The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.
Identifieur interne : 003A53 ( Main/Exploration ); précédent : 003A52; suivant : 003A54The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.
Auteurs : Katica Ilic [États-Unis] ; Elizabeth A. Kellogg ; Pankaj Jaiswal ; Felipe Zapata ; Peter F. Stevens ; Leszek P. Vincent ; Shulamit Avraham ; Leonore Reiser ; Anuradha Pujar ; Martin M. Sachs ; Noah T. Whitman ; Susan R. Mccouch ; Mary L. Schaeffer ; Doreen H. Ware ; Lincoln D. Stein ; Seung Y. RheeSource :
- Plant physiology [ 0032-0889 ] ; 2007.
Descripteurs français
- KwdFr :
- Interface utilisateur (MeSH), Magnoliopsida (anatomie et histologie), Protéines végétales (génétique), Protéines végétales (métabolisme), Régulation de l'expression des gènes végétaux (MeSH), Structures de plante (anatomie et histologie), Structures de plante (classification), Terminologie comme sujet (MeSH).
- MESH :
- anatomie et histologie : Magnoliopsida, Structures de plante.
- génétique : Protéines végétales, Structures de plante.
- métabolisme : Protéines végétales.
- Interface utilisateur, Régulation de l'expression des gènes végétaux, Terminologie comme sujet.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Plant Proteins.
- anatomy & histology : Magnoliopsida, Plant Structures.
- classification : Plant Structures.
- chemical , metabolism : Plant Proteins.
- Gene Expression Regulation, Plant, Terminology as Topic, User-Computer Interface.
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.
DOI: 10.1104/pp.106.092825
PubMed: 17142475
PubMed Central: PMC1803752
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17142475</PMID><DateCompleted><Year>2007</Year><Month>04</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0032-0889</ISSN><JournalIssue CitedMedium="Print"><Volume>143</Volume><Issue>2</Issue><PubDate><Year>2007</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Plant physiology</Title><ISOAbbreviation>Plant Physiol</ISOAbbreviation></Journal><ArticleTitle>The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.</ArticleTitle><Pagination><MedlinePgn>587-99</MedlinePgn></Pagination><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ilic</LastName><ForeName>Katica</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Plant Biology, Carnegie Institution, Stanford, California 94305, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kellogg</LastName><ForeName>Elizabeth A</ForeName><Initials>EA</Initials></Author><Author ValidYN="Y"><LastName>Jaiswal</LastName><ForeName>Pankaj</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Zapata</LastName><ForeName>Felipe</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Stevens</LastName><ForeName>Peter F</ForeName><Initials>PF</Initials></Author><Author ValidYN="Y"><LastName>Vincent</LastName><ForeName>Leszek P</ForeName><Initials>LP</Initials></Author><Author ValidYN="Y"><LastName>Avraham</LastName><ForeName>Shulamit</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Reiser</LastName><ForeName>Leonore</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Pujar</LastName><ForeName>Anuradha</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Sachs</LastName><ForeName>Martin M</ForeName><Initials>MM</Initials></Author><Author ValidYN="Y"><LastName>Whitman</LastName><ForeName>Noah T</ForeName><Initials>NT</Initials></Author><Author ValidYN="Y"><LastName>McCouch</LastName><ForeName>Susan R</ForeName><Initials>SR</Initials></Author><Author ValidYN="Y"><LastName>Schaeffer</LastName><ForeName>Mary L</ForeName><Initials>ML</Initials></Author><Author ValidYN="Y"><LastName>Ware</LastName><ForeName>Doreen H</ForeName><Initials>DH</Initials></Author><Author ValidYN="Y"><LastName>Stein</LastName><ForeName>Lincoln D</ForeName><Initials>LD</Initials></Author><Author ValidYN="Y"><LastName>Rhee</LastName><ForeName>Seung Y</ForeName><Initials>SY</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>12</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Plant Physiol</MedlineTA><NlmUniqueID>0401224</NlmUniqueID><ISSNLinking>0032-0889</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019684" MajorTopicYN="N">Magnoliopsida</DescriptorName><QualifierName UI="Q000033" MajorTopicYN="Y">anatomy & histology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018514" MajorTopicYN="N">Plant Structures</DescriptorName><QualifierName UI="Q000033" MajorTopicYN="Y">anatomy & histology</QualifierName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009626" MajorTopicYN="Y">Terminology as Topic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014584" MajorTopicYN="N">User-Computer Interface</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate 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IdType="pubmed">18629207</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Avraham, Shulamit" sort="Avraham, Shulamit" uniqKey="Avraham S" first="Shulamit" last="Avraham">Shulamit Avraham</name><name sortKey="Jaiswal, Pankaj" sort="Jaiswal, Pankaj" uniqKey="Jaiswal P" first="Pankaj" last="Jaiswal">Pankaj Jaiswal</name><name sortKey="Kellogg, Elizabeth A" sort="Kellogg, Elizabeth A" uniqKey="Kellogg E" first="Elizabeth A" last="Kellogg">Elizabeth A. Kellogg</name><name sortKey="Mccouch, Susan R" sort="Mccouch, Susan R" uniqKey="Mccouch S" first="Susan R" last="Mccouch">Susan R. Mccouch</name><name sortKey="Pujar, Anuradha" sort="Pujar, Anuradha" uniqKey="Pujar A" first="Anuradha" last="Pujar">Anuradha Pujar</name><name sortKey="Reiser, Leonore" sort="Reiser, Leonore" uniqKey="Reiser L" first="Leonore" last="Reiser">Leonore Reiser</name><name sortKey="Rhee, Seung Y" sort="Rhee, Seung Y" uniqKey="Rhee S" first="Seung Y" last="Rhee">Seung Y. Rhee</name><name sortKey="Sachs, Martin M" sort="Sachs, Martin M" uniqKey="Sachs M" first="Martin M" last="Sachs">Martin M. Sachs</name><name sortKey="Schaeffer, Mary L" sort="Schaeffer, Mary L" uniqKey="Schaeffer M" first="Mary L" last="Schaeffer">Mary L. Schaeffer</name><name sortKey="Stein, Lincoln D" sort="Stein, Lincoln D" uniqKey="Stein L" first="Lincoln D" last="Stein">Lincoln D. Stein</name><name sortKey="Stevens, Peter F" sort="Stevens, Peter F" uniqKey="Stevens P" first="Peter F" last="Stevens">Peter F. Stevens</name><name sortKey="Vincent, Leszek P" sort="Vincent, Leszek P" uniqKey="Vincent L" first="Leszek P" last="Vincent">Leszek P. Vincent</name><name sortKey="Ware, Doreen H" sort="Ware, Doreen H" uniqKey="Ware D" first="Doreen H" last="Ware">Doreen H. Ware</name><name sortKey="Whitman, Noah T" sort="Whitman, Noah T" uniqKey="Whitman N" first="Noah T" last="Whitman">Noah T. Whitman</name><name sortKey="Zapata, Felipe" sort="Zapata, Felipe" uniqKey="Zapata F" first="Felipe" last="Zapata">Felipe Zapata</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Ilic, Katica" sort="Ilic, Katica" uniqKey="Ilic K" first="Katica" last="Ilic">Katica Ilic</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|wiki= Bois
|area= PoplarV1
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|clé= pubmed:17142475
|texte= The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.
}}
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