{"ok":true,"site":"uniprot","host":"uniprot.org","about":"UniProt, the Universal Protein Resource. This CLI wraps the public rest.uniprot.org JSON API to search and fetch UniProtKB protein entries, sequences, publications, version history, taxonomy, keywords, diseases, UniRef clusters and proteomes, plus AlphaFold structure predictions.","commands":[{"command":"search-proteins","summary":"Search UniProtKB protein entries with a query; filters such as reviewed or organism go inside the query string","params":[{"name":"query","type":"string","required":true,"description":"UniProt query syntax. Free text or field queries joined with AND/OR/NOT, e.g. 'hemoglobin', '(hemoglobin) AND (reviewed:true)', '(hemoglobin) AND (model_organism:9606)', 'gene:HBB AND organism_id:9606"},{"name":"api_fields","type":"string","description":"Comma-separated result fields. list-result-fields --database uniprotkb lists the valid names (sent to the site as \"fields\"; clify's own --fields only shapes the output)","default":"accession,reviewed,id,protein_name,gene_names,organism_name,length"},{"name":"sort","type":"string","description":"Sort as '<field> asc|desc'. Sortable fields include accession, id, gene, length, mass, organism_name, protein_name, annotation_score. Example: 'length desc'"},{"name":"size","type":"number","description":"Number of results to return (max 500)","default":25}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/search-proteins?query=%28hemoglobin%29+AND+%28reviewed%3Atrue%29&sort=length+desc"},{"command":"count-protein-facets","summary":"Get facet counts (reviewed status, model organism, existence level, annotation score, length bins, etc.) for a UniProtKB query without fetching entries","params":[{"name":"query","type":"string","required":true,"description":"UniProt query, e.g. 'hemoglobin' or '*' for everything"},{"name":"facets","type":"string","description":"Comma-separated facet names: reviewed, model_organism, proteins_with, existence, annotation_score, length","default":"reviewed,model_organism,proteins_with,existence,annotation_score,length"}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/count-protein-facets?query=hemoglobin"},{"command":"get-protein","summary":"Get the full UniProtKB entry (names, genes, organism, function comments, features, cross-references, sequence) for an accession","params":[{"name":"accession","type":"string","required":true,"description":"UniProtKB accession, e.g. P68871"},{"name":"api_fields","type":"string","description":"Optional comma-separated fields that limit the returned entry, e.g. 'accession,protein_name,cc_function,sequence' (sent to the site as \"fields\"; clify's own --fields only shapes the output)"}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/get-protein"},{"command":"download-protein","summary":"Download a UniProtKB entry as plain text: a FASTA sequence, the flat file, or GFF features","params":[{"name":"accession","type":"string","required":true,"description":"UniProtKB accession"},{"name":"format","type":"string","description":"Download format: fasta (sequence), txt (UniProt flat file) or gff (features)","oneOf":["fasta","txt","gff"],"default":"fasta"}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/download-protein"},{"command":"get-protein-gene-centric","summary":"Get the gene-centric view of a protein: the canonical protein of its proteome plus related isoforms and fragments from the same gene","params":[{"name":"accession","type":"string","required":true,"description":"UniProtKB accession"}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/get-protein-gene-centric"},{"command":"get-protein-history","summary":"List all historical versions of a UniProtKB entry (UniSave) with release dates and sequence versions","params":[{"name":"accession","type":"string","required":true,"description":"UniProtKB accession"}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/get-protein-history"},{"command":"list-result-fields","summary":"List the valid result field names (for --fields) and the sortable fields of a UniProt database","params":[{"name":"database","type":"string","required":true,"description":"Database name","oneOf":["uniprotkb","taxonomy","keywords","diseases","uniref","proteomes"]}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/list-result-fields"},{"command":"list-protein-search-fields","summary":"List the query field terms usable in UniProtKB queries (e.g. accession, gene, organism_id, reviewed), with examples","params":[],"exampleUrl":"https://clify-dev.netlify.app/uniprot/list-protein-search-fields"},{"command":"search-taxonomy","summary":"Search taxonomy nodes by name, or list children/descendants with parent:<taxId> or ancestor:<taxId>","params":[{"name":"query","type":"string","required":true,"description":"Name text (e.g. 