120 lines
9.5 KiB
XML
120 lines
9.5 KiB
XML
<?xml version="1.0" encoding="utf-8"?>
|
|
<!--re3data.org Schema for the Description of Research Data Repositories. Version 2.2, December 2014. doi:10.2312/re3.006-->
|
|
<r3d:re3data xmlns:r3d="http://www.re3data.org/schema/2-2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.re3data.org/schema/2-2 http://schema.re3data.org/2-2/re3dataV2-2.xsd">
|
|
<r3d:repository>
|
|
<r3d:re3data.orgIdentifier>r3d100012568</r3d:re3data.orgIdentifier>
|
|
<r3d:repositoryName language="eng">The Adaptive Evolution Database</r3d:repositoryName>
|
|
<r3d:additionalName language="eng">TAED</r3d:additionalName>
|
|
<r3d:repositoryURL>https://liberles.cst.temple.edu/TAED/index.html</r3d:repositoryURL>
|
|
<r3d:repositoryIdentifier>RRID:SCR_006930</r3d:repositoryIdentifier>
|
|
<r3d:repositoryIdentifier>RRID:nif-0000-03533</r3d:repositoryIdentifier>
|
|
<r3d:description language="eng">TAED is a database of phylogenetically indexed gene families. It contains multiple sequence alignments from MAFFT1, maximum likelihood phylogenetic trees from PhyML2, bootstrap values for each node, dN/dS ratios for each lineage from the free ratios model in PAML3, and labels for each node of speciation or duplication from gene tree/species tree reconciliation using SoftParsMap4. The phylogenetic indexing enables simultaneous viewing of lineages with high dN/dS that occurred along the same species tree branches. Resources from the Protein Data Bank (PDB) and the Kyoto Encyclopedia of Genes and Genomes (KEGG)5, have been incorporated into the TAED analysis to detect substitutions along each branch within the phylogenetic tree and to assess selection within pathways.</r3d:description>
|
|
<r3d:repositoryContact>daliberles@temple.edu</r3d:repositoryContact>
|
|
<r3d:type>disciplinary</r3d:type>
|
|
<r3d:size updated="2017-12-05">143.806 completed protein families; 3.185.986 proteins; 3.214 species</r3d:size>
|
|
<r3d:startDate>2016</r3d:startDate>
|
|
<r3d:endDate></r3d:endDate>
|
|
<r3d:repositoryLanguage>eng</r3d:repositoryLanguage>
|
|
<r3d:subject subjectScheme="DFG">2 Life Sciences</r3d:subject>
|
|
<r3d:subject subjectScheme="DFG">201 Basic Biological and Medical Research</r3d:subject>
|
|
<r3d:subject subjectScheme="DFG">21 Biology</r3d:subject>
|
|
<r3d:missionStatementURL>https://liberles.cst.temple.edu/TAED/index.html</r3d:missionStatementURL>
|
|
<r3d:contentType contentTypeScheme="parse">Scientific and statistical data formats</r3d:contentType>
|
|
<r3d:contentType contentTypeScheme="parse">Structured graphics</r3d:contentType>
|
|
<r3d:contentType contentTypeScheme="parse">other</r3d:contentType>
|
|
<r3d:providerType>dataProvider</r3d:providerType>
|
|
<r3d:keyword>bioinformatics</r3d:keyword>
|
|
<r3d:keyword>epigenomics</r3d:keyword>
|
|
<r3d:keyword>evolution</r3d:keyword>
|
|
<r3d:keyword>genomics</r3d:keyword>
|
|
<r3d:keyword>molecular evolution</r3d:keyword>
|
|
<r3d:keyword>phylogenetic tree</r3d:keyword>
|
|
<r3d:keyword>phylogenomics</r3d:keyword>
|
|
<r3d:keyword>species diversification</r3d:keyword>
|
|
<r3d:keyword>taxonomy</r3d:keyword>
|
|
<r3d:institution>
|
|
<r3d:institutionName language="eng">Institute for Genomics and Evolutionary Medicine</r3d:institutionName>
|
|
<r3d:institutionAdditionalName language="eng">IGEM</r3d:institutionAdditionalName>
|
|
<r3d:institutionCountry>USA</r3d:institutionCountry>
|
|
<r3d:responsibilityType>general</r3d:responsibilityType>
|
|
<r3d:institutionType>non-profit</r3d:institutionType>
|
|
<r3d:institutionURL>https://igem.temple.edu/home</r3d:institutionURL>
|
|
<r3d:responsibilityStartDate>2016</r3d:responsibilityStartDate>
|
|
<r3d:responsibilityEndDate></r3d:responsibilityEndDate>
|
|
</r3d:institution>
|
|
<r3d:institution>
|
|
<r3d:institutionName language="eng">National Science Foundation</r3d:institutionName>
