biodata-registry is an open-weight model from Anne Voigt. Its published files total 8.0 MB.
A pip-installable Python package that provides a YAML-based dataset manifest registry for bioinformatics agents. It also exposes a FastMCP server so agent processes can query dataset metadata over MCP.
Parameters—
Context—
Weights8.0 MB
License—
AccessOpen weights
Monthly Downloads—
Model Card
A pip-installable Python package that provides a YAML-based dataset manifest registry for bioinformatics agents. It also exposes a FastMCP server so agent processes can query dataset metadata over MCP. - Discovers and indexes dataset manifests (one YAML file per dataset) at import time - Validates manifests against a typed schema (DatasetManifest) - Ships with the Moffitt et al. 2015 PDAC bulk microarray dataset as the first entry - Exposes registry tools over MCP via a FastMCP server Or from within the repo directory: The server exposes four MCP tools: 1. Create a YAML file in biodataregistry/manifests/.yaml. 2. The file must contain at minimum: datasetid, title, accession, organism…
Excerpt from the card by Anne Voigt.
Identity and Version
- Repository
- anne-voigt/biodata-registry
- Publisher
- Anne Voigt
- Task
- Not stated by the source
- Modality
- Other
- Library
- Not stated by the source
- Parameters
- Not stated by the source
- Languages
- Not stated by the source
- Revision
- 2c167c154db2830c394cb2bb4ee18f8d2b232610
- First published
- 2026-06-16
- Last updated
- 2026-10-06
Files and Weights
188 files, 8.0 MB in total.
Configuration112 files · 1.1 MB
Documentation20 files · 182.1 KB
Other53 files · 6.8 MB
Repository3 files · 6.2 KB
Every file
| File | Type | Size | SHA-256 |
|---|---|---|---|
| .pre-commit-config.yaml | Configuration | 970 B | — |
| bandit.yaml | Configuration | 916 B | — |
| biodata_registry/__init__.py | Configuration | 2.3 KB | — |
| biodata_registry/_manifest_checks.py | Configuration | 29.1 KB | — |
| biodata_registry/_manifest_vocab.py | Configuration | 10.2 KB | — |
| biodata_registry/_plan_gates.py | Configuration | 42.0 KB | — |
| biodata_registry/_plan_vocab.py | Configuration | 5.1 KB | — |
| biodata_registry/data_access.py | Configuration | 12.0 KB | — |
| biodata_registry/data_transitions.py | Configuration | 12.4 KB | — |
| biodata_registry/integration.py | Configuration | 14.4 KB | — |
| biodata_registry/manifest_schema.py | Configuration | 34.2 KB | — |
| biodata_registry/manifests/__init__.py | Configuration | — | |
| biodata_registry/manifests/ccle_broad_2019.yaml | Configuration | 3.8 KB | — |
| biodata_registry/manifests/cptac_pda.yaml | Configuration | 9.9 KB | — |
| biodata_registry/manifests/cptac_pda_counts.yaml | Configuration | 16.3 KB | — |
| biodata_registry/manifests/cptac_pda_proteome.yaml | Configuration | 17.7 KB | — |
| biodata_registry/manifests/gse111672_moncada_indrop.yaml | Configuration | 10.7 KB | — |
| biodata_registry/manifests/gse111672_moncada_st.yaml | Configuration | 13.5 KB | — |
| biodata_registry/manifests/gse15471_badea.yaml | Configuration | 7.4 KB | — |
| biodata_registry/manifests/gse155698_steele.yaml | Configuration | 14.2 KB | — |
