@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 {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 {1609, title = {Annotating the Maize B73 Gene Expression Atlas {\textendash} A Plant Ontology Use Case for Genomics Data Curation}, year = {2012}, month = {April 2012}, address = {Washington DC, USA}, abstract = {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}, url = {http://pir.georgetown.edu/biocuration2012.html/index.html}, author = {Cooper, Laurel D.}, editor = {Schaeffer, Mary and Walls, Ramona L and Justin L. Elser and Preece, Justin and Smith, Barry and Mungall, Christopher J and Gandolfo, Maria A and Dennis Wm. Stevenson and Jaiswal, Pankaj} } @article {1608, title = {Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa}, 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. 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.}, url = {http://pag.confex.com/pag/xx/webprogrampreliminary/Paper1716.html}, author = {Cooper, Laurel D.}, editor = {Walls, Ramona L and Justin L. Elser and Preece, Justin and Smith, Barry and Mungall, Christopher J and Gandolfo, Maria Alejandra and Dennis Wm. Stevenson and Jaiswal, Pankaj} } @conference {242, title = {Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources}, booktitle = {3rd International Conference on Biomedical Ontology (ICBO 2012)}, series = {Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012)}, year = {2012}, month = {2012}, publisher = {KR-MED Series}, organization = {KR-MED Series}, address = {Graz, Austria}, abstract = {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: {\textquotedblleft}{\textellipsis}Leaves usually alternate or opposite, sometimes in basal rosettes, rarely in whorls; rarely stipulate, usually petiolate, sometimes sessile{\textellipsis}{\textquotedblright} 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.}, url = {http://ceur-ws.org/Vol-897/}, author = {Walls, Ramona L}, editor = {Cornet, R. and Steven, R. and Cooper, Laurel D. and Macklin, James A. and Cui, Hong and Mungall, Chris and Dennis Wm. Stevenson and Jaiswal, Pankaj} } @article {1607, title = {The Plant Ontology: Linking Genomic and Phenomic Data Across Plant Taxa}, year = {2012}, month = {2012}, address = {San Diego, CA}, abstract = {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.}, url = {http://pag.confex.com/pag/xx/webprogram/Paper1878.html}, author = {Cooper, Laurel D.}, editor = {Walls, Ramona L and Gandolfo, Maria A and Dennis Wm. Stevenson and Smith, Barry and Justin L. Elser and Preece, Justin and Mungall, Christopher J and Jaiswal, Pankaj} } @article {1606, title = {The Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa}, year = {2012}, month = {2012}, address = {San Diego, CA}, url = {https://pag.confex.com/pag/xx/webprogram/Paper3536.html}, author = {Cooper, Laurel D.} }