83 lines
7.1 KiB
XML
83 lines
7.1 KiB
XML
<?xml version="1.0" encoding="utf-8"?>
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<!--re3data.org Schema for the Description of Research Data Repositories. Version 2.2, December 2014. doi:10.2312/re3.006-->
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<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">
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<r3d:repository>
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<r3d:re3data.orgIdentifier>r3d100010557</r3d:re3data.orgIdentifier>
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<r3d:repositoryName language="eng">Universal PBM Resource for Oligonucleotide Binding Evaluation</r3d:repositoryName>
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<r3d:additionalName language="eng">UniPROBE</r3d:additionalName>
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<r3d:repositoryURL>http://thebrain.bwh.harvard.edu/uniprobe/</r3d:repositoryURL>
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<r3d:repositoryIdentifier>FAIRSHARING_doi:10.25504/FAIRsharing.8zf3ny</r3d:repositoryIdentifier>
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<r3d:repositoryIdentifier>RRID:OMICS_00546</r3d:repositoryIdentifier>
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<r3d:repositoryIdentifier>RRID:SCR_005803</r3d:repositoryIdentifier>
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<r3d:repositoryIdentifier>RRID:nif-0000-03611</r3d:repositoryIdentifier>
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<r3d:description language="eng">The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins. This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In total, the database currently hosts DNA binding data for 406 nonredundant proteins from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, mouse, and human. The database's web tools (on the right) include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences</r3d:description>
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<r3d:repositoryContact>uniprobe@genetics.med.harvard.edu</r3d:repositoryContact>
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<r3d:type>disciplinary</r3d:type>
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<r3d:size updated=""></r3d:size>
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<r3d:startDate>2008-05</r3d:startDate>
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<r3d:endDate></r3d:endDate>
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<r3d:repositoryLanguage>eng</r3d:repositoryLanguage>
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<r3d:subject subjectScheme="DFG">2 Life Sciences</r3d:subject>
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<r3d:subject subjectScheme="DFG">204 Microbiology, Virology and Immunology</r3d:subject>
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<r3d:subject subjectScheme="DFG">21 Biology</r3d:subject>
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<r3d:subject subjectScheme="DFG">22 Medicine</r3d:subject>
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<r3d:missionStatementURL>http://the_brain.bwh.harvard.edu/index.html</r3d:missionStatementURL>
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<r3d:contentType contentTypeScheme="parse">Images</r3d:contentType>
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<r3d:contentType contentTypeScheme="parse">Raw data</r3d:contentType>
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<r3d:contentType contentTypeScheme="parse">Scientific and statistical data formats</r3d:contentType>
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<r3d:contentType contentTypeScheme="parse">Structured graphics</r3d:contentType>
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<r3d:contentType contentTypeScheme="parse">other</r3d:contentType>
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<r3d:providerType>dataProvider</r3d:providerType>
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<r3d:keyword>DNA</r3d:keyword>
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<r3d:keyword>biology</r3d:keyword>
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<r3d:keyword>cells</r3d:keyword>
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<r3d:keyword>gene ontology</r3d:keyword>
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<r3d:keyword>molecular</r3d:keyword>
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<r3d:keyword>mouse</r3d:keyword>
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<r3d:keyword>protein</r3d:keyword>
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<r3d:institution>
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<r3d:institutionName language="eng">Brigham and Women's Hospital, Bulyk Laboratory</r3d:institutionName>
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<r3d:institutionAdditionalName language="eng">Bulyk Lab</r3d:institutionAdditionalName>
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<r3d:institutionCountry>USA</r3d:institutionCountry>
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<r3d:responsibilityType>general</r3d:responsibilityType>
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<r3d:responsibilityType>technical</r3d:responsibilityType>
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<r3d:institutionType>non-profit</r3d:institutionType>
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<r3d:institutionURL>http://thebrain.bwh.harvard.edu/</r3d:institutionURL>
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<r3d:responsibilityStartDate></r3d:responsibilityStartDate>
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<r3d:responsibilityEndDate></r3d:responsibilityEndDate>
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<r3d:institutionContact>http://the_brain.bwh.harvard.edu/contact.html</r3d:institutionContact>
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</r3d:institution>
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<r3d:policy>
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<r3d:policyName>Downloads</r3d:policyName>
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<r3d:policyURL>http://thebrain.bwh.harvard.edu/uniprobe/downloads.php</r3d:policyURL>
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</r3d:policy>
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<r3d:databaseAccess>
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<r3d:databaseAccessType>open</r3d:databaseAccessType>
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</r3d:databaseAccess>
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<r3d:dataAccess>
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<r3d:dataAccessType>open</r3d:dataAccessType>
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</r3d:dataAccess>
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<r3d:dataLicense>
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<r3d:dataLicenseName>ODC</r3d:dataLicenseName>
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<r3d:dataLicenseURL>https://opendatacommons.org/licenses/pddl/1-0/</r3d:dataLicenseURL>
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</r3d:dataLicense>
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<r3d:dataLicense>
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<r3d:dataLicenseName>other</r3d:dataLicenseName>
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<r3d:dataLicenseURL>http://thebrain.bwh.harvard.edu/uniprobe/academic-license.php</r3d:dataLicenseURL>
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</r3d:dataLicense>
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<r3d:dataUpload>
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<r3d:dataUploadType>closed</r3d:dataUploadType>
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</r3d:dataUpload>
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<r3d:software>
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<r3d:softwareName>other</r3d:softwareName>
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</r3d:software>
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<r3d:versioning>yes</r3d:versioning>
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<r3d:pidSystem>none</r3d:pidSystem>
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<r3d:citationGuidelineURL>http://the_brain.bwh.harvard.edu/uniprobe/about.php</r3d:citationGuidelineURL>
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<r3d:enhancedPublication>yes</r3d:enhancedPublication>
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<r3d:qualityManagement>unknown</r3d:qualityManagement>
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<r3d:remarks>UniPROBE is covered by Thomson Reuters Data Citation Index.</r3d:remarks>
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<r3d:entryDate>2013-12-02</r3d:entryDate>
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<r3d:lastUpdate>2022-12-14</r3d:lastUpdate>
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</r3d:repository>
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</r3d:re3data> |