Using a perennial identifier. The UniProt entry also possess an “entry
With a perennial identifier. The UniProt entry also possess an “entry name” (the SwissProt “identifier”), a “protein name”, “synonyms” etc. Only the “accession” is perennial and need to be applied. The value of a rdf:resource attribute is usually a URI that each uniquely identifies the resource, and the data inside the resource. The worth on the rdf:resource attribute can be a URI, not a URL; as such, a URI does not have to reference a physical internet object but simply identifies a controlled vocabulary term or database object (a URI is actually a label). For instance, a accurate URL for an World-wide-web resource such as http:uniprot.orgentryP2999 could possibly correspond for the URI http:identifiers.orguniprotP2999. SBML will not specify how a parser is to interpret a URI. In the case of a transformation into a physical URL, there could possibly be several solutions. As an example, the URI http: identifiers.orggoGO:0007268 could be translated into any one of several following: http:ebi.ac.ukegoDisplayGoTermselectedGO:0007268 http:godatabase.orgcgibinamigogo.cgiviewdetails queryGO: 0007268 http:informatics.jax.orgsearchesGO.cgiidGO:0007268 To allow interoperability, the neighborhood has agreed on an initial set of standardized valid URI syntax rules which could be utilised within the common annotation format. This set of rules just isn’t part from the SBML common but will develop independently from distinct SBML Levels and Versions. As the set changes, a given URI syntax rule will not be modified, even though the physical sources linked together with the rule may possibly change. These URIs will generally be composed as resource:id. MIRIAM Resources, located at http:sbml.orgmiriam, lists URI syntaxes and feasible physical links to controlled vocabularies and databases. Every entry contains a list of SBML and relation components in which the offered URI may be appropriately embedded. To enable consistent and thus useful links to external sources, the URI syntax rule set must have a consistent view of your ideas represented by the various SBML components for the purposes of this format. One example is, as the rule set is made to link SBML biological and biochemical sources the rule set assumes that a Species element represents the notion of a biochemical entity sort instead of mathematical symbol. The URI rule list will evolve with the evolution of databases and resources. The annotationJ Integr Bioinform. A-1155463 chemical information Author manuscript; obtainable in PMC 207 June 02.Hucka et al.Pageformat described in this section will not require a uncomplicated parser of this format to access this list. six.five Relation components To allow the format to encode various sorts of relationships amongst SBML components and resources, qualifier components are utilised to enclose a set of rdf:li components. The relation elements imply a distinct connection involving the enclosing SBML element along with the resources referenced by the rdf:li elements. The detailed semantics (i.e. from the viewpoint of automatic parser) on the relation elements is defined by the URI list at http:sbml.orgmiriam, and thus is outside the PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23814047 scope of SBML. The URI list commonly assumes that the biological entity represented by the element is the concept linked towards the reference resource.Author Manuscript Author Manuscript Author Manuscript Author ManuscriptSeveral relation elements having a given tag, enclosed inside the same SBML element, every single represent an option annotation to the SBML element. For instance two bqbiol:hasPart components within a Species SBML element represent two distinct sets of references towards the.
