23:34:13.539907
CHEBI:33373,promethium atom,2026-01-30T18:48:58.387369
CHEBI:33374,samarium atom,2026-01-30T18:48:58.387899
CHEBI:33375,gadolinium atom,2026-01-30T18:48:58.388278
CHEBI:49648,holmium atom,2026-01-30T18:48:58.389147
CHEBI:33379,erbium,2026-01-30T18:48:58.389830
CHEBI:33380,thulium atom,2026-01-30T18:48:58.390225
CHEBI:33381,ytterbium,2026-01-30T18:48:58.390560
CHEBI:33382,lutetium atom,2026-01-30T18:48:58.391037
CHEBI:27573,silicon atom,2026-02-14T13:12:08.187733
CHEBI:29390,silicon carbide,2026-02-14T13:12:08.189109
CHEBI:82281,Indium phosphide,2026-02-14T13:12:08.190378
CHEBI:33371,technetium-99,2026-02-14T13:12:45.429091
CHEBI:33388,plutonium atom,2026-02-14T13:12:45.429768
CHEBI:33389,americium atom,2026-02-14T13:12:45.430292
CHEBI:52636,iodine-129 atom,2026-02-14T13:12:45.431463
7 changes: 7 additions & 0 deletions cache/chmo/terms.csv
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Expand Up @@ -63,3 +63,10 @@ CHMO:0000896,rotational-echo double-resonance spectroscopy,2025-12-19T10:23:50.4
CHMO:0000701,liquid chromatography-tandem mass spectrometry,2025-12-19T10:23:50.442059
CHMO:0000817,impedance spectrum,2025-12-19T10:23:50.442354
CHMO:0001009,high-performance liquid chromatography,2025-12-19T10:23:51.583446
CHMO:0001430,injection moulding,2026-02-14T13:11:57.085965
CHMO:0001613,extrusion,2026-02-14T13:11:57.086674
CHMO:0000414,gamma-ray spectroscopy,2026-02-14T13:13:05.885585
CHMO:0000230,alpha-particle spectroscopy,2026-02-14T13:13:05.886238
CHMO:0000782,neutron activation analysis,2026-02-14T13:13:05.886825
CHMO:0000068,electron microscopy,2026-02-14T13:13:05.887378
CHMO:0002119,granulometry,2026-02-15T15:45:57.306305
19 changes: 19 additions & 0 deletions cache/envo/terms.csv
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Expand Up @@ -93,3 +93,22 @@ ENVO:00002244,gleysol,2025-12-19T09:48:32.851266
ENVO:00002252,solonchak,2025-12-19T09:48:39.303320
ENVO:00002254,vertisol,2025-12-19T09:48:41.590102
ENVO:01001320,fresh water body,2025-12-19T09:48:43.832579
ENVO:00012408,aquifer,2026-02-14T13:11:34.028669
ENVO:00000175,karst,2026-02-14T13:11:34.029277
ENVO:01000505,salt dome,2026-02-14T13:11:34.029563
ENVO:00002056,shale,2026-02-14T13:11:34.029807
ENVO:00002185,oil reservoir,2026-02-14T13:12:11.178064
ENVO:01000851,methane clathrate,2026-02-14T13:12:11.179029
ENVO:00000354,volcanic field,2026-02-14T13:12:11.179698
ENVO:00002042,surface water,2026-02-14T13:12:25.875964
ENVO:01001004,groundwater,2026-02-14T13:12:25.876965
ENVO:00002019,brackish water,2026-02-14T13:12:25.877294
ENVO:00002149,sea water,2026-02-14T13:12:25.877834
ENVO:01001267,stormwater,2026-02-14T13:12:25.880279
ENVO:01000722,meltwater,2026-02-14T13:12:25.880967
ENVO:00000003,mine tailing,2026-02-14T13:12:45.427518
ENVO:02000127,coal ash,2026-02-14T13:12:45.428552
ENVO:02000130,boiler slag,2026-02-14T13:12:45.428924
ENVO:02000128,fly ash,2026-02-14T13:12:45.429293
ENVO:00003044,brine,2026-02-14T13:12:45.429918
ENVO:01000470,building envelope,2026-02-14T13:12:52.142467
13 changes: 13 additions & 0 deletions cache/ncit/terms.csv
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Expand Up @@ -415,3 +415,16 @@ NCIT:C8509,Primary Neoplasm,2025-12-22T08:19:09.518825
NCIT:C122534,Other Architecture and Engineering Workers,2025-12-22T08:19:09.519891
NCIT:C116701,Spectrophotometry,2025-12-22T08:19:09.525228
NCIT:C122936,Patient Derived Xenograft,2025-12-22T08:19:25.480593
NCIT:C62378,Quantum Dot,2026-02-14T13:11:57.130239
NCIT:C28169,Linear Accelerator,2026-02-14T13:12:45.427776
NCIT:C48205,Synchrotron,2026-02-14T13:12:45.428917
NCIT:C94881,Cyclotron,2026-02-14T13:12:45.430407
NCIT:C307,Biological Agent,2026-02-15T15:41:30.218030
NCIT:C18472,High Throughput Screening,2026-02-15T15:43:03.912026
NCIT:C50227,Transformer Device,2026-02-15T15:45:56.748457
NCIT:C156494,Magnetic Field Strength,2026-02-15T15:46:23.291483
NCIT:C18097,Molecular Dynamics,2026-02-15T15:46:23.783307
NCIT:C68769,Decontamination,2026-02-15T15:46:36.956886
NCIT:C28239,Cobalt Co-60,2026-02-15T15:46:57.873654
NCIT:C120576,Improvised Nuclear Device,2026-02-15T15:47:04.484150
NCIT:C120580,Radiological Dispersal Device,2026-02-15T15:47:13.265115
2 changes: 2 additions & 0 deletions cache/obi/terms.csv
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Expand Up @@ -76,3 +76,5 @@ OBI:0001186,epitope protection from infectious challenge experiment based on pat
OBI:0001937,has specified numeric value,2025-12-19T11:06:30.227493
OBI:0000659,specimen collection process,2025-12-22T08:16:54.248591
OBI:0000094,material processing,2025-12-22T08:16:54.249148
OBI:0000854,western blot assay,2026-02-22T14:59:00.342925
OBI:0302736,comet assay,2026-02-22T14:59:17.858350
4 changes: 4 additions & 0 deletions cache/pato/terms.csv
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Expand Up @@ -16,3 +16,7 @@ PATO:0002477,brittle,2025-10-19T07:20:50.014732
PATO:0040070,thermoplastic,2025-10-19T07:20:50.023960
PATO:0001421,alive,2025-10-19T07:20:51.275331
PATO:0001422,dead,2025-10-19T07:20:51.275821
PATO:0000973,porosity,2026-02-14T13:11:36.077664
PATO:0000970,permeability,2026-02-14T13:11:36.080996
PATO:0000146,temperature,2026-02-14T13:12:25.889278
PATO:0001756,heat conductivity,2026-02-14T13:12:51.425663
64 changes: 64 additions & 0 deletions docs/plans/2026-02-12-genesis-mission-valuesets-design.md
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@@ -0,0 +1,64 @@
# Genesis Mission Valuesets Coverage Design

