MorphoBank: phylophenomics in the “cloud”
Identifieur interne : 000606 ( Istex/Corpus ); précédent : 000605; suivant : 000607MorphoBank: phylophenomics in the “cloud”
Auteurs : Maureen A. O Eary ; Seth KaufmanSource :
- Cladistics [ 0748-3007 ] ; 2011-10.
Abstract
A highly interoperable informatics infrastructure rapidly emerged to handle genomic data used for phylogenetics and was instrumental in the growth of molecular systematics. Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single‐user, file‐based desktop software wholly unsuitable for real‐time, team‐based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e.g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with “cloud” computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at‐large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self‐assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e.g. if X is absent, Y is inapplicable, or X–Z characters share a media view). MorphoBank has enabled an order of magnitude increase in phylophenomic data collection: a recent collaboration by more than 25 researchers has produced a database of > 4500 phenomic characters supported by > 10 000 media.
© The Willi Hennig Society 2011.
Url:
DOI: 10.1111/j.1096-0031.2011.00355.x
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© The Willi Hennig Society 2011.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>Maureen A. O’Leary</name><affiliations><json:string>Department of Anatomical Sciences, HSC T‐8 (040), Stony Brook University, Stony Brook, NY 11794‐8081, USA</json:string></affiliations></json:item><json:item><name>Seth Kaufman</name><affiliations><json:string>Whirl‐i‐Gig, 220 5th Street, Greenport, NY 11944, USA</json:string></affiliations></json:item></author><articleId><json:string>CLA355</json:string></articleId><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>A highly interoperable informatics infrastructure rapidly emerged to handle genomic data used for phylogenetics and was instrumental in the growth of molecular systematics. Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single‐user, file‐based desktop software wholly unsuitable for real‐time, team‐based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e.g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with “cloud” computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at‐large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self‐assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e.g. if X is absent, Y is inapplicable, or X–Z characters share a media view). 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Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single‐user, file‐based desktop software wholly unsuitable for real‐time, team‐based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e.g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with “cloud” computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at‐large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self‐assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e.g. if X is absent, Y is inapplicable, or X–Z characters share a media view). MorphoBank has enabled an order of magnitude increase in phylophenomic data collection: a recent collaboration by more than 25 researchers has produced a database of > 4500 phenomic characters supported by > 10 000 media.
© The Willi Hennig Society 2011.</p></abstract></profileDesc><revisionDesc><change when="2011-10">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/DE08887DD4861B9FE39E1332DD51BCA0B637DB33/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1096-0031</doi><issn type="print">0748-3007</issn><issn type="electronic">1096-0031</issn><idGroup><id type="product" value="CLA"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="CLADISTICS">Cladistics</title></titleGroup></publicationMeta><publicationMeta level="part" position="10105"><doi origin="wiley">10.1111/cla.2011.27.issue-5</doi><numberingGroup><numbering type="journalVolume" number="27">27</numbering><numbering type="journalIssue" number="5">5</numbering></numberingGroup><coverDate startDate="2011-10">October 2011</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="5" status="forIssue"><doi origin="wiley">10.1111/j.1096-0031.2011.00355.x</doi><idGroup><id type="unit" value="CLA355"></id></idGroup><countGroup><count type="pageTotal" number="9"></count></countGroup><titleGroup><title type="tocHeading1">SOFTWARE</title></titleGroup><copyright>© The Willi Hennig Society 2011</copyright><eventGroup><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:2.9.3 mode:FullText" date="2011-09-08"></event><event type="publishedOnlineEarlyUnpaginated" date="2011-04-28"></event><event type="firstOnline" date="2011-04-28"></event><event type="publishedOnlineFinalForm" date="2011-09-08"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-01-15"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-10-16"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="529">529</numbering><numbering type="pageLast" number="537">537</numbering></numberingGroup><correspondenceTo> Corresponding author:
<i>E‐mail address</i>: <email>maureen.oleary@stonybrook.edu</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:CLA.CLA355.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Accepted 3 March 2011</unparsedEditorialHistory><countGroup><count type="figureTotal" number="3"></count><count type="tableTotal" number="0"></count></countGroup><titleGroup><title type="main">MorphoBank: phylophenomics in the “cloud”</title><title type="shortAuthors"><i>M.A. O’Leary and S. Kaufman</i></title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1" corresponding="yes"><personName><givenNames>Maureen A.</givenNames><familyName>O’Leary</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a2"><personName><givenNames>Seth</givenNames><familyName>Kaufman</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="US"><unparsedAffiliation>Department of Anatomical Sciences, HSC T‐8 (040), Stony Brook University, Stony Brook, NY 11794‐8081, USA</unparsedAffiliation></affiliation><affiliation xml:id="a2" countryCode="US"><unparsedAffiliation>Whirl‐i‐Gig, 220 5th Street, Greenport, NY 11944, USA</unparsedAffiliation></affiliation></affiliationGroup><supportingInformation><p><b>Appendix S1.</b> MorphoBank 2.7 technical description.</p><p><b>Appendix S2.</b> MorphoBank 2.7 architecture.</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:07483007:media:cla355:CLA_355_sm_AppendixS1"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:07483007:media:cla355:CLA_355_sm_AppendixS2"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title><p>A highly interoperable informatics infrastructure rapidly emerged to handle genomic data used for phylogenetics and was instrumental in the growth of molecular systematics. Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single‐user, file‐based desktop software wholly unsuitable for real‐time, team‐based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e.g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with “cloud” computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at‐large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self‐assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e.g. if X is absent, Y is inapplicable, or X–Z characters share a media view). MorphoBank has enabled an order of magnitude increase in phylophenomic data collection: a recent collaboration by more than 25 researchers has produced a database of > 4500 phenomic characters supported by > 10 000 media.
© The Willi Hennig Society 2011.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>MorphoBank: phylophenomics in the “cloud”</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>MorphoBank: phylophenomics in the “cloud”</title></titleInfo><name type="personal"><namePart type="given">Maureen A.</namePart><namePart type="family">O’Leary</namePart><affiliation>Department of Anatomical Sciences, HSC T‐8 (040), Stony Brook University, Stony Brook, NY 11794‐8081, USA</affiliation><description>Correspondence: Corresponding author:: </description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Seth</namePart><namePart type="family">Kaufman</namePart><affiliation>Whirl‐i‐Gig, 220 5th Street, Greenport, NY 11944, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article"></genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2011-10</dateIssued><edition>Accepted 3 March 2011</edition><copyrightDate encoding="w3cdtf">2011</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="figures">3</extent></physicalDescription><abstract lang="en">A highly interoperable informatics infrastructure rapidly emerged to handle genomic data used for phylogenetics and was instrumental in the growth of molecular systematics. Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single‐user, file‐based desktop software wholly unsuitable for real‐time, team‐based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e.g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with “cloud” computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at‐large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self‐assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e.g. if X is absent, Y is inapplicable, or X–Z characters share a media view). MorphoBank has enabled an order of magnitude increase in phylophenomic data collection: a recent collaboration by more than 25 researchers has produced a database of > 4500 phenomic characters supported by > 10 000 media.
© The Willi Hennig Society 2011.</abstract><relatedItem type="host"><titleInfo><title>Cladistics</title></titleInfo><genre type="journal">journal</genre><note type="content"> Appendix S1. MorphoBank 2.7 technical description. Appendix S2. MorphoBank 2.7 architecture. Appendix S1. MorphoBank 2.7 technical description. Appendix S2. MorphoBank 2.7 architecture.Supporting Info Item: Supporting info item - Supporting info item - </note><identifier type="ISSN">0748-3007</identifier><identifier type="eISSN">1096-0031</identifier><identifier type="DOI">10.1111/(ISSN)1096-0031</identifier><identifier type="PublisherID">CLA</identifier><part><date>2011</date><detail type="volume"><caption>vol.</caption><number>27</number></detail><detail type="issue"><caption>no.</caption><number>5</number></detail><extent unit="pages"><start>529</start><end>537</end><total>9</total></extent></part></relatedItem><identifier type="istex">DE08887DD4861B9FE39E1332DD51BCA0B637DB33</identifier><identifier type="DOI">10.1111/j.1096-0031.2011.00355.x</identifier><identifier type="ArticleID">CLA355</identifier><accessCondition type="use and reproduction" contentType="copyright">© The Willi Hennig Society 2011</accessCondition><recordInfo><recordContentSource>WILEY</recordContentSource><recordOrigin>Blackwell Publishing Ltd</recordOrigin></recordInfo></mods></metadata><enrichments><json:item><type>multicat</type><uri>https://api.istex.fr/document/DE08887DD4861B9FE39E1332DD51BCA0B637DB33/enrichments/multicat</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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