Enriching OBI for Web Service Annotation
With the increasing development and use of ontologies in the biomedical domain, opportunities for their utilization in applications and
workflows are being created. We are working towards enriching the Ontology for Biomedical Investigations (OBI) to provide for annotation of Web services.
In this effort we use terms/definitions from the EDAM ontology wherever applicable.
Visit http://code.google.com/p/obi-webservice/ for the latest version of the Extended OBI ontology and more.
Ontologies
Some of the Web Services Modelled
BLAST Web Services (NCBI Blast and WuBlast at EBI)
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NCBI Blast and WuBlast are web services that implement BLAST, a heuristic search algorithm for comparing primary biological sequence information, such as the amino-acid or nucleotides sequences with a database of sequences, and identify sequences that resemble the query sequence above a certain threshold. BLAST stands for Basic Local Alignment Search Tool
Documentation At EBI for WUBlast
Documentation At EBI for NCBIBlast
Ontology analysis diagram for Blast
Definitions for Blast Web services
WUBlast fully annotated with terms from enriched OBI
ClustalW2 Web Service
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ClustalW web service is an implementation of Clustal Program: (Multiple Sequence Alignment). ClustalW is a fully automatic program for global multiple alignment of DNA or protein sequences. The alignment is progressive and considers sequence redundancy.
Documentation At EBI for ClustalW2
Ontology analysis diagram for ClustalW2
Definitions for ClustalW2
ClustalW fully annotated with terms from enriched OBI
tCoffee Web Service
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The t-Coffee web service is an implementation of T-Coffee a multiple sequence alignment program to align a set of sequences previously gathered using other programs such as BLAST or FASTA. The main characteristic of T-Coffee is that it will allow you to combine results obtained with several alignment methods.
Documentation At EBI for tCoffee
Ontology analysis diagram for tCoffee
Definitions for tCoffee
tCoffee fully annotated with terms from enriched OBI
signalP Web Service
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This Web Service implements SignalP v. 3.1. It predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks and hidden Markov models.
Documentation for signalP
Ontology analysis diagram for signalP
Definitions for signalP
WSDbfetch Web Service
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WSDbfetch allows you to retrieve entries from various up-to-date biological databases using entry identifiers or accession numbers. This is equivalent to the CGI based dbfetch service. Like the CGI service a request can return a maximum of 200 entries.
Documentation for WSDbfetch
Ontology analysis diagram for WSDbfetch
Definitions for WSDbfetch
WSDBFetch fully annotated with terms from enriched OBI