| biodata_registry/manifests/gse16515_mayo.yaml | Configuration | 7.1 KB | — |
| biodata_registry/manifests/gse167525_brown.yaml | Configuration | 8.2 KB | — |
| biodata_registry/manifests/gse17891_collisson.yaml | Configuration | 11.4 KB | — |
| biodata_registry/manifests/gse202051_hwang.yaml | Configuration | 13.8 KB | — |
| biodata_registry/manifests/gse205013_werba.yaml | Configuration | 11.2 KB | — |
| biodata_registry/manifests/gse205154_sears.yaml | Configuration | 15.5 KB | — |
| biodata_registry/manifests/gse205154_sears_counts.yaml | Configuration | 14.5 KB | — |
| biodata_registry/manifests/gse205154_sears_filtered_tmm.yaml | Configuration | 16.5 KB | — |
| biodata_registry/manifests/gse205154_sears_tmm.yaml | Configuration | 14.6 KB | — |
| biodata_registry/manifests/gse205154_sears_vst.yaml | Configuration | 17.4 KB | — |
| biodata_registry/manifests/gse21501_stratford.yaml | Configuration | 8.1 KB | — |
| biodata_registry/manifests/gse221250_mccarthy.yaml | Configuration | 11.8 KB | — |
| biodata_registry/manifests/gse278687_chen_st.yaml | Configuration | 15.9 KB | — |
| biodata_registry/manifests/gse278688_chen_sc.yaml | Configuration | 11.5 KB | — |
| biodata_registry/manifests/gse287307_guo.yaml | Configuration | 8.4 KB | — |
| biodata_registry/manifests/gse28735_pdac.yaml | Configuration | 8.1 KB | — |
| biodata_registry/manifests/gse50827_nones.yaml | Configuration | 7.9 KB | — |
| biodata_registry/manifests/gse57495.yaml | Configuration | 6.9 KB | — |
| biodata_registry/manifests/gse62165_jiang.yaml | Configuration | 6.1 KB | — |
| biodata_registry/manifests/gse71729_moffitt.yaml | Configuration | 13.7 KB | — |
| biodata_registry/manifests/gse71989_chen.yaml | Configuration | 6.7 KB | — |
| biodata_registry/manifests/paad_cptac_2021.yaml | Configuration | 3.8 KB | — |
| biodata_registry/manifests/paad_qcmg_uq_2016.yaml | Configuration | 4.9 KB | — |
| biodata_registry/manifests/paad_tcga.yaml | Configuration | 5.4 KB | — |
| biodata_registry/manifests/paad_utsw_2015.yaml | Configuration | 3.4 KB | — |
| biodata_registry/manifests/paca_au_array.yaml | Configuration | 13.8 KB | — |
| biodata_registry/manifests/paca_au_rnaseq.yaml | Configuration | 15.6 KB | — |
| biodata_registry/manifests/paca_ca_rnaseq.yaml | Configuration | 12.1 KB | — |
| biodata_registry/manifests/puleo_2018.yaml | Configuration | 11.5 KB | — |
| biodata_registry/manifests/shiau_2024_smi.yaml | Configuration | 17.9 KB | — |
| biodata_registry/manifests/tcga_paad.yaml | Configuration | 19.7 KB | — |
| biodata_registry/manifests/tcga_paad_tpm.yaml | Configuration | 23.8 KB | — |
| biodata_registry/registry.py | Configuration | 8.4 KB | — |
| biodata_registry/server.py | Configuration | 8.7 KB | — |
| memory.py | Configuration | 18.6 KB | — |
| scripts/ingest/chen/assemble_gse278687_chen_st.py | Configuration | 11.7 KB | — |
| scripts/ingest/chen/assemble_gse278688_chen_sc.py | Configuration | 8.2 KB | — |
| scripts/ingest/cptac/assemble_cptac_pda_counts.py | Configuration | 14.8 KB | — |
| scripts/ingest/cptac/assemble_cptac_pda_proteome.py | Configuration | 6.9 KB | — |
| scripts/ingest/geo/_geo.py | Configuration | 3.9 KB | — |
