Sequence ontology

K. Eilbeck, S. E. Lewis, C. J. Mungall, M. Yandell, L. Stein, R. Durbin, and M. Ashbumer. 2005. The Sequence Ontology a tool for the unification of genome annotations, Genome Biology, 6 R44. 

Figure 11.2 Gene Ontology assignments of the M. truncatula expressed sequence tags.

Each SOAP Web service is described in terms of Web Service Description Language (Booth and Liu 2007), which is a specification in XML. This enables data passed over the Web, say a sequence of characters such as CMRSGGCTRRYAC, to have its type specified according to an ontology, thus telling the code that that sequence of characters is a consensus DNA sequence rather than an author name or a geographical location. A RESTful Web service works in terms of HTTP requests and thus has potentially a less constrained syntax. 

Quick ontology matching (QOM) was one of the first approaches to implement this idea (Ehrig and Staab 2004). It iteratively applies a sequence of matchers and can restrict the search space for every matcher. The considered approaches to restrict the search space include focusing on elements with similar names (labels) or similar structural properties. The authors showed that the runtime complexity of QOM can be reduced to (0(n log(n)) instead of 0(n2) for ontologies of size n. 

The data are collected daily from a number of sources, including the National Center for Biotechnology Information (NCBI) and Gene Ontology (GO) Consortium. The warehouse includes sequences, structures, and complete genomes from Gen-Bank as well as annotation links such as NCBI taxon database terms, redundant sequences, sequence neighbors, conserved domains, Online Mendehan Inheritance in Man identifiers, GO terms, LocusLink identifiers, and PubMed links. 

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