Reference "Curation of QTLs with default ontology mapping files"

Reference ID	11453
Title	Curation of QTLs with default ontology mapping files
Source	Gramene Internal reference, 2007, vol. , pp. 1-1
Author (1)	Gramene curators
Abstract	QTL data in the Gramene database is semantically described by the use of multiple ontologies such as Trait ontology (TO), Gene Ontology (GO), Plant Ontology (PO), Environment Ontology (EO). This task is done by expert curators extracting the information from experiments described in the cited literature, expert knowledge or by creating a default mapping between these ontologies based on the existing data. As part of the curation strategy, majority of the ontology associations in QTL database with IC (inferred by curator) evidence code are derived from default TO-PO and TO-EO mappings. These mapping files are developed as follows, terms from different ontologies that have common concepts associated with the terms in the TO are mapped in a simple and straightforward manner. For example; The term Root Length is decomposed into ‘root’ and ‘length’ and only the anatomical plant part ‘root’ is mapped to its exact equivalent root: PO:0009005 from the PO. Trait terms that do not have the anatomical part embedded within themselves have been mapped to higher level terms such as plant structure PO:0009011. In addition, the trait terms have been mapped to the growth stage or stage of development that plant is likely to be in, when the assay is performed. This is done in the following manner: The trait stigma color: TO:0000185 is mapped to the anatomical part stigma: PO:0009073, which is seen at the stage of flowering: PO:0007016. Automatic mapping is followed by manual curation and the annotations are validated by providing references.