Dataset Open Access
Jacqueline A. Robinson;
Saurabh Belsare;
Shifra Birnbaum;
Deborah E. Newman;
Jeannie Chan;
Jeremy P. Glenn;
Betsy Ferguson;
Laura A. Cox;
Jeffrey D. Wall
<?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.2583292"> <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.2583292</dct:identifier> <foaf:page rdf:resource="https://doi.org/10.5281/zenodo.2583292"/> <dct:creator> <rdf:Description rdf:about="http://orcid.org/0000-0002-5556-815X"> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-5556-815X</dct:identifier> <foaf:name>Jacqueline A. Robinson</foaf:name> <org:memberOf> <foaf:Organization> <foaf:name>University of California, San Francisco</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Saurabh Belsare</foaf:name> <org:memberOf> <foaf:Organization> <foaf:name>University of California, San Francisco</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Shifra Birnbaum</foaf:name> <org:memberOf> <foaf:Organization> <foaf:name>Texas Biomedical Research Institute</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Deborah E. Newman</foaf:name> <org:memberOf> <foaf:Organization> <foaf:name>Texas Biomedical Research Institute</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Jeannie Chan</foaf:name> <org:memberOf> <foaf:Organization> <foaf:name>Texas Biomedical Research Institute</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Jeremy P. Glenn</foaf:name> <org:memberOf> <foaf:Organization> <foaf:name>Texas Biomedical Research Institute</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Betsy Ferguson</foaf:name> <org:memberOf> <foaf:Organization> <foaf:name>Oregon National Primate Research Center</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Laura A. Cox</foaf:name> <org:memberOf> <foaf:Organization> <foaf:name>Wake Forest School of Medicine</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Jeffrey D. Wall</foaf:name> <org:memberOf> <foaf:Organization> <foaf:name>University of California, San Francisco</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:title>Resources for genomic analyses in baboons (genus Papio)</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> <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2019-03-01</dct:issued> <owl:sameAs rdf:resource="https://zenodo.org/record/2583292"/> <adms:identifier> <adms:Identifier> <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/2583292</skos:notation> <adms:schemeAgency>url</adms:schemeAgency> </adms:Identifier> </adms:identifier> <dct:isVersionOf rdf:resource="https://doi.org/10.5281/zenodo.2583291"/> <dct:description><p>Resources for genomic analyses in baboons (genus <em>Papio</em>). See &quot;Analysis of 100 high coverage genomes from a pedigreed captive baboon colony&quot; by Robinson et al. 2019 for further details.</p> <p><strong>Panu_2.0_Panu_3.0_chain_files.tar.gz</strong> Chain files for converting coordinates between Panu_2.0 and Panu_3.0. All coordinates in the files below correspond to Panu_2.0, but can be converted to coordinates in the new assembly, Panu_3.0, using the chain files with liftOver (Hinrichs et al. 2006, DOI:10.1093/nar/gkj144).</p> <p><strong>baboon_100_highcoverage_SNPRC_sample_info.txt</strong> Sample information: Sample ID, Sequencing ID, Type, Sex, Fped (%), Admixed, Mean coverage (X). The type, sex, inbreeding coefficient (Fped), and admixture status are all based on the SNPRC pedigree.</p> <p><strong>baboon_24_olive_founders_phased.vcf.gz</strong> Phased VCF files for 24 olive baboon founders. Phasing was performed with Beagle (Browning and Browning 2007, DOI:10.1086/521987), assuming an effective population size of 40,000 individuals (Boissinot et al. 2014, DOI:10.1002/ajpa.22618). SNPs were filtered to remove singletons and thinned so that no two sites were closer than 10 bp. <strong>baboon_24_olive_founders_phased.vcf.gz.tbi</strong> is the index for the VCF file.</p> <p><br> <strong>baboon_ldhelmet_recombination_maps.tar.gz</strong> Fine-scale recombination maps produced with LDhelmet (Chan et al. 2012, DOI:10.1371/journal.pgen.1003090) based on phased genotypes from 24 olive baboon founders. Results from three block penalties are provided (5, 25, 50).</p> <p><strong>baboon_AIMs_33founders_fixed_yellow_olive.txt</strong> List of ancestry informative markers for distinguishing olive and yellow baboon ancestry. These sites represent fixed differences between 7 genetically yellow and 24 genetically olive baboons.</p> <p><strong>baboon_plink_ROH.bed</strong> Coordinates of runs of homozygosity in BED format, inferred with PLINK (Chang et al. 2015, DOI:10.1186/s13742-015-0047-8) using the default behavior of the --homozyg function. The following parameters were used to prune SNPs beforehand: --indep-pairwise 50 5 0.5. The columns are: chromosome, start position, end position, sample name.</p> <p><strong>baboon_LOF_mutations.txt</strong> List of putative LOF mutations annotated with SnpEff (Cingolani et al. 2012, DOI:10.4161/fly.19695). 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Data volume | 8.6 GB | 8.6 GB |
Unique views | 315 | 315 |
Unique downloads | 89 | 89 |