## Context

The DOE Genesis Mission defines 26 national science and technology challenges.
Four BER (Biological and Environmental Research) lighthouse concepts provide
deeper detail: GEO-AI, AI-Driven Living Mine, Change, and G2P.

This design adds valuesets coverage for all 26 challenges using a tiered
depth approach, organized into the existing domain-based directory structure.

## Tiering

### Tier 1 (Deep) - BER lighthouses + adjacent

| Challenge | New Schema Files |
|---|---|
| GEO-AI lighthouse | `earth_science/subsurface.yaml`, `earth_science/hydrogeology.yaml`, `earth_science/remote_sensing.yaml` |
| AI-Driven Living Mine lighthouse | `bio/biogeochemistry.yaml`, `industry/unconventional_resources.yaml` |
| Change lighthouse | `bio/stress_response.yaml`, `bio/microbial_ecology.yaml`, `bio/synthetic_biology.yaml` |
| G2P lighthouse | `bio/omics_data_types.yaml`, `bio/enzyme_function.yaml` |
| #3 Biotechnology Revolution | `bioprocessing/biomanufacturing.yaml` |
| #4 Critical Minerals Supply | (covered by Living Mine + existing mining enums) |
| #14 Autonomous Labs | `lab_automation/autonomous_labs.yaml` |
| #17 Water for Energy | `earth_science/water_resources.yaml` |
| #19 Subsurface Energy Assets | `energy/subsurface_energy.yaml` |

### Tier 2 (Moderate) - extensions to existing domains

| Challenge | New Schema Files |
|---|---|
| #1 Advanced Manufacturing | `industry/manufacturing.yaml` |
| #5 Nuclear Energy | (covered by existing 46 nuclear enums) |
| #6 Fusion Energy | `energy/nuclear/fusion.yaml` |
| #7 Nuclear Cleanup | `energy/nuclear/nuclear_cleanup.yaml` |
| #12 Materials Discovery | `materials_science/computational_materials.yaml` |
| #13 Materials Design | (covered by #12 + existing materials_science enums) |
| #18 Grid Scaling | `energy/grid.yaml` |

### Tier 3 (Light) - 1-2 enums each

| Challenge | New Schema Files |
|---|---|
| #2 Buildings | `industry/construction.yaml` |
| #8-9 Quantum | `computing/quantum.yaml` |
| #10 Microelectronics | `computing/microelectronics.yaml` |
| #11 Data Centers | `computing/data_centers.yaml` |
| #15-16 Physics | `physics/particle_physics.yaml` |
| #20-26 Nuclear Security | `energy/nuclear/nuclear_forensics.yaml` |

## Estimated New Enums

- Tier 1: ~40-50 new enums across 13 files
- Tier 2: ~15-20 new enums across 5 files
- Tier 3: ~8-12 new enums across 6 files
- Total: ~65-80 new enums

## Conventions

- Follow existing pattern: CamelCase enum names, UPPER_CASE permissible values
- Use `meaning:` with OBO CURIEs where possible (verify via OLS)
- All enums get `status: DRAFT`, contributor ORCID, and `valuesets_meta:ValueSetEnumDefinition`
- Schema IDs use `https://w3id.org/valuesets/{path}`
- New files must be added to `valuesets.yaml` imports
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