{"ok":true,"site":"ebi","host":"ebi.ac.uk","about":"EBI Search (EMBL-EBI): keyword search across all EMBL-EBI data resources such as UniProt, PDBe, Ensembl, Europe PMC, ChEBI and Reactome, with entry lookup, cross-references, gene/protein identification and FASTA sequence download.","commands":[{"command":"search-domain","summary":"Keyword search within one EBI Search domain (e.g. uniprot, proteinSequences, pubmed, chebi, pdbe), with field selection, facet filters, sorting and offset paging","params":[{"name":"domain","type":"string","required":true,"description":"Domain id, e.g. uniprot, proteinSequences, pubmed, chebi, pdbe, ensembl_gene, reactome, allebi. Run list-domains for all ids."},{"name":"query","type":"string","required":true,"description":"Lucene-style query, e.g. insulin, or field:value such as name:insulin AND TAXONOMY:9606"},{"name":"api_fields","type":"string","description":"Comma-separated retrievable fields to return for each entry. Valid fields depend on the domain (see get-domain-info). uniprot example: descRecName,organism_scientific_name,acc,status. Sent to the site"},{"name":"facets","type":"string","description":"Facet filters as facetId:value, comma-separated, e.g. TAXONOMY:9606,status:Reviewed (see get-search-facets for values)"},{"name":"sort","type":"string","description":"Sort as field:ascending|descending, e.g. publication_date:descending. Only sortable fields are allowed (see get-domain-info); uniprot does not allow sorting on id or length."},{"name":"size","type":"number","description":"Results per page (max 100)","default":15},{"name":"start","type":"number","description":"Zero-based result offset for paging","default":0}],"exampleUrl":"https://clify-dev.netlify.app/ebi/search-domain?query=insulin&api_fields=descRecName%2Corganism_scientific_name%2Cacc%2Cstatus&facets=TAXONOMY%3A9606%2Cstatus%3AReviewed"},{"command":"get-search-facets","summary":"Get facet value counts for a query in a domain, e.g. source database, organism (TAXONOMY) or review status, to discover filter values for search-domain","params":[{"name":"domain","type":"string","required":true,"description":"Domain id, e.g. uniprot, proteinSequences, pubmed"},{"name":"query","type":"string","required":true,"description":"Search query"},{"name":"facetfields","type":"string","description":"Comma-separated facet ids to return, e.g. domain_source, TAXONOMY, status. Omit to get all facets."},{"name":"facetcount","type":"number","description":"Maximum number of values per facet","default":11},{"name":"facets","type":"string","description":"Facet filters already applied, e.g. TAXONOMY:9606"}],"exampleUrl":"https://clify-dev.netlify.app/ebi/get-search-facets?query=insulin&facetfields=domain_source&facetcount=50"},{"command":"count-all-domains","summary":"Search all EMBL-EBI data at once and get hit counts per domain and subdomain (the tree behind the 'All results' page)","params":[{"name":"query","type":"string","required":true,"description":"Keyword query"}],"exampleUrl":"https://clify-dev.netlify.app/ebi/count-all-domains?query=insulin"},{"command":"list-domains","summary":"List all EBI Search domains and subdomains (ids, names, descriptions, index info) as a tree","params":[],"exampleUrl":"https://clify-dev.netlify.app/ebi/list-domains"},{"command":"get-domain-info","summary":"Get one domain's metadata: searchable/retrievable/sortable fields, facets, and index info. Use it to find valid values for fields, facets and sort.","params":[{"name":"domain","type":"string","required":true,"description":"Domain id, e.g. uniprot, pubmed, pdbe"}],"exampleUrl":"https://clify-dev.netlify.app/ebi/get-domain-info"},{"command":"get-entries","summary":"Fetch one or more entries by id or accession from a domain, with selected fields","params":[{"name":"domain","type":"string","required":true,"description":"Domain id, e.g. uniprot"},{"name":"ids","type":"string","required":true,"description":"Entry id(s), comma-separated, e.g. P01308 or P06213,P08069"},{"name":"api_fields","type":"string","description":"Comma-separated