Scientific Research

Life Sciences Databases

Name: Life Sciences Databases
Author: OpenAI

OpenAI v0.1.5

Helps you query and interpret structured public life-science resources across human genetics, variants, expression, functional genomics, proteins, structures, pathways, chemistry, pharmacology, clinical evidence, and public omics datasets. Use focused skills for source-specific lookups or combine a small set of orthogonal databases for evidence-backed research.

Language: English · Automatically detected from descriptions.

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Package details

Publisher declarations from the archived package. These are separate from our research and the live service's terms.

Package license: Proprietary
Package author: OpenAI
Keywords: life-science, databases, bioinformatics, genetics, omics, proteins, chemistry, clinical-research

Declared capabilities

Interactive
Read
Write

Package observed Sep 30, 2026.

.codex-plugin/plugin.json

Files & skills

File archives

Plugin package116 files · 99.8 KBBrowse files →

Skill instructions

alphafold-skill2.8 KB

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---
name: alphafold-skill
description: Submit compact AlphaFold Protein Structure Database API requests for prediction, UniProt summary, sequence summary, and annotation lookups. Use when a user wants AlphaFold metadata or concise structure summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `alphafold-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all AlphaFold API calls.
- Use `base_url=https://alphafold.ebi.ac.uk/api`.
- The script accepts `max_items`, but set it explicitly only when trimming array-heavy responses; single-entry lookups usually do not need it.
- For `sequence/summary` or `annotations`, start around `max_items=3` to `5`.
- Re-run the request if the conversation is long instead of trusting older tool output.
- Treat displayed `...` in tool previews as UI truncation, not part of the real request.
- If the user asks for full JSON, set `save_raw=true` and report the saved file path instead of pasting the payload into chat.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
- Prefer these paths: `prediction/<qualifier>`, `uniprot/summary/<qualifier>.json`, `sequence/summary`, and `annotations/<qualifier>.json`.
- Keep sequence-style inputs compact and prefer rerunning instead of copying prior output back into context.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common AlphaFold patterns:
- `{"base_url":"https://alphafold.ebi.ac.uk/api","path":"prediction/Q5VSL9"}`
- `{"base_url":"https://alphafold.ebi.ac.uk/api","path":"uniprot/summary/Q5VSL9.json"}`
- `{"base_url":"https://alphafold.ebi.ac.uk/api","path":"annotations/Q5VSL9.json","params":{"type":"MUTAGEN"},"max_items":3}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` such as `invalid_json`, `invalid_input`, `network_error`, or `invalid_response`.

## Execution
```bash
echo '{"base_url":"https://alphafold.ebi.ac.uk/api","path":"prediction/Q5VSL9"}' | python scripts/rest_request.py
```

Referenced files: 1

bgee-skill1.97 KB

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---
name: bgee-skill
description: Submit compact Bgee SPARQL requests for healthy wild-type expression metadata and ontology-aware lookup patterns. Use when a user wants concise Bgee summaries; save raw results only on request.
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `bgee-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/sparql_request.py` for all Bgee SPARQL work.
- Start with small `SELECT` or `ASK` queries and add `LIMIT` early.
- Prefer ontology-aware, healthy wild-type expression questions over broad triple dumps.
- Use `query_path` for longer SPARQL documents instead of pasting large inline queries.
- Re-run requests in long conversations instead of relying on older tool output.

## Execution behavior
- Return concise markdown summaries from the SPARQL JSON by default.
- Return raw results only if the user explicitly asks for machine-readable output.
- Default to JSON result format unless the user explicitly asks for text output.

## Input
- Read one JSON object from stdin.
- Required field: `query` or `query_path`
- Optional fields: `method`, `params`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common Bgee patterns:
- `{"query":"ASK {}"}`
- `{"query":"SELECT * WHERE { ?s ?p ?o } LIMIT 3","max_items":3}`

## Output
- Success returns `ok`, `source`, a compact `summary`, and `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` such as `invalid_json`, `invalid_input`, `network_error`, or `invalid_response`.

## Execution
```bash
echo '{"query":"ASK {}"}' | python scripts/sparql_request.py
```

Referenced files: 1

bindingdb-skill2.7 KB

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---
name: bindingdb-skill
description: Submit compact BindingDB REST API requests for ligand-target binding lookups by PDB, UniProt, or similarity search. Use when a user wants concise BindingDB summaries; save raw payloads only on request.
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `bindingdb-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all BindingDB API calls.
- Use `base_url=https://bindingdb.org`.
- Add `response=application/json` in `params` when you want structured output; some empty-result cases may still return an empty body.
- For broad lookup endpoints, start around `max_items=10`; similarity-style queries are better with `5-10`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer these paths: `rest/getLigandsByPDBs`, `rest/getLigandsByUniprots`, `rest/getLigandsBySmiles`, and `rest/getTargetsByCompound`.
- If the user needs the full payload, set `save_raw=true` and report the saved file path instead of pasting large response bodies into chat.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common BindingDB patterns:
- `{"base_url":"https://bindingdb.org","path":"rest/getLigandsByPDBs","params":{"pdb":"1Q0L","cutoff":100,"identity":92,"response":"application/json"},"max_items":10}`
- `{"base_url":"https://bindingdb.org","path":"rest/getLigandsBySmiles","params":{"smiles":"CC(=O)OC1=CC=CC=C1C(=O)O","cutoff":0.9,"response":"application/json"},"max_items":5}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records`, a compact `summary`, or `text_head`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://bindingdb.org","path":"rest/getLigandsByPDBs","params":{"pdb":"1Q0L","cutoff":100,"identity":92,"response":"application/json"},"max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

biobankjapan-phewas-skill2.71 KB

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---
name: biobankjapan-phewas-skill
description: Fetch compact BioBank Japan PheWAS summaries for single variants by accepting rsID, GRCh38, or GRCh37 input and resolving to the required GRCh37 query. Use when a user wants concise BBJ association results for one variant
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `biobankjapan-phewas-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/biobankjapan_phewas.py` for all BioBank Japan PheWAS lookups.
- Accept exactly one of `rsid`, `grch37`, `grch38`, or `variant`; resolve to the canonical GRCh37 `chr:pos-ref-alt` query before calling BioBank Japan.
- The script accepts `max_results`; start with `max_results=10` and only increase it if the first slice is insufficient.
- Re-run the lookup in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.
- If the user needs the full association payload, set `save_raw=true` and report `raw_output_path` instead of pasting large arrays into chat.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the JSON verbatim only if the user explicitly asks for machine-readable output.
- Surface the canonical queried variant, total association count, and whether the results were truncated.
- Increase `max_results` gradually instead of asking for large association dumps in one call.

## Input
- Read one JSON object from stdin, or a single JSON string containing the variant.
- Required input: exactly one of `rsid`, `grch37`, `grch38`, or `variant`
- Optional fields: `max_results`, `save_raw`, `raw_output_path`, `timeout_sec`
- Common patterns:
- `{"grch37":"10:114758349-C-T","max_results":10}`
- `{"grch38":"10:112998590-C-T","max_results":10}`
- `{"rsid":"rs7903146","max_results":10}`
- `{"variant":"10:114758349:C:T","max_results":25,"save_raw":true}`

