UniProtKB

The UniProtKB syntactic ontology was generated using Protégé 3.4 RC1 via the XMLTab plugin. The classes represent the element and attribute types, while the instances represent the data themselves as retrieved from UniProtKB. While the original intent was to make use of the UniProtKB RDF format, problems were experienced in reasoning and importing the full set of ontology and RDF files required.

Figure 4: The UniProtKB syntactic ontology. As with the other syntactic ontologies, instances represent the data itself, while classes represent the structure.
Image uniprot-full

The UniProtKB is a comprehensive public protein sequence and function database, consisting both of manually-curated and automatically-annotated data. Unambiguous assignment of a UniProtKB primary accession to a new species in an SBML document provides a useful way to link disparate instances. For the use cases, UniProtKB was primarily useful for localisation and identification information. Often, new models contain little more than species ids and skeletons of reactions, making even the simple addition of cross-references to UniProtKB useful.



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