# bioservices **Repository Path**: tyejdslhk/bioservices ## Basic Information - **Project Name**: bioservices - **Description**: Access to Biological Web Services from Python. - **Primary Language**: Unknown - **License**: GPL-3.0 - **Default Branch**: master - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2020-12-22 - **Last Updated**: 2020-12-22 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README BioServices ############## .. image:: https://badge.fury.io/py/bioservices.svg :target: https://pypi.python.org/pypi/bioservices .. image:: https://secure.travis-ci.org/cokelaer/bioservices.png :target: http://travis-ci.org/cokelaer/bioservices .. image:: https://coveralls.io/repos/cokelaer/bioservices/badge.png?branch=master :target: https://coveralls.io/r/cokelaer/bioservices?branch=master .. image:: http://readthedocs.org/projects/bioservices/badge/?version=master :target: http://bioservices.readthedocs.org/en/master/?badge=master :alt: Documentation Status :Python_version_available: BioServices is tested for Python 2.7, 3.6, 3.7 :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). .. image:: https://raw.githubusercontent.com/cokelaer/bioservices/master/doc/bioservices.png :target: https://raw.githubusercontent.com/cokelaer/bioservices/master/doc/bioservices.png 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 here `github cokelaer/bioservices `_ and here `github bioservices `_. 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 `_. Revision 1.7.X -------------- * Fix ENA new API * Fix NCBIBlast and Muscle services (new API) * Update Quickgo * New module: mygeneinfom pdbe * Integration new Biomodels API following Combine/Harmony meetng * Update ChEMBL after an ChEMBL API change * General fixes and update from @thobalose (https://github.com/cokelaer/bioservices/pull/149) to * added panther module (pantherdb.org) * added tests for pubchem, pfam and eva modules, which are still in draft version though * deprecated PICR and TCGA modules (the latter was not really available anyway) * Fixed wikipathway, kegg, reactome tests and code (issues 148 and 151) 1.6.X ----- * rewrote entirely the ChEMBL wrapper due to new ChEMBL API. * removed the quickgo_old module and its tests * Fix typo for a "valid colum," in uniprot module * Changed biomodels WSDL endpoint (thanks to https://github.com/thobalose. ) * uses colorlog to have more robust and consistent logging. * Fixed wikipathway XML issues by outputing dictionaries now. This fixes https://github.com/cokelaer/bioservices/issues/131 * Fix https://github.com/cokelaer/bioservices/issues/137 to handle KEGG GENE field properly in KEGGParse * Fix https://github.com/cokelaer/bioservices/issues/125 thanks to https://github.com/thobalose. 1.5.X --------- * Support for Python 3.6 on Travis. * No more support for Python 2.6 * biodbnet and wikipathways services now uses the REST protocol (instead of WSDL). * move readseq to seqret and uses new EBI API * move wsdbfetch to dbfetch (and switch to REST protocol) * quickgo uses the new API from EBI * New Reactome API * For developers: use pytest instead of nosetests. 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