Access to Biological Web Services from Python
|BioServices is tested for Python 3.6, 3.7, 3.8|
|Contributions:||Please join https://github.com/cokelaer/bioservices and share your notebooks https://github.com/bioservices/notebooks/|
|Issues:||Please use https://github.com/cokelaer/bioservices/issues|
|How to cite:||Cokelaer et al. BioServices: a common Python package to access biological Web Services programmatically Bioinformatics (2013) 29 (24): 3241-3242|
Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols).
The primary goal of BioServices is to use Python as a glue language to provide a programmatic access to several Bioinformatics Web Services. By doing so, elaboration of new applications that combine several of the wrapped Web Services is fostered.
One of the main philosophy of BioServices is to make use of the existing biological databases (not to re-invent new databases) and to alleviates the needs for expertise in Web Services for the developers/users.
Here is a small example using the UniProt Web Service to search for the zap70 specy in human organism:
>>> from bioservices import UniProt >>> u = UniProt(verbose=False) >>> data = u.search("zap70+and+taxonomy:9606", frmt="tab", limit=3, ... columns="entry name,length,id, genes") >>> print(data) Entry name Length Entry Gene names ZAP70_HUMAN 619 P43403 ZAP70 SRK B4E0E2_HUMAN 185 B4E0E2 RHOH_HUMAN 191 Q15669 RHOH ARHH TTF
More examples and tutorials are available in the On-line documentation
Here is the list of services available and their testing status (non exhaustive). Not all services are currently tested (WIP, july 2021)
Contributions to implement new wrappers are more than welcome. See BioServices github page to join the development, and the Developer guide on how to implement new wrappers.
This is a summary of the changelog. Complete change can be found in the <main documentation.
- Include RNASEQ (EBI) in module rnaseq_ebi
- Renamed kegg.KEGG.info into dbinfo , which was overloaded with Logging
- Replaced deprecated HGNC with the official web service from genenames.org
- Fully updated EUtils since WSDL is now down; implementation uses REST now.
- Removed the apps/taxonomy module now part of http://github.com/biokit.
- added http_delete in services.py
- CACHE files are now stored in a general directory in the home, rather than locally
- Source code moved to github.com
- New REST class to use requests package instead of urllib2.
- Creation of a global configuration file in .config/bioservice/bioservices.cfg
- NEW services: Reactome, Readseq, Ensembl, EUtils
- add try/except for pandas library.
- added sub-package called apps with some useful tools (fasta,peptides, taxon) in bioservices.apps directory
- NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf
- NEW services: biocarta, pfam, ChEBI, UniChem
- Add documentation and examples related to Galaxy/BioPython.
- NEW Service : HGNC
- Use BeautifulSoup4 instead of 3
- add PDB, ArrayExpress, biomart, chemspider draft, eutils, miriam, arrayexpress
- First release of bioservices
- Stable version of bioservices including the following services:
- BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt, WSDbfetch, NCBIblast, PSICQUIC, Wikipath
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