Dataset Open Access

Ortholog data from the tuatara genome project

Patricio, Mateus; Muffato, Matthieu; Rutherford, Kim Matthew; Gemmell, Neil J.


DCAT Export

<?xml version='1.0' encoding='utf-8'?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:adms="http://www.w3.org/ns/adms#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dct="http://purl.org/dc/terms/" xmlns:dctype="http://purl.org/dc/dcmitype/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:duv="http://www.w3.org/ns/duv#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:frapo="http://purl.org/cerif/frapo/" xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:gsp="http://www.opengis.net/ont/geosparql#" xmlns:locn="http://www.w3.org/ns/locn#" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:schema="http://schema.org/" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:vcard="http://www.w3.org/2006/vcard/ns#" xmlns:wdrs="http://www.w3.org/2007/05/powder-s#">
  <rdf:Description rdf:about="https://doi.org/10.5281/zenodo.2542571">
    <rdf:type rdf:resource="http://www.w3.org/ns/dcat#Dataset"/>
    <dct:type rdf:resource="http://purl.org/dc/dcmitype/Dataset"/>
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://doi.org/10.5281/zenodo.2542571</dct:identifier>
    <foaf:page rdf:resource="https://doi.org/10.5281/zenodo.2542571"/>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0003-2056-3946">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0003-2056-3946</dct:identifier>
        <foaf:name>Patricio, Mateus</foaf:name>
        <foaf:givenName>Mateus</foaf:givenName>
        <foaf:familyName>Patricio</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>European Bioinformatics Institute</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-7860-3560">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-7860-3560</dct:identifier>
        <foaf:name>Muffato, Matthieu</foaf:name>
        <foaf:givenName>Matthieu</foaf:givenName>
        <foaf:familyName>Muffato</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>European Bioinformatics Institute</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0001-6277-726X">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0001-6277-726X</dct:identifier>
        <foaf:name>Rutherford, Kim Matthew</foaf:name>
        <foaf:givenName>Kim Matthew</foaf:givenName>
        <foaf:familyName>Rutherford</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>University of Cambridge</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0003-0671-3637">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0003-0671-3637</dct:identifier>
        <foaf:name>Gemmell, Neil J.</foaf:name>
        <foaf:givenName>Neil J.</foaf:givenName>
        <foaf:familyName>Gemmell</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>University of Otago</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:title>Ortholog data from the tuatara genome project</dct:title>
    <dct:publisher>
      <foaf:Agent>
        <foaf:name>Zenodo</foaf:name>
      </foaf:Agent>
    </dct:publisher>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2019</dct:issued>
    <dcat:keyword>tuatara</dcat:keyword>
    <dcat:keyword>orthologs</dcat:keyword>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2019-01-24</dct:issued>
    <owl:sameAs rdf:resource="https://zenodo.org/record/2542571"/>
    <adms:identifier>
      <adms:Identifier>
        <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/2542571</skos:notation>
        <adms:schemeAgency>url</adms:schemeAgency>
      </adms:Identifier>
    </adms:identifier>
    <dct:isVersionOf rdf:resource="https://doi.org/10.5281/zenodo.2542570"/>
    <dct:description>&lt;p&gt;This record contains orthology predictions based on the Maker gene annotation&lt;br&gt; of the tuatara (Sphenodon punctatus) and a set of 25 other species, using the&lt;br&gt; Ensembl methodology.&lt;/p&gt; &lt;p&gt;See http://doi.org/10.5281/zenodo.1489354 for the Maker annotation in GFF&lt;br&gt; format.&lt;/p&gt; &lt;p&gt;The files all_trees.emf.gz and all_homologies.tsv.gz contain the phylogenetic&lt;br&gt; trees (all_trees.emf.gz, in the EMF alignment format) and the derived pairwise&lt;br&gt; orthologies and paralogies (all_homologies.tsv.gz, in tabular format).&lt;/p&gt; &lt;p&gt;From the phylogenetic trees, sets of 1-to-1 orthologues across all 26 species&lt;br&gt; were extracted (pure_one2one_orthologies.txt).&amp;nbsp; Sets of orthologues that span&lt;br&gt; all the species but include paralogues were reduced to 1 copy per species&lt;br&gt; using gene order conservation and sequence similarity. This extra dataset is&lt;br&gt; available in promoted_one2one_orthologies.txt&lt;/p&gt; &lt;p&gt;The main Ensembl entry point for tuatara is:&lt;br&gt; &amp;nbsp; http://www.ensembl.org/Sphenodon_punctatus/&lt;/p&gt; &lt;p&gt;This work is supported by Ngatiwai iwi, Allan Wilson Centre, University of&lt;br&gt; Otago, New Zealand Genomics Limited, Illumina, National eScience&lt;br&gt; Infrastructure (NeSI NZ).&lt;/p&gt;</dct:description>
    <dct:accessRights rdf:resource="http://publications.europa.eu/resource/authority/access-right/PUBLIC"/>
    <dct:accessRights>
      <dct:RightsStatement rdf:about="info:eu-repo/semantics/openAccess">
        <rdfs:label>Open Access</rdfs:label>
      </dct:RightsStatement>
    </dct:accessRights>
    <dcat:distribution>
      <dcat:Distribution>
        <dct:license rdf:resource="https://creativecommons.org/licenses/by/4.0/legalcode"/>
        <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.2542571"/>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.2542571"/>
        <dcat:byteSize>505410515</dcat:byteSize>
        <dcat:downloadURL rdf:resource="https://zenodo.org/record/2542571/files/all_homologies.tsv.gz"/>
        <dcat:mediaType>text/tab-separated-values</dcat:mediaType>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.2542571"/>
        <dcat:byteSize>229435651</dcat:byteSize>
        <dcat:downloadURL rdf:resource="https://zenodo.org/record/2542571/files/all_trees.emf.gz"/>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.2542571"/>
        <dcat:byteSize>1396156</dcat:byteSize>
        <dcat:downloadURL rdf:resource="https://zenodo.org/record/2542571/files/promoted_one2one_orthologies.txt"/>
        <dcat:mediaType>text/plain</dcat:mediaType>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.2542571"/>
        <dcat:byteSize>58875</dcat:byteSize>
        <dcat:downloadURL rdf:resource="https://zenodo.org/record/2542571/files/pure_one2one_orthologies.txt"/>
        <dcat:mediaType>text/plain</dcat:mediaType>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.2542571"/>
        <dcat:byteSize>1102</dcat:byteSize>
        <dcat:downloadURL rdf:resource="https://zenodo.org/record/2542571/files/README.txt"/>
        <dcat:mediaType>text/plain</dcat:mediaType>
      </dcat:Distribution>
    </dcat:distribution>
  </rdf:Description>
</rdf:RDF>
247
122
views
downloads
All versions This version
Views 247247
Downloads 122122
Data volume 8.0 GB8.0 GB
Unique views 222222
Unique downloads 100100

Share

Cite as