%0 Journal Article %J PLoS Biol %D 2015 %T Finding Our Way through Phenotypes %A Deans, Andrew R. %A Lewis, Suzanna E. %A Huala, Eva %A Anzaldo, Salvatore S. %A Ashburner, Michael %A Balhoff, James P. %A Blackburn, David C. %A Blake, Judith A. %A Burleigh, J. Gordon %A Chanet, Bruno %A Cooper, Laurel D. %A Courtot, Mélanie %A Csösz, Sándor %A Cui, Hong %A Dahdul, Wasila %A Das, Sandip %A Dececchi, T. Alexander %A Dettai, Agnes %A Diogo, Rui %A Druzinsky, Robert E. %A Dumontier, Michel %A Franz, Nico M. %A Friedrich, Frank %A Gkoutos, George V. %A Haendel, Melissa %A Harmon, Luke J. %A Hayamizu, Terry F. %A He, Yongqun %A Hines, Heather M. %A Ibrahim, Nizar %A Jackson, Laura M. %A Jaiswal, Pankaj %A James-Zorn, Christina %A Köhler, Sebastian %A Lecointre, Guillaume %A Lapp, Hilmar %A Carolyn J. Lawrence %A Le Novère, Nicolas %A Lundberg, John G. %A Macklin, James %A Mast, Austin R. %A Midford, Peter E. %A Mikó, István %A Mungall, Christopher J %A Oellrich, Anika %A Osumi-Sutherland, David %A Parkinson, Helen %A Ramírez, Martín J. %A Richter, Stefan %A Robinson, Peter N. %A Ruttenberg, Alan %A Schulz, Katja S. %A Segerdell, Erik %A Seltmann, Katja C. %A Sharkey, Michael J. %A Smith, Aaron D. %A Smith, Barry %A Specht, Chelsea D. %A Squires, R. Burke %A Thacker, Robert W. %A Thessen, Anne %A Fernandez-Triana, Jose %A Vihinen, Mauno %A Vize, Peter D. %A Vogt, Lars %A Wall, Christine E. %A Walls, Ramona L %A Westerfeld, Monte %A Wharton, Robert A. %A Wirkner, Christian S. %A Woolley, James B. %A Yoder, Matthew J. %A Zorn, Aaron M. %A Mabee, Paula %X

Imagine if we could compute across phenotype data as easily as genomic data; this article calls for efforts to realize this vision and discusses the potential benefits.

%B PLoS Biol %I Public Library of Science %V 13 %P e1002033 %8 01 %G eng %U http://dx.doi.org/10.1371%2Fjournal.pbio.1002033 %R 10.1371/journal.pbio.1002033 %0 Generic %D 2014 %T Common Reference Ontologies for Plant Biology (cROP): A Platform for Integrative Plant Genomics %A Cooper, Laurel %E Justin L. Elser %E Preece, Justin %E Arnaud, Elizabeth %E Sinisa Todorovic %E Eugene Zhang %E Christopher Mungall %E Smith, Barry %E Dennis Wm. Stevenson %E Jaiswal, Pankaj %X Around the world, a small number of plant species serve as the primary source of food for the human population, yet these crops are vulnerable to multiple stressors, such as diseases, nutrient deficiencies and unfavorable environmental conditions. Traditional breeding methods for plant improvement may be combined with next-generation methods such as automated scoring of traits and phenotypes to develop improved varieties. Linking these analyses to the growing corpus of genomics data generated by high-throughput sequencing, transcriptomics, proteomics, phenomics and genome annotation projects requires common, interoperable, reference vocabularies (ontologies) for the description of the data. The ‘Common Reference Ontologies for Plant Biology’ (cROP) initiative is building the needed suite of reference ontologies, together with enhanced data storage and visualization technologies. The cROP will assume the further development of the existing Plant Ontology (PO), Plant Trait Ontology (TO), and Plant Environment Ontology (EO) and will develop the Plant Stress Ontology (PSO) for abiotic and biotic stresses. It will also include relevant aspects of ontologies such as Gene Ontology (GO), Cell Type (CL), Chemical Entities of Biological Interest (ChEBI), Protein Ontology (PRO) and the Phenotypic Qualities Ontology (PATO). It will include a centralized platform where reference ontologies for plants will be used to access cutting-edge data resources for plant traits, phenotypes, diseases, genomes and semantically-queried gene expression and genetic diversity data across a wide range of plant species. cROP will unify and streamline a fragmented semantic framework and will support allele discovery, advance the understanding of crop evolution, and facilitate crop development. %B Plant and Animal Genome XXII Meeting %C San Diego, CA %8 Jan. 11-15, 2014 %G eng %U https://pag.confex.com/pag/xxii/webprogram/Paper9799.html %0 Generic %D 2014 %T Plant Environmental Condition Ontology (EO) %A Jaiswal, Pankaj %E Cooper, Laurel %E Laura Moore %B Fourth Annual Summit of the Phenotype Ontology Research Coordination Network %I Phenotype Research Coordination Network %C Biosphere2, Tucson, AZ %8 Feb. 21-23, 2014 %G eng %0 Generic %D 2013 %T Development of a Unified Phenotype Dataset for Plants %A Huala, Eva %E Steven B. Cannon %E Cooper, Laurel %E George Gkoutos %E Lisa C Harper %E Jaiswal, Pankaj %E Carolyn J. Lawrence %E Johnny Lloyd %E David Meinke %E Menda, Naama %E Laura Moore %E Mueller, Lukas %E Nelson, Rex T %E Walls, Ramona L %X Plant phenotype datasets can be found in a range of formats including free text and species-specific or knowledge domain-specific controlled vocabularies. While this enables some limited comparison of phenotype data across a single species or within a knowledge domain such as crop breeding, queries or analyses that span a broader set of species are not possible in the absence of a common vocabulary for describing phenotypes. To enable cross-species and cross-domain phenotype comparisons and analyses in plants, we have launched an effort to convert existing phenotype datasets for 8 plant species, encompassing both model species and crops, into a common format using taxonomically broad ontologies representing plant anatomical parts and developmental stages (Plant Ontology), biological processes (Gene Ontology), chemicals (ChEBI), and phenotypic qualities (PATO). Our effort focuses on mutant and overexpression phenotypes associated with genes of known sequence in Arabidopsis, tomato, potato, pepper, maize, rice, soybean and Medicago. Shared use of ontologies, annotation standards, formats and best practices across these eight plant species ensures that the resulting dataset will produce valid results for cross-species querying and semantic similarity analyses. Additionally, the dataset will enable us to explore the relationship between sequence similarity and phenotypic similarity across a range of plant species. %B Plant and Animal Genome 2013 %C San Diego, CA %8 Jan. 11-16, 2013 %G eng %U https://pag.confex.com/pag/xxi/webprogram/Paper5616.html %9 Poster presentationPoster presentation %0 Generic %D 2013 %T Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics %A Cooper, Laurel %E Laura Moore %E Arnaud, Elizabeth %E Nelson, Rex T %E Menda, Naama %E Shrestha, Rosemary %E Grant, David %E L. Matteis %E Mungall, Christopher J %E Bastow, Ruth %E McLaren, Graham %E Jaiswal, Pankaj %X One of the central principles of biology is the concept that an organism’s genotype interacts with the environment to produce the observable characteristics, or phenotype. Understanding this interaction is a core goal of modern biology, and enables development of organisms with commercially useful characteristics through modern breeding programs. A number of crop- or clade-specific plant trait ontologies have been developed to describe plant traits important for agriculture in order to address major scientific challenges such as food security. Traditionally, phenotype information has been captured in a free text manner, which cannot be easily indexed and presents an obstacle to data sharing. Recent advances in next generation sequencing and phenotyping technologies have allowed researchers to access a growing mountain of data, resulting in an emerging gap between the genomics information and the quantitative information describing phenotypes and traits. One approach to overcome this obstacle is through the annotation of data using a common controlled vocabulary or “ontology". We present our vision of a species-neutral Reference Plant Trait Ontology (Ref-TO) which would be the basis for linking the disparate knowledge domains and that will support data integration and data mining across species. The Ref-TO is one of the modules for the Common Reference Ontology for Plant Science (cROP) which is being developed. %B Plant and Animal Genome XXI Conference %C San Diego, CA %8 Jan. 11-16, 2013 %G eng %U https://pag.confex.com/pag/xxi/webprogram/Paper7640.html %9 PosterPoster %0 Journal Article %J Database %D 2013 %T An overview of the BioCreative 2012 Workshop Track III: interactive text mining task %A Arighi, Cecilia N. %A Carterette, Ben %A Cohen, K. Bretonnel %A Krallinger, Martin %A Wilbur, W. John %A Fey, Petra %A Dodson, Robert %A Cooper, Laurel %A Van Slyke, Ceri E. %A Dahdul, Wasila %A Mabee, Paula %A Li, Donghui %A Harris, Bethany %A Gillespie, Marc %A Jimenez, Silvia %A Roberts, Phoebe %A Matthews, Lisa %A Becker, Kevin %A Drabkin, Harold %A Bello, Susan %A Licata, Luana %A Chatr-aryamontri, Andrew %A Schaeffer, Mary L %A Park, Julie %A Haendel, Melissa %A Van Auken, Kimberly %A Li, Yuling %A Chan, Juancarlos %A Muller, Hans-Michael %A Cui, Hong %A Balhoff, James P. %A Chi-Yang Wu, Johnny %A Lu, Zhiyong %A Wei, Chih-Hsuan %A Tudor, Catalina O. %A Raja, Kalpana %A Subramani, Suresh %A Natarajan, Jeyakumar %A Cejuela, Juan Miguel %A Dubey, Pratibha %A Wu, Cathy %X In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have developed tools for text mining from a computer science/linguistics perspective, and