## Output
- Success returns `ok`, `source`, `input`, `query_variant`, `max_results_applied`, `association_count`, `association_count_total`, `truncated`, `associations`, `variant`, `variant_url`, `raw_output_path`, and `warnings`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"grch37":"10:114758349-C-T","max_results":10}' | python scripts/biobankjapan_phewas.py
```

Referenced files: 3

biostudies-arrayexpress-skill2.63 KB

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---
name: biostudies-arrayexpress-skill
description: Submit compact BioStudies and ArrayExpress API requests for free-text search and accession-based study retrieval. Use when a user wants concise BioStudies summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `biostudies-arrayexpress-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all BioStudies and ArrayExpress calls.
- Use `base_url=https://www.ebi.ac.uk/biostudies/api/v1`.
- Search pages are better with `pageSize=10` and `max_items=10`; accession lookups usually do not need `max_items`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer these paths: `search`, `ArrayExpress/search`, `studies/<accession>`, and `studies/<accession>/info`.
- If the user needs the full payload, set `save_raw=true` and report the saved file path instead of pasting large study records into chat.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common BioStudies patterns:
- `{"base_url":"https://www.ebi.ac.uk/biostudies/api/v1","path":"search","params":{"query":"rna","page":1,"pageSize":10},"record_path":"hits","max_items":10}`
- `{"base_url":"https://www.ebi.ac.uk/biostudies/api/v1","path":"ArrayExpress/search","params":{"query":"single cell","page":1,"pageSize":10},"record_path":"hits","max_items":10}`
- `{"base_url":"https://www.ebi.ac.uk/biostudies/api/v1","path":"studies/E-MTAB-6701"}`

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk/biostudies/api/v1","path":"search","params":{"query":"rna","page":1,"pageSize":10},"record_path":"hits","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

cbioportal-skill2.78 KB

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---
name: cbioportal-skill
description: Submit compact cBioPortal API requests for studies, molecular profiles, mutations, clinical data, and samples. Use when a user wants concise cBioPortal summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `cbioportal-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all cBioPortal API calls.
- Use `base_url=https://www.cbioportal.org/api`.
- Collection endpoints are better with `pageSize=10` and `max_items=10`; single study or profile lookups usually do not need `max_items`.
- Use `method=POST` plus `json_body` for fetch-style endpoints such as mutation fetches.
- Send `Accept: application/json` in `headers`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer these paths: `studies`, `studies/<studyId>/molecular-profiles`, `molecular-profiles/<profileId>/mutations/fetch`, and study-level clinical or sample endpoints.
- If the user needs the full payload, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common cBioPortal patterns:
  - `{"base_url":"https://www.cbioportal.org/api","path":"studies","params":{"keyword":"breast","projection":"SUMMARY","pageSize":10},"headers":{"Accept":"application/json"},"max_items":10}`
  - `{"base_url":"https://www.cbioportal.org/api","path":"molecular-profiles/brca_tcga_mutations/mutations/fetch","method":"POST","json_body":{"sampleListId":"brca_tcga_all","entrezGeneIds":[7157]},"headers":{"Accept":"application/json"},"max_items":10}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://www.cbioportal.org/api","path":"studies","params":{"keyword":"breast","projection":"SUMMARY","pageSize":10},"headers":{"Accept":"application/json"},"max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

cellxgene-skill2.4 KB

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---
name: cellxgene-skill
description: Submit compact CELLxGENE Discover API requests for public collection and dataset metadata. Use when a user wants concise single-cell collection summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `cellxgene-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all CELLxGENE Discover calls.
- Use `base_url=https://api.cellxgene.cziscience.com/curation/v1`.
- Prefer targeted collection detail lookups rather than full archive dumps by default.
- The public `collections` list can be large and may require a higher `timeout_sec`; collection detail lookups are usually the better first call.
- Re-run requests in long conversations instead of relying on older tool output.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common CELLxGENE patterns:
- `{"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections/db468083-041c-41ca-8f6f-bf991a070adf","max_items":5}`
- `{"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections","timeout_sec":60,"max_items":5}`

## Execution
```bash
echo '{"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections/db468083-041c-41ca-8f6f-bf991a070adf","max_items":5}' | python scripts/rest_request.py
```

Referenced files: 1

chebi-skill2.45 KB

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---
name: chebi-skill
description: Submit compact ChEBI 2.0 API requests for chemical search, compound lookup, ontology traversal, and structure metadata. Use when a user wants concise ChEBI summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `chebi-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all ChEBI calls.
- Use `base_url=https://www.ebi.ac.uk`.
- Prefer the documented public routes under `chebi/backend/api/public/`.
- Start with `es_search/` for free-text lookup and use `compound/<CHEBI:id>/` for targeted records.
- Re-run requests in long conversations instead of relying on older tool output.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return raw JSON only if the user explicitly asks for machine-readable output.
- Prefer these paths: `chebi/backend/api/public/es_search/`, `chebi/backend/api/public/compound/<CHEBI:id>/`, and ontology child or parent routes.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common ChEBI patterns:
- `{"base_url":"https://www.ebi.ac.uk","path":"chebi/backend/api/public/es_search/","params":{"query":"caffeine","size":10},"record_path":"results","max_items":10}`
- `{"base_url":"https://www.ebi.ac.uk","path":"chebi/backend/api/public/compound/CHEBI:27732/"}`
- `{"base_url":"https://www.ebi.ac.uk","path":"chebi/backend/api/public/ontology/children/CHEBI:27732/"}`

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk","path":"chebi/backend/api/public/es_search/","params":{"query":"caffeine","size":10},"record_path":"results","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

chembl-skill2.73 KB

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---
name: chembl-skill
description: Submit compact ChEMBL API requests for activity, molecule, target, mechanism, and text-search endpoints. Use when a user wants concise ChEMBL summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `chembl-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all ChEMBL API calls.
- Use `base_url=https://www.ebi.ac.uk/chembl/api/data`.
- The script accepts `max_items`; for activity, mechanism, and text-search collections, start with API `limit=10` and `max_items=10`.
- Single molecule or target lookups usually do not need `max_items`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
- Prefer these paths: `activity.json`, `molecule/<id>.json`, `target/<id>.json`, `mechanism.json`, and `molecule/search.json`.
- Use `record_path` to target list fields like `activities`, `mechanisms`, or `molecules`.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common ChEMBL patterns:
  - `{"base_url":"https://www.ebi.ac.uk/chembl/api/data","path":"activity.json","params":{"molecule_chembl_id":"CHEMBL25","limit":10},"record_path":"activities","max_items":10}`
  - `{"base_url":"https://www.ebi.ac.uk/chembl/api/data","path":"molecule/CHEMBL25.json"}`
  - `{"base_url":"https://www.ebi.ac.uk/chembl/api/data","path":"molecule/search.json","params":{"q":"imatinib","limit":10},"record_path":"molecules","max_items":10}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk/chembl/api/data","path":"activity.json","params":{"molecule_chembl_id":"CHEMBL25","limit":10},"record_path":"activities","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

civic-skill2.03 KB

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---
name: civic-skill
description: Submit compact CIViC GraphQL requests for cancer variant interpretation schema inspection and targeted evidence retrieval. Use when a user wants concise CIViC summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `civic-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/civic_graphql.py` for all CIViC GraphQL work.
- Keep selection sets narrow and start with targeted, evidence-bearing entity queries; reserve schema introspection for resolving a concrete query failure.
- Use `query_path` for longer GraphQL documents instead of pasting large inline queries.
- Re-run requests in long conversations instead of relying on older tool output.

## Input
- Read one JSON object from stdin.
- Required field: `query` or `query_path`
- Optional fields: `variables`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common CIViC patterns:
- `{"query":"query { search(query:\"BRAF\") { id name matchingText resultType } }","max_items":5}`

## Output
- Success returns `ok`, `source`, `top_keys`, a compact `summary`, and `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` such as `invalid_json`, `invalid_input`, `network_error`, `invalid_response`, or `graphql_error`.

## Execution
```bash
echo '{"query":"query { search(query:\"BRAF\") { id name matchingText resultType } }","max_items":5}' | python scripts/civic_graphql.py
```

Referenced files: 1

clinicaltrials-skill2.65 KB

View saved version →

---
name: clinicaltrials-skill
description: Submit compact ClinicalTrials.gov API v2 requests for study search, metadata, enums, search areas, and field statistics. Use when a user wants concise ClinicalTrials.gov summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `clinicaltrials-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/clinicaltrials_client.py` for all ClinicalTrials.gov v2 calls.
- Study searches are better with `max_items=10` and `max_pages=1`; only increase pages when the user explicitly wants more than the first page.
- Use targeted `params` instead of broad unfiltered study dumps.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer `action=studies` for search and `action=metadata|search_areas|enums|stats_size|field_values|field_sizes` for API introspection and field stats.
- If the user needs full pages or aggregated responses, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required field: `action`
- Supported actions: `studies`, `metadata`, `search_areas`, `enums`, `stats_size`, `field_values`, `field_sizes`, `request`
- Optional fields: `path` for `action=request`, `params`, `max_items`, `max_depth`, `max_pages`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common ClinicalTrials.gov patterns:
- `{"action":"studies","params":{"query.cond":"prostate cancer","filter.overallStatus":"RECRUITING","pageSize":10},"max_items":10,"max_pages":1}`
- `{"action":"metadata"}`
- `{"action":"field_values","params":{"field":"protocolSection.identificationModule.organization.fullName"}}`

## Output
- `action=studies` returns `pages_fetched`, `next_page_token`, count metadata, and compact `records`.
- Other actions return either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"action":"studies","params":{"query.cond":"prostate cancer","filter.overallStatus":"RECRUITING","pageSize":10},"max_items":10,"max_pages":1}' | python scripts/clinicaltrials_client.py
```

Referenced files: 1

clinvar-variation-skill2.29 KB

View saved version →

---
name: clinvar-variation-skill
description: Submit compact ClinVar Clinical Tables and NCBI Variation requests for search, VCV, RCV, SCV, and RefSNP lookups. Use when a user wants variant-level summaries or identifier mapping
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `clinvar-variation-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/clinvar_variation.py` for all ClinVar and NCBI Variation work.
- The script accepts `max_items`; for `action=search`, start around `max_items=10`.
- For `vcv`, `rcv`, `scv`, and `refsnp`, omit `max_items` unless you need to trim nested arrays in the summary.
- Re-run requests in long conversations instead of relying on prior tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.
- If the user asks for full JSON, set `save_raw=true` and report the saved file path instead of pasting large payloads into chat.

