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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 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, yaml, psycopg2, tqdm, etc.


AllenAMP-T2DBindingDbBioGridBRENDACDCChem2Bio2RDFChEMBLDisease OntologyDisGeNetDNormDrugCentralEnsEMBLFDAGene OntologyGWAS CatalogHUGOHumanBaseiCiteIDGJensenLabLINCSMaayanLabMeSHMONARCHMyGeneNCBOOMIMOpen TargetsPantherPDBPubChemPubMedPubTatorReactomeRXNormSTRINGDBTCGA • • UMLSUniProtWikidataWikiPathways

Miscellaneous utilities: UTIL

Usage Example

$ python3 -m BioClients.pubchem.Client -h

Design pattern

Generally each module includes command-line app which calls functions in a corresponding, providing all capabilities by import of the module. Functions can write to an output file or return a Pandas dataframe (if output file unspecified).

Data structures and formats, XML, JSON, and TSV

BioClients is designed to be simple and practical, and XML, JSON and 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. TSV represents tables of rows and columns, related by common keys, reflecting the development of SQL and relational databases. Transforming JSON to TSV, as these clients generally do, projects data objects to tables useful for many applications (e.g. machine learning).

Project details

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BioClients-0.1.6.tar.gz (366.0 kB view hashes)

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