there are many initiatives to curate some aspect of biology from the literature. Some biocuration efforts already make use of a text mining tool, but there have not been many broad-based systematic efforts to study which aspects of a text mining tool contribute to its usefulness for a curation task. Here, we report on an effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools. Six text mining systems presenting diverse biocuration tasks participated in a formal evaluation, and appropriate biocurators were recruited for testing. The performance results from this evaluation indicate that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly (\~{}1.7- to 2.5-fold) over manual curation. In addition, some of the systems were able to improve annotation accuracy when compared with the performance on the manually curated set. In terms of inter-annotator agreement, the factors that contributed to significant differences for some of the systems included the expertise of the biocurator on the given curation task, the inherent difficulty of the curation and attention to annotation guidelines. After the task, annotators were asked to complete a survey to help identify strengths and weaknesses of the various systems. The analysis of this survey highlights how important task completion is to the biocurators’ overall experience of a system, regardless of the system’s high score on design, learnability and usability. In addition, strategies to refine the annotation guidelines and systems documentation, to adapt the tools to the needs and query types the end user might have and to evaluate performance in terms of efficiency, user interface, result export and traditional evaluation metrics have been analyzed during this task. This analysis will help to plan for a more intense study in BioCreative IV. %B Database %V 2013 %8 2013 %G eng %U http://database.oxfordjournals.org/content/2013/bas056.abstract %0 Generic %D 2013 %T Plant Ontology, a controlled and structured plant vocabulary for all botanical disciplines %A Brian Atkinson %E Cooper, Laurel %E Laura Moore %E Preece, Justin %E Nikhil TV Lingutla %E Sinisa Todorovic %E Walls, Ramona L %E Ruth Stockey %E Gar Rothwell %E Smith, Barry %E Gandolfo, Maria A %E Dennis Wm. Stevenson %E Jaiswal, Pankaj %X Recently, plant genome sequencing has expanded to different species of plants. This has dramatically expanded our knowledge of gene expression in plant structures and development, as well as plant evolution. However, due to the vast phylogenetic diversity within the plant kingdom some inconsistencies with terminology have occurred. These conflicting plant vocabularies challenge advancement in the plant sciences; therefore, it is important to have a consistent plant structure vocabulary that encompasses all green plants. The Plant Ontology (PO) has been constructed as a well-structured vocabulary whether the terms are anatomical or developmental. The PO also annotates gene expression data to a wide diversity of plant parts and stages of development, for example, terms can be linked with relevant genes that are expressed during the development of a certain structure. Terms are arranged in a hierarchical structure in which taxon-specific annotations occur; this provides the opportunity for users to compare gene expression in homologous structures across clades. This serves as a critical aid for plant scientists who incorporate large data sets to engage questions on genomics, development, and comparative genetics across different plant groups. The Plant Ontology also provides other resources for plant biologists to use such as the Annotation of Image Segments with Ontologies program (AISO), allowing users to annotate plant structures with relevant terminology and genes from images from digital photography or scanned copies. For example digital images of fossil flowers can be segmented and annotated with Plant Ontology terms, to create an image database where structures can be easily identified and compared with other structures from different specimens in longitudinal and cross sections. The goal of the Plant Ontology is to cultivate a consistent vocabulary for plant biologists across all disciplines of botany. %B Botany 2013 %C New Orleans, LA %8 July 27-31, 2013 %G eng %U http://www.2013.botanyconference.org/engine/search/index.php?func=detail&aid=1337 %9 Poster presentationPoster presentation %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 2013 %T The Species-Specific Crop Ontology (Generation Challenge Programme): Application and Integration into the Reference Plant Trait Ontology to Enable Data Mining on Phenotypes %A Arnaud, Elizabeth %E Shrestha, Rosemary %E Kulakow, Peter %E Bakare, Moshood %E Antonio Lopez-Montes %E Ofodile, Sam %E T., Praveen Reddy %E Prasad, Peteti %E Shah, Trushar %E Hash, Charles Thomas %E Weltzien-Rattunde, Eva %E Sissoko, Ibrahima %E Guerrero, Alberto Fabio %E Simon, Reinhard %E Borja-Borja, Nikki Frances %E Ramil, Mauleon %E L. Matteis %E Skofic, Milko %E Hazekamp, Tom %E McLaren, Graham %E Cooper, Laurel %E Jaiswal, Pankaj %E Menda, Naama %E Nelson, Rex %E Grant, David %E Bastow, Ruth %E Rami, Jean-Francois %X The Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) currently contains eleven crop-specific ontologies and has been developed for the Integrated Breeding Platform (IBP) (https://www.integratedbreeding.net/) by several CGIAR centers. The CO provides validated trait names used by crop communities of practice (CoP) for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries. The trait information is completed by the description of the measurement methods and scales and images. The trait dictionaries used to produce the Integrated Breeding (IB) fieldbooks are synchronized with the CO terms for automatic annotation of the phenotypic data measured in the field. The CO acts as a trait name server for various sites and databases: the Genotyping Data Management System (GDMS); the cassava database at Cornell University (http://cassavadb.org); Agtrials, the Global Repository for Evaluation Trials of Climate Change, Agriculture and Food Security (CCAFS), a CGIAR Research Program (http://agtrials.org ); and the EU-Sol BreedDB website (https://www.eu-sol.wur.nl/). The vision will be presented of a species-neutral and overarching Reference Plant Trait Ontology to support data annotation, integration and data mining across species, which has resulted from the successful collaboration between the CO project, the Plant Ontology (PO; http://www.plantontology.org/), the Trait Ontology (TO;http://www.gramene.org/plant_ontology/) the USDA-ARS SoyBase Database (http://www.soybase.org/), the Solanaceae Genomic Network (http://solgenomics.net/), and GarNet (http://www.garnetcommunity.org.uk/). %B Plant and Animal Genome XXI Conference %C San Diego, CA %8 Jan. 11-16, 2013 %G eng %U https://pag.confex.com/pag/xxi/webprogram/Paper5002.html %9 Ontology Workshop TalkOntology Workshop Talk %0 Generic %D 2012 %T Annotating Gene Expression in Physcomitrella patens using the Plant Ontology: Facilitating Cross-Taxa Comparisons %A Cooper, Laurel D. %E Walls, Ramona L %E Justin L. Elser %E Preece, Justin %E Smith, Barry %E Mungall, Christopher J %E Rensing, Stefan %E Hiss, Manuel %E Szövényi, Péter %E Lang, Daniel %E Gandolfo, Maria A %E Dennis Wm. Stevenson %E Jaiswal, Pankaj %X The Plant Ontology (PO: http://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. Recent changes in the PO include the addition of more than 80 new terms to accommodate non-seed plants, with an emphasis on those needed to annotate gene expression from the Physcomitrella patens genome. The primary purpose of the PO is to facilitate cross-database querying and to foster consistent use of vocabularies in annotation. The use of ontologies ensures consistent annotations within and across species, enabling both prediction of gene function and cross-species comparisons of gene expression. An essential, powerful feature of the PO is the set of links from terms to associated annotations, which are structure- or development-specific genes, proteins and phenotypes sourced from numerous plant genomics datasets. Currently, the PO includes over 2 million annotations associated with over 1,300 terms. We will give a brief tutorial on how to access the PO and associated data, and demonstrate the utility of linking Physcomitrella gene expression data to PO terms. The combination of ontology terms and the annotation of diverse gene expression and phenotype data sets facilitates diverse analyses, including assessing the similarity between genes of inter- or intra-specific origin and the exploration of structural homologies among organs, tissues and cell types. %B Plant and Animal Genome XX Conference %S Non-seed plants workshop %C San Diego, CA %8 Jan 2012 %G eng %U http://pag.confex.com/pag/xx/webprogram/Paper1640.html %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 Generic %D 2012 %T Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa %A Cooper, Laurel D. %E Walls, Ramona L %E Justin L. Elser %E Preece, Justin %E Smith, Barry %E Mungall, Christopher J %E Gandolfo, Maria Alejandra %E Dennis Wm. Stevenson %E Jaiswal, Pankaj %X The Plant Ontology (PO: http://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. Originally designed to span the monocot-dicot divide in flowering plants, the PO has been redesigned to encompass a wider variety of angiosperm species, as well as gymnosperms, pteridophytes (ferns), lycophytes (lycopods) and bryophytes (liverworts, mosses and hornworts). Recent changes in the PO include the addition of more than 80 new terms to accommodate non-seed plants, with an emphasis on those needed to annotate gene expression from the Physcomitrella patens genome. 