| scripts/ingest/geo/assemble_gse167525_brown.py | Configuration | 4.8 KB | — |
| scripts/ingest/geo/assemble_gse221250_mccarthy.py | Configuration | 5.0 KB | — |
| scripts/ingest/geo/assemble_gse287307_guo.py | Configuration | 3.4 KB | — |
| scripts/ingest/hwang/assemble_gse202051_hwang.py | Configuration | 5.9 KB | — |
| scripts/ingest/loveless/assemble_h5ad.py | Configuration | 3.3 KB | — |
| scripts/ingest/loveless/derive_profiles.py | Configuration | 6.7 KB | — |
| scripts/ingest/loveless/derive_signatures.py | Configuration | 10.1 KB | — |
| scripts/ingest/loveless/merge_runs_h5ad.py | Configuration | 8.5 KB | — |
| scripts/ingest/loveless/slim_h5ad.py | Configuration | 2.2 KB | — |
| scripts/ingest/loveless/subset_h5ad.py | Configuration | 2.5 KB | — |
| scripts/ingest/moncada/assemble_gse111672_moncada_indrop.py | Configuration | 5.4 KB | — |
| scripts/ingest/moncada/assemble_gse111672_moncada_st.py | Configuration | 7.7 KB | — |
| scripts/ingest/shiau/assemble_shiau_2024_smi.py | Configuration | 9.2 KB | — |
| scripts/ingest/tcga/_gdc.py | Configuration | 7.8 KB | — |
| scripts/ingest/tcga/assemble_tcga_paad_counts.py | Configuration | 7.1 KB | — |
| scripts/ingest/tcga/assemble_tcga_paad_tpm.py | Configuration | 5.9 KB | — |
| scripts/ingest/tcga/bake_tcga_paad_clinical.py | Configuration | 12.8 KB | — |
| scripts/record_integrity.py | Configuration | 9.4 KB | — |
| security/bandit-baseline.json | Configuration | 2.4 KB | — |
| tests/__init__.py | Configuration | — | |
| tests/integration_plan/__init__.py | Configuration | — | |
| tests/integration_plan/_helpers.py | Configuration | 4.5 KB | — |
| tests/integration_plan/test_final_plan.py | Configuration | 3.6 KB | — |
| tests/integration_plan/test_gate_arity.py | Configuration | 1.1 KB | — |
| tests/integration_plan/test_gate_atlas.py | Configuration | 3.2 KB | — |
| tests/integration_plan/test_gate_confounded_design.py | Configuration | 6.4 KB | — |
| tests/integration_plan/test_gate_cross_modality.py | Configuration | 1.1 KB | — |
| tests/integration_plan/test_gate_cross_organism.py | Configuration | 3.1 KB | — |
| tests/integration_plan/test_gate_cross_resolution.py | Configuration | 2.9 KB | — |
| tests/integration_plan/test_gate_deconvolution_pairing.py | Configuration | 6.8 KB | — |
| tests/integration_plan/test_gate_dna.py | Configuration | 1.5 KB | — |
| tests/integration_plan/test_gate_duplicate_cohort.py | Configuration | 6.8 KB | — |
| tests/integration_plan/test_gate_model_system.py | Configuration | 6.0 KB | — |
| tests/integration_plan/test_gate_shared_feature_space.py | Configuration | 1.0 KB | — |
| tests/integration_plan/test_gate_spatial.py | Configuration | 2.9 KB | — |
| tests/integration_plan/test_gate_subject_group.py | Configuration | 8.7 KB | — |
| tests/integration_plan/test_group_by.py | Configuration | 3.3 KB | — |
| tests/integration_plan/test_mcp_wiring.py | Configuration | 856 B | — |
| tests/integration_plan/test_output_contract.py | Configuration | 3.2 KB | — |
| tests/integration_plan/test_subject_group_mgh.py | Configuration | 1.2 KB | — |
| tests/test_data_access.py | Configuration | 10.7 KB | — |
