MorphoBank: phylophenomics in the “cloud”
Identifieur interne : 000773 ( Main/Exploration ); précédent : 000772; suivant : 000774MorphoBank: phylophenomics in the “cloud”
Auteurs : Maureen A. O Eary [États-Unis] ; Seth Kaufman [États-Unis]Source :
- 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
Affiliations:
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O Eary</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Anatomical Sciences, HSC T‐8 (040), Stony Brook University, Stony Brook, NY 11794‐8081</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Kaufman, Seth" sort="Kaufman, Seth" uniqKey="Kaufman S" first="Seth" last="Kaufman">Seth Kaufman</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Whirl‐i‐Gig, 220 5th Street, Greenport, NY 11944</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author></analytic><monogr></monogr><series><title level="j">Cladistics</title><idno type="ISSN">0748-3007</idno><idno type="eISSN">1096-0031</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2011-10">2011-10</date><biblScope unit="volume">27</biblScope><biblScope unit="issue">5</biblScope><biblScope unit="page" from="529">529</biblScope><biblScope unit="page" to="537">537</biblScope></imprint><idno type="ISSN">0748-3007</idno></series><idno type="istex">DE08887DD4861B9FE39E1332DD51BCA0B637DB33</idno><idno type="DOI">10.1111/j.1096-0031.2011.00355.x</idno><idno type="ArticleID">CLA355</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0748-3007</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml: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.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>État de New York</li></region></list><tree><country name="États-Unis"><region name="État de New York"><name sortKey="O Eary, Maureen A" sort="O Eary, Maureen A" uniqKey="O Eary M" first="Maureen A." last="O Eary">Maureen A. O Eary</name></region><name sortKey="Kaufman, Seth" sort="Kaufman, Seth" uniqKey="Kaufman S" first="Seth" last="Kaufman">Seth Kaufman</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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