ForestTreeDB: a database dedicated to the mining of tree transcriptomes.
Identifieur interne : 003B91 ( Main/Exploration ); précédent : 003B90; suivant : 003B92ForestTreeDB: a database dedicated to the mining of tree transcriptomes.
Auteurs : Nathalie Pavy [Canada] ; James J. Johnson ; John A. Crow ; Charles Paule ; Timothy Kunau ; John Mackay ; Ernest F. RetzelSource :
- Nucleic acids research [ 1362-4962 ] ; 2007.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Arbres (génétique), Bases de données d'acides nucléiques (MeSH), Génomique (MeSH), Interface utilisateur (MeSH), Internet (MeSH), Polymorphisme de nucléotide simple (MeSH), Populus (génétique), Tracheobionta (génétique), Transcription génétique (MeSH), Étiquettes de séquences exprimées (composition chimique).
- MESH :
English descriptors
- KwdEn :
- Databases, Nucleic Acid (MeSH), Expressed Sequence Tags (chemistry), Gene Expression Profiling (MeSH), Genomics (MeSH), Internet (MeSH), Polymorphism, Single Nucleotide (MeSH), Populus (genetics), Tracheophyta (genetics), Transcription, Genetic (MeSH), Trees (genetics), User-Computer Interface (MeSH).
- MESH :
Abstract
ForestTreeDB is intended as a resource that centralizes large-scale expressed sequence tag (EST) sequencing results from several tree species (http://foresttree.org/ftdb). It currently encompasses 344,878 quality sequences from 68 libraries, from diverse organs of conifer and hybrid poplar trees. It utilizes the Nimbus data model to provide a hosting system for multiple projects, and uses object-relational mapping APIs in Java and Perl for data accesses within an Oracle database designed to be scalable, maintainable and extendable. Transcriptome builds or unigene sets occupy the focal point of the system. Several of the five current species-specific unigenes were used to design microarrays and SNP resources. The ForestTreeDB web application provides the means for multiple combination database queries. It presents the user with a list of discrete queries to retrieve and download large EST datasets or sequences from precompiled unigene assemblies. Functional annotation assignment is not trivial in conifers which are distantly related to angiosperm model plants. Optimal annotations are achieved through database queries that integrate results from several procedures based open-source tools. ForestTreeDB aims to facilitate sequence mining of coherent annotations in multiple species to support comparative genomic approaches. We plan to continuously enrich ForestTreeDB with other resources through collaborations with other genomic projects.
DOI: 10.1093/nar/gkl882
PubMed: 17130142
PubMed Central: PMC1716727
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">ForestTreeDB: a database dedicated to the mining of tree transcriptomes.</title><author><name sortKey="Pavy, Nathalie" sort="Pavy, Nathalie" uniqKey="Pavy N" first="Nathalie" last="Pavy">Nathalie Pavy</name><affiliation wicri:level="4"><nlm:affiliation>Laval University, Centre de Recherche en Biologie Forestière, Québec, Canada G1K 7P4. nathalie.pavy@rsvs.ulaval.ca</nlm:affiliation><country>Canada</country><wicri:regionArea>Laval University, Centre de Recherche en Biologie Forestière, Québec</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author><author><name sortKey="Johnson, James J" sort="Johnson, James J" uniqKey="Johnson J" first="James J" last="Johnson">James J. Johnson</name></author><author><name sortKey="Crow, John A" sort="Crow, John A" uniqKey="Crow J" first="John A" last="Crow">John A. Crow</name></author><author><name sortKey="Paule, Charles" sort="Paule, Charles" uniqKey="Paule C" first="Charles" last="Paule">Charles Paule</name></author><author><name sortKey="Kunau, Timothy" sort="Kunau, Timothy" uniqKey="Kunau T" first="Timothy" last="Kunau">Timothy Kunau</name></author><author><name sortKey="Mackay, John" sort="Mackay, John" uniqKey="Mackay J" first="John" last="Mackay">John Mackay</name></author><author><name sortKey="Retzel, Ernest F" sort="Retzel, Ernest F" uniqKey="Retzel E" first="Ernest F" last="Retzel">Ernest F. Retzel</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2007">2007</date><idno type="RBID">pubmed:17130142</idno><idno type="pmid">17130142</idno><idno type="doi">10.1093/nar/gkl882</idno><idno type="pmc">PMC1716727</idno><idno type="wicri:Area/Main/Corpus">003C74</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003C74</idno><idno type="wicri:Area/Main/Curation">003C74</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003C74</idno><idno type="wicri:Area/Main/Exploration">003C74</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">ForestTreeDB: a database dedicated to the mining of tree transcriptomes.</title><author><name sortKey="Pavy, Nathalie" sort="Pavy, Nathalie" uniqKey="Pavy N" first="Nathalie" last="Pavy">Nathalie Pavy</name><affiliation wicri:level="4"><nlm:affiliation>Laval University, Centre de Recherche en Biologie Forestière, Québec, Canada G1K 7P4. nathalie.pavy@rsvs.ulaval.ca</nlm:affiliation><country>Canada</country><wicri:regionArea>Laval University, Centre de Recherche en Biologie Forestière, Québec</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author><author><name sortKey="Johnson, James J" sort="Johnson, James J" uniqKey="Johnson J" first="James J" last="Johnson">James J. Johnson</name></author><author><name sortKey="Crow, John A" sort="Crow, John A" uniqKey="Crow J" first="John A" last="Crow">John A. Crow</name></author><author><name sortKey="Paule, Charles" sort="Paule, Charles" uniqKey="Paule C" first="Charles" last="Paule">Charles Paule</name></author><author><name sortKey="Kunau, Timothy" sort="Kunau, Timothy" uniqKey="Kunau T" first="Timothy" last="Kunau">Timothy