| tests/test_data_transitions.py | Configuration | 8.9 KB | — |
| tests/test_derive_profiles.py | Configuration | 2.3 KB | — |
| tests/test_derive_signatures.py | Configuration | 3.3 KB | — |
| tests/test_live_cache.py | Configuration | 3.9 KB | — |
| tests/test_loveless_merge_runs.py | Configuration | 3.4 KB | — |
| tests/test_manifest_integrity.py | Configuration | 3.9 KB | — |
| tests/test_manifests_against_data.py | Configuration | 50.6 KB | — |
| tests/test_memory_tool.py | Configuration | 14.7 KB | — |
| tests/test_registry.py | Configuration | 47.5 KB | — |
| tests/test_tcga_paad_clinical_bake.py | Configuration | 5.5 KB | — |
| tests/test_tcga_paad_counts_assembler.py | Configuration | 6.3 KB | — |
| README.md | Documentation | 4.0 KB | — |
| docs/INTAKE-CHECKLIST.md | Documentation | 6.3 KB | — |
| docs/adr/ADR-0001-decision-matrix.md | Documentation | 18.5 KB | — |
| docs/adr/ADR-0015-vst-data-level-mapping.md | Documentation | 5.8 KB | — |
| docs/adr/ADR-0026-subject-group-id.md | Documentation | 9.3 KB | — |
| docs/adr/ADR-0027-proteomics-block.md | Documentation | 5.5 KB | — |
| docs/adr/ADR-0028-spatial-modality-split.md | Documentation | 7.1 KB | — |
| docs/adr/ADR-0029-spatial-specialist-contract.md | Documentation | 6.2 KB | — |
| docs/adr/ADR-0030-data-access-seam.md | Documentation | 5.3 KB | — |
| docs/adr/ADR-0031-curated-mouse-manifests.md | Documentation | 3.7 KB | — |
| docs/adr/ADR-0033-model-system-in-the-integration-engine.md | Documentation | 4.7 KB | — |
| docs/adr/RESERVED.md | Documentation | 2.8 KB | — |
| docs/design/DESIGN-spatial-specialist.md | Documentation | 23.2 KB | — |
| docs/history/DONE.md | Documentation | 8.2 KB | — |
| docs/plans/CANDIDATES-spatial-hur-2026-10.md | Documentation | 28.8 KB | — |
| docs/plans/PLAN-hur-perturbation-datasets.md | Documentation | 8.2 KB | — |
| docs/plans/PLAN-modality-expansion.md | Documentation | 14.5 KB | — |
| docs/plans/PLAN-model-system-pooling.md | Documentation | 12.3 KB | — |
| scripts/ingest/loveless/README.md | Documentation | 5.7 KB | — |
| security/ACCEPTED-FINDINGS.md | Documentation | 2.1 KB | — |
| Makefile | Other | 2.4 KB | — |
| biodata_registry-0.1.0-py3-none-any.whl | Other | 62.8 KB | — |
| biodata_registry-0.1.1-py3-none-any.whl | Other | 63.0 KB | — |
| biodata_registry-0.1.10-py3-none-any.whl | Other | 107.3 KB | 5f11b80bc9fa |
| biodata_registry-0.1.11-py3-none-any.whl | Other | 119.1 KB | 6b3f53747d90 |
| biodata_registry-0.1.12-py3-none-any.whl | Other | 119.3 KB | a2c0ea70ef93 |
| biodata_registry-0.1.13-py3-none-any.whl | Other | 122.9 KB | f6441e81f093 |
| biodata_registry-0.1.14-py3-none-any.whl | Other | 130.1 KB | f6babb2e42d1 |
| biodata_registry-0.1.15-py3-none-any.whl | Other | 134.4 KB | 7aa2b03a2162 |
| biodata_registry-0.1.16-py3-none-any.whl | Other | 134.9 KB | dcfe54e3cd5c |
| biodata_registry-0.1.17-py3-none-any.whl | Other | 151.4 KB | df0f683f5311 |
| biodata_registry-0.1.18-py3-none-any.whl | Other | 152.7 KB | 2ece094de1b2 |
| biodata_registry-0.1.19-py3-none-any.whl | Other | 160.0 KB | 91af26065065 |
| biodata_registry-0.1.2-py3-none-any.whl | Other | 70.1 KB | — |