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. Currently, the PO includes over 2 million such annotations associated with over 1,300 terms. Outreach activities include workshops, conference presentations and outreach booths. Also, image libraries are being created through PlantSystematics.org and linked to PO terms to provide reference images for plant structure terms. 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 Plant and Animal Genome XX Conference %C San Diego, CA %8 Jan 2012 %G eng %U http://pag.confex.com/pag/xx/webprogrampreliminary/Paper1716.html %0 Conference Paper %B 3rd International Conference on Biomedical Ontology (ICBO 2012) %D 2012 %T Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources %A Walls, Ramona L %E Cornet, R. %E Steven, R. %E Cooper, Laurel D. %E Macklin, James A. %E Cui, Hong %E Mungall, Chris %E Dennis Wm. Stevenson %E Jaiswal, Pankaj %X Traditional taxonomic literature can provide a wealth ofdata, but access to that data is limited by its free-text format. Taxonomic treatments such as the Flora of North America (FNA Editorial Committee 1993) consist of terse descriptions of the characters used to identify taxa, such as: “…Leaves usually alternate or opposite, sometimes in basal rosettes, rarely in whorls; rarely stipulate, usually petiolate, sometimes sessile…” Converting taxonomic descriptions to computer-readable format makes them available for automatic retrieval and large-scale analyses. Ontologies such as the Plant Ontology (PO) play a central role in automatic annotation, by providing semantic meaning for the words in a description. We used automated and manual methods to map terms from the Categorical Glossary for the Flora of North America Project (http://128.2.21.109/fmi/xsl/FNA/home.xsl) to the PO. %B 3rd International Conference on Biomedical Ontology (ICBO 2012) %S Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012) %I KR-MED Series %C Graz, Austria %8 2012 %G eng %U http://ceur-ws.org/Vol-897/ %0 Journal Article %J American Journal of Botany %D 2012 %T Ontologies as Integrative Tools for Plant Science %A Walls, Ramona L %A Athreya, Balaji %A Cooper, Laurel %A Elser, Justin %A Gandolfo, Maria A %A Jaiswal, Pankaj %A Mungall, Christopher J %A Preece, Justin %A Rensing, Stefan %A Smith, Barry %A Stevenson, Dennis W %K Botany %K Computational Biology %K Data Interpretation, Statistical %K Database Management Systems %K Databases, Factual %K Genome, Plant %K Genomics %K Molecular Sequence Annotation %K Phenotype %K Plants %K Semantics %K Terminology as Topic %K Vocabulary, Controlled %X PREMISE OF THE STUDY: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web. METHODS: This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). KEY RESULTS: Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education. CONCLUSIONS: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. %B American Journal of Botany %V 99 %P 1263-75 %8 2012 Aug %G eng %N 8 %1 http://www.ncbi.nlm.nih.gov/pubmed/22847540?dopt=Abstract %& 1263 %R 10.3732/ajb.1200222 %0 Generic %D 2012 %T The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa %A Preece, Justin %E Cooper, Laurel %E Walls, Ramona L %E Justin L. Elser %E Smith, Barry %E Mungall, Christopher J %E Rensing, Stefan %E Gandolfo, Maria A %E Dennis Wm. Stevenson %E Jaiswal, Pankaj %X The Plant Ontology (PO: http://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 the consistent use of vocabularies in annotation of genomics data. The PO encompasses all plant species, ranging from angiosperms to gymnosperms, pteridophytes (ferns), lycophytes (lycopods) and bryophytes (liverworts, mosses and hornworts). Recent changes in the PO include the addition of new ontology terms and annotations to describe non-seed plants, such as Physcomitrella and woody plant species. 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. Currently, the PO includes over 2 million such annotations associated with over 1,300 terms. Outreach activities include workshops, conference presentations and outreach booths. The combination of ontology terms and the annotation of diverse gene expression and phenotype data sets facilitates diverse analyses, including assessing the similarity between genes of inter- or intra-specific origin and the exploration of structural homologies among organs, tissues and cell types. 