{"ok":true,"site":"pubchem-ncbi","host":"pubchem.ncbi.nlm.nih.gov","about":"PubChem (NCBI) open chemistry database. This CLI searches compounds, genes, bioassays and literature, runs structure searches, fetches compound, gene, assay and element records, exports 2D/3D structures, and browses the periodic table, classification trees and data sources.","commands":[{"command":"search-compounds","summary":"Keyword search of PubChem compounds (name, synonym, formula, etc.) with sorting and paging","params":[{"name":"q","type":"string","required":true,"description":"Search keyword, e.g. a compound name, synonym or formula. Do not include double quotes."},{"name":"sort","type":"string","description":"Sort order as 'field,dir'. Examples: relevancescore,desc; cid,asc; complexity,desc; mw,asc; mw,desc; annothitcnt,desc","default":"relevancescore,desc"},{"name":"start","type":"number","description":"1-based index of the first row. Page 2 with limit 10 is start=11.","default":1},{"name":"api_limit","type":"number","description":"Rows per page (sent to the site as \"limit\"; clify's own --limit only shapes the output)","default":10}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/search-compounds"},{"command":"search-genes","summary":"Keyword search of PubChem gene targets","params":[{"name":"q","type":"string","required":true,"description":"Search keyword (gene symbol, name, related term)"},{"name":"sort","type":"string","description":"Sort order 'field,dir', e.g. relevancescore,desc","default":"relevancescore,desc"},{"name":"start","type":"number","description":"1-based index of the first row","default":1},{"name":"api_limit","type":"number","description":"Rows per page (sent to the site as \"limit\"; clify's own --limit only shapes the output)","default":10}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/search-genes"},{"command":"search-bioassays","summary":"Keyword search of PubChem bioassays (AIDs)","params":[{"name":"q","type":"string","required":true,"description":"Search keyword"},{"name":"sort","type":"string","description":"Sort order 'field,dir', e.g. relevancescore,desc","default":"relevancescore,desc"},{"name":"start","type":"number","description":"1-based index of the first row","default":1},{"name":"api_limit","type":"number","description":"Rows per page (sent to the site as \"limit\"; clify's own --limit only shapes the output)","default":10}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/search-bioassays"},{"command":"search-literature","summary":"Keyword search of literature (PubMed articles) linked to PubChem records","params":[{"name":"q","type":"string","required":true,"description":"Search keyword"},{"name":"sort","type":"string","description":"Sort order 'field,dir', e.g. relevancescore,desc or articlepubdate,desc","default":"relevancescore,desc"},{"name":"start","type":"number","description":"1-based index of the first row","default":1},{"name":"api_limit","type":"number","description":"Rows per page (sent to the site as \"limit\"; clify's own --limit only shapes the output)","default":10}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/search-literature"},{"command":"count-search-hits","summary":"Count keyword hits in every PubChem collection (compound, substance, bioassay, gene, protein, taxonomy, pathway, cell, literature, patent)","params":[{"name":"q","type":"string","required":true,"description":"Search keyword"}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/count-search-hits"},{"command":"structure-search","summary":"Run an identity, similarity, substructure, superstructure or 3D-similarity search seeded by a compound CID. Returns the hit count and a cache key.","params":[{"name":"cid","type":"string","required":true,"description":"PubChem Compound ID used as the query structure"},{"name":"type","type":"string","description":"Structure search type","oneOf":["similarity","substructure","superstructure","identity","similarity_3d"],"default":"similarity"}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/structure-search"},{"command":"resolve-name","summary":"Resolve a chemical name or identifier to PubChem records (preferred CID, RefChem); also reports whether the input is valid SMILES, SMARTS, InChI, etc.","params":[{"name":"name","type":"string","required":true,"description":"Chemical name or identifier"}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/resolve-name?name=caffeine"},{"command":"autocomplete","summary":"Autocomplete suggestions for compound, gene or taxonomy names from a prefix","params":[{"name":"q","type":"string","required":true,"description":"Name prefix"},{"name":"dictionary","type":"string","description":"Dictionary to suggest from. Comma-separated lists such as compound,gene are also accepted.","oneOf":["compound","gene","taxonomy","compound,gene,taxonomy"],"default":"compound"},{"name":"api_limit","type":"number","description":"Maximum suggestions per dictionary (sent to the site as \"limit\"; clify's own --limit only shapes the output)","default":10}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/autocomplete"},{"command":"get-compound","summary":"Full PubChem compound summary record (names, identifiers, properties, safety, pharmacology, etc.) by CID","params":[{"name":"cid","type":"number","required":true,"description":"PubChem Compound ID, e.g. 2519 (caffeine), 2244 (aspirin)"},{"name":"heading","type":"string","description":"Optional TOC heading that limits the record to one section, e.g. 'Melting Point' or 'IUPAC Name'"}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/get-compound"},{"command":"get-gene","summary":"PubChem gene target record by NCBI Gene ID","params":[{"name":"geneid","type":"number","required":true,"description":"NCBI Gene ID"}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/get-gene"},{"command":"get-bioassay","summary":"PubChem bioassay record (description, protocol, targets, results summary) by AID","params":[{"name":"aid","type":"number","required":true,"description":"PubChem BioAssay ID (AID)"}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/get-bioassay"},{"command":"get-element","summary":"PubChem element record (identifiers, properties, history, uses) by atomic number","params":[{"name":"atomic_number","type":"number","required":true,"description":"Atomic number, e.g. 6 for Carbon"}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/get-element"},{"command":"get-compound-structure","summary":"Compound structure record as JSON (atoms, bonds, 2D or 3D coordinates, computed props) by CID","params":[{"name":"cid","type":"number","required":true,"description":"PubChem Compound ID"},{"name":"record_type","type":"string","description":"2d for a 2D depiction, 3d for the computed 3D conformer","oneOf":["2d","3d"],"default":"2d"}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/get-compound-structure?record_type=3d"},{"command":"export-compound-sdf","summary":"Download a compound's 2D or 3D structure as SDF (MOL) text by CID","params":[{"name":"cid","type":"number","required":true,"description":"PubChem Compound ID"},{"name":"record_type","type":"string","description":"2d or 3d coordinates","oneOf":["2d","3d"],"default":"2d"}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/export-compound-sdf?record_type=3d"},{"command":"list-elements","summary":"Periodic table: every element with symbol, mass, electron configuration, electronegativity, state, melting/boiling point, etc.","params":[],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/list-elements"},{"command":"list-classifications","summary":"List the classification hierarchies in the PubChem Classification Browser (MeSH, ChEBI, ATC, Compound TOC, ...) with their HIDs","params":[],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/list-classifications"},{"command":"get-classification-node","summary":"Expand a classification hierarchy node to show its children and record counts","params":[{"name":"hid","type":"number","required":true,"description":"Hierarchy ID from list-classifications"},{"name":"start","type":"string","description":"Node to expand: 'root' or a node id such as node_3607744","default":"root"},{"name":"depth","type":"number","description":"Number of child levels to return","default":1}],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/get-classification-node?hid=2&start=root"},{"command":"list-sources","summary":"List all PubChem data sources (depositors) with substance/assay counts, category, organization, URL and license","params":[],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/list-sources"},{"command":"list-news","summary":"Recent PubChem news and announcements","params":[],"exampleUrl":"https://clify-dev.netlify.app/pubchem-ncbi/list-news"}]}