@article {10.1371/journal.pbio.1002033, title = {Finding Our Way through Phenotypes}, journal = {PLoS Biol}, volume = {13}, number = {1}, year = {2015}, month = {01}, pages = {e1002033}, publisher = {Public Library of Science}, abstract = {

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.

}, doi = {10.1371/journal.pbio.1002033}, url = {http://dx.doi.org/10.1371\%2Fjournal.pbio.1002033}, author = {Deans, Andrew R. and Lewis, Suzanna E. and Huala, Eva and Anzaldo, Salvatore S. and Ashburner, Michael and Balhoff, James P. and Blackburn, David C. and Blake, Judith A. and Burleigh, J. Gordon and Chanet, Bruno and Cooper, Laurel D. and Courtot, M{\'e}lanie and Cs{\"o}sz, S{\'a}ndor and Cui, Hong and Dahdul, Wasila and Das, Sandip and Dececchi, T. Alexander and Dettai, Agnes and Diogo, Rui and Druzinsky, Robert E. and Dumontier, Michel and Franz, Nico M. and Friedrich, Frank and Gkoutos, George V. and Haendel, Melissa and Harmon, Luke J. and Hayamizu, Terry F. and He, Yongqun and Hines, Heather M. and Ibrahim, Nizar and Jackson, Laura M. and Jaiswal, Pankaj and James-Zorn, Christina and K{\"o}hler, Sebastian and Lecointre, Guillaume and Lapp, Hilmar and Carolyn J. Lawrence and Le Nov{\`e}re, Nicolas and Lundberg, John G. and Macklin, James and Mast, Austin R. and Midford, Peter E. and Mik{\'o}, Istv{\'a}n and Mungall, Christopher J and Oellrich, Anika and Osumi-Sutherland, David and Parkinson, Helen and Ram{\'\i}rez, Mart{\'\i}n J. and Richter, Stefan and Robinson, Peter N. and Ruttenberg, Alan and Schulz, Katja S. and Segerdell, Erik and Seltmann, Katja C. and Sharkey, Michael J. and Smith, Aaron D. and Smith, Barry and Specht, Chelsea D. and Squires, R. Burke and Thacker, Robert W. and Thessen, Anne and Fernandez-Triana, Jose and Vihinen, Mauno and Vize, Peter D. and Vogt, Lars and Wall, Christine E. and Walls, Ramona L and Westerfeld, Monte and Wharton, Robert A. and Wirkner, Christian S. and Woolley, James B. and Yoder, Matthew J. and Zorn, Aaron M. and Mabee, Paula} } @article {1612, title = {An overview of the BioCreative 2012 Workshop Track III: interactive text mining task}, journal = {Database}, volume = {2013}, year = {2013}, month = {2013}, abstract = {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{\textquoteright} overall experience of a system, regardless of the system{\textquoteright}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.}, url = {http://database.oxfordjournals.org/content/2013/bas056.abstract}, author = {Arighi, Cecilia N. and Carterette, Ben and Cohen, K. Bretonnel and Krallinger, Martin and Wilbur, W. John and Fey, Petra and Dodson, Robert and Cooper, Laurel and Van Slyke, Ceri E. and Dahdul, Wasila and Mabee, Paula and Li, Donghui and Harris, Bethany and Gillespie, Marc and Jimenez, Silvia and Roberts, Phoebe and Matthews, Lisa and Becker, Kevin and Drabkin, Harold and Bello, Susan and Licata, Luana and Chatr-aryamontri, Andrew and Schaeffer, Mary L and Park, Julie and Haendel, Melissa and Van Auken, Kimberly and Li, Yuling and Chan, Juancarlos and Muller, Hans-Michael and Cui, Hong and Balhoff, James P. and Chi-Yang Wu, Johnny and Lu, Zhiyong and Wei, Chih-Hsuan and Tudor, Catalina O. and Raja, Kalpana and Subramani, Suresh and Natarajan, Jeyakumar and Cejuela, Juan Miguel and Dubey, Pratibha and Wu, Cathy} } @article {234, title = {Plant Ontology, a controlled and structured plant vocabulary for all botanical disciplines}, year = {2013}, month = {July 27-31, 2013}, type = {Poster presentationPoster presentation}, address = {New Orleans, LA}, abstract = {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.