BioClients

Python package for access to online biomedical resources, usually via REST APIs. Modules generally include Client.py for command-line use and Utils.py for integration into other code.

Dependencies

• Python3

Modules

biogrid, brenda, chembl, diseaseontology, disgenet, dnorm, ensembl, fda, geneontology, gwascatalog, hugo, humanbase, icite, lincs, mesh, omim, opentargets, pdb, pubchem, pubmed, pubtator, reactome, rxnorm, stringdb, umls, uniprot

Usage

$ python3 -m BioClients.stringdb.Client -h

usage: Client.py [-h] [--id ID] [--ids IDS] [--idfile IDFILE] [--o OFILE]
                 [--species SPECIES] [--minscore MINSCORE]
                 [--netflavor {evidence,confidence,actions}]
                 [--imgfmt {image,highres_image,svg}] [--api_host API_HOST]
                 [--api_base_path API_BASE_PATH] [-v]
                 {getIds,getInteractionPartners,getNetwork,getNetworkImage,getEnrichment,getPPIEnrichment,getInteractors,getActions,getAbstracts}

STRING-DB REST API client utility

positional arguments:
  {getIds,getInteractionPartners,getNetwork,getNetworkImage,getEnrichment,getPPIEnrichment,getInteractors,getActions,getAbstracts}
                        operation

optional arguments:
  -h, --help            show this help message and exit
  --id ID               protein ID (ex:DRD1_HUMAN)
  --ids IDS             protein IDs, comma-separated
  --idfile IDFILE       input file, protein IDs
  --o OFILE             output file
  --species SPECIES     taxon code, ex: 9606 (human)
  --minscore MINSCORE   signifcance threshold 0-1000
  --netflavor {evidence,confidence,actions}
                        network flavor
  --imgfmt {image,highres_image,svg}
                        image format
  --api_host API_HOST
  --api_base_path API_BASE_PATH
  -v, --verbose

Example protein IDs: DRD1 DRD1_HUMAN DRD2 DRD2_HUMAN ; Example species: 9606 (human, via taxon identifiers, http://www.uniprot.org/taxonomy) ; Image formats: PNG PNG_highres SVG ; MAY BE DEPRECATED: getInteractors, getActions, getAbstracts

UMLS

From the NIH National Library of Medicine (NLM).

• Registration is required for both browser and API access. See https://www.nlm.nih.gov/research/umls/. To use BioClients.umls.Client, create ~/.umls.yaml with format:

API_KEY: "===REPLACE-WITH-KEY-HERE==="

RxNorm

From the NIH National Library of Medicine (NLM).

• https://www.nlm.nih.gov/research/umls/rxnorm/

Usage examples

python3 -m BioClients.rxnorm.Client -h
python3 -m BioClients.rxnorm.Client list_sourcetypes
python3 -m BioClients.rxnorm.Client list_relationtypes
python3 -m BioClients.rxnorm.Client list_termtypes
python3 -m BioClients.rxnorm.Client list_propnames
python3 -m BioClients.rxnorm.Client list_propcategories
python3 -m BioClients.rxnorm.Client list_idtypes
python3 -m BioClients.rxnorm.Client list_class_types
python3 -m BioClients.rxnorm.Client list_classes
python3 -m BioClients.rxnorm.Client list_classes --class_types 'MESHPA,ATC1-4'

Requiring names:

python3 -m BioClients.rxnorm.Client get_name --ids "prozac,tamiflu"
python3 -m BioClients.rxnorm.Client get_name2rxcui --ids "prozac,tamiflu"

Requiring external IDs:

python3 -m BioClients.rxnorm.Client get_id2rxcui --ids "C2709711" --idtype UMLSCUI

Requiring RxCUI IDs:

python3 -m BioClients.rxnorm.Client get_rxcui_status --ids "131725,213269"
python3 -m BioClients.rxnorm.Client get_rxcui_properties --ids "131725,213269"
python3 -m BioClients.rxnorm.Client get_rxcui_ndcs --ids "131725,213269"
python3 -m BioClients.rxnorm.Client get_rxcui_allrelated --ids "131725,213269"

MeSH

From the NIH National Library of Medicine (NLM). Currently XML processing tools only.

• https://meshb.nlm.nih.gov/

PubChem

Tools for obtaining and processing PubChem data (REST, SOAP, FTP).

python3 -m BioClients.pubchem.Client --name remdesivir name2sid
python3 -m BioClients.pubchem.Client --name remdesivir name2cid

ChEMBL

Tools for obtaining and processing ChEMBL data.

• https://www.ebi.ac.uk/chembl/
• https://chembl.gitbook.io/chembl-interface-documentation/web-services
• https://chembl.gitbook.io/chembl-interface-documentation/downloads

PubMed, PubTator, iCite

PubMed and related NIH literature resources.

• (PubMed)[https://pubmed.ncbi.nlm.nih.gov/]
• (iCite)[https://icite.od.nih.gov/]
• (PubTator)[https://www.ncbi.nlm.nih.gov/research/pubtator/]