@article {230, title = {Common Reference Ontologies for Plant Biology (cROP): A Platform for Integrative Plant Genomics}, year = {2014}, month = {Jan. 11-15, 2014}, address = {San Diego, CA}, abstract = {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 {\textquoteleft}Common Reference Ontologies for Plant Biology{\textquoteright} (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.}, url = {https://pag.confex.com/pag/xxii/webprogram/Paper9799.html}, author = {Cooper, Laurel}, editor = {Justin L. Elser and Preece, Justin and Arnaud, Elizabeth and Sinisa Todorovic and Eugene Zhang and Christopher Mungall and Smith, Barry 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 {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 {1605, title = {Annotating the Maize B73 Gene Expression Atlas in the Plant Ontology- A Tool for Plant Genomics.}, year = {2012}, month = {March 2012}, address = {Portland, OR}, 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). 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.}, url = {http://maizemeeting.maizegdb.org/mm2012/see_abstract.php?id=302}, author = {Jaiswal, Pankaj}, editor = {Cooper, Laurel and 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} } @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} } @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} } @conference {1617, title = {A plant disease extension of the Infectious Disease Ontology}, booktitle = {International Conference on Biomedical Ontology (ICBO-2012)}, volume = {897}, year = {2012}, month = {July 2012}, publisher = {CEUR Workshop Proceedings}, organization = {CEUR Workshop Proceedings}, address = {Graz, Austria}, abstract = {Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this chal{\textendash}- lenge, and methods such as high{\textendash}-throughput sequencing and automat{\textendash}- ed scoring of phenotypes can provide significant new insights. Ontolo{\textendash}- gies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease On{\textendash}- tology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geo{\textendash}- graphic location and ecology of diseases and hosts, and molecular func{\textendash}- tions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting in{\textendash}-house ontology development comple{\textendash}- mented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism.}, url = {http://ceur-ws.org/Vol-897/}, author = {Walls, Ramona and Smith, Barry and Elser, Justin and Goldfain, Albert} } @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 {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 {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} } @conference {1618, title = {Planteome Annotation Wiki: A Semantic Application for the Community Curation of Plant Genotypes and Phenotypes}, booktitle = {SWAT4LS 2011}, series = {Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences 2011}, year = {2011}, month = {Dec 7-9, 2011}, pages = {96-97}, publisher = {ACM New York, NY}, organization = {ACM New York, NY}, address = {London, UK}, isbn = {978-1-4503-1076-5}, doi = {10.1145/2166896.2166921}, author = {Preece, Justin}, editor = {Elser, Justin and Jaiswal, Pankaj} } @conference {1603, title = {Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotype.}, booktitle = {4th International Workshop on Semantic Web Applications and Tools for Life Sciences}, year = {2011}, month = {Dec 6-9, 2011}, address = {Univ. of London and the Wellcome Trust Collection Conference Center (London, UK)}, abstract = {Two notable trends currently impacting biology curationare 1) the use of wikis to input, store, and disseminate research data and 2) the development of semantic technologies to facilitate higher-order data description and exploration. These separate developments, when brought together, have the potential to deliver on one promise of the "semantic web": structured, self-described data used to further scientific c research and analysis. The Semantic MediaWiki [5] extension, when used in conjunction with Semantic Forms [4], provides an avenue to create a semantically-driven, community-powered research platform on the web.}, url = {http://dl.acm.org/citation.cfm?doid=2166896.2166921}, author = {Preece, Justin}, editor = {Justin L. Elser and Jaiswal, Pankaj} } @article {1601, title = {Using the Plant Ontology to improve the interoperability of genomic and phenomic data sets}, year = {2011}, month = {Nov. 30 - Dec 3}, address = {Cold Spring Harbor Laboratory, New York}, abstract = {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 {\textquoteleft}petal{\textquoteright} in dicots and {\textquoteleft}lemma{\textquoteright} in monocot grasses are both subtypes of {\textquoteleft}phyllome{\textquoteright} (leaf-like structures) and that both are associated with {\textquoteleft}flower{\textquoteright} ({\textquoteleft}petal{\textquoteright} is part_of {\textquoteleft}flower{\textquoteright} and {\textquoteleft}lemma{\textquoteright} is part_of {\textquoteleft}inflorescence{\textquoteright} which has_part {\textquoteleft}flower{\textquoteright}). 