}, url = {http://www.2013.botanyconference.org/engine/search/index.php?func=detail\&aid=1337}, author = {Brian Atkinson}, editor = {Cooper, Laurel and Laura Moore and Preece, Justin and Nikhil TV Lingutla and Sinisa Todorovic and Walls, Ramona L and Ruth Stockey and Gar Rothwell and Smith, Barry and Gandolfo, Maria A and Dennis Wm. Stevenson and Jaiswal, Pankaj} } @article {211, title = {The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses}, journal = {Plant \& Cell Physiology}, volume = {54}, year = {2013}, month = {2013 Feb}, pages = {1-23}, chapter = {1}, abstract = {The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ({\textquoteright}ontology{\textquoteright}) 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.}, keywords = {Alkyl and Aryl Transferases, bioinformatics, comparative genomics, genome annotation, Molecular Sequence Annotation, Multigene Family, ontology, Phenotype, plant anatomy, Plant Proteins, Software, terpene synthase}, issn = {1471-9053}, doi = {10.1093/pcp/pcs163}, url = {http://pcp.oxfordjournals.org/content/54/2/e1}, author = {Cooper, Laurel and Walls, Ramona L and Elser, Justin and Gandolfo, Maria A and Stevenson, Dennis W and Smith, Barry and Preece, Justin and Athreya, Balaji and Mungall, Christopher J and Rensing, Stefan and Hiss, Manuel and Lang, Daniel and Reski, Ralf and Berardini, Tanya Z and Li, Donghui and Huala, Eva and Schaeffer, Mary and Menda, Naama and Arnaud, Elizabeth and Shrestha, Rosemary and Yamazaki, Yukiko and Jaiswal, Pankaj} } @article {231, title = {A Resource for a Common Reference Ontology for Plants}, year = {2013}, month = {Jan. 11-16, 2013}, address = {San Diego, CA}, abstract = {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.}, url = {https://pag.confex.com/pag/xxi/webprogram/Paper5587.html}, author = {Jaiswal, Pankaj}, editor = {Smith, Barry and R. Bastow and Paul J. Kersey and Arnaud, Elizabeth and Cooper, Laurel and Christopher Rawlings} } @article {236, title = {The Species-Specific Crop Ontology (Generation Challenge Programme): Application and Integration into the Reference Plant Trait Ontology to Enable Data Mining on Phenotypes}, year = {2013}, month = {Jan. 11-16, 2013}, type = {Ontology Workshop TalkOntology Workshop Talk}, address = {San Diego, CA}, abstract = {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/).}, url = {https://pag.confex.com/pag/xxi/webprogram/Paper5002.html}, author = {Arnaud, Elizabeth}, editor = {Shrestha, Rosemary and Kulakow, Peter and Bakare, Moshood and Antonio Lopez-Montes and Ofodile, Sam and T., Praveen Reddy and Prasad, Peteti and Shah, Trushar and Hash, Charles Thomas and Weltzien-Rattunde, Eva and Sissoko, Ibrahima and Guerrero, Alberto Fabio and Simon, Reinhard and Borja-Borja, Nikki Frances and Ramil, Mauleon and L. Matteis and Skofic, Milko and Hazekamp, Tom and McLaren, Graham and Cooper, Laurel and Jaiswal, Pankaj and Menda, Naama and Nelson, Rex and Grant, David and Bastow, Ruth and Rami, Jean-Francois} } @article {822, title = {Annotating Gene Expression in Physcomitrella patens using the Plant Ontology: Facilitating Cross-Taxa Comparisons}, year = {2012}, month = {Jan 2012}, address = {San Diego, CA}, abstract = {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.}, url = {http://pag.confex.com/pag/xx/webprogram/Paper1640.html}, author = {Cooper, Laurel D.}, editor = {Walls, Ramona L and Justin L. Elser and Preece, Justin and Smith, Barry and Mungall, Christopher J and Rensing, Stefan and Hiss, Manuel and Sz{\"o}v{\'e}nyi, P{\'e}ter and Lang, Daniel and Gandolfo, Maria A and Dennis Wm. Stevenson and Jaiswal, Pankaj} } @article {212, title = {Ontologies as Integrative Tools for Plant Science}, journal = {American Journal of Botany}, volume = {99}, year = {2012}, month = {2012 Aug}, pages = {1263-75}, chapter = {1263}, abstract = {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.