@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 {822,
	title = {Annotating Gene Expression in <i>Physcomitrella patens</i> 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 {219,
	title = {An extension of the Plant Ontology project supporting wood anatomy and development research},
	journal = {IAWA Journal},
	volume = {33},
	year = {2012},
	pages = {113-117},
	chapter = {113},
	abstract = {A wealth of information on plant anatomy and morphology is available in the current and historical literature, and molecular biologists are producing massive amounts of transcriptome and genome data that can be used to gain better insights into the development, evolution, ecology, and physiological function of plant anatomical attributes. Integrating anatomical and molecular data sets is of major importance to the field of wood science, but this is often hampered by the lack of a standardized, controlled vocabulary that allows for cross-referencing among disparate data types. One approach to overcome this obstacle is through the annotation of data using a common controlled vocabulary or "ontology" (Ashburner et al. 2000; Smith et al. 2007). An ontology is a way of representing knowledge in a given domain that includes a set of terms to describe the classes in that domain, as well as the relationships among terms. Each term can be associated with an array of data such as names, definitions, identification numbers, and genes involved. Ontologies are fundamental for unifying diverse terminologies and are increasingly used by scientists, philosophers, the military and online web search engines. In an ontology, terms are carefully defined, allowing a wide array of researchers to (1) use terms consistently in scientific publications or standardized handbooks on quality/trait evaluations, and (2) search for and integrate data linked to these terms in anatomical, genetic, genomic, and other types of biological databases. The Plant Ontology (PO, www.plantontology.org) is a structured vocabulary and database resource that links plant anatomy and development to gene expression and phenotypic datasets from all areas of plant biology.},
	url = {http://www.researchgate.net/publication/232271560_An_extension_of_the_Plant_Ontology_project_supporting_wood_anatomy_and_development_research},
	author = {Lens, F and Cooper, Laurel and Gandolfo, Maria A and Groover, P and Jaiswal, Pankaj and Lachenbruch, R and Spicer, R and Staton, D and Dennis Wm. Stevenson and Walls, Ramona L and Wegrzyn, J}
}
@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 {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 {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 <i>Physcomitrella patens</i>},
	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}
}