'mouse') or field query such as 'parent:9606' or 'ancestor:9605'"},{"name":"api_fields","type":"string","description":"Comma-separated result fields (sent to the site as \"fields\"; clify's own --fields only shapes the output)","default":"id,common_name,scientific_name,lineage,links"},{"name":"size","type":"number","description":"Number of results (max 500)","default":25}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/search-taxonomy?query=mouse"},{"command":"get-taxonomy","summary":"Get a taxonomy node by NCBI taxon id: names, rank, parent, full lineage, links and protein/proteome counts","params":[{"name":"taxonId","type":"number","required":true,"description":"NCBI taxonomy id, e.g. 9606 for human"}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/get-taxonomy"},{"command":"search-keywords","summary":"Search UniProt controlled keywords (KW-xxxx) by name","params":[{"name":"query","type":"string","required":true,"description":"Keyword text, e.g. 'heme'"},{"name":"api_fields","type":"string","description":"Comma-separated result fields (sent to the site as \"fields\"; clify's own --fields only shapes the output)","default":"id,name,category,gene_ontologies"},{"name":"size","type":"number","description":"Number of results","default":25}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/search-keywords?query=heme"},{"command":"get-keyword","summary":"Get a UniProt keyword: definition, synonyms, parent hierarchy, category and protein counts","params":[{"name":"keywordId","type":"string","required":true,"description":"Keyword id, e.g. KW-0349"}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/get-keyword"},{"command":"search-diseases","summary":"Search UniProt human disease entries (DI-xxxxx) by name","params":[{"name":"query","type":"string","required":true,"description":"Disease text, e.g. 'thalassemia'"},{"name":"api_fields","type":"string","description":"Comma-separated result fields (sent to the site as \"fields\"; clify's own --fields only shapes the output)","default":"id,name,keywords"},{"name":"size","type":"number","description":"Number of results","default":25}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/search-diseases?query=thalassemia"},{"command":"get-disease","summary":"Get a disease entry: definition, alternative names, cross-references (MIM, MedGen, etc.), keywords and protein counts","params":[{"name":"diseaseId","type":"string","required":true,"description":"Disease id, e.g. DI-01275"}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/get-disease"},{"command":"search-uniref","summary":"Search UniRef sequence clusters (100%, 90% and 50% identity); filter identity in the query, e.g. 'hemoglobin AND identity:0.9'","params":[{"name":"query","type":"string","required":true,"description":"UniRef query; add 'AND identity:1.0|0.9|0.5' to restrict the cluster level"},{"name":"api_fields","type":"string","description":"Comma-separated result fields (sent to the site as \"fields\"; clify's own --fields only shapes the output)","default":"id,name,types,count,organism,length,identity"},{"name":"size","type":"number","description":"Number of results","default":25}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/search-uniref?query=hemoglobin"},{"command":"search-proteomes","summary":"Search proteomes by organism name; filter in the query, e.g. 'human AND proteome_type:1' for reference proteomes","params":[{"name":"query","type":"string","required":true,"description":"Proteome query, e.g. 'human' or 'organism_id:9606'"},{"name":"api_fields","type":"string","description":"Comma-separated result fields (sent to the site as \"fields\"; clify's own --fields only shapes the output)","default":"upid,organism,organism_id,protein_count,busco,cpd"},{"name":"size","type":"number","description":"Number of results","default":25}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/search-proteomes?query=human"},{"command":"get-proteome","summary":"Get a proteome by UPID: description, taxonomy, type, and components (chromosomes) with protein counts","params":[{"name":"upid","type":"string","required":true,"description":"Proteome id, e.g. UP000005640 (human reference proteome)"}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/get-proteome"},{"command":"get-alphafold-prediction","summary":"Get the AlphaFold predicted structure for a UniProt accession: confidence (pLDDT) and download URLs for PDB, CIF and PAE files","params":[{"name":"accession","type":"string","required":true,"description":"UniProtKB accession"}],"exampleUrl":"https://clify-dev.netlify.app/uniprot/get-alphafold-prediction"}]}