}, keywords = {Botany, Computational Biology, Data Interpretation, Statistical, Database Management Systems, Databases, Factual, Genome, Plant, Genomics, Molecular Sequence Annotation, Phenotype, Plants, Semantics, Terminology as Topic, Vocabulary, Controlled}, issn = {1537-2197}, doi = {10.3732/ajb.1200222}, author = {Walls, Ramona L and Athreya, Balaji and Cooper, Laurel and Elser, Justin and Gandolfo, Maria A and Jaiswal, Pankaj and Mungall, Christopher J and Preece, Justin and Rensing, Stefan and Smith, Barry and Stevenson, Dennis W} } @article {240, title = {The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa}, year = {2012}, month = {Sept. 6-9, 2012}, type = {posterposter}, address = {Robinson College, Cambridge, UK}, abstract = {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.}, author = {Preece, Justin}, editor = {Cooper, Laurel and Walls, Ramona L and Justin L. Elser and Smith, Barry and Mungall, Christopher J and Rensing, Stefan and Gandolfo, Maria A and Dennis Wm. Stevenson and Jaiswal, Pankaj} } @article {241, title = {The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa}, year = {2012}, month = {July 20-24, 2012}, type = {poster}, address = {Austin, Tx}, abstract = {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.}, author = {Cooper, Laurel}, editor = {Walls, Ramona L and Justin L. Elser and Preece, Justin and Smith, Barry and Mungall, Christopher J and Rensing, Stefan and Gandolfo, Maria A and Dennis Wm. Stevenson and Jaiswal, Pankaj} } @article {1615, title = {The genome of woodland strawberry (Fragaria vesca)}, journal = {Nat Genet}, volume = {43}, year = {2011}, month = {2011}, pages = {109 - 116}, isbn = {1061-4036}, url = {http://dx.doi.org/10.1038/ng.740}, author = {Shulaev, Vladimir and Sargent, Daniel J and Crowhurst, Ross N and Mockler, Todd C and Folkerts, Otto and Delcher, Arthur L and Jaiswal, Pankaj and Mockaitis, Keithanne and Liston, Aaron and Mane, Shrinivasrao P and Burns, Paul and Davis, Thomas M and Slovin, Janet P and Bassil, Nahla and Hellens, Roger P and Evans, Clive and Harkins, Tim and Kodira, Chinnappa and Desany, Brian and Crasta, Oswald R and Jensen, Roderick V and Allan, Andrew C and Michael, Todd P and Setubal, Joao Carlos and Celton, Jean-Marc and Rees, D Jasper G and Williams, Kelly P and Holt, Sarah H and Rojas, Juan Jairo Ruiz and Chatterjee, Mithu and Liu, Bo and Silva, Herman and Meisel, Lee and Adato, Avital and Filichkin, Sergei A and Troggio, Michela and Viola, Roberto and Ashman, Tia-Lynn and Wang, Hao and Dharmawardhana, Palitha and Elser, Justin and Raja, Rajani and Priest, Henry D and Bryant, Douglas W and Fox, Samuel E and Givan, Scott A and Wilhelm, Larry J and Naithani, Sushma and Christoffels, Alan and Salama, David Y and Carter, Jade and Girona, Elena Lopez and Zdepski, Anna and Wang, Wenqin and Kerstetter, Randall A and Schwab, Wilfried and Korban, Schuyler S and Davik, Jahn and Monfort, Amparo and Denoyes-Rothan, Beatrice and Arus, Pere and Mittler, Ron and Flinn, Barry and Aharoni, Asaph and Bennetzen, Jeffrey L and Salzberg, Steven L and Dickerman, Allan W and Velasco, Riccardo and Borodovsky, Mark and Veilleux, Richard E and Folta, Kevin M} } @article {214, title = {The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations}, journal = {Nucleic Acids Research}, volume = {36}, year = {2008}, month = {2008 Jan}, pages = {D449-54}, abstract = {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{\textquoteright}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.