For access to online biomedical resources, usually via REST APIs.
Project description
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).
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.
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/]
Project details
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