## Input
- Read one JSON object from stdin.
- Required field: `action`
- Action-specific required fields:
- `search`: `terms`
- `vcv`: `vcv`
- `rcv`: `rcv`
- `scv`: `scv`
- `refsnp`: `refsnp`
- Optional fields: `params`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`

## Output
- `search` returns `total`, `identifiers`, `display_rows`, `extra_fields`, and truncation metadata.
- `vcv|rcv|scv|refsnp` return a compact `summary` and optional `top_keys`.
- Use `raw_output_path` when `save_raw=true`.
- Failures return `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"action":"search","terms":"VCV000013080","max_items":10}' | python scripts/clinvar_variation.py
```

Referenced files: 1

efo-ontology-skill2.68 KB

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---
name: efo-ontology-skill
description: Submit compact EFO OLS4 requests for search, term lookup, children, and descendants. Use when a user wants concise EFO resolution or ontology-expansion summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `efo-ontology-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all OLS4 and EFO API calls.
- Use `base_url=https://www.ebi.ac.uk/ols4/api`.
- Search, children, and descendant endpoints are better with `max_items=10`; single term lookups usually do not need `max_items`.
- Use the smallest ontology expansion that answers the question.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer these paths: `search`, `ontologies/efo/terms/<double-encoded-iri>`, and the corresponding `children` or `descendants` paths.
- If the user needs the full payload, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common OLS4 patterns:
  - `{"base_url":"https://www.ebi.ac.uk/ols4/api","path":"search","params":{"q":"asthma","ontology":"efo"},"record_path":"response.docs","max_items":10}`
  - `{"base_url":"https://www.ebi.ac.uk/ols4/api","path":"ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000270"}`
  - `{"base_url":"https://www.ebi.ac.uk/ols4/api","path":"ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000270/descendants","record_path":"_embedded.terms","max_items":10}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk/ols4/api","path":"search","params":{"q":"asthma","ontology":"efo"},"record_path":"response.docs","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

encode-skill2.68 KB

View saved version →

---
name: encode-skill
description: Submit compact ENCODE REST API requests for object lookups, portal-style search, and metadata retrieval. Use when a user wants concise ENCODE summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `encode-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all ENCODE API calls.
- Use `base_url=https://www.encodeproject.org`.
- Object lookups usually do not need `max_items`; portal-style search endpoints are better with `limit=10` and `max_items=10`.
- Send `Accept: application/json` in `headers` and add `format=json` in `params` when needed.
- Keep request volume modest and avoid large unfiltered searches.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer accession paths such as `biosamples/<accession>/` and search paths such as `search/`.
- If the user needs the full payload, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common ENCODE patterns:
- `{"base_url":"https://www.encodeproject.org","path":"biosamples/ENCBS000AAA/","params":{"frame":"object","format":"json"},"headers":{"Accept":"application/json"}}`
- `{"base_url":"https://www.encodeproject.org","path":"search/","params":{"type":"Experiment","assay_title":"RNA-seq","limit":10,"format":"json"},"record_path":"@graph","headers":{"Accept":"application/json"},"max_items":10}`

## Execution
```bash
echo '{"base_url":"https://www.encodeproject.org","path":"search/","params":{"type":"Experiment","assay_title":"RNA-seq","limit":10,"format":"json"},"record_path":"@graph","headers":{"Accept":"application/json"},"max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

ensembl-skill2.63 KB

View saved version →

---
name: ensembl-skill
description: Submit compact Ensembl REST API requests for lookup, overlap, cross-reference, and variation endpoints. Use when a user wants concise Ensembl summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `ensembl-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all Ensembl API calls.
- Use `base_url=https://rest.ensembl.org`.
- The script accepts `max_items`; object lookups usually do not need it, but `overlap` and `xrefs` are better with `max_items=10`.
- Send JSON-friendly headers such as `Accept: application/json` and `Content-Type: application/json`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not part of the true request.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
- Prefer these paths: `lookup/id/<id>`, `overlap/region/<species>/<region>`, `xrefs/id/<id>`, and `variation/<species>/<id>`.
- Use `save_raw=true` when the user needs the full payload.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common Ensembl patterns:
- `{"base_url":"https://rest.ensembl.org","path":"lookup/id/ENSG00000141510","headers":{"Accept":"application/json","Content-Type":"application/json"}}`
- `{"base_url":"https://rest.ensembl.org","path":"overlap/region/homo_sapiens/1:1000000-1002000","params":{"feature":"gene"},"headers":{"Accept":"application/json","Content-Type":"application/json"},"max_items":10}`

## Execution
```bash
echo '{"base_url":"https://rest.ensembl.org","path":"lookup/id/ENSG00000141510","headers":{"Accept":"application/json","Content-Type":"application/json"}}' | python scripts/rest_request.py
```

Referenced files: 1

epigraphdb-skill2.58 KB

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---
name: epigraphdb-skill
description: Submit compact EpiGraphDB API requests for ontology, literature, MR, gene-drug, and support-path evidence. Use when a user wants concise EpiGraphDB summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `epigraphdb-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all EpiGraphDB API calls.
- Use `base_url=https://api.epigraphdb.org`.
- Start with `max_items=10` for list-style endpoints; use smaller caps for literature-heavy or pairwise endpoints if the response fans out quickly.
- Prefer the connectivity guard endpoints first when endpoint availability matters: `ping`, `builds`, and `meta/api-endpoints`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer targeted paths such as `ontology/gwas-efo`, `gene/drugs`, `gene/druggability/ppi`, `mr`, and `literature/gwas`.
- If the user needs the full payload, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common EpiGraphDB patterns:
  - `{"base_url":"https://api.epigraphdb.org","path":"ping"}`
  - `{"base_url":"https://api.epigraphdb.org","path":"ontology/gwas-efo","params":{"trait":"asthma","score_threshold":0.8,"fuzzy":true},"max_items":10}`
  - `{"base_url":"https://api.epigraphdb.org","path":"gene/drugs","params":{"gene_name":"IL6R"},"max_items":10}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://api.epigraphdb.org","path":"ontology/gwas-efo","params":{"trait":"asthma","score_threshold":0.8,"fuzzy":true},"max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

eqtl-catalogue-skill2.76 KB

View saved version →

---
name: eqtl-catalogue-skill
description: Submit compact eQTL Catalogue API requests for association retrieval and documented metadata endpoints. Use when a user wants concise public eQTL Catalogue summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `eqtl-catalogue-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all eQTL Catalogue calls.
- Use the current `base_url=https://www.ebi.ac.uk/eqtl/api/v3`; avoid deprecated, unversioned v1 routes.
- Prefer targeted association endpoints over broad list endpoints.
- Prefer documented v3 dataset-scoped association requests with explicit `rsid` and a small upstream `size`.
- Legacy compatibility defaults apply only to deprecated unversioned routes; they are unnecessary for the current v3 API.
- Re-run requests in long conversations instead of relying on older tool output.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return raw JSON only if the user explicitly asks for machine-readable output.
- Prefer documented v3 association paths such as `datasets/QTD000021/associations` or `associations` with an explicit `rsid`; do not send unresolved placeholder identifiers or deprecated routes. For upstream `400`/`500` responses, report only the HTTP status and query-free endpoint path; never reproduce an upstream error body that may echo private query data.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common eQTL Catalogue patterns:
- `{"base_url":"https://www.ebi.ac.uk/eqtl/api/v3","path":"datasets/QTD000021/associations","params":{"rsid":"rs4239702","size":1},"max_items":5}`
- `{"base_url":"https://www.ebi.ac.uk/eqtl/api/v3","path":"associations","params":{"rsid":"rs7412","size":1},"max_items":5}`

