- Python_version_available
BioServices is tested for Python 3.7, 3.8, 3.9, 3.10
- Contributions
Please join 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
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.
Maintaining BioServices would not have been possible without users and contributors. Each contribution has been an encouragement to pursue this project. Thanks to all:
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_id:9606", frmt="tsv", limit=3,
... columns="id,length,accession, gene_names")
>>> print(data)
Entry name Length Entry Gene names
ZAP70_HUMAN 619 P43403 ZAP70 SRK
B4E0E2_HUMAN 185 B4E0E2
RHOH_HUMAN 191 Q15669 RHOH ARHH TTFNote
major changes of UniProt API changed all columns names in June 2022. The code above is valid for bioservices versions >1.10. Earlier version used:
>>> data = u.search("zap70+and+taxonomy:9606", frmt="tab", limit=3, ... columns="entry name,length,id, genes")
Note that columns names have changed, the frmt was changed from tab to tsv and taxonomy is now taxonomy_id. Names correspondences can be found in:
u._legacy_names
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 |
|
biocontainers |
|
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 |
|
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.
In version 1.8.2, we included a bioservices command. For now it has only one subcommand to download a NCBI accession number and possibly it genbank or GFF file (if available):
bioservices download-accession --accession K01711.1 --with-gbk | Version | Description |
|---|---|
| 1.12.0 | * migrating to pyproject |
1.11.2 |
|
1.11.1 |
|
1.11.0 |
|
| 1.10.4 | * Fix v1.10.3 adding missing requirements.txt |
1.10.3 |
|
1.10.2 |
|
1.10.1 |
|
| 1.10.0 | * Update uniprot to use the new API (june 2022) |
| 1.9.0 | * Update unichem to reflect new API |
1.8.4 |
|
1.8.3 |
|
| 1.8.2 | * Fix suds package in code and requirements |
1.8.1 |
|
1.8.0 |
|
1.4.X |
|
1.3.X |
|
| 1.2.X | * NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf |
| 1.1.X | * NEW services: biocarta, pfam, ChEBI, UniChem |
| 1.0.0: | * first stable release |
0.9.X: |
|