Bioinformatics Web APIs

Documentation on bioinformatics web accessible programming interfaces (APIs), other wise known as Web Services.

• The EBI has a variety of (poorly documented) web services available through SOAP at http://www.ebi.ac.uk/Tools/webservices/, including EMBOSS, WUBLAST and WSDBFETCH, which enables you to retrieve sequences from various databases.

• XEMBL

• NCBI's Entrez has both SOAP and REST based web services - see the help pages there at http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html .

• BIND, a database of protein interactions, has a SOAP API too - see http://soap.bind.ca/ .

• PathPort at the Virginia Bioinformatics Institute has a selection of SOAP based services including Phylip, glimmer, some statistical tools and a Smith Waterman implementation. See http://staff.vbi.vt.edu/pathport/services/

• The DNA Databank of Japan (DDBJ) has a collection of SOAP services at http://xml.ddbj.nig.ac.jp/soapp.html

• My GRID project's list: http://twiki.mygrid.org.uk/twiki/bin/view/Bioinformatics/BioinformaticsWebServices
• XML.com article: http://webservices.xml.com/pub/a/ws/2002/05/14/biows.html
• There are lots of web services included in Taverna (You can either browse them via the Taverna GUI facilities, or search for the “DEFAULT SERVICES” paragraph of the “mygrid.properties” file under 'taverna/conf' directory using the text editor of your choice)