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk/eqtl/api/v3","path":"datasets/QTD000021/associations","params":{"rsid":"rs4239702","size":1},"max_items":5}' | python scripts/rest_request.py
```

Referenced files: 2

eva-skill2.5 KB

View saved version →

---
name: eva-skill
description: Submit compact EVA REST requests for species metadata and archived variant lookups. Use when a user wants concise European Variation Archive summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `eva-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all EVA calls.
- Use `base_url=https://www.ebi.ac.uk/eva/webservices/identifiers/v1` for compact clustered-variant records or `base_url=https://www.ebi.ac.uk/eva/webservices/rest/v1` for documented study and assembly routes.
- Prefer targeted, evidence-bearing variant or study lookups over broad genomic window pulls and metadata-only checks.
- Keep region queries narrow by species, assembly, or small coordinate windows when possible.
- Re-run requests in long conversations instead of relying on older tool output.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return raw JSON only if the user explicitly asks for machine-readable output.
- Prefer compact paths such as `clustered-variants/17870277`; use `meta/species/list` only to discover supported assemblies, never as biological evidence.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common EVA patterns:
- `{"base_url":"https://www.ebi.ac.uk/eva/webservices/identifiers/v1","path":"clustered-variants/17870277","max_items":5}`
- `{"base_url":"https://www.ebi.ac.uk/eva/webservices/rest/v1","path":"studies/PRJEB4019/summary","record_path":"response.0.result","max_items":5}`

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk/eva/webservices/identifiers/v1","path":"clustered-variants/17870277","max_items":5}' | python scripts/rest_request.py
```

Referenced files: 1

finngen-phewas-skill2.69 KB

View saved version →

---
name: finngen-phewas-skill
description: Fetch compact FinnGen PheWAS summaries for single variants by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query. Use when a user wants concise FinnGen association results for one variant
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `finngen-phewas-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/finngen_phewas.py` for all FinnGen PheWAS lookups.
- Accept exactly one of `rsid`, `grch37`, `grch38`, or `variant`; resolve to the canonical GRCh38 `chr:pos-ref-alt` query before calling FinnGen.
- The script accepts `max_results`; start with `max_results=10` and only increase it if the first slice is insufficient.
- Re-run the lookup in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.
- If the user needs the full association payload, set `save_raw=true` and report `raw_output_path` instead of pasting large arrays into chat.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the JSON verbatim only if the user explicitly asks for machine-readable output.
- Surface the canonical queried variant, total association count, truncation status, and any returned `regions`.
- Increase `max_results` gradually instead of asking for large association dumps in one call.

## Input
- Read one JSON object from stdin, or a single JSON string containing the variant.
- Required input: exactly one of `rsid`, `grch37`, `grch38`, or `variant`
- Optional fields: `max_results`, `save_raw`, `raw_output_path`, `timeout_sec`
- Common patterns:
- `{"grch38":"10:112998590-C-T","max_results":10}`
- `{"grch37":"10:114758349-C-T","max_results":10}`
- `{"rsid":"rs7903146","max_results":10}`
- `{"variant":"10:112998590:C:T","max_results":25,"save_raw":true}`

## Output
- Success returns `ok`, `source`, `input`, `query_variant`, `max_results_applied`, `association_count`, `association_count_total`, `truncated`, `associations`, `variant`, `regions`, `variant_url`, `raw_output_path`, and `warnings`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"grch38":"10:112998590-C-T","max_results":10}' | python scripts/finngen_phewas.py
```

Referenced files: 3

genebass-gene-burden-skill2.04 KB

View saved version →

---
name: genebass-gene-burden-skill
description: Submit compact Genebass gene burden requests for one Ensembl gene ID and one burden set. Use when a user wants concise Genebass PheWAS summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `genebass-gene-burden-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/genebass_gene_burden.py` for all Genebass calls.
- This skill accepts one Ensembl gene ID per invocation.
- `max_results` is flexible; start around `25` for broad summaries and increase only if the user explicitly wants more associations.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return raw JSON only if the user explicitly asks for machine-readable output.
- Supported burden sets are `pLoF`, `missense|LC`, and `synonymous`, with the aliases already handled by the script.
- If the user needs the full result set, increase `max_results` deliberately instead of dumping everything by default.

## Input
- Read JSON from stdin as either a string Ensembl ID or an object.
- String form:
- `"ENSG00000173531"`
- Object form:
- `{"ensembl_gene_id":"ENSG00000173531","burden_set":"pLoF","max_results":25}`

## Output
- Success returns `ok`, `source`, input metadata, `gene`, association counts, `truncated`, and compact `associations`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"ensembl_gene_id":"ENSG00000173531","burden_set":"pLoF","max_results":25}' | python scripts/genebass_gene_burden.py
```

Referenced files: 1

gnomad-graphql-skill2.51 KB

View saved version →

---
name: gnomad-graphql-skill
description: Submit compact gnomAD GraphQL requests for frequency, gene constraint, and variant context queries. Use when a user wants concise gnomAD summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `gnomad-graphql-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/gnomad_graphql.py` for all gnomAD GraphQL work.
- For nested GraphQL results, start with `max_items=3` to `5`.
- Keep selection sets narrow and page or filter at the query level instead of asking for broad dumps.
- Use `query_path` for long GraphQL documents instead of pasting large inline queries.
- Re-run requests in long conversations instead of relying on earlier tool output.
- Treat displayed `...` in tool previews as UI truncation, not part of the real query.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return raw JSON only if the user explicitly asks for machine-readable output.
- Prefer targeted queries for variant frequency, gene constraint, or transcript consequence context.
- If the user needs the full payload, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required field: `query` or `query_path`
- Optional fields: `variables`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common gnomAD patterns:
  - `{"query":"query Variant($variantId: String!, $dataset: DatasetId!) { variant(variantId: $variantId, dataset: $dataset) { variantId genome { ac an af } } }","variables":{"variantId":"10-112998590-C-T","dataset":"gnomad_r4"},"max_items":5}`

## Output
- Success returns `ok`, `source`, `top_keys`, a compact `summary`, and `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` such as `invalid_json`, `invalid_input`, `network_error`, `invalid_response`, or `graphql_error`.

## Execution
```bash
echo '{"query":"query Variant($variantId: String!, $dataset: DatasetId!) { variant(variantId: $variantId, dataset: $dataset) { variantId genome { ac an af } } }","variables":{"variantId":"10-112998590-C-T","dataset":"gnomad_r4"},"max_items":5}' | python scripts/gnomad_graphql.py
```

Referenced files: 1

gtex-eqtl-skill2.42 KB

View saved version →

---
name: gtex-eqtl-skill
description: Fetch GTEx single-tissue eQTL associations from one variant input by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query for the GTEx v2 API. Use when a user wants eQTL associations returned as JSON.
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `gtex-eqtl-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

# Operating rules

- Use Python `requests` for all network calls.
- Accept exactly one of `rsid`, `grch37`, `grch38`, or `variant`, and resolve to a GRCh38 `chrom-pos-ref-alt` query.
- Convert to GTEx `variantId` format: `chr{chrom}_{pos}_{ref}_{alt}_b38`.
- The script returns one JSON object; summarize its evidence with claim-adjacent citations unless the user requests machine-readable output.

# Input

Accept JSON on stdin as either:

- A string: `"10-112998590-C-T"` (treated as GRCh38)
- An object:

```json
{
  "grch38": "10-112998590-C-T",
  "max_results": 200
}
```

Other accepted object forms include:

```json
{
  "grch37": "10-114758349-C-T"
}
```

```json
{
  "rsid": "rs7903146",
  "max_results": 50
}
```

Allowed variant separators include `-`, `:`, `_`, `/`, or whitespace, for example:

- `10-112998590-C-T`
- `10:112998590-C-T`
- `10:112998590:C:T`
- `chr10 112998590 C T`

`max_results` is optional and truncates returned eQTL rows when provided.

