New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
Abstract The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which...
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| Veröffentlicht in: | Nucleic acids research 2020-01, Vol.48 (D1), p.D882-D889 |
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| creator | Luo, Yunhai Hitz, Benjamin C Gabdank, Idan Hilton, Jason A Kagda, Meenakshi S Lam, Bonita Myers, Zachary Sud, Paul Jou, Jennifer Lin, Khine Baymuradov, Ulugbek K Graham, Keenan Litton, Casey Miyasato, Stuart R Strattan, J Seth Jolanki, Otto Lee, Jin-Wook Tanaka, Forrest Y Adenekan, Philip O’Neill, Emma Cherry, J Michael |
| description | Abstract
The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation. |
| doi_str_mv | 10.1093/nar/gkz1062 |
| format | Article |
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The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkz1062</identifier><identifier>PMID: 31713622</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Animals ; Database Issue ; Databases, Genetic ; DNA - genetics ; Genome, Human ; Genomics ; Humans ; Mice ; Software</subject><ispartof>Nucleic acids research, 2020-01, Vol.48 (D1), p.D882-D889</ispartof><rights>The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019</rights><rights>The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c520t-fa42606c049eb7930d4e259031686dfee73f45e365834af3342bd8b1c1e24ac53</citedby><cites>FETCH-LOGICAL-c520t-fa42606c049eb7930d4e259031686dfee73f45e365834af3342bd8b1c1e24ac53</cites><orcidid>0000-0001-6948-2042 ; 0000-0001-5094-282X ; 0000-0001-5025-5886 ; 0000-0002-8649-6611 ; 0000-0003-3361-3594</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061942/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061942/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31713622$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Luo, Yunhai</creatorcontrib><creatorcontrib>Hitz, Benjamin C</creatorcontrib><creatorcontrib>Gabdank, Idan</creatorcontrib><creatorcontrib>Hilton, Jason A</creatorcontrib><creatorcontrib>Kagda, Meenakshi S</creatorcontrib><creatorcontrib>Lam, Bonita</creatorcontrib><creatorcontrib>Myers, Zachary</creatorcontrib><creatorcontrib>Sud, Paul</creatorcontrib><creatorcontrib>Jou, Jennifer</creatorcontrib><creatorcontrib>Lin, Khine</creatorcontrib><creatorcontrib>Baymuradov, Ulugbek K</creatorcontrib><creatorcontrib>Graham, Keenan</creatorcontrib><creatorcontrib>Litton, Casey</creatorcontrib><creatorcontrib>Miyasato, Stuart R</creatorcontrib><creatorcontrib>Strattan, J Seth</creatorcontrib><creatorcontrib>Jolanki, Otto</creatorcontrib><creatorcontrib>Lee, Jin-Wook</creatorcontrib><creatorcontrib>Tanaka, Forrest Y</creatorcontrib><creatorcontrib>Adenekan, Philip</creatorcontrib><creatorcontrib>O’Neill, Emma</creatorcontrib><creatorcontrib>Cherry, J Michael</creatorcontrib><title>New developments on the Encyclopedia of DNA Elements (ENCODE) data portal</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation.</description><subject>Animals</subject><subject>Database Issue</subject><subject>Databases, Genetic</subject><subject>DNA - genetics</subject><subject>Genome, Human</subject><subject>Genomics</subject><subject>Humans</subject><subject>Mice</subject><subject>Software</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kE1Lw0AQhhdRbP04eZc9SUViZz-yaS5CqVEL0l70vGw3kzaaZmM2reivN6VV9OJpYObhfYeHkDMG1wxi0S9N3Z-_fjJQfI90mVA8kLHi-6QLAsKAgRx0yJH3LwBMslAeko5g0YbjXTKe4DtNcY2Fq5ZYNp66kjYLpElpP2y7xDQ31GX0djKkSYFbppdMRtPb5JKmpjG0cnVjihNykJnC4-luHpPnu-Rp9BA8Tu_Ho-FjYEMOTZAZyRUoCzLGWRQLSCXyMAbB1EClGWIkMhmiUOFASJMJIfksHcyYZcilsaE4Jjfb3Go1W2Jq24dqU-iqzpem_tDO5PrvpcwXeu7WOgLFYsnbgN4uoHZvK_SNXubeYlGYEt3Kay6YBIhEuOm62qK2dt7XmP3UMNAb-bqVr3fyW_r892c_7LftFrjYAm5V_Zv0BV78jJM</recordid><startdate>20200108</startdate><enddate>20200108</enddate><creator>Luo, Yunhai</creator><creator>Hitz, Benjamin C</creator><creator>Gabdank, Idan</creator><creator>Hilton, Jason A</creator><creator>Kagda, Meenakshi S</creator><creator>Lam, Bonita</creator><creator>Myers, Zachary</creator><creator>Sud, Paul</creator><creator>Jou, Jennifer</creator><creator>Lin, Khine</creator><creator>Baymuradov, Ulugbek K</creator><creator>Graham, Keenan</creator><creator>Litton, Casey</creator><creator>Miyasato, Stuart R</creator><creator>Strattan, J Seth</creator><creator>Jolanki, Otto</creator><creator>Lee, Jin-Wook</creator><creator>Tanaka, Forrest Y</creator><creator>Adenekan, Philip</creator><creator>O’Neill, Emma</creator><creator>Cherry, J Michael</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-6948-2042</orcidid><orcidid>https://orcid.org/0000-0001-5094-282X</orcidid><orcidid>https://orcid.org/0000-0001-5025-5886</orcidid><orcidid>https://orcid.org/0000-0002-8649-6611</orcidid><orcidid>https://orcid.org/0000-0003-3361-3594</orcidid></search><sort><creationdate>20200108</creationdate><title>New developments on the Encyclopedia of DNA Elements (ENCODE) data portal</title><author>Luo, Yunhai ; 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The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>31