|
|
<r3d:institutionCountry>USA</r3d:institutionCountry>
|
|
<r3d:responsibilityType>funding</r3d:responsibilityType>
|
|
<r3d:institutionType>non-profit</r3d:institutionType>
|
|
<r3d:institutionURL>https://www.nsf.gov/</r3d:institutionURL>
|
|
<r3d:institutionIdentifier>ROR:021nxhr62</r3d:institutionIdentifier>
|
|
<r3d:responsibilityStartDate>2016</r3d:responsibilityStartDate>
|
|
<r3d:responsibilityEndDate></r3d:responsibilityEndDate>
|
|
<r3d:institutionContact>https://www.nsf.gov/help/contact.jsp</r3d:institutionContact>
|
|
</r3d:institution>
|
|
<r3d:institution>
|
|
<r3d:institutionName language="eng">Temple University, Department of Biology, Center for Computational Genetics and Genomics</r3d:institutionName>
|
|
<r3d:institutionAdditionalName language="eng">CCGG</r3d:institutionAdditionalName>
|
|
<r3d:institutionCountry>USA</r3d:institutionCountry>
|
|
<r3d:responsibilityType>technical</r3d:responsibilityType>
|
|
<r3d:institutionType>non-profit</r3d:institutionType>
|
|
<r3d:institutionURL>https://ccgg.temple.edu/</r3d:institutionURL>
|
|
<r3d:responsibilityStartDate>2016</r3d:responsibilityStartDate>
|
|
<r3d:responsibilityEndDate></r3d:responsibilityEndDate>
|
|
</r3d:institution>
|
|
<r3d:institution>
|
|
<r3d:institutionName language="eng">Temple University, Liberles group</r3d:institutionName>
|
|
<r3d:institutionCountry>USA</r3d:institutionCountry>
|
|
<r3d:responsibilityType>general</r3d:responsibilityType>
|
|
<r3d:institutionType>non-profit</r3d:institutionType>
|
|
<r3d:institutionURL>https://sites.temple.edu/liberles/</r3d:institutionURL>
|
|
<r3d:responsibilityStartDate></r3d:responsibilityStartDate>
|
|
<r3d:responsibilityEndDate></r3d:responsibilityEndDate>
|
|
<r3d:institutionContact>daliberles@temple.edu</r3d:institutionContact>
|
|
</r3d:institution>
|
|
<r3d:policy>
|
|
<r3d:policyName>Contracts and Agreements</r3d:policyName>
|
|
<r3d:policyURL>https://research.temple.edu/innovation/contracts-and-agreements</r3d:policyURL>
|
|
</r3d:policy>
|
|
<r3d:policy>
|
|
<r3d:policyName>Data Usage, Governance and Integrity Policy</r3d:policyName>
|
|
<r3d:policyURL>https://secretary.temple.edu/sites/secretary/files/policies/04.71.10.pdf</r3d:policyURL>
|
|
</r3d:policy>
|
|
<r3d:policy>
|
|
<r3d:policyName>Policies & Bylaws</r3d:policyName>
|
|
<r3d:policyURL>https://secretary.temple.edu/policies</r3d:policyURL>
|
|
</r3d:policy>
|
|
<r3d:databaseAccess>
|
|
<r3d:databaseAccessType>open</r3d:databaseAccessType>
|
|
</r3d:databaseAccess>
|
|
<r3d:dataAccess>
|
|
<r3d:dataAccessType>open</r3d:dataAccessType>
|
|
</r3d:dataAccess>
|
|
<r3d:dataLicense>
|
|
<r3d:dataLicenseName>Copyrights</r3d:dataLicenseName>
|
|
<r3d:dataLicenseURL>https://liberles.cst.temple.edu/TreeThrasher/TreeThrasher_license.html</r3d:dataLicenseURL>
|
|
</r3d:dataLicense>
|
|
<r3d:dataLicense>
|
|
<r3d:dataLicenseName>Copyrights</r3d:dataLicenseName>
|
|
<r3d:dataLicenseURL>https://secretary.temple.edu/sites/secretary/files/policies/04.71.10.pdf</r3d:dataLicenseURL>
|
|
</r3d:dataLicense>
|
|
<r3d:dataUpload>
|
|
<r3d:dataUploadType>closed</r3d:dataUploadType>
|
|
</r3d:dataUpload>
|
|
<r3d:software>
|
|
<r3d:softwareName>MySQL</r3d:softwareName>
|
|
</r3d:software>
|
|
<r3d:versioning>yes</r3d:versioning>
|
|
<r3d:api apiType="other">https://liberles.cst.temple.edu/TAED/TAEDKEGG.php</r3d:api>
|
|
<r3d:api apiType="other">https://liberles.cst.temple.edu/TAED/TAED_API.php</r3d:api>
|
|
<r3d:pidSystem>none</r3d:pidSystem>
|
|
<r3d:citationGuidelineURL></r3d:citationGuidelineURL>
|
|
<r3d:aidSystem>none</r3d:aidSystem>
|
|
<r3d:enhancedPublication>unknown</r3d:enhancedPublication>
|
|
<r3d:qualityManagement>yes</r3d:qualityManagement>
|
|
<r3d:remarks></r3d:remarks>
|
|
<r3d:entryDate>2017-12-05</r3d:entryDate>
|
|
<r3d:lastUpdate>2022-12-19</r3d:lastUpdate>
|
|
</r3d:repository>
|
|
</r3d:re3data> |