{"files":{"SKILL.md":"---\nname: crossbar-data-api\ndescription: \"CROssBAR Data API skill. Use when working with CROssBAR Data for activities, assays, drugs. Covers 13 endpoints.\"\nversion: 1.0.0\ngenerator: lapsh\n---\n\n# CROssBAR Data API\nAPI version: 1.0\n\n## Auth\nNo authentication required.\n\n## Base URL\nhttps://www.ebi.ac.uk/Tools/crossbar\n\n## Setup\n1. No auth setup needed\n2. GET /activities -- verify access\n\n## Endpoints\n\n13 endpoints across 10 groups. See references/api-spec.lap for full details.\n\n### activities\n| Method | Path | Description |\n|--------|------|-------------|\n| GET | /activities | Get ChEMBL activities |\n\n### assays\n| Method | Path | Description |\n|--------|------|-------------|\n| GET | /assays | Get ChEMBL assays |\n\n### drugs\n| Method | Path | Description |\n|--------|------|-------------|\n| GET | /drugs | drugs collected from Drugbank |\n\n### efo\n| Method | Path | Description |\n|--------|------|-------------|\n| GET | /efo | Get EFO diseases data |\n\n### hpo\n| Method | Path | Description |\n|--------|------|-------------|\n| GET | /hpo | Get HPO phenotypes data |\n\n### intact\n| Method | Path | Description |\n|--------|------|-------------|\n| GET | /intact | Molecular Interactions collected from IntAct |\n\n### molecules\n| Method | Path | Description |\n|--------|------|-------------|\n| GET | /molecules | Get ChEMBL molecules |\n\n### proteins\n| Method | Path | Description |\n|--------|------|-------------|\n| GET | /proteins | Proteins collected from Uniprot for selective tax ids  HUMAN(9606), MOUSE(10090), RAT(10116), BOVINE(9913), ESCHERICHIA_COLI(83333), SUS_SCROFA(9823), MYCOBACTERIUM_TUBERCULOSIS(83332), ORYCTOLAGUS_CUNICULUS(9986), SACCHAROMYCES_CEREVISIAE(559292), CVHSA(694009) & SARS2(2697049) |\n\n### pubchem\n| Method | Path | Description |\n|--------|------|-------------|\n| GET | /pubchem/bioassays | Get pubchem bioassays |\n| GET | /pubchem/bioassays/sids | Get pubchem bioassays associated to particular substance ids (sid) & outcome |\n| GET | /pubchem/compounds | Get pubchem compounds |\n| GET | /pubchem/substances | Get pubchem substances |\n\n### targets\n| Method | Path | Description |\n|--------|------|-------------|\n| GET | /targets | Get ChEMBL targets |\n\n## Common Questions\n\nMatch user requests to endpoints in references/api-spec.lap. Key patterns:\n- \"List all activities?\" -> GET /activities\n- \"List all assays?\" -> GET /assays\n- \"List all drugs?\" -> GET /drugs\n- \"List all efo?\" -> GET /efo\n- \"List all hpo?\" -> GET /hpo\n- \"List all intact?\" -> GET /intact\n- \"List all molecules?\" -> GET /molecules\n- \"List all proteins?\" -> GET /proteins\n- \"List all bioassays?\" -> GET /pubchem/bioassays\n- \"List all sids?\" -> GET /pubchem/bioassays/sids\n- \"List all compounds?\" -> GET /pubchem/compounds\n- \"List all substances?\" -> GET /pubchem/substances\n- \"List all targets?\" -> GET /targets\n\n## Response Tips\n- Check response schemas in references/api-spec.lap for field details\n\n## CLI\n\n```bash\n# Update this spec to the latest version\nnpx @lap-platform/lapsh get crossbar-data-api -o references/api-spec.lap\n\n# Search for related APIs\nnpx @lap-platform/lapsh search crossbar-data-api\n```\n\n## References\n- Full spec: See references/api-spec.lap for complete endpoint details, parameter tables, and response schemas\n\n> Generated from the official API spec by [LAP](https://lap.sh)\n","references/api-spec.lap":"@lap v0.3\n# Machine-readable API spec. Each @endpoint block is one API call.