Libraries tagged by biology
amelaye/biophp
97 Downloads
Enjoy my BioPHP version !
amelaye/biotools
22 Downloads
Symfony forms and services for the BioPHP minitools
omniscient/omnilab
0 Downloads
Omnilab: one contract for the public science-data APIs - entities (a compound, a gene, a protein, a species, a star, an earthquake) with their properties, units and cross-references, series (a variable measured at a place over time: weather, climate, air) and catalogued products (a satellite scene, a dataset, STAC-like) - whatever the domain; a Collector that follows cross-references from one base to the next, and a Symfony bundle.
omnilab/uniprot
0 Downloads
Omnilab UniProt: a protein of UniProtKB by accession or entry name - its names, gene, organism, function, length, mass and sequence, cofactors, ligands, location and keywords, its NCBI Gene and Ensembl genes as cross-references, its organism, PDB structures and ligands as related things - and UniProt's search, through the UniProt REST API, no key needed.
omnilab/string
0 Downloads
Omnilab STRING: a protein by its STRING id (9606.ENSP00000269305), UniProt accession, Ensembl protein or name - its preferred name, protein name, annotation, species and Ensembl protein - its interaction partners as related things with their combined scores, the network among proteins with each evidence channel's score, and their functional enrichment (GO, KEGG, Reactome, Pfam, InterPro, diseases), through STRING's API, no key needed.
omnilab/reactome
0 Downloads
Omnilab Reactome: a pathway or a reaction by its stable identifier (R-HSA-70171) - its names, species, summary, compartments, GO biological process, Rhea reaction, inputs, outputs and catalysts, review status, release dates, DOI and diagram - its participants (UniProt proteins, ChEBI small molecules), organism, sub-events and orthologous events as related things, a search by text, and the pathways of a protein or a molecule (UniProt, ChEBI), through Reactome's Content Service, no key needed.
omnilab/quickgo
0 Downloads
Omnilab QuickGO: a Gene Ontology term (GO:0005829) - its name, definition, aspect, synonyms, comment, obsolescence, direct parents by relation and children - a UniProt protein with the GO terms it is annotated to by aspect and evidence, its annotations with their evidence, reference and curator, and a search of terms, through the EBI's QuickGO services, no key needed.
omnilab/pdb
0 Downloads
Omnilab PDB: an entry of the Protein Data Bank by its PDB id through RCSB PDB's GraphQL Data API - its title, keywords, method, resolution, weight, dates, primary citation and authors, its polymer entities and ligands, an image of its assembly; the UniProt proteins of its chains, their organisms and its ligands (ChEBI, PubChem or InChIKey) as related things, never its identifiers; a removed entry's only replacement - and RCSB's full-text search, no key needed.
omnilab/opentargets
0 Downloads
Omnilab Open Targets: a target by its Ensembl gene, a disease or phenotype by its EFO, Mondo, HPO or Orphanet id, a drug by its ChEMBL id - names, descriptions, locations, classes, therapeutic areas, parents, mechanisms of action, indications - their associations with scores, drugs and clinical candidates, UniProt, HGNC, OMIM and Orphanet ids, InterPro domains and Reactome pathways, a search, and the associations paged, through the Open Targets Platform's GraphQL API, no key needed.
omnilab/ncbi
0 Downloads
Omnilab NCBI: a gene of NCBI Gene by its GeneID - symbol, name, organism, place on the genome, summary, its UniProt and Ensembl ids - and a taxon of NCBI Taxonomy by its id or a name - scientific name, rank, lineage, common name, GBIF key - and a search of either, through NCBI Datasets v2 and E-utilities, no key needed (one for ten calls a second).
omnilab/interpro
0 Downloads
Omnilab InterPro: an InterPro entry (IPR000971) or a Pfam family (PF00042) - its name, type, description, member signatures, GO terms, protein and structure counts, Pfam clan, representative structure, overlapping entries and hierarchy - a UniProt protein with the InterPro entries and Pfam families it matches, by type and position, as related things, and a search of InterPro entries, through the InterPro API, no key needed.
omnilab/hgnc
0 Downloads
Omnilab HGNC: a human gene by its HGNC id (HGNC:4827), approved, previous or alias symbol, or an id HGNC records (NCBI Gene, Ensembl, UniProt, OMIM) - its approved name, locus group and type, location, previous symbols and names, aliases, gene groups, status, dates, MANE Select, RefSeq and CCDS ids - its NCBI Gene, Ensembl, UniProt and OMIM ids as cross-references, and a search, through HGNC's REST service, no key needed.
omnilab/gwas
0 Downloads
Omnilab GWAS Catalog: a study by its accession (GCST000854), a variant by its rs id, a trait by its EFO, Mondo or HPO id - reported and mapped traits, samples, ancestries, platforms, functional class, location, mapped genes, studies - each with its strongest associations and the studies, variants and traits they tie it to as related things, a search of traits, and the associations paged with their p-values, effect sizes and risk alleles, through the NHGRI-EBI GWAS Catalog's REST API v2, no key needed.
omnilab/ensembl
0 Downloads
Omnilab Ensembl: a gene, transcript, protein or exon of Ensembl by its id, or a gene by its symbol in a species - its symbol, name, biotype, species, assembly and place on the genome, a gene's NCBI Gene record and Swiss-Prot proteins and a protein's UniProt entries as cross-references, its species, gene, transcripts and protein as related things - and the genes a symbol names, through the Ensembl REST API, no key needed.
omnilab/clinvar
0 Downloads
Omnilab ClinVar: a variation by its VariationID or VCV accession - its name, type, germline classification, review status, conditions, genes, protein change, consequence, location, SPDI, allele frequencies, aliases - its dbSNP id as a cross-reference, its genes and conditions (Mondo, OMIM, Orphanet, HPO) as related things, and a search in ClinVar's query language, through the NCBI's E-utilities, no key needed.