Kunau</name></author><author><name sortKey="Mackay, John" sort="Mackay, John" uniqKey="Mackay J" first="John" last="Mackay">John Mackay</name></author><author><name sortKey="Retzel, Ernest F" sort="Retzel, Ernest F" uniqKey="Retzel E" first="Ernest F" last="Retzel">Ernest F. Retzel</name></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2007" type="published">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Nucleic Acid (MeSH)</term><term>Expressed Sequence Tags (chemistry)</term><term>Gene Expression Profiling (MeSH)</term><term>Genomics (MeSH)</term><term>Internet (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (genetics)</term><term>Tracheophyta (genetics)</term><term>Transcription, Genetic (MeSH)</term><term>Trees (genetics)</term><term>User-Computer Interface (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Arbres (génétique)</term><term>Bases de données d'acides nucléiques (MeSH)</term><term>Génomique (MeSH)</term><term>Interface utilisateur (MeSH)</term><term>Internet (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (génétique)</term><term>Tracheobionta (génétique)</term><term>Transcription génétique (MeSH)</term><term>Étiquettes de séquences exprimées (composition chimique)</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Expressed Sequence Tags</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Étiquettes de séquences exprimées</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term><term>Tracheophyta</term><term>Trees</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arbres</term><term>Populus</term><term>Tracheobionta</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Nucleic Acid</term><term>Gene Expression Profiling</term><term>Genomics</term><term>Internet</term><term>Polymorphism, Single Nucleotide</term><term>Transcription, Genetic</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Bases de données d'acides nucléiques</term><term>Génomique</term><term>Interface utilisateur</term><term>Internet</term><term>Polymorphisme de nucléotide simple</term><term>Transcription génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">ForestTreeDB is intended as a resource that centralizes large-scale expressed sequence tag (EST) sequencing results from several tree species (http://foresttree.org/ftdb). It currently encompasses 344,878 quality sequences from 68 libraries, from diverse organs of conifer and hybrid poplar trees. It utilizes the Nimbus data model to provide a hosting system for multiple projects, and uses object-relational mapping APIs in Java and Perl for data accesses within an Oracle database designed to be scalable, maintainable and extendable. Transcriptome builds or unigene sets occupy the focal point of the system. Several of the five current species-specific unigenes were used to design microarrays and SNP resources. The ForestTreeDB web application provides the means for multiple combination database queries. It presents the user with a list of discrete queries to retrieve and download large EST datasets or sequences from precompiled unigene assemblies. Functional annotation assignment is not trivial in conifers which are distantly related to angiosperm model plants. Optimal annotations are achieved through database queries that integrate results from several procedures based open-source tools. ForestTreeDB aims to facilitate sequence mining of coherent annotations in multiple species to support comparative genomic approaches. We plan to continuously enrich ForestTreeDB with other resources through collaborations with other genomic projects.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17130142</PMID><DateCompleted><Year>2007</Year><Month>03</Month><Day>16</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>35</Volume><Issue>Database issue</Issue><PubDate><Year>2007</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res</ISOAbbreviation></Journal><ArticleTitle>ForestTreeDB: a database dedicated to the mining of tree transcriptomes.</ArticleTitle><Pagination><MedlinePgn>D888-94</MedlinePgn></Pagination><Abstract><AbstractText>ForestTreeDB is intended as a resource that centralizes large-scale expressed sequence tag (EST) sequencing results from several tree species (http://foresttree.org/ftdb). It currently encompasses 344,878 quality sequences from 68 libraries, from diverse organs of conifer and hybrid poplar trees. It utilizes the Nimbus data model to provide a hosting system for multiple projects, and uses object-relational mapping APIs in Java and Perl for data accesses within an Oracle database designed to be scalable, maintainable and extendable. Transcriptome builds or unigene sets occupy the focal point of the system. Several of the five current species-specific unigenes were used to design microarrays and SNP resources. The ForestTreeDB web application provides the means for multiple combination database queries. It presents the user with a list of discrete queries to retrieve and download large EST datasets or sequences from precompiled unigene assemblies. Functional annotation assignment is not trivial in conifers which are distantly related to angiosperm model plants. Optimal annotations are achieved through database queries that integrate results from several procedures based open-source tools. ForestTreeDB aims to facilitate sequence mining of coherent annotations in multiple species to support comparative genomic approaches. We plan to continuously enrich ForestTreeDB with other resources through collaborations with other genomic projects.