| biodata_registry-0.1.20-py3-none-any.whl | Other | 160.3 KB | 7afceaf86f2d |
| biodata_registry-0.1.21-py3-none-any.whl | Other | 167.6 KB | 4159047ead39 |
| biodata_registry-0.1.22-py3-none-any.whl | Other | 171.7 KB | fdd61b097988 |
| biodata_registry-0.1.23-py3-none-any.whl | Other | 176.2 KB | e6d960c89669 |
| biodata_registry-0.1.24-py3-none-any.whl | Other | 177.3 KB | 085aac782ddd |
| biodata_registry-0.1.25-py3-none-any.whl | Other | 177.5 KB | 255d8e1871c1 |
| biodata_registry-0.1.26-py3-none-any.whl | Other | 179.5 KB | 9710fea1aff0 |
| biodata_registry-0.1.27-py3-none-any.whl | Other | 185.7 KB | ec9bb3023c6b |
| biodata_registry-0.1.28-py3-none-any.whl | Other | 188.0 KB | 958b2780efc6 |
| biodata_registry-0.1.29-py3-none-any.whl | Other | 188.4 KB | 1759faf0c3ad |
| biodata_registry-0.1.3-py3-none-any.whl | Other | 70.7 KB | — |
| biodata_registry-0.1.30-py3-none-any.whl | Other | 202.0 KB | 9508a9c9cdf2 |
| biodata_registry-0.1.31-py3-none-any.whl | Other | 206.5 KB | 4a0a4b3cee6f |
| biodata_registry-0.1.32-py3-none-any.whl | Other | 207.8 KB | 04a2d57f6cd7 |
| biodata_registry-0.1.33-py3-none-any.whl | Other | 208.7 KB | ab67754d8812 |
| biodata_registry-0.1.34-py3-none-any.whl | Other | 209.5 KB | 8b8a3d4857af |
| biodata_registry-0.1.35-py3-none-any.whl | Other | 220.2 KB | 76fa83d7cb45 |
| biodata_registry-0.1.36-py3-none-any.whl | Other | 228.5 KB | 6f2ac8c47c84 |
| biodata_registry-0.1.37-py3-none-any.whl | Other | 234.2 KB | 29c1f9c5d376 |
| biodata_registry-0.1.4-py3-none-any.whl | Other | 84.9 KB | — |
| biodata_registry-0.1.5-py3-none-any.whl | Other | 87.2 KB | — |
| biodata_registry-0.1.6-py3-none-any.whl | Other | 89.8 KB | — |
| biodata_registry-0.1.7-py3-none-any.whl | Other | 95.8 KB | — |
| biodata_registry-0.1.8-py3-none-any.whl | Other | 103.7 KB | b7edc1aa7405 |
| biodata_registry-0.1.9-py3-none-any.whl | Other | 107.0 KB | e6bbfc1900a3 |
| pyproject.toml | Other | 1.7 KB | — |
| scripts/hooks/pre-push | Other | 1.1 KB | — |
| scripts/ingest/chen/gse278688_chen_sc_celltype_profiles_chen_st_genes.csv | Other | 252.5 KB | — |
| scripts/ingest/chen/gse278688_chen_sc_celltype_signatures.csv | Other | 15.0 KB | — |
| scripts/ingest/chen/gse278688_chen_sc_celltype_signatures_chen_st_genes.csv | Other | 14.5 KB | — |
| scripts/ingest/loveless/Dockerfile | Other | 1.8 KB | — |
| scripts/ingest/loveless/convert_rds_to_h5ad.R | Other | 5.5 KB | — |
| scripts/ingest/loveless/gse155698_steele_celltype_profiles_v2.csv | Other | 260.5 KB | — |
| scripts/ingest/loveless/gse155698_steele_celltype_signatures_v2.csv | Other | 17.8 KB | — |
| scripts/ingest/loveless/gse205013_werba_celltype_signatures.csv | Other | 17.9 KB | — |
| scripts/ingest/loveless/run_job.sh | Other | 5.2 KB | — |
| scripts/release.sh | Other | 12.6 KB | — |
| scripts/security_scan.sh | Other | 9.3 KB | — |
| uv.lock | Other | 482.9 KB | — |
| .gitattributes | Repository | 2.6 KB | — |
| .gitignore | Repository | 520 B | — |
| .gitleaks.toml | Repository | 3.1 KB | — |
License and Download
- License
- Not stated by the source
- Access
- Open weights, no gate
Download from Anne Voigt
Released by Anne Voigt through its official repository on Hugging Face.