\n@api CROssBAR Data API\n@base https://www.ebi.ac.uk/Tools/crossbar\n@version 1.0\n@common_fields {limit: any # limit, page: any # page}\n@endpoints 13\n@toc activities(1), assays(1), drugs(1), efo(1), hpo(1), intact(1), molecules(1), proteins(1), pubchem(4), targets(1)\n\n@group activities\n@endpoint GET /activities\n@desc Get ChEMBL activities\n@optional {assayChemblId: any # assayChemblId, moleculeChemblId: any # moleculeChemblId, pchemblValue: any # pchemblValue, targetChemblId: any # targetChemblId}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endgroup\n\n@group assays\n@endpoint GET /assays\n@desc Get ChEMBL assays\n@optional {assayChemblId: any # assayChemblId, assayOrg: any # assayOrg, assayType: any # assayType, targetChemblId: any # targetChemblId}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endgroup\n\n@group drugs\n@endpoint GET /drugs\n@desc drugs collected from Drugbank\n@optional {accession: any # accession, chemblId: any # chemblId, identifier: any # identifier, name: any # name, pubchemCid: any # pubchemCid}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endgroup\n\n@group efo\n@endpoint GET /efo\n@desc Get EFO diseases data\n@optional {doid: any # doid, label: any # label, mesh: any # mesh, oboId: any # oboId, omimId: any # omimId, synonym: any # synonym}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endgroup\n\n@group hpo\n@endpoint GET /hpo\n@desc Get HPO phenotypes data\n@optional {genesymbol: any # genesymbol, hpotermname: any # hpotermname, synonym: any # synonym}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endgroup\n\n@group intact\n@endpoint GET /intact\n@desc Molecular Interactions collected from IntAct\n@optional {accession: any # accession, confidence: any # confidence, gene: any # gene}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endgroup\n\n@group molecules\n@endpoint GET /molecules\n@desc Get ChEMBL molecules\n@optional {canonicalSmiles: any # canonicalSmiles, inchiKey: any # inchiKey, moleculeChemblId: any # moleculeChemblId}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endgroup\n\n@group proteins\n@endpoint GET /proteins\n@desc Proteins collected from Uniprot for selective tax ids  HUMAN(9606), MOUSE(10090), RAT(10116), BOVINE(9913), ESCHERICHIA_COLI(83333), SUS_SCROFA(9823), MYCOBACTERIUM_TUBERCULOSIS(83332), ORYCTOLAGUS_CUNICULUS(9986), SACCHAROMYCES_CEREVISIAE(559292), CVHSA(694009) & SARS2(2697049)\n@optional {accession: any # accession, ec: any # ec, fullName: any # fullName, gene: any # gene, go: any # go, interpro: any # interpro, omim: any # omim, orphanet: any # orphanet, pfam: any # pfam, reactome: any # reactome, taxId: any # taxId}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endgroup\n\n@group pubchem\n@endpoint GET /pubchem/bioassays\n@desc Get pubchem bioassays\n@optional {accession: any # accession, assayPubchemId: any # assayPubchemId, ncbiProteinId: any # ncbiProteinId}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endpoint GET /pubchem/bioassays/sids\n@desc Get pubchem bioassays associated to particular substance ids (sid) & outcome\n@optional {outcome: any # outcome, sids: any # sids}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endpoint GET /pubchem/compounds\n@desc Get pubchem compounds\n@optional {canonicalSmiles: any # canonicalSmiles, cid: any # cid, inchiKey: any # inchiKey}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endpoint GET /pubchem/substances\n@desc Get pubchem substances\n@optional {cid: any # cid, sid: any # sid}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endgroup\n\n@group targets\n@endpoint GET /targets\n@desc Get ChEMBL targets\n@optional {accession: any # accession, targetIds: any # targetIds}\n@returns(200) OK\n@errors {401: Unauthorized, 403: Forbidden, 404: Not Found}\n\n@endgroup\n\n@end\n"}}