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pavy</LastName><ForeName>Nathalie</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Laval University, Centre de Recherche en Biologie Forestière, Québec, Canada G1K 7P4. nathalie.pavy@rsvs.ulaval.ca</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Johnson</LastName><ForeName>James J</ForeName><Initials>JJ</Initials></Author><Author ValidYN="Y"><LastName>Crow</LastName><ForeName>John A</ForeName><Initials>JA</Initials></Author><Author ValidYN="Y"><LastName>Paule</LastName><ForeName>Charles</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Kunau</LastName><ForeName>Timothy</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>MacKay</LastName><ForeName>John</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Retzel</LastName><ForeName>Ernest F</ForeName><Initials>EF</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>11</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nucleic Acids Res</MedlineTA><NlmUniqueID>0411011</NlmUniqueID><ISSNLinking>0305-1048</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="Y">Databases, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="N">Expressed Sequence Tags</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020407" MajorTopicYN="N">Internet</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D064028" MajorTopicYN="N">Tracheophyta</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="N">Transcription, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014197" MajorTopicYN="N">Trees</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014584" MajorTopicYN="N">User-Computer Interface</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>11</Month><Day>30</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2007</Year><Month>3</Month><Day>17</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>11</Month><Day>30</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">17130142</ArticleId><ArticleId IdType="pii">gkl882</ArticleId><ArticleId IdType="doi">10.1093/nar/gkl882</ArticleId><ArticleId IdType="pmc">PMC1716727</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Nucleic Acids Res. 2003 Jan 1;31(1):371-3</Citation><ArticleIdList><ArticleId IdType="pubmed">12520025</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7383-8</Citation><ArticleIdList><ArticleId IdType="pubmed">12771380</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Biol. 1990 Oct 5;215(3):403-10</Citation><ArticleIdList><ArticleId IdType="pubmed">2231712</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 1998 Mar;8(3):175-85</Citation><ArticleIdList><ArticleId IdType="pubmed">9521921</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 1998 Mar;8(3):186-94</Citation><ArticleIdList><ArticleId IdType="pubmed">9521922</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9693-8</Citation><ArticleIdList><ArticleId IdType="pubmed">9689143</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 1998;14(9):755-63</Citation><ArticleIdList><ArticleId IdType="pubmed">9918945</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2005 Jan 1;33(Database issue):D71-4</Citation><ArticleIdList><ArticleId IdType="pubmed">15608288</ArticleId></ArticleIdList></Reference><Reference><Citation>Tree Physiol. 2006 Jan;26(1):1-16</Citation><ArticleIdList><ArticleId IdType="pubmed">16203709</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Physiol. 2005 Oct;139(2):610-8</Citation><ArticleIdList><ArticleId IdType="pubmed">16219921</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2005;6:144</Citation><ArticleIdList><ArticleId IdType="pubmed">16236172</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51</Citation><ArticleIdList><ArticleId IdType="pubmed">16381856</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2006 Jan 1;34(Database issue):D257-60</Citation><ArticleIdList><ArticleId IdType="pubmed">16381859</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Mol Biol. 2006 Jan;60(1):21-40</Citation><ArticleIdList><ArticleId IdType="pubmed">16463097</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2006;7:174</Citation><ArticleIdList><ArticleId IdType="pubmed">16824208</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2003 Jan 1;31(1):224-8</Citation><ArticleIdList><ArticleId IdType="pubmed">12519987</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Biol. 2001 Nov 2;313(4):903-19</Citation><ArticleIdList><ArticleId IdType="pubmed">11697912</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country><region><li>Québec</li></region><settlement><li>Québec (ville)</li></settlement><orgName><li>Université Laval</li></orgName></list><tree><noCountry><name sortKey="Crow, John A" sort="Crow, John A" uniqKey="Crow J" first="John A" last="Crow">John A. Crow</name><name sortKey="Johnson, James J" sort="Johnson, James J" uniqKey="Johnson J" first="James J" last="Johnson">James J. Johnson</name><name sortKey="Kunau, Timothy" sort="Kunau, Timothy" uniqKey="Kunau T" first="Timothy" last="Kunau">Timothy Kunau</name><name sortKey="Mackay, John" sort="Mackay, John" uniqKey="Mackay J" first="John" last="Mackay">John Mackay</name><name sortKey="Paule, Charles" sort="Paule, Charles" uniqKey="Paule C" first="Charles" last="Paule">Charles Paule</name><name sortKey="Retzel, Ernest F" sort="Retzel, Ernest F" uniqKey="Retzel E" first="Ernest F" last="Retzel">Ernest F. Retzel</name></noCountry><country name="Canada"><region name="Québec"><name sortKey="Pavy, Nathalie" sort="Pavy, Nathalie" uniqKey="Pavy N" first="Nathalie" last="Pavy">Nathalie Pavy</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 003B91 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 003B91 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:17130142
|texte= ForestTreeDB: a database dedicated to the mining of tree transcriptomes.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:17130142" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |