%0 Journal Article %J Plant & Cell Physiology %D 2013 %T The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses %A Cooper, Laurel %A Walls, Ramona L %A Elser, Justin %A Gandolfo, Maria A %A Stevenson, Dennis W %A Smith, Barry %A Preece, Justin %A Athreya, Balaji %A Mungall, Christopher J %A Rensing, Stefan %A Hiss, Manuel %A Lang, Daniel %A Reski, Ralf %A Berardini, Tanya Z %A Li, Donghui %A Huala, Eva %A Schaeffer, Mary %A Menda, Naama %A Arnaud, Elizabeth %A Shrestha, Rosemary %A Yamazaki, Yukiko %A Jaiswal, Pankaj %K Alkyl and Aryl Transferases %K bioinformatics %K comparative genomics %K genome annotation %K Molecular Sequence Annotation %K Multigene Family %K ontology %K Phenotype %K plant anatomy %K Plant Proteins %K Software %K terpene synthase %X The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. %B Plant & Cell Physiology %V 54 %P 1-23 %8 2013 Feb %G eng %U http://pcp.oxfordjournals.org/content/54/2/e1 %N 2 %1 http://www.ncbi.nlm.nih.gov/pubmed/23220694?dopt=Abstract %& 1 %R 10.1093/pcp/pcs163 %0 Generic %D 2012 %T Annotating the Maize B73 Gene Expression Atlas – A Plant Ontology Use Case for Genomics Data Curation %A Cooper, Laurel D. %E Schaeffer, Mary %E Walls, Ramona L %E Justin L. Elser %E Preece, Justin %E Smith, Barry %E Mungall, Christopher J %E Gandolfo, Maria A %E Dennis Wm. Stevenson %E Jaiswal, Pankaj %X The Plant Ontology (www.plantontology.org) is a structured vocabulary and database resource for all plant scientists that links plant anatomy, morphology, and development to the rapidly expanding field of plant genomics. The primary purpose of the PO is to facilitate cross-database querying and to foster consistent use of vocabularies in annotation. An essential feature of the PO is the set of freely accessible web links from terms to associated annotations, which are structure- or development-specific genes, proteins, and phenotypes sourced from numerous plant genomics datasets. In collaboration with MaizeGDB (www.maizegdb.org), we have recently added approximately 1.5 million new associations between maize (Zea mays) gene models and Plant Ontology terms. These associations are based on a large NimbleGen microarray data set profiling genome-wide transcription patterns in 60 tissues, representing 11 distinct organs over the life cycle of a maize plant of the inbred line B73 (Sekhon, et al, Plant Journal, 2011). The microarray data was associated with  35,000 maize gene models developed from the recent sequencing of its genome and updated to the current assembly, B73 RefGen_v2, as a collaboration between MaizeGDB and PLEXdb (www.plexdb.org). The curation path used to associate the PO terms to the maize gene atlas began at MaizeGDB, by mapping each microarray tissue sample to Plant %B Biocuration 2012 %C Washington DC, USA %8 April 2012 %G eng %U http://pir.georgetown.edu/biocuration2012.html/index.html %0 Generic %D 2012 %T Annotating the Maize B73 Gene Expression Atlas in the Plant Ontology- A Tool for Plant Genomics. %A Jaiswal, Pankaj %E Cooper, Laurel %E Schaeffer, Mary %E Walls, Ramona L %E Justin L. Elser %E Preece, Justin %E Smith, Barry %E Mungall, Christopher J %E Gandolfo, Maria A %E Dennis Wm. Stevenson %X The Plant Ontology (www.plantontology.org) is a structured vocabulary and database resource for all plant scientists that links plant anatomy, morphology, and development to the rapidly expanding field of plant genomics. The primary purpose of the PO is to facilitate cross-database querying and to foster consistent use of vocabularies in annotation. An essential feature of the PO is the set of freely accessible web links from terms to associated annotations, which are structure- or development-specific genes, proteins, and phenotypes sourced from numerous plant genomics datasets. In collaboration with MaizeGDB (www.maizegdb.org), we have recently added approximately 1.5 million new associations between maize (Zea mays) gene models and Plant Ontology terms. These associations are based on a large NimbleGen microarray data set profiling genome-wide transcription patterns in 60 tissues, representing 11 distinct organs over the life cycle of a maize plant of the inbred line B73 (Sekhon, et al, Plant Journal, 2011). The microarray data was associated with  35,000 maize gene models developed from the recent sequencing of its genome and updated to the current assembly, B73 RefGen_v2, as a collaboration between MaizeGDB and PLEXdb (www.plexdb.org). PO association files in gaf 2.0 format (www.geneontology.org) were further enhanced by the inclusion of classical gene names, mapped by CoGe (www.genomevolution.org/CoGe/). The maize gene atlas associations were made public in the Plant Ontology Release #16 in October 2011. They are available for download, and can be viewed in various browser modes, both at the PO and at MaizeGDB. The