# Output

Success shape:

```json
{
  "ok": true,
  "source": "gtex-v2",
  "input": {"type": "grch38", "value": "10-112998590-C-T"},
  "query_variant": {
    "chr": "10",
    "pos": 112998590,
    "ref": "C",
    "alt": "T",
    "canonical": "10:112998590-C-T",
    "variant_id": "chr10_112998590_C_T_b38"
  },
  "eqtl_count": 2,
  "eqtl_count_total": 2,
  "truncated": false,
  "eqtls": [],
  "paging_info": {},
  "warnings": []
}
```

Failure shape:

```json
{
  "ok": false,
  "error": {"code": "...", "message": "..."},
  "warnings": []
}
```

# Execution

Use:

- `scripts/gtex_eqtl.py`

The script reads JSON from stdin and prints JSON to stdout.

Example:

```bash
echo '{"grch38":"10-112998590-C-T","max_results":5}' | python scripts/gtex_eqtl.py
```

Referenced files: 5

gwas-catalog-skill2.83 KB

View saved version →

---
name: gwas-catalog-skill
description: Submit compact GWAS Catalog REST API v2 requests for studies, associations, SNPs, EFO traits, genes, publications, loci, and metadata. Use when a user wants concise GWAS Catalog summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `gwas-catalog-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all GWAS Catalog API calls.
- Use `base_url=https://www.ebi.ac.uk/gwas/rest/api/v2`.
- The script accepts `max_items`; for collection endpoints, start with API `size=10` and `max_items=10`.
- Single-resource endpoints such as `studies/<accession>` generally do not need `max_items`.
- Use `record_path` to target `_embedded.<resource>` lists.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
- Prefer these paths: `metadata`, `studies`, `studies/<accession>`, `associations`, `snps`, `efoTraits`, `genes`, `publications`, and `loci`.
- Use `save_raw=true` if the user needs the full HATEOAS payload or pagination links.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common GWAS Catalog patterns:
  - `{"base_url":"https://www.ebi.ac.uk/gwas/rest/api/v2","path":"metadata"}`
  - `{"base_url":"https://www.ebi.ac.uk/gwas/rest/api/v2","path":"studies","params":{"efo_trait":"asthma","size":10},"record_path":"_embedded.studies","max_items":10}`
  - `{"base_url":"https://www.ebi.ac.uk/gwas/rest/api/v2","path":"associations","params":{"mapped_gene":"BRCA1","size":10},"record_path":"_embedded.associations","max_items":10}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk/gwas/rest/api/v2","path":"studies","params":{"efo_trait":"asthma","size":10},"record_path":"_embedded.studies","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

human-protein-atlas-skill2.79 KB

View saved version →

---
name: human-protein-atlas-skill
description: Submit compact Human Protein Atlas requests for gene JSON, search downloads, and page-level tissue or cell-line lookups. Use when a user wants concise Human Protein Atlas summaries; save raw JSON or HTML only on request.
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `human-protein-atlas-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all Human Protein Atlas calls.
- Use `base_url=https://www.proteinatlas.org`.
- The script accepts `max_items`; single gene entry lookups usually do not need it, while search and download endpoints are better with `max_items=10`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.
- If the user asks for full HTML or JSON, set `save_raw=true` and report the saved file path instead of pasting large payloads into chat.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
- Prefer these paths: `<ENSG>.json`, `api/search_download.php`, `search/tissue/<symbol>`, and `search/cellline/<symbol>`.
- For page-level search endpoints, prefer `response_format=text` so the script returns only `text_head` unless raw output is requested.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common HPA patterns:
- `{"base_url":"https://www.proteinatlas.org","path":"ENSG00000141510.json"}`
- `{"base_url":"https://www.proteinatlas.org","path":"api/search_download.php","params":{"search":"TP53","format":"json","columns":"g,gs,tissue","compress":"no"},"max_items":10}`
- `{"base_url":"https://www.proteinatlas.org","path":"search/tissue/TP53","response_format":"text"}`

## Execution
```bash
echo '{"base_url":"https://www.proteinatlas.org","path":"ENSG00000141510.json"}' | python scripts/rest_request.py
```

Referenced files: 1

ipd-skill2.44 KB

View saved version →

---
name: ipd-skill
description: Submit compact IPD REST requests for HLA allele and cell-level metadata using the public IPD query API. Use when a user wants concise IPD summaries; save raw JSON or text only on request.
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `ipd-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all IPD calls.
- Use `base_url=https://www.ebi.ac.uk/cgi-bin/ipd/api`.
- The most stable public routes are `allele` and `cell`.
- For HLA allele browsing, pass `project=HLA` and keep `limit` modest.
- Re-run requests in long conversations instead of relying on older tool output.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return raw JSON or text only if the user explicitly asks for machine-readable output.
- Prefer these paths: `allele`, `cell`, and `allele/download`.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common IPD patterns:
- `{"base_url":"https://www.ebi.ac.uk/cgi-bin/ipd/api","path":"allele","params":{"project":"HLA","limit":10},"record_path":"data","max_items":10}`
- `{"base_url":"https://www.ebi.ac.uk/cgi-bin/ipd/api","path":"allele","params":{"project":"HLA","query":"contains(name,\"A*01\")","limit":10},"record_path":"data","max_items":10}`
- `{"base_url":"https://www.ebi.ac.uk/cgi-bin/ipd/api","path":"cell","params":{"limit":10},"record_path":"data","max_items":10}`

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk/cgi-bin/ipd/api","path":"allele","params":{"project":"HLA","limit":10},"record_path":"data","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

metabolights-skill2.17 KB

View saved version →

---
name: metabolights-skill
description: Submit compact MetaboLights requests for study discovery and study-level metabolomics metadata. Use when a user wants concise MetaboLights summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `metabolights-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all MetaboLights calls.
- Use `base_url=https://www.ebi.ac.uk/metabolights/ws`.
- Start with `studies` for archive browsing and `studies/<MTBLS accession>` for targeted records.
- Keep study discovery narrow and paged rather than pulling very large pages.
- Re-run requests in long conversations instead of relying on older tool output.

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk/metabolights/ws","path":"studies","record_path":"content","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

mgnify-skill2.25 KB

View saved version →

---
name: mgnify-skill
description: Submit compact MGnify API requests for microbiome studies, samples, and biome metadata. Use when a user wants concise MGnify summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `mgnify-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all MGnify calls.
- Use `base_url=https://www.ebi.ac.uk/metagenomics/api/v1`.
- MGnify uses JSON:API-style responses. Prefer `record_path=data` for collection endpoints.
- Keep requests narrow by study accession, sample accession, or biome whenever possible.
- Re-run requests in long conversations instead of relying on older tool output.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return raw JSON only if the user explicitly asks for machine-readable output.
- Prefer these paths: `studies`, `samples`, and `biomes`.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common MGnify patterns:
  - `{"base_url":"https://www.ebi.ac.uk/metagenomics/api/v1","path":"studies","params":{"page_size":10},"record_path":"data","max_items":10}`
  - `{"base_url":"https://www.ebi.ac.uk/metagenomics/api/v1","path":"biomes","params":{"page_size":10},"record_path":"data","max_items":10}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk/metagenomics/api/v1","path":"studies","params":{"page_size":10},"record_path":"data","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

ncbi-clinicaltables-skill2.63 KB

View saved version →

---
name: ncbi-clinicaltables-skill
description: Submit compact Clinical Tables NCBI Gene requests for human gene lookup, pagination, and field selection. Use when a user wants concise autocomplete-style human gene search results
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `ncbi-clinicaltables-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/ncbi_gene_clinicaltables.py` for all Clinical Tables gene searches.
- The script accepts `max_items`; for search pages, start with `count=10` and `max_items=10`.
- Use `params` for endpoint options like `df`, `ef`, `sf`, `q`, `offset`, and `count`.
- Prefer `ncbi-entrez-skill` when the user wants general Entrez Gene records rather than autocomplete/search rows.
- Page with `offset` instead of asking for large pulls.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.
- If the user asks for the full payload, set `save_raw=true` and report the saved file path instead of pasting large response arrays into chat.