}, keywords = {Controlled, databases, Genes, genetic, genome, Internet, plant, Plant Development, Plants, User-Computer Interface, Vocabulary}, issn = {1362-4962}, doi = {10.1093/nar/gkm908}, author = {Avraham, Shulamit and Tung, Chih-Wei and Ilic, Katica and Jaiswal, Pankaj and Kellogg, Elizabeth A and McCouch, Susan and Pujar, Anuradha and Reiser, Leonore and Rhee, Seung Y and Sachs, Martin M and Schaeffer, Mary and Stein, Lincoln and Stevens, Peter and Vincent, Leszek and Zapata, Felipe and Ware, Doreen} } @inbook {217, title = {Plant Structure Ontology (PSO) - A Morphological and Anatomical Ontology of Flowering Plants}, booktitle = {Anatomy Ontologies for Bioinformatics}, series = {Computational Biology}, volume = {6}, year = {2008}, pages = {27-42}, publisher = {Springer}, organization = {Springer}, address = {London}, abstract = {The Plant Structure Ontology (PSO) is a controlled vocabulary of anatomy and morphology of a generic flowering plant, developed by the Plant Ontology Consortium (POC) The main goal of the POC was to reduce the problem of heterogeneity of terminology used to describe comparable object types in plant genomic databases. PSO provides standardized set of terms describing anatomical and morphological structures pertinent to flowering plants during their normal course of development. Created as a tool for annotation of gene expression patterns and description of phenotypes across angiosperms, PSO is intended for plant genomics databases and broad plant genomic research community. Currently, this ontology encompasses diverse angiosperm taxa; further development will include new model organisms and important crop species. This chapter describes the rationales for creating PSO and discusses the guiding principles for its development and maintenance. The content of the PSO and the ontology browsing functionalities are outlined. The PSO can be browsed and downloaded at www.plantontology.org.}, issn = {978-1-84628-884-5}, doi = {10.1007/978-1-84628-885-2_2}, author = {Ilic, Katica and Rhee, Seung Y and Kellogg, Elizabeth A and Stevens, Peter F}, editor = {Burger, Albert and Davidson, Duncan and Baldock, Richard} } @article {215, title = {The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant}, journal = {Plant Physiology}, volume = {143}, year = {2007}, month = {2007 Feb}, pages = {587-99}, abstract = {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.}, keywords = {Angiosperms, Gene Expression Regulation, plant, Plant Proteins, Plant Structures, Terminology as Topic, User-Computer Interface}, issn = {0032-0889}, doi = {10.1104/pp.106.092825}, author = {Ilic, Katica and Kellogg, Elizabeth A and Jaiswal, Pankaj and Zapata, Felipe and Stevens, Peter F and Vincent, Leszek P and Avraham, Shulamit and Reiser, Leonore and Pujar, Anuradha and Sachs, Martin M and Whitman, Noah T and McCouch, Susan R and Schaeffer, Mary L and Ware, Doreen H and Stein, Lincoln D and Rhee, Seung Y} } @article {216, title = {Whole-plant growth stage ontology for angiosperms and its application in plant biology}, journal = {Plant Physiology}, volume = {142}, year = {2006}, month = {2006 Oct}, pages = {414-28}, abstract = {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.}, keywords = {Arabidopsis, Botany, Germination, Oryza sativa, Plant Leaves, Plant Shoots, Reproduction, Software, Terminology as Topic, Zea mays}, issn = {0032-0889}, doi = {10.1104/pp.106.085720}, author = {Pujar, Anuradha and Jaiswal, Pankaj and Kellogg, Elizabeth A and Ilic, Katica and Vincent, Leszek and Avraham, Shulamit and Stevens, Peter and Zapata, Felipe and Reiser, Leonore and Rhee, Seung Y and Sachs, Martin M and Schaeffer, Mary and Stein, Lincoln and Ware, Doreen and McCouch, Susan} } @article {213, title = {Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages}, journal = {Comparative and Functional Genomics}, volume = {6}, year = {2005}, month = {2005}, pages = {388-97}, abstract = {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.}, issn = {1531-6912}, doi = {10.1002/cfg.496}, author = {Jaiswal, Pankaj and Avraham, Shulamit and Ilic, Katica and Kellogg, Elizabeth A and McCouch, Susan and Pujar, Anuradha and Reiser, Leonore and Rhee, Seung Y and Sachs, Martin M and Schaeffer, Mary and Stein, Lincoln and Stevens, Peter and Vincent, Leszek and Ware, Doreen and Zapata, Felipe} }