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 Genome Informatics 2012 %C Robinson College, Cambridge, UK %8 Sept. 6-9, 2012 %G eng %9 posterposter %0 Generic %D 2012 %T The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa %A Cooper, Laurel %E Walls, Ramona L %E Justin L. Elser %E Preece, Justin %E Smith, Barry %E Mungall, Christopher J %E Rensing, Stefan %E Gandolfo, Maria A %E Dennis Wm. Stevenson %E Jaiswal, Pankaj %X The Plant Ontology (PO: http://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 the consistent use of vocabularies in annotation of genomics data. The PO encompasses all plant species, ranging from angiosperms to gymnosperms, pteridophytes (ferns), lycophytes (lycopods) and bryophytes (liverworts, mosses and hornworts). Recent changes in the PO include the addition of new ontology terms and annotations to describe non-seed plants, such as Physcomitrella and woody plant species. 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. Currently, the PO includes over 2 million such annotations associated with over 1,300 terms. Outreach activities include workshops, conference presentations and outreach booths. The combination of ontology terms and the annotation of diverse gene expression and phenotype data sets facilitates diverse analyses, including assessing the similarity between genes of inter- or intra-specific origin and the exploration of structural homologies among organs, tissues and cell types. 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 Plant Biology 2012 %C Austin, Tx %8 July 20-24, 2012 %G eng %9 poster %0 Generic %D 2012 %T The Plant Ontology: Linking Genomic and Phenomic Data Across Plant Taxa %A Cooper, Laurel D. %E Walls, Ramona L %E Gandolfo, Maria A %E Dennis Wm. Stevenson %E Smith, Barry %E Justin L. Elser %E Preece, Justin %E Mungall, Christopher J %E Jaiswal, Pankaj %X The Plant Ontology (PO: http://plantontology.org) consists of over 1,300 rigorously-defined ontology terms and their relations that describe plant anatomy, morphology and developmental stages. Approximately 400 new plant anatomy terms have been recently added to enhance the framework for cross-species comparisons and to accommodate work in economically important plant species such as Musa and Eucalyptus, along with an additional 80 new terms needed to describe gene expression in the moss Physcomitrella patens and other non-vascular plants. In addition, the PO provides associations between the ontology terms and a variety of plant genomics resources including characterized genes, proteins, mRNA sequences, germplasm resources and QTLs. Currently, the PO includes freely accessible web links to over 2 million such annotations from maize, Arabidopsis, rice, strawberry, tomato and eggplant (along with other members of the Solanaceae family) and P. patens, with additional associations to grape, potato, cotton and many other plant species being added soon. Terms from the PO can be combined with ones from other ontologies such as the TO (Trait Ontology) and GO (Gene Ontology) to describe plant phenotypes. The combination of ontology terms and the annotation of diverse gene expression and phenotype data sets facilitates diverse analyses, including assessing the similarity between genes of inter- or intra-specific origin and the exploration of structural homologies among organs, tissues and cell types. In this presentation, we will provide an overview of the Plant Ontology and its resources and present a comparison of phenotypes across species, based on the orthology of gene expression profiles and the ontological relations among plant structures. %B Plant and Animal Genome XX Conference %S Plant Phenotypes Workshop %C San Diego, CA %8 2012 %G eng %U http://pag.confex.com/pag/xx/webprogram/Paper1878.html %0 Journal Article %J Database %D 2012 %T Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR %A Van Auken, Kimberly %A Fey, Petra %A Berardini, Tanya Z %A Dodson, Robert %A Cooper, Laurel %A Li, Donghui %A Chan, Juancarlos %A Li, Yuling %A Basu, Siddhartha %A Muller, Hans-Michael %A Chisholm, Rex %A Huala, Eva %A Sternberg, Paul W. %X WormBase, dictyBase and The Arabidopsis Information Resource (TAIR) are model organism databases containing information about Caenorhabditis elegans and other nematodes, the social amoeba Dictyostelium discoideum and related Dictyostelids and the flowering plant Arabidopsis thaliana, respectively. Each database curates multiple data types from the primary research literature. In this article, we