## Input
- Read one JSON object from stdin.
- Required field: `terms`
- Optional fields: `params`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common NCBI Gene patterns:
- `{"terms":"TP53","params":{"df":"GeneID,Symbol,description"}}`
- `{"terms":"BRCA","params":{"count":10,"df":"chromosome,GeneID,Symbol,description,type_of_gene"},"max_items":10}`
- `{"terms":"kinase","params":{"count":10,"offset":10,"df":"GeneID,Symbol,description"},"max_items":10}`

## Output
- Success returns `ok`, `source`, `terms`, `total`, `codes`, `display_rows`, `extra_fields`, and truncation metadata.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"terms":"TP53","params":{"count":10,"df":"GeneID,Symbol,description"},"max_items":10}' | python scripts/ncbi_gene_clinicaltables.py
```

Referenced files: 1

ncbi-datasets-skill2.23 KB

View saved version →

---
name: ncbi-datasets-skill
description: Submit compact NCBI Datasets v2 requests for assembly, genome, taxonomy, and related metadata endpoints. Use when a user wants concise NCBI Datasets summaries; save raw JSON or text only on request.
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `ncbi-datasets-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/ncbi_datasets.py` for all Datasets v2 calls in this package.
- Use explicit REST `path` values relative to `https://api.ncbi.nlm.nih.gov/datasets/v2`.
- Prefer targeted metadata paths instead of broad unfiltered pulls.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script output by default.
- Return raw JSON or text only if the user explicitly asks for machine-readable output.
- Prefer targeted endpoint calls instead of broad unfiltered dumps.
- If the user needs the full raw response, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required field: `path`
- Optional fields: `params`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common Datasets patterns:
- `{"path":"genome/taxon/assembly_descriptors","params":{"taxons":"9606"}}`
- `{"path":"genome/accession/GCF_000001405.40/dataset_report"}`
- `{"path":"taxonomy/taxon/9606"}`

## Output
- Success returns `ok`, `source`, path metadata, and either compact `records`, a compact `summary`, or `text_head`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"path":"genome/taxon/assembly_descriptors","params":{"taxons":"9606"}}' | python scripts/ncbi_datasets.py
```

Referenced files: 1

ncbi-entrez-skill3.03 KB

View saved version →

---
name: ncbi-entrez-skill
description: Submit compact NCBI Entrez E-Utilities requests for PubMed, Gene, Protein, Nucleotide, PMC metadata, and GEO metadata workflows. Use when a user wants concise Entrez search, fetch, summary, or link results; save raw JSON or XML only on request.
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `ncbi-entrez-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/ncbi_entrez.py` for all Entrez calls in this package.
- Use explicit `endpoint` values such as `esearch`, `esummary`, `efetch`, `elink`, or `einfo`.
- Search-style Entrez calls are better with `retmax=10` and `max_items=10`.
- GEO is nested under this skill. Use `db=gds` or `db=geoprofiles` for GEO metadata and load `references/geo.md` only when the user is specifically asking about GEO.
- BLAST workflows belong in `ncbi-blast-skill`. PMC Open Access workflows belong in `ncbi-pmc-skill`. Datasets v2 workflows belong in `ncbi-datasets-skill`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script output by default.
- Return raw JSON or XML only if the user explicitly asks for machine-readable output.
- Prefer targeted endpoint calls instead of broad unfiltered dumps.
- If the user needs the full raw response, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required field: `endpoint`
- Optional fields: `params`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common Entrez patterns:
- `{"endpoint":"esearch","params":{"db":"pubmed","term":"KRAS AND colorectal cancer","retmode":"json","retmax":10},"max_items":10}`
- `{"endpoint":"esummary","params":{"db":"gene","id":"7157","retmode":"json"},"max_items":10}`
- `{"endpoint":"efetch","params":{"db":"protein","id":"NP_000537.3","retmode":"xml"},"response_format":"xml","max_items":10}`
- `{"endpoint":"elink","params":{"dbfrom":"gds","db":"pubmed","id":"200000001","retmode":"json"},"max_items":10}`

## Output
- Success returns `ok`, `source`, endpoint metadata, and either compact `records`, a compact `summary`, or `text_head`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"endpoint":"esearch","params":{"db":"gene","term":"TP53[gene] AND human[orgn]","retmode":"json","retmax":10},"max_items":10}' | python scripts/ncbi_entrez.py
```

## References
- Load `references/geo.md` only when the user specifically needs GEO query patterns.

Referenced files: 2

opentargets-skill3.59 KB

View saved version →

---
name: opentargets-skill
description: Submit compact Open Targets Platform GraphQL requests for target, disease, drug, variant, study, and search data, including associated-disease datasource heatmap matrices. Use when a user wants concise Open Targets summaries or per-datasource evidence context
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `opentargets-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/opentargets_graphql.py` for all Open Targets GraphQL work.
- Use `scripts/opentargets_disease_heatmap.py` when the user wants the associated-disease bubble grid or a disease-by-datasource evidence matrix.
- The script accepts `max_items`; for nested GraphQL results, start with `max_items=3` to `5`.
- Keep GraphQL selection sets narrow and page connection-style fields conservatively.
- Use `query_path` for long GraphQL documents instead of pasting large inline query strings.
- Re-run requests in long conversations instead of relying on earlier tool output.
- Treat displayed `...` in tool previews as UI truncation, not part of the real query.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the JSON verbatim only if the user explicitly asks for machine-readable output.
- Prefer targeted GraphQL queries that select only the fields needed for the user task.
- Use schema introspection only when necessary; do not dump large schema payloads into chat.
- For the associated-disease heatmap, treat `datasourceScores` as evidence-source breadth/context. Do not treat heatmap breadth alone as proof of causal target assignment, mechanism, or direction of effect.

## Input
- Read one JSON object from stdin.
- Required field: `query` or `query_path`
- Optional fields: `variables`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common Open Targets patterns:
- `{"query":"query searchAny($q: String!) { search(queryString: $q) { total hits { entity score object { ... on Target { id approvedSymbol } } } } }","variables":{"q":"MST1"},"max_items":3}`

## Execution
```bash
echo '{"query":"query searchAny($q: String!) { search(queryString: $q) { total hits { entity score object { ... on Target { id approvedSymbol } } } } }","variables":{"q":"MST1"},"max_items":5}' | python scripts/opentargets_graphql.py
```

Associated-disease heatmap helper:

