- Python version available:
BioServices is tested for Python 2.6,2.7, 3.3, 3.4, 3.5
- Contributions:
Please join https://github.com/cokelaer/bioservices and share your notebooks https://github.com/bioservices/notebooks/
- Issues:
- How to cite:
Cokelaer et al. BioServices: a common Python package to access biological Web Services programmatically Bioinformatics (2013) 29 (24): 3241-3242
- Documentation:
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.
BioServices provides access to 25 Web Services including. For a quick start, look at some notebooks related to
UniProt on uniprot nbviewer
BioModels on biomodels nbviewer
ChEMBL on chembl nbviewer
Ensembl on Ensembl nbviewer
KEGG on KEGG nbviewer
MUSCLE on MUSCLE nbviewer
NCBIBlast on ncbiblast nbviewer
WikiPathway on wikipathway nbviewer
and more on nbviewer.
An up-to-date list of Web Services is provided within the online documentation.
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 exhaustive On-line documentation
Release History
This is a summary of the changelog. Complete change can be found in the main documentation.
1.4.X
Update uniprot valid column names.
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
1.3.X
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, PRIDE, clinvitae, Intact (complex)
CHANGES: all parameters called format have been renamed frmt (to avoid using Python keyword)
1.2.X
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
1.1.X
NEW services: biocarta, pfam, ChEBI, UniChem
Add documentation and examples related to Galaxy/BioPython.
NEW Service : HGNC
Use BeautifulSoup4 instead of 3
1.0.X
add PDB, ArrayExpress, biomart, chemspider draft, eutils, miriam, arrayexpress
1.0.0
First release of bioservices including the following services: BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt, WSDbfetch, NCBIblast, PSICQUIC, Wikipath
Release History
This is a summary of the changelog. Complete change can be found in the <main documentation.
1.4.X
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
1.3.X
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
1.2.X
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
1.1.X
NEW services: biocarta, pfam, ChEBI, UniChem
Add documentation and examples related to Galaxy/BioPython.
NEW Service : HGNC
Use BeautifulSoup4 instead of 3
1.0.X
add PDB, ArrayExpress, biomart, chemspider draft, eutils, miriam, arrayexpress
1.0.0:
First release of bioservices
0.9.X:
- Stable version of bioservices including the following services:
BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt, WSDbfetch, NCBIblast, PSICQUIC, Wikipath
1 maintainer
Release files for bioservices 1.4.8
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| bioservices-1.4.8.tar.gz | 195.8 kB | Details |
Release files / bioservices-1.4.8.tar.gz
| Download URL | bioservices-1.4.8.tar.gz |
|---|---|
| Size | 195.8 kB |
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