describe the curation workflow at WormBase, with particular emphasis on our use of text-mining tools (BioCreative 2012, Workshop Track II). We then describe the application of a specific component of that workflow, Textpresso for Cellular Component Curation (CCC), to Gene Ontology (GO) curation at dictyBase and TAIR (BioCreative 2012, Workshop Track III). We find that, with organism-specific modifications, Textpresso can be used by dictyBase and TAIR to annotate gene productions to GO’s Cellular Component (CC) ontology. %B Database %V 2012 %8 2012 %G eng %U http://database.oxfordjournals.org/content/2012/bas040.abstract %0 Conference Paper %B International Conference on Knowledge Discovery and Information Retrieval (IC3K2012) %D 2012 %T Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotype %A Arnaud, Elizabeth %A Cooper, Laurel %A Shrestha, Rosemary %A Menda, Naama %A Nelson, Rex T %A L. Matteis %A M. Skofic %A R. Bastow %A Jaiswal, Pankaj %A Mueller, Lukas %A McLaren, Graham %B International Conference on Knowledge Discovery and Information Retrieval (IC3K2012) %C Barcelona, Spain %8 10/2012 %G eng %0 Journal Article %J Nat Genet %D 2011 %T The genome of woodland strawberry (Fragaria vesca) %A Shulaev, Vladimir %A Sargent, Daniel J %A Crowhurst, Ross N %A Mockler, Todd C %A Folkerts, Otto %A Delcher, Arthur L %A Jaiswal, Pankaj %A Mockaitis, Keithanne %A Liston, Aaron %A Mane, Shrinivasrao P %A Burns, Paul %A Davis, Thomas M %A Slovin, Janet P %A Bassil, Nahla %A Hellens, Roger P %A Evans, Clive %A Harkins, Tim %A Kodira, Chinnappa %A Desany, Brian %A Crasta, Oswald R %A Jensen, Roderick V %A Allan, Andrew C %A Michael, Todd P %A Setubal, Joao Carlos %A Celton, Jean-Marc %A Rees, D Jasper G %A Williams, Kelly P %A Holt, Sarah H %A Rojas, Juan Jairo Ruiz %A Chatterjee, Mithu %A Liu, Bo %A Silva, Herman %A Meisel, Lee %A Adato, Avital %A Filichkin, Sergei A %A Troggio, Michela %A Viola, Roberto %A Ashman, Tia-Lynn %A Wang, Hao %A Dharmawardhana, Palitha %A Elser, Justin %A Raja, Rajani %A Priest, Henry D %A Bryant, Douglas W %A Fox, Samuel E %A Givan, Scott A %A Wilhelm, Larry J %A Naithani, Sushma %A Christoffels, Alan %A Salama, David Y %A Carter, Jade %A Girona, Elena Lopez %A Zdepski, Anna %A Wang, Wenqin %A Kerstetter, Randall A %A Schwab, Wilfried %A Korban, Schuyler S %A Davik, Jahn %A Monfort, Amparo %A Denoyes-Rothan, Beatrice %A Arus, Pere %A Mittler, Ron %A Flinn, Barry %A Aharoni, Asaph %A Bennetzen, Jeffrey L %A Salzberg, Steven L %A Dickerman, Allan W %A Velasco, Riccardo %A Borodovsky, Mark %A Veilleux, Richard E %A Folta, Kevin M %B Nat Genet %V 43 %P 109 - 116 %8 2011 %@ 1061-4036 %G eng %U http://dx.doi.org/10.1038/ng.740 %0 Generic %D 2011 %T Using the Plant Ontology to improve the interoperability of genomic and phenomic data sets %A Walls, Ramona L %E Cooper, Laurel %E Gandolfo, Maria A %E Dennis Wm. Stevenson %E Smith, Barry %E Justin L. Elser %E Preece, Justin %E Mungall, Christopher J %E Jaiswal, Pankaj %X The Plant Ontology (PO: http://plantontology.org) is a structured vocabulary (ontology) consisting of terms, attributes, and relations that describe anatomy, morphology, and development stages of green plants. In addition, the PO provides access to genes and phenotypes that have been associated with ontology terms via the annotation of samples from specific tissues and developmental stages. The PO is an essential, powerful tool for the annotation of diverse gene-expression and phenotype data sets that can be used to assess the similarity between genes of inter- or intra-specific origin and to explore structural homologies among organs, tissues and cell types. The PO facilitates computational reasoning, based on ontological relationships and biological context, allowing researchers to probe the complex relationships among data sets for gene expression, phenotypes, gene-gene interactions, and molecular functions (via the Gene Ontology). For example, the logical definitions and relationships in the PO can be used to deduce that ‘petal’ in dicots and ‘lemma’ in monocot grasses are both subtypes of ‘phyllome’ (leaf-like structures) and that both are associated with ‘flower’ (‘petal’ is part_of ‘flower’ and ‘lemma’ is part_of ‘inflorescence’ which has_part ‘flower’). Researchers can use the association data in the PO to compare the expression patterns of orthologous genes in these structures in maize and Arabidopsis, or to determine if similar phenotypes in the two structures are linked to orthologous genes. Currently, the PO includes over 2 million annotations from maize, Arabidopsis,strawberry, rice, solanaceous crops (such as tomato), and the moss