| Python_version_available: | BioServices is tested for Python 3.6, 3.7, 3.8, 3.9 |
|---|---|
| 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 |
| Documentation: | RTD 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 about 40 Web Services.
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.
| Service | CI testing |
|---|---|
| arrayexpress | 
|
| bigg | 
|
| biocarta | 
|
| biodbnet | 
|
| biogrid | 
|
| biomart | 
|
| biomodels | 
|
| chebi | 
|
| chembl | 
|
| cog | 
|
| dbfetch | 
|
| ena | 
|
| ensembl | 
|
| eutils | 
|
| eva | 
|
| hgnc | 
|
| intact_complex | 
|
| kegg | 
|
| muscle | 
|
| mygeneinfo | 
|
| ncbiblast | 
|
| omicsdi | 
|
| omnipath | 
|
| panther | 
|
| pathwaycommons | 
|
| pdb | 
|
| pdbe | 
|
| pfam | 
|
| pride | 
|
| psicquic | 
|
| pubchem | 
|
| quickgo | 
|
| reactome | 
|
| rhea | 
|
| rnaseq_ebi | 
|
| seqret | 
|
| unichem | 
|
| uniprot | 
|
| wikipathway | 
|
Note
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.
| Version | Description |
|---|---|
| 1.8.0 |
|