BioClients 0.0.3

For access to online biomedical resources, usually via REST APIs.

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/]