Physcomitrella patens. These annotations are associated with over 1,400 ontology terms. Almost 400 new anatomical terms have been added to the PO recently, to enhance the framework for cross-species comparisons and accommodate work in future agricultural models such as Musa and Eucalyptus. Approximately 80 new terms were added specifically for non-vascular plants, with an emphasis on those needed to describe gene expression in P. patens. In this presentation, we will provide an overview of the Plant Ontology and its resources and present a pilot study comparing inter-specific gene expression profiles, based on the orthology of genes and ontological relations among plant structures. %B Plant Genomes & Biotechnology: from Genes to Networks %C Cold Spring Harbor Laboratory, New York %8 Nov. 30 - Dec 3 %G eng %0 Generic %D 2011 %T Using the Plant Ontology to Link Anatomical Structures to Gene Annotations in Physcomitrella patens %A Walls, Ramona L %E Cooper, Laurel %E Gandolfo, Maria A %E Dennis Wm. Stevenson %E Smith, Barry %E Justin L. Elser %E Preece, Justin %E Mungall, Christopher J %E Jaiswal, Pankaj %X To fully explore the research possibilities created by the recent sequencing of the Physcomitrella patens genome, biological information must be linked to the genome sequence through the process of annotation. The use of ontologies ensures consistent annotations within and across species, enabling both gene prediction and cross-species comparisons of gene expression. While the Gene Ontology (GO) is an excellent tool for describing gene function and localization at the subcellular level, comprehensive annotation also requires ontology terms to describe plant anatomy and morphology, as well as growth and development stages. The Plant Ontology (PO) provides these terms through its two branches: the Plant Anatomy Ontology and the Plant Growth and Development Stage Ontology. The PO allows for uniform descriptions of the phenotypes and tissues used in gene expression studies. With the addition of over 80 new terms to describe bryophytes, the PO is well suited for the description of Physcomitrella anatomy and morphology. In this presentation, we will provide an overview of the Plant Ontology and its principles and review the new terms and changes that have been made to accommodate mosses. We will give a brief tutorial on how to access the PO and associated data, and conclude by showing examples of association files that other groups have contributed, in order to illustrate the utility of linking Physcomitrella genome data to PO terms. %B Moss 2011 %S Webinar %C Black Forest, Germany %8 Sept 12, 2011 %G eng %U http://plantco.de/MOSS2011/index.html %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 2007 %T The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant %A Ilic, Katica %A Kellogg, Elizabeth A %A Jaiswal, Pankaj %A Zapata, Felipe %A Stevens, Peter F %A Vincent, Leszek P %A Avraham, Shulamit %A Reiser, Leonore %A Pujar, Anuradha %A Sachs, Martin M %A Whitman, Noah T %A McCouch, Susan R %A Schaeffer, Mary L %A Ware, Doreen H %A Stein, Lincoln D %A Rhee, Seung Y %K Angiosperms %K Gene Expression Regulation %K plant %K Plant Proteins %K Plant Structures %K Terminology as Topic %K User-Computer Interface %X Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological representation of anatomy and morphology of a flowering plant. The PSO is intended for a broad plant research community, including bench scientists, curators in genomic databases, and bioinformaticians. The initial releases of the PSO integrated existing ontologies for Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa); more recent versions of the ontology encompass terms relevant to Fabaceae, Solanaceae, additional cereal crops, and poplar (Populus spp.). Databases such as The Arabidopsis Information Resource, Nottingham Arabidopsis Stock Centre, Gramene, MaizeGDB, and SOL Genomics Network are using the PSO to describe expression patterns of genes and phenotypes of mutants and natural variants and are regularly contributing new annotations to the Plant Ontology database. The PSO is also used in specialized public databases, such as BRENDA, GENEVESTIGATOR, NASCArrays, and others. Over 10,000 gene annotations and phenotype descriptions from participating databases can be queried and retrieved using the Plant Ontology browser. The PSO, as well as contributed gene associations, can be obtained at www.plantontology.org. %B Plant Physiology %V 143 %P 587-99 %8 2007 Feb %G eng %N 2 %1 http://www.ncbi.nlm.nih.gov/pubmed/17142475?dopt=Abstract %R 10.1104/pp.106.092825 %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