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.}, author = {Walls, Ramona L}, editor = {Cooper, Laurel 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 {1600, title = {Using the Plant Ontology to Link Anatomical Structures to Gene Annotations in Physcomitrella patens}, year = {2011}, month = {Sept 12, 2011}, address = {Black Forest, Germany}, abstract = {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.}, url = {http://plantco.de/MOSS2011/index.html}, author = {Walls, Ramona L}, editor = {Cooper, Laurel 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 {1552, title = {Plant Ontology: Databases And Applications}, year = {2010}, month = {2010}, address = {San Diego, CA}, abstract = {As data is generated from multiple plant genome projects and comparative genomics approaches, the vocabulary from group to group and species to species can be disparate. To enable researchers across species to draw conclusions from known or predicted experiments, we are developing controlled vocabularies (ontologies) to describe plant morphological, anatomical, and growth and developmental stages. Since the inception of the Plant Ontology (PO) database in 2003, plant biologists have been able to consistently use the PO terms in the database for annotation of tissue and/or growth stage specific expression of proteins, genes, and phenotypes that were observed in experiments. The PO terms documented number over 1,100, and there are over 500,000 associations, of which over 85\% have been added within the last year. The terms and associations can be used in tandem with information (such as their biochemical charcterization from their source database) to predict plant phenotypes, determine function of gene products, and possibly initiate new gene discovery with comparative genomics analysis. Future development by the Plant Ontology Consortium will be centered on adding additional species-specific terms to accommodate annotations from Rutaceae (citrus), Fabaceae (Medicago and soybean), Solanaceae (tomato), Triticeae (wheat, oat, and barley), and Populus (poplar).}, url = {http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_924.html}, author = {Justin L. Elser}, editor = {Cooper, Laurel and Jaiswal, Pankaj} } @article {1596, title = {Plant Ontology: Databases And Applications}, year = {2010}, month = {Jan 9-13, 2010}, address = {San Diego, CA}, abstract = {As data is generated from multiple plant genome projects and comparative genomics approaches, the vocabulary from group to group and species to species can be disparate. To enable researchers across species to draw conclusions from known or predicted experiments, we are developing controlled vocabularies (ontologies) to describe plant morphological, anatomical, and growth and developmental stages. Since the inception of the Plant Ontology (PO) database in 2003, plant biologists have been able to consistently use the PO terms in the database for annotation of tissue and/or growth stage specific expression of proteins, genes, and phenotypes that were observed in experiments. The PO terms documented number over 1,100, and there are over 500,000 associations, of which over 85\% have been added within the last year. The terms and associations can be used in tandem with information (such as their biochemical characterization from their source database) to predict plant phenotypes, determine function of gene products, and possibly initiate new gene discovery with comparative genomics analysis. Future development by the Plant Ontology Consortium will be centered on adding additional species-specific terms to accommodate annotations from Rutaceae (citrus), Fabaceae (Medicago and soybean), Solanaceae (tomato), Triticeae (wheat, oat, and barley), and Populus (poplar).}, author = {Justin L. Elser}, editor = {Cooper, Laurel and Jaiswal, Pankaj} } @conference {1616, title = {A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species}, booktitle = {NETTAB 2010 conference on Biological Wikis}, series = {Network Tools and Applications in Biology-NETTAB-BBCC 2010 Biological Wikis}, year = {2010}, month = {2010}, pages = {109-112}, publisher = {Aracne}, organization = {Aracne}, address = {Naples, Italy}, url = {http://www.nettab.org/2010/}, author = {Preece, Justin}, editor = {Elser, Justin and Jaiswal, Pankaj} }