retrievable fields for the domain, e.g. descRecName,organism_scientific_name,status,length (sent to the site as \"fields\"; clify's own --fields only shapes the output)"},{"name":"fieldurl","type":"boolean","description":"Include links to the source resource page","default":true},{"name":"viewurl","type":"boolean","description":"Include alternative view links such as FASTA","default":true}],"exampleUrl":"https://clify-dev.netlify.app/ebi/get-entries?api_fields=descRecName%2Corganism_scientific_name%2Cstatus"},{"command":"list-entry-xref-domains","summary":"List the domains an entry is cross-referenced to, with the number of referenced entries in each (e.g. pdbe, alphafold, europepmc)","params":[{"name":"domain","type":"string","required":true,"description":"Source domain id, e.g. uniprot, omim, reactome, hgnc"},{"name":"id","type":"string","required":true,"description":"Entry id in the source domain, e.g. INS_HUMAN or P01308 for uniprot, 176730 for omim"}],"exampleUrl":"https://clify-dev.netlify.app/ebi/list-entry-xref-domains"},{"command":"get-entry-xrefs","summary":"Get the entries in a target domain that cross-reference a given entry (e.g. AlphaFold or BioModels entries for UniProt INS_HUMAN)","params":[{"name":"domain","type":"string","required":true,"description":"Source domain id, e.g. uniprot"},{"name":"id","type":"string","required":true,"description":"Entry id(s) in the source domain, comma-separated, e.g. INS_HUMAN or P01308"},{"name":"targetDomain","type":"string","required":true,"description":"Target domain id taken from list-entry-xref-domains for this entry (only those with referenceEntryCount > 0 return results), e.g. alphafold, biomodels, complex-portal, europepmc"},{"name":"api_fields","type":"string","description":"Comma-separated retrievable fields of the target domain to return, e.g. name,description. Sent to the site as \"fields\"; clify's own --fields only shapes the output."},{"name":"size","type":"number","description":"Number of references per page (max 100)","default":15},{"name":"start","type":"number","description":"Zero-based offset into the references","default":0}],"exampleUrl":"https://clify-dev.netlify.app/ebi/get-entry-xrefs"},{"command":"identify-term","summary":"Identify what a search term refers to (gene, protein, etc., grouped by orthology and organism) with links to summary pages","params":[{"name":"term","type":"string","required":true,"description":"Gene or protein name or symbol, e.g. insulin, INS, INSR, IDE"}],"exampleUrl":"https://clify-dev.netlify.app/ebi/identify-term?term=INSR"},{"command":"get-summary-details","summary":"Get the gene/protein summary details (expression, structures, literature...) for an identification returned by identify-term","params":[{"name":"term","type":"string","required":true,"description":"The original search term"},{"name":"spine","type":"string","description":"Spine id from identify-term, e.g. molecular","default":"molecular"},{"name":"tid","type":"string","required":true,"description":"Identification id (iid) from identify-term, e.g. synENSG00000144749"},{"name":"classification","type":"string","description":"NCBI taxonomy id of the organism, e.g. 9606 for human"}],"exampleUrl":"https://clify-dev.netlify.app/ebi/get-summary-details?term=insulin&spine=molecular&tid=synENSG00000144749&classification=9606"},{"command":"fetch-sequence","summary":"Download raw database entries such as a FASTA sequence via dbfetch (e.g. UniProtKB P01308 in FASTA)","params":[{"name":"id","type":"string","required":true,"description":"Accession(s), comma-separated, e.g. P01308"},{"name":"db","type":"string","description":"dbfetch database name","oneOf":["uniprotkb","embl","pdb","ensemblgene","interpro","chebi"],"default":"uniprotkb"},{"name":"format","type":"string","description":"Output format; available formats depend on the database","oneOf":["fasta","default","uniprot"],"default":"fasta"}],"exampleUrl":"https://clify-dev.netlify.app/ebi/fetch-sequence?id=P01308&db=uniprotkb&format=fasta"}]}