2004
DOI: 10.1002/cfg.432
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The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature

Abstract: In general, it is not easy to specify a single sequence identity for each molecule name that appears in a pathway in the scientific literature. A molecule name may stand for concepts of various granularities, from concrete objects such as H-Ras and ERK1 to abstract concepts or categories such as Ras and MAPK. Typically, the relations among molecule names derive a hierarchical structure; without a proper way to handle this knowledge, it becomes ever more difficult to develop a reliable pathway database. This pa… Show more

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Cited by 12 publications
(10 citation statements)
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“…Synonyms for the terms are entered in the Synonyms column. In addition, if terms related to specific proteins or chemicals are found, their corresponding IDs in the MoleculeRole ontology 15 are entered in the General Dbxrefs column (Figure 1).…”
Section: Curation Methodsmentioning
confidence: 99%
See 2 more Smart Citations
“…Synonyms for the terms are entered in the Synonyms column. In addition, if terms related to specific proteins or chemicals are found, their corresponding IDs in the MoleculeRole ontology 15 are entered in the General Dbxrefs column (Figure 1).…”
Section: Curation Methodsmentioning
confidence: 99%
“…Each term name of a sub-pathway has a compositional structure and is based on molecular interaction types and the relevant molecule names. For molecular names (protein and chemical names), terms are defined in MoleculeRole Ontology, 15 an ontology of protein names that appear in the scientific literature. It manages the relations among "function names" and "abstract (generic) names" and "concrete names".…”
Section: Classification Of Sub-pathways Using Moleculerole Ontologymentioning
confidence: 99%
See 1 more Smart Citation
“…PSI-MI [17] and INOH Event Ontology (EO) [22] are ontologies that, in part, describe the events of protein interaction. Finally, the Molecule Role Ontology [38], another ontology developed for INOH pathway (http://www.inoh.org/) curation, contains molecular functional group names, abstract molecule names and concrete molecule names manually collected from literature. The structure of each of these resources aligns well with PRO.…”
Section: Other Protein-related Ontologiesmentioning
confidence: 99%
“…PSI-MI [ 16 ] and the INOH Event Ontology (EO) [ 17 ] are ontologies that describe some of the types of protein interaction events. Finally, both the INOH Molecule Role Ontology [ 18 ] and Reactome [ 19 ], contain molecular functional group names, abstract molecule names and concrete molecule names manually collected from literature. The structure of each of the other protein-related resources described above aligns well with PRO.…”
Section: Introductionmentioning
confidence: 99%