A Resource for a Common Reference Ontology for Plants

TitleA Resource for a Common Reference Ontology for Plants
Publication TypeConference Presentation
Presenting AuthorJaiswal P
Secondary AuthorsSmith B, Bastow R, Kersey PJ, Arnaud E, Cooper L, Rawlings C
Conference NamePlant and Animal Genome XXI Meeting
Tertiary TitleOntology Workshop Presentation
Conference LocationSan Diego, CA

In the new age of comparative plant biology, we are looking at datasets from numerous inter and intra-specific comparative analysis experiments on transcriptome, proteomics, phenomics and genome annotation projects. These experiments may describe, for example, a set of genes from one or more plant species that are differentially expressed in response to some type of treatment. These genes may have associations to phenotypes and molecular functions, in addition to various gene and protein features. For a researcher looking at this data, the value comes from the analysis of this data. Unfortunately, the data is present in many locations in online data repositories and is also annotated using different vocabularies and keywords that often do not match descriptions between different resources. The problem can be solved in two ways: (1) keep the data in different locations, but annotate it with common reference vocabularies that can be queried in real time using common query words and/or (2) keep the data in a centralized location, and resolve the conflicting descriptions by adopting a single standard. Considering the limited resources and enormous amount of data distributed at many sites, an integrated approach of adopting common annotation standards and a set of reference ontologies is desired. We will present a vision of an international resource for a Common Reference Ontology for Plants (cROP), in order to develop common standards for annotating plant gene function, expression and phenotypes, in addition to describing the anatomy and responses such as diseases, reported in various experiments and resources.