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Clients to online biomedical resources, usually REST APIs.

Project description

BioClients BioClients logo

Python package for access to online biomedical resources, usually via REST APIs. Modules generally include for command-line use and for integration into other code. With the advent of HTTP web services, first SOAP/XML and then mostly REST/JSON, many online APIs require very similar methods for data search, requests and transforms into usable formats, often CSV/TSV.

Availability and installation

Source at; releases available via (pip3 install BioClients).

However, current development snapshot recommended.

(First download or clone.)

$ cd BioClients
$ python3 install


  • Python 3.6+
  • Python packages: pandas, requests, urllib, json, xml, etc.


AMP-T2DBioGridBRENDAChem2Bio2RDFChEMBLDisease OntologyDisGeNetDNormDrugCentralEnsEMBLFDAGene OntologyGWAS CatalogHUGOHumanBaseiCiteIDGJensenLabLINCSMaayanLabMeSHMONARCHOMIMOpen TargetsPantherPDBPubChemPubMedPubTatorReactomeRXNormSTRINGDBTCGATIN-XUMLSUniProt


$ python3 -m BioClients.pubchem.Client -h

Data structures and formats, XML, JSON, and CSV/TSV

BioClients is designed to be simple and practical, and XML, JSON and CSV/TSV are likewise simple in many respects, yet a great deal of conceptual and technological progress is reflected. XML and JSON can represent arbitrarily complex data objects, comprised of nested lists, dictionaries, and trees of primary types. CSV/TSV represents tables of rows and columns, the relational db view, flattened as needed for many applications (e.g. ML) but related by common keys. Transforming REST JSON results to CSV/TSV, as these clients generally do, projects data structures to tables useful for many applications.

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