addition of the maize gene atlas annotations to the PO represents an example of how ontologies provide access to large genomics data sets. Currently, the PO includes over 2 million such annotations from 17 species associated with over 1,300 terms. Other recent additions include annotations to cotton (Gossypium) and the moss Physcomitrella patens, with plans for the future inclusion of grape (Vitis) and potato (Solanum). The PO is a valuable resource for both research and teaching that can be used as a guide to plant structures and growth and developmental landmarks in life cycles of plants across many taxa. %B 54th Annual Maize Genetics Conference %C Portland, OR %8 March 2012 %G eng %U http://maizemeeting.maizegdb.org/mm2012/see_abstract.php?id=302 %0 Journal Article %J Nucleic Acids Research %D 2008 %T The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations %A Avraham, Shulamit %A Tung, Chih-Wei %A Ilic, Katica %A Jaiswal, Pankaj %A Kellogg, Elizabeth A %A McCouch, Susan %A Pujar, Anuradha %A Reiser, Leonore %A Rhee, Seung Y %A Sachs, Martin M %A Schaeffer, Mary %A Stein, Lincoln %A Stevens, Peter %A Vincent, Leszek %A Zapata, Felipe %A Ware, Doreen %K Controlled %K databases %K Genes %K genetic %K genome %K Internet %K plant %K Plant Development %K Plants %K User-Computer Interface %K Vocabulary %X The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC’s principles, existing software and database structure. Over the past year, POC has added hundreds of ontology terms to associate with thousands of genes and gene products from Arabidopsis, rice and maize, which are available through a newly updated web-based browser (http://www.plantontology.org/amigo/go.cgi) for viewing, searching and querying. The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current. In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement. %B Nucleic Acids Research %V 36 %P D449-54 %8 2008 Jan %G eng %R 10.1093/nar/gkm908 %0 Journal Article %J Plant Physiology %D 2006 %T Whole-plant growth stage ontology for angiosperms and its application in plant biology %A Pujar, Anuradha %A Jaiswal, Pankaj %A Kellogg, Elizabeth A %A Ilic, Katica %A Vincent, Leszek %A Avraham, Shulamit %A Stevens, Peter %A Zapata, Felipe %A Reiser, Leonore %A Rhee, Seung Y %A Sachs, Martin M %A Schaeffer, Mary %A Stein, Lincoln %A Ware, Doreen %A McCouch, Susan %K Arabidopsis %K Botany %K Germination %K Oryza sativa %K Plant Leaves %K Plant Shoots %K Reproduction %K Software %K Terminology as Topic %K Zea mays %X Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth and development. Each species or family specific community developed distinct terminologies for describing whole-plant growth stages. This semantic heterogeneity made it impossible to use growth stage description contained within plant biology databases to make meaningful computational comparisons. The Plant Ontology Consortium (http://www.plantontology.org) was founded to develop standard ontologies describing plant anatomical as well as growth and developmental stages that can be used for annotation of gene expression patterns and phenotypes of all flowering plants. In this article, we describe the development of a generic whole-plant growth stage ontology that describes the spatiotemporal stages of plant growth as a set of landmark events that progress from germination to senescence. This ontology represents a synthesis and integration of terms and concepts from a variety of species-specific vocabularies previously used for describing phenotypes and genomic information. It provides a common platform for annotating gene function and gene expression in relation to the developmental trajectory of a plant described at the organismal level. As proof of concept the Plant Ontology Consortium used the plant ontology growth stage ontology to annotate genes and phenotypes in plants with initial emphasis on those represented in The Arabidopsis Information Resource, Gramene database, and MaizeGDB. %B Plant Physiology %V 142 %P 414-28 %8 2006 Oct %G eng %N 2 %1 http://www.ncbi.nlm.nih.gov/pubmed/16905665?dopt=Abstract %R 10.1104/pp.106.085720 %0 Journal Article %J Comparative and Functional Genomics %D 2005 %T Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages %A Jaiswal, Pankaj %A Avraham, Shulamit %A Ilic, Katica %A Kellogg, Elizabeth A %A McCouch, Susan %A Pujar, Anuradha %A Reiser, Leonore %A Rhee, Seung Y %A Sachs, Martin M %A Schaeffer, Mary %A Stein, Lincoln %A Stevens, Peter %A Vincent, Leszek %A Ware, Doreen %A Zapata, Felipe %X The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) for Arabidopsis, Gramene for rice and MaizeGDB for maize, can now be queried and retrieved. %B Comparative and Functional Genomics %V 6 %P 388-97 %8 2005 %G eng %N 7-8 %1 http://www.ncbi.nlm.nih.gov/pubmed/18629207?dopt=Abstract %R 10.1002/cfg.496