```bash
echo '{
"ensembl_id":"ENSG00000186868",
"page_size":50,
"max_pages":4,
"disease_name_filter":"alzh"
}' | python scripts/opentargets_disease_heatmap.py
```

The helper paginates `associatedDiseases`, collects `datasourceScores`, and returns:

- `matrix.columns`: datasource IDs plus display labels
- `matrix.rows`: diseases with `datasource_scores`
- `summary.rows_preview`: top datasource signals per disease

Use the disease-name filter as a client-side substring filter similar to the UI. If you later need the overall association score column, inspect the GraphQL row type first before adding candidate fields such as `score` or `associationScore`.

Referenced files: 2

pharmgkb-skill2.43 KB

View saved version →

---
name: pharmgkb-skill
description: Submit compact PharmGKB API requests for genes, variants, clinical annotations, dosing guidelines, and search. Use when a user wants concise PharmGKB summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `pharmgkb-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all PharmGKB API calls.
- Use the current `base_url=https://api.clinpgx.org/v1/data`; the former `api.pharmgkb.org` hostname was retired.
- Single object lookups usually do not need `max_items`; list and search endpoints are better with `max_items=10`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer these paths: `gene/<id>`, `variant/<id>`, `clinicalAnnotation`, `dosingGuideline`, and search endpoints.
- If the user needs the full payload, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common PharmGKB patterns:
- `{"base_url":"https://api.clinpgx.org/v1/data","path":"gene/PA128","max_items":5}`
- `{"base_url":"https://api.clinpgx.org/v1/data","path":"clinicalAnnotation","params":{"relatedChemicals.accessionId":"PA449726","limit":10},"max_items":10}`
- `{"base_url":"https://api.clinpgx.org/v1/data","path":"variant/PA166158545","max_items":5}`

## Execution
```bash
echo '{"base_url":"https://api.clinpgx.org/v1/data","path":"gene/PA128","max_items":5}' | python scripts/rest_request.py
```

Referenced files: 1

pride-skill2.18 KB

View saved version →

---
name: pride-skill
description: Submit compact PRIDE Archive API requests for proteomics project discovery and project-level metadata. Use when a user wants concise PRIDE summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `pride-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all PRIDE Archive calls.
- Use `base_url=https://www.ebi.ac.uk/pride/ws/archive/v2`.
- Start with `projects` for discovery and keep page sizes modest.
- Prefer project-level metadata lookups over broad archive dumps.
- Re-run requests in long conversations instead of relying on older tool output.

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk/pride/ws/archive/v2","path":"projects","params":{"keyword":"proteomics","pageSize":10},"max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

proteomexchange-skill2.54 KB

View saved version →

---
name: proteomexchange-skill
description: Submit compact ProteomeXchange PROXI requests for datasets, libraries, peptidoforms, proteins, PSMs, spectra, and USI examples. Use when a user wants concise PROXI summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `proteomexchange-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all ProteomeXchange PROXI calls.
- Use `base_url=https://proteomecentral.proteomexchange.org/api/proxi/v0.1`.
- Collection endpoints are better with `max_items=10`; targeted identifier lookups usually do not need `max_items`.
- Keep requests narrow by identifier, spectrum, or dataset whenever possible.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer these paths: `datasets`, `datasets/<identifier>`, `libraries`, `peptidoforms`, `proteins`, `psms`, `spectra`, and `usi_examples`.
- If the user needs the full payload, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common PROXI patterns:
  - `{"base_url":"https://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"datasets","max_items":10}`
  - `{"base_url":"https://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"datasets/PXD000001"}`
  - `{"base_url":"https://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"usi_examples","max_items":10}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"datasets","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

pubchem-pug-skill2.64 KB

View saved version →

---
name: pubchem-pug-skill
description: Submit compact PubChem PUG REST requests for compound properties, descriptions, assay summaries, and substance metadata. Use when a user wants concise PubChem summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `pubchem-pug-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all PubChem PUG calls.
- Use `base_url=https://pubchem.ncbi.nlm.nih.gov/rest/pug`.
- Property and description endpoints usually return a single focused record; assay or broader list endpoints are better with `max_items=10`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer property, description, assay summary, and substance paths instead of broad record dumps.
- If the user needs the full payload, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common PubChem patterns:
- `{"base_url":"https://pubchem.ncbi.nlm.nih.gov/rest/pug","path":"compound/name/aspirin/property/MolecularFormula,MolecularWeight/JSON","record_path":"PropertyTable.Properties"}`
- `{"base_url":"https://pubchem.ncbi.nlm.nih.gov/rest/pug","path":"compound/cid/2244/description/JSON","record_path":"InformationList.Information","max_items":10}`
- `{"base_url":"https://pubchem.ncbi.nlm.nih.gov/rest/pug","path":"assay/aid/1706/summary/JSON","record_path":"AssaySummaries","max_items":10}`

## Execution
```bash
echo '{"base_url":"https://pubchem.ncbi.nlm.nih.gov/rest/pug","path":"compound/name/aspirin/property/MolecularFormula,MolecularWeight/JSON","record_path":"PropertyTable.Properties"}' | python scripts/rest_request.py
```

Referenced files: 1

quickgo-skill2.58 KB

View saved version →

---
name: quickgo-skill
description: Submit compact QuickGO requests for GO terms, annotations, and ontology traversal. Use when a user wants concise QuickGO summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `quickgo-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all QuickGO API calls.
- Use `base_url=https://www.ebi.ac.uk/QuickGO/services`.
- GO term lookups usually do not need `max_items`; annotation and traversal endpoints are better with `limit=10` and `max_items=10`.
- Send `Accept: application/json` in `headers`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer these paths: `ontology/go/terms/<id>`, `annotation/search`, and ontology child or ancestor endpoints.
- If the user needs the full payload, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common QuickGO patterns:
  - `{"base_url":"https://www.ebi.ac.uk/QuickGO/services","path":"ontology/go/terms/GO:0008150,GO:0003674","headers":{"Accept":"application/json"},"record_path":"results","max_items":10}`
  - `{"base_url":"https://www.ebi.ac.uk/QuickGO/services","path":"annotation/search","params":{"geneProductId":"P04637","limit":10},"headers":{"Accept":"application/json"},"record_path":"results","max_items":10}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://www.ebi.ac.uk/QuickGO/services","path":"annotation/search","params":{"geneProductId":"P04637","limit":10},"headers":{"Accept":"application/json"},"record_path":"results","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

rcsb-pdb-skill2.7 KB

View saved version →

---
name: rcsb-pdb-skill
description: Submit compact RCSB PDB requests for core metadata, Search API queries, and FASTA downloads. Use when a user wants concise RCSB summaries; save raw JSON or FASTA only on request.
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `rcsb-pdb-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all RCSB PDB and Search API calls.
- Use `base_url=https://data.rcsb.org/rest/v1` for core metadata, `https://search.rcsb.org/rcsbsearch/v2` for Search API, and `https://www.rcsb.org` for FASTA downloads.
- Core entry or assembly lookups usually do not need `max_items`; Search API results are better with query pager rows around `10` and `max_items=10`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer core metadata endpoints for focused lookups and Search API POST requests for discovery.
- For FASTA downloads, use `response_format=text` so the script returns a short `text_head` unless raw output is requested.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common RCSB patterns:
- `{"base_url":"https://data.rcsb.org/rest/v1","path":"core/entry/4hhb"}`
- `{"base_url":"https://search.rcsb.org/rcsbsearch/v2","path":"query","method":"POST","json_body":{"query":{"type":"terminal","service":"full_text","parameters":{"value":"hemoglobin"}},"return_type":"entry","request_options":{"pager":{"start":0,"rows":10}}},"record_path":"result_set","max_items":10}`
- `{"base_url":"https://www.rcsb.org","path":"fasta/entry/4HHB/download","response_format":"text"}`

## Execution
```bash
echo '{"base_url":"https://data.rcsb.org/rest/v1","path":"core/entry/4hhb"}' | python scripts/rest_request.py
```

Referenced files: 1

reactome-skill2.66 KB

View saved version →

---
name: reactome-skill
description: Submit compact Reactome ContentService requests for pathway, event, participant, search, and diagram-related data. Use when a user wants concise Reactome summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `reactome-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all Reactome ContentService calls.
- Use `base_url=https://reactome.org/ContentService`.
- Single pathway or event lookups usually do not need `max_items`; list-style pathway membership calls are better with `max_items=10`.
- Send `Accept: application/json` in `headers` when requesting JSON.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer these paths: `data/query/<eventId>`, `data/pathways/low/entity/<identifier>`, `data/participants/<eventId>`, and search endpoints.
- If the user needs the full payload, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common Reactome patterns:
  - `{"base_url":"https://reactome.org/ContentService","path":"data/query/R-HSA-199420","headers":{"Accept":"application/json"}}`
  - `{"base_url":"https://reactome.org/ContentService","path":"data/pathways/low/entity/P38398","params":{"species":"Homo sapiens"},"headers":{"Accept":"application/json"},"max_items":10}`
  - `{"base_url":"https://reactome.org/ContentService","path":"data/participants/R-HSA-199420","headers":{"Accept":"application/json"},"max_items":10}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://reactome.org/ContentService","path":"data/query/R-HSA-199420","headers":{"Accept":"application/json"}}' | python scripts/rest_request.py
```

Referenced files: 1

rhea-skill2.67 KB

View saved version →

---
name: rhea-skill
description: Submit compact Rhea reaction search requests for biochemical reactions and reaction IDs. Use when a user wants concise Rhea summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `rhea-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all Rhea calls.
- Use Rhea's official `base_url=https://sparql.rhea-db.org` SPARQL endpoint for compact JSON reaction records.
- The website search API supports TSV, not `format=json`; avoid website requests that fail with Cloudflare HTTP 403.
- Keep queries narrow by reaction ID, compound name, EC number, or free-text reaction term.
- Re-run requests in long conversations instead of relying on older tool output.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return raw JSON only if the user explicitly asks for machine-readable output.
- Prefer a targeted SPARQL reaction identifier, `LIMIT 1`, `format=json`, and `record_path=results.bindings`.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common Rhea patterns:
  - `{"base_url":"https://sparql.rhea-db.org","path":"sparql","params":{"query":"PREFIX rh: <http://rdf.rhea-db.org/> SELECT ?accession ?equation WHERE { <http://rdf.rhea-db.org/47148> rh:accession ?accession ; rh:equation ?equation . } LIMIT 1","format":"json"},"headers":{"Accept":"application/sparql-results+json"},"record_path":"results.bindings","max_items":5}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://sparql.rhea-db.org","path":"sparql","params":{"query":"PREFIX rh: <http://rdf.rhea-db.org/> SELECT ?accession ?equation WHERE { <http://rdf.rhea-db.org/47148> rh:accession ?accession ; rh:equation ?equation . } LIMIT 1","format":"json"},"headers":{"Accept":"application/sparql-results+json"},"record_path":"results.bindings","max_items":5}' | python scripts/rest_request.py
```

Referenced files: 1

rnacentral-skill2.32 KB

View saved version →

---
name: rnacentral-skill
description: Submit compact RNAcentral API requests for RNA entry browsing, single-entry lookup, and cross-reference retrieval. Use when a user wants concise RNAcentral summaries
---

## Source presentation
<!-- source-presentation-contract:v2 -->
- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `rnacentral-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all RNAcentral calls.
- Use `base_url=https://rnacentral.org/api/v1`.
- Keep the trailing slash on collection and record paths to avoid redirects.
- Start with `rna/` for browsing and `rna/<URS>/` or `rna/<URS>/xrefs/` for targeted lookups.
- Re-run requests in long conversations instead of relying on older tool output.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return raw JSON only if the user explicitly asks for machine-readable output.
- Prefer these paths: `rna/`, `rna/<URS>/`, and `rna/<URS>/xrefs/`.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common RNAcentral patterns:
  - `{"base_url":"https://rnacentral.org/api/v1","path":"rna/","params":{"page_size":10},"record_path":"results","max_items":10}`
  - `{"base_url":"https://rnacentral.org/api/v1","path":"rna/URS0000000001/"}`
  - `{"base_url":"https://rnacentral.org/api/v1","path":"rna/URS0000000001/xrefs/","record_path":"results","max_items":10}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://rnacentral.org/api/v1","path":"rna/","params":{"page_size":10},"record_path":"results","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

string-skill2.81 KB

View saved version →

---
name: string-skill
description: Submit compact STRING API requests for network, interaction partner, and enrichment endpoints. Use when a user wants concise STRING summaries
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `string-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all STRING API calls.
- Use `base_url=https://string-db.org/api/json`.
- Use `method=POST` with `form_body` for STRING endpoints.
- Include `caller_identity` in `form_body`; keep it stable within a session when possible.
- The script accepts `max_items`; for `network` and `interaction_partners`, start with API `limit=10` and `max_items=10`.
- For `enrichment`, summarize the top `5` to `10` rows unless the user asks for more.
- Re-run requests in long conversations instead of relying on prior tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
- Prefer these paths: `network`, `interaction_partners`, and `enrichment`.
- For long identifier lists, keep the request small and paged; if full results are needed, use `save_raw=true`.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common STRING patterns:
- `{"base_url":"https://string-db.org/api/json","path":"network","method":"POST","form_body":{"identifiers":"TP53","species":9606,"caller_identity":"chatgpt-skill","limit":10},"max_items":10}`
- `{"base_url":"https://string-db.org/api/json","path":"interaction_partners","method":"POST","form_body":{"identifier":"TP53","species":9606,"caller_identity":"chatgpt-skill","limit":10},"max_items":10}`

## Execution
```bash
echo '{"base_url":"https://string-db.org/api/json","path":"network","method":"POST","form_body":{"identifiers":"TP53","species":9606,"caller_identity":"chatgpt-skill","limit":10},"max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

tpmi-phewas-skill2.64 KB

View saved version →

---
name: tpmi-phewas-skill
description: Fetch compact TPMI PheWAS summaries for single variants by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query. Use when a user wants concise TPMI association results for one variant
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `tpmi-phewas-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/tpmi_phewas.py` for all TPMI PheWAS lookups.
- Accept exactly one of `rsid`, `grch37`, `grch38`, or `variant`; resolve to the canonical GRCh38 `chr:pos-ref-alt` query before calling TPMI.
- The script accepts `max_results`; start with `max_results=10` and only increase it if the first slice is insufficient.
- Re-run the lookup in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.
- If the user needs the full association payload, set `save_raw=true` and report `raw_output_path` instead of pasting large arrays into chat.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the JSON verbatim only if the user explicitly asks for machine-readable output.
- Surface the canonical queried variant, total association count, and whether the results were truncated.
- Increase `max_results` gradually instead of asking for large association dumps in one call.

## Input
- Read one JSON object from stdin, or a single JSON string containing the variant.
- Required input: exactly one of `rsid`, `grch37`, `grch38`, or `variant`
- Optional fields: `max_results`, `save_raw`, `raw_output_path`, `timeout_sec`
- Common patterns:
- `{"grch38":"6:160540105-T-C","max_results":10}`
- `{"grch37":"6:162447146-T-C","max_results":10}`
- `{"rsid":"rs9273363","max_results":10}`
- `{"variant":"6:160540105:T:C","max_results":25,"save_raw":true}`

## Execution
```bash
echo '{"grch38":"6:160540105-T-C","max_results":10}' | python scripts/tpmi_phewas.py
```

Referenced files: 3

ukb-topmed-phewas-skill2.7 KB

View saved version →

---
name: ukb-topmed-phewas-skill
description: Fetch compact UKB-TOPMed PheWAS summaries for single variants by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query. Use when a user wants concise UKB-TOPMed association results for one variant
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `ukb-topmed-phewas-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/ukb_topmed_phewas.py` for all UKB-TOPMed PheWAS lookups.
- Accept exactly one of `rsid`, `grch37`, `grch38`, or `variant`; resolve to the canonical GRCh38 `chr:pos-ref-alt` query before calling UKB-TOPMed.
- The script accepts `max_results`; start with `max_results=10` and only increase it if the first slice is insufficient.
- Re-run the lookup in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.
- If the user needs the full association payload, set `save_raw=true` and report `raw_output_path` instead of pasting large arrays into chat.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the JSON verbatim only if the user explicitly asks for machine-readable output.
- Surface the canonical queried variant, total association count, and whether the results were truncated.
- Increase `max_results` gradually instead of asking for large association dumps in one call.

## Input
- Read one JSON object from stdin, or a single JSON string containing the variant.
- Required input: exactly one of `rsid`, `grch37`, `grch38`, or `variant`
- Optional fields: `max_results`, `save_raw`, `raw_output_path`, `timeout_sec`
- Common patterns:
- `{"grch38":"10:112998590-C-T","max_results":10}`
- `{"grch37":"10:114758349-C-T","max_results":10}`
- `{"rsid":"rs7903146","max_results":10}`
- `{"variant":"10:112998590:C:T","max_results":25,"save_raw":true}`

## Execution
```bash
echo '{"grch38":"10:112998590-C-T","max_results":10}' | python scripts/ukb_topmed_phewas.py
```

Referenced files: 3

uniprot-skill2.99 KB

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---
name: uniprot-skill
description: Submit compact UniProt REST API requests for UniProtKB, UniRef, UniParc, and FASTA stream endpoints. Use when a user wants concise UniProt summaries; save raw JSON or FASTA only on request.
---

## Source presentation

- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.
- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.
- Use the `uniprot-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.

## Operating rules
- Use `scripts/rest_request.py` for all UniProt API calls.
- Use `base_url=https://rest.uniprot.org`.
- The script accepts `max_items`; for search endpoints, start with API `size=10` and `max_items=10`.
- Single accession or cluster lookups usually do not need `max_items`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not part of the real request.
- If the user asks for full JSON or FASTA, set `save_raw=true` and report the saved file path instead of pasting the payload into chat.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
- Prefer these paths: `uniprotkb/search`, `uniprotkb/<accession>`, `uniref/<cluster>`, `uniparc/search`, and `uniprotkb/stream`.
- For `stream`, use `response_format=text` so the script returns only a short `text_head` unless raw output is requested.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common UniProt patterns:
- `{"base_url":"https://rest.uniprot.org","path":"uniprotkb/search","params":{"query":"gene:TP53 AND organism_id:9606","fields":"accession,gene_names","size":10,"format":"json"},"record_path":"results","max_items":10}`
- `{"base_url":"https://rest.uniprot.org","path":"uniprotkb/P04637","params":{"format":"json"}}`
- `{"base_url":"https://rest.uniprot.org","path":"uniprotkb/stream","params":{"query":"organism_id:562","format":"fasta","size":2},"response_format":"text"}`

## Execution
```bash
echo '{"base_url":"https://rest.uniprot.org","path":"uniprotkb/search","params":{"query":"gene:TP53 AND organism_id:9606","fields":"accession,gene_names","size":10,"format":"json"},"record_path":"results","max_items":10}' | python scripts/rest_request.py
```

Referenced files: 1

Technical details

First seen: Sep 30, 2026 · 22:02 UTC
Last seen: Oct 1, 2026 · 12:00 UTC
Collection status: Collected

Plugin_054ff933a434819187c4f95db80afc7f

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