114 lines
10 KiB
XML
114 lines
10 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>r3d100010071</r3d:re3data.orgIdentifier>
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<r3d:repositoryName language="eng">DOE Joint Genome Institute Genome Web Portal</r3d:repositoryName>
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<r3d:additionalName language="eng">JGI Genome Portal</r3d:additionalName>
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<r3d:additionalName language="eng">US Department of Energy Joint Genome Institute Genome Web Portal</r3d:additionalName>
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<r3d:repositoryURL>https://genome.jgi.doe.gov/portal/</r3d:repositoryURL>
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<r3d:repositoryIdentifier>RRID:nif-0000-30425</r3d:repositoryIdentifier>
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<r3d:description language="eng">The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms.
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Databases: Genome Online Database (GOLD), Integrated Microbial Genomes (IGM), MycoCosm, Phytozome</r3d:description>
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<r3d:repositoryContact>degilbert@lbl.gov</r3d:repositoryContact>
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<r3d:type>disciplinary</r3d:type>
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<r3d:size updated="2019-05-15">148.551 Trillions Total sequencing</r3d:size>
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<r3d:startDate>1997</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">21 Biology</r3d:subject>
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<r3d:subject subjectScheme="DFG">3 Natural Sciences</r3d:subject>
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<r3d:subject subjectScheme="DFG">31 Chemistry</r3d:subject>
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<r3d:missionStatementURL>https://jgi.doe.gov/about-us/</r3d:missionStatementURL>
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<r3d:contentType contentTypeScheme="parse">Archived data</r3d:contentType>
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<r3d:contentType contentTypeScheme="parse">Databases</r3d:contentType>
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<r3d:contentType contentTypeScheme="parse">Images</r3d:contentType>
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<r3d:contentType contentTypeScheme="parse">Standard office documents</r3d:contentType>
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<r3d:providerType>dataProvider</r3d:providerType>
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<r3d:providerType>serviceProvider</r3d:providerType>
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<r3d:keyword>fungal genomics</r3d:keyword>
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<r3d:keyword>gene sequencing</r3d:keyword>
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<r3d:keyword>metagenomics</r3d:keyword>
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<r3d:keyword>microbial genomics</r3d:keyword>
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<r3d:keyword>plant genomics</r3d:keyword>
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<r3d:institution>
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<r3d:institutionName language="eng">DOE Joint Geonome Institute</r3d:institutionName>
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<r3d:institutionAdditionalName language="eng">DOE JGI</r3d:institutionAdditionalName>
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<r3d:institutionCountry>USA</r3d:institutionCountry>
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<r3d:responsibilityType>funding</r3d:responsibilityType>
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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>https://jgi.doe.gov/</r3d:institutionURL>
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<r3d:responsibilityStartDate>1997</r3d:responsibilityStartDate>
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<r3d:responsibilityEndDate></r3d:responsibilityEndDate>
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<r3d:institutionContact>https://jgi.doe.gov/contact-us/</r3d:institutionContact>
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</r3d:institution>
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<r3d:institution>
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<r3d:institutionName language="eng">U.S. Department of Energy, Office of Science</r3d:institutionName>
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<r3d:institutionAdditionalName language="eng">DOE</r3d:institutionAdditionalName>
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<r3d:institutionCountry>USA</r3d:institutionCountry>
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<r3d:responsibilityType>funding</r3d:responsibilityType>
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<r3d:institutionType>non-profit</r3d:institutionType>
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<r3d:institutionURL>https://science.energy.gov/</r3d:institutionURL>
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<r3d:responsibilityStartDate>1997</r3d:responsibilityStartDate>
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<r3d:responsibilityEndDate></r3d:responsibilityEndDate>
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<r3d:institutionContact>daniel.drell@science.doe.gov</r3d:institutionContact>
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</r3d:institution>
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<r3d:institution>
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<r3d:institutionName language="eng">University of California, Office of the President</r3d:institutionName>
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<r3d:institutionAdditionalName language="eng">UCOP</r3d:institutionAdditionalName>
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<r3d:institutionCountry>USA</r3d:institutionCountry>
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<r3d:responsibilityType>funding</r3d:responsibilityType>
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<r3d:institutionType>non-profit</r3d:institutionType>
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<r3d:institutionURL>https://www.ucop.edu/</r3d:institutionURL>
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<r3d:responsibilityStartDate>1997</r3d:responsibilityStartDate>
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<r3d:responsibilityEndDate></r3d:responsibilityEndDate>
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</r3d:institution>
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<r3d:policy>
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<r3d:policyName>GOLD Data Usage Policy</r3d:policyName>
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<r3d:policyURL>https://gold.jgi.doe.gov/usagepolicy</r3d:policyURL>
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</r3d:policy>
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<r3d:policy>
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<r3d:policyName>JGI Policies</r3d:policyName>
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<r3d:policyURL>https://jgi.doe.gov/user-programs/pmo-overview/policies/</r3d:policyURL>
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</r3d:policy>
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<r3d:policy>
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<r3d:policyName>MycoCosm Data Usage Policy</r3d:policyName>
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<r3d:policyURL>https://genome.jgi.doe.gov/pages/data-usage-policy.jsf</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:dataAccessRestriction>registration</r3d:dataAccessRestriction>
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</r3d:dataAccess>
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<r3d:dataLicense>
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<r3d:dataLicenseName>Copyrights</r3d:dataLicenseName>
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<r3d:dataLicenseURL>https://jgi.doe.gov/disclaimer/</r3d:dataLicenseURL>
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</r3d:dataLicense>
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<r3d:dataUpload>
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<r3d:dataUploadType>restricted</r3d:dataUploadType>
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<r3d:dataUploadRestriction>registration</r3d:dataUploadRestriction>
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</r3d:dataUpload>
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<r3d:dataUploadLicense>
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<r3d:dataUploadLicenseName>Data submission guide</r3d:dataUploadLicenseName>
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<r3d:dataUploadLicenseURL>https://img.jgi.doe.gov/submit/doc/Submission_User_Guide.pdf</r3d:dataUploadLicenseURL>
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</r3d:dataUploadLicense>
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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:api apiType="FTP">ftp://ftp.jgi-psf.org/</r3d:api>
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<r3d:api apiType="SWORD">https://genome.jgi.doe.gov/portal/help/download.jsf</r3d:api>
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<r3d:pidSystem>none</r3d:pidSystem>
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<r3d:citationGuidelineURL>https://genome.jgi.doe.gov/pages/citeUs.jsf</r3d:citationGuidelineURL>
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<r3d:enhancedPublication>unknown</r3d:enhancedPublication>
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<r3d:qualityManagement>yes</r3d:qualityManagement>
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<r3d:remarks>DOE Joint Genome Institute Genome Web Portal is covered by Clarivate Data Citation Index. The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) was created in 1997 to unite the expertise and resources in DNA sequencing, informatics, and technology development pioneered at the U.S. Department of Energy (DOE) genome centers at Lawrence Berkeley National Laboratory (LBNL), Lawrence Livermore National Laboratory (LLNL), and Los Alamos National Laboratory (LANL). In 1999, to accelerate the completion of DOE’s commitment to the Human Genome Project, the University of California, which manages the DOE JGI lead laboratory in LBNL, leased laboratory and office space in a light industrial park in Walnut Creek, California, to consolidate activities</r3d:remarks>
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<r3d:entryDate>2012-08-08</r3d:entryDate>
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<r3d:lastUpdate>2021-08-25</r3d:lastUpdate>
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</r3d:repository>
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</r3d:re3data> |