├── .gitignore ├── BioClients ├── __init__.py ├── allen │ ├── __init__.py │ └── brain │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── amp │ ├── __init__.py │ └── t2d │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── badapple │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── bindingdb │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── biogrid │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── biomarkerkb │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── bioregistry │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── brenda │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── cas │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── cdc │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── cfde │ ├── __init__.py │ └── cfchemdb │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── chebi │ ├── Client.py │ ├── Client_SOAP.py │ ├── Utils.py │ └── __init__.py ├── chem2bio2rdf │ ├── Client.py │ ├── Utils.py │ ├── __init__.py │ └── slap │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── chembl │ ├── Client.py │ ├── FetchByID.py │ ├── UnichemClient.py │ ├── Utils.py │ └── __init__.py ├── chemidplus │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── clinicaltrials │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── diseaseontology │ └── Client.py ├── disgenet │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── dnorm │ ├── Client.py │ └── __init__.py ├── drugcentral │ ├── Client.py │ ├── Test.py │ ├── Utils.py │ └── __init__.py ├── emblebi │ ├── __init__.py │ ├── identifiers │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py │ └── unichem │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── ensembl │ ├── Client.py │ ├── Utils.py │ ├── __init__.py │ └── biomart │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── entrez │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── fda │ ├── __init__.py │ └── aer │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── geneontology │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── glygen │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── gtex │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── gwascatalog │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── hubmap │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── hugo │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── humanbase │ ├── Client.py │ └── __init__.py ├── icite │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── idg │ ├── Client.py │ ├── Utils.py │ ├── __init__.py │ ├── pharos │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py │ ├── rss │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py │ ├── tcrd │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py │ ├── tiga │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py │ └── tinx │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── iuphar │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── jensenlab │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── lincs │ ├── Client.py │ ├── Client_lincscloud.py │ ├── Utils.py │ ├── __init__.py │ ├── clue │ │ ├── Client.py │ │ └── Utils.py │ └── sigcom │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── maayanlab │ ├── __init__.py │ ├── archs4 │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py │ └── harmonizome │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── medline │ ├── __init__.py │ ├── connect │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py │ └── genetics │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── mesh │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── monarch │ ├── Biolink.py │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── mygene │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── ncats │ ├── __init__.py │ └── gsrs │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py ├── ncbo │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── omim │ ├── Client.py │ └── __init__.py ├── oncotree │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── openphacts │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── opentargets │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── panther │ ├── Client.py │ └── __init__.py ├── pdb │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── pubchem │ ├── Client.py │ ├── Utils.py │ ├── __init__.py │ ├── ftp │ │ ├── Client.py │ │ ├── Utils.py │ │ ├── __init__.py │ │ ├── pubchem_ftp_actives.py │ │ ├── pubchem_ftp_assay_fetch.py │ │ ├── pubchem_ftp_assay_results.py │ │ ├── pubchem_ftp_assay_search.py │ │ ├── pubchem_ftp_assaysim.py │ │ ├── pubchem_ftp_compound_assaystats.py │ │ └── pubchem_ftp_gini_index.py │ ├── rdf │ │ ├── Client.py │ │ └── __init__.py │ └── soap │ │ ├── Client.py │ │ ├── Utils.py │ │ ├── __init__.py │ │ ├── pug_aids2assays.py │ │ ├── pug_ids2mols.py │ │ └── pug_substance_search.py ├── pubmed │ ├── App_XML.py │ ├── Client.py │ ├── Utils.py │ ├── Utils_XML.py │ └── __init__.py ├── pubtator │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── reactome │ ├── Client.py │ ├── SMBL_utils.py │ ├── Utils.py │ └── __init__.py ├── rxnorm │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── stringdb │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── tcga │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── ubkg │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── umls │ ├── CPTClient.py │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── uniprot │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── util │ ├── __init__.py │ ├── db │ │ ├── Utils.py │ │ └── __init__.py │ ├── graphql │ │ ├── Utils.py │ │ └── __init__.py │ ├── hdf │ │ ├── Utils.py │ │ └── __init__.py │ ├── igraph │ │ ├── App.py │ │ ├── Utils.py │ │ └── __init__.py │ ├── neo4j │ │ ├── App.py │ │ ├── Utils.py │ │ └── __init__.py │ ├── obo │ │ ├── App.py │ │ ├── Utils.py │ │ └── __init__.py │ ├── owl │ │ ├── App.py │ │ ├── Utils.py │ │ └── __init__.py │ ├── pandas │ │ ├── App.py │ │ ├── Csv2Html.py │ │ ├── Csv2Markdown.py │ │ ├── Csv2Sql.py │ │ ├── Utils.py │ │ └── __init__.py │ ├── pdf │ │ └── PDF2Txt.py │ ├── rdf │ │ ├── App.py │ │ ├── Utils.py │ │ └── __init__.py │ ├── rest │ │ ├── Utils.py │ │ └── __init__.py │ ├── sparql │ │ ├── Client.py │ │ ├── Utils.py │ │ └── __init__.py │ ├── xml │ │ ├── Utils.py │ │ └── __init__.py │ └── yaml │ │ ├── Utils.py │ │ └── __init__.py ├── wikidata │ ├── Client.py │ ├── Utils.py │ └── __init__.py └── wikipathways │ ├── Client.py │ ├── Utils.py │ └── __init__.py ├── LICENSE ├── README.md ├── conda └── environment.yml ├── doc ├── allen.md ├── amp_t2d.md ├── badapple.md ├── bindingdb.md ├── biogrid.md ├── biomarkerkb.md ├── bioregistry.md ├── brenda.md ├── cas.md ├── cdc.md ├── cfde.md ├── chebi.md ├── chem2bio2rdf.md ├── chembl.md ├── chemidplus.md ├── clinicaltrials.md ├── disgenet.md ├── dnorm.md ├── drugcentral.md ├── emblebi.md ├── ensembl.md ├── entrez.md ├── fda.md ├── geneontology.md ├── glygen.md ├── gtex.md ├── gwascatalog.md ├── hugo.md ├── humanbase.md ├── icite.md ├── idg.md ├── images │ └── BioClients_logo.png ├── iuphar.md ├── jensenlab.md ├── lincs.md ├── maayanlab.md ├── medline.md ├── mesh.md ├── monarch.md ├── mygene.md ├── ncats.md ├── ncbo.md ├── omim.md ├── oncotree.md ├── opentargets.md ├── panther.md ├── pdb.md ├── pubchem.md ├── pubmed.md ├── pubtator.md ├── reactome.md ├── rxnorm.md ├── stringdb.md ├── tcga.md ├── ubkg.md ├── umls.md ├── uniprot.md ├── util.md ├── wikidata.md └── wikipathways.md └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeremyjyang/BioClients/HEAD/.gitignore -------------------------------------------------------------------------------- /BioClients/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeremyjyang/BioClients/HEAD/BioClients/__init__.py -------------------------------------------------------------------------------- /BioClients/allen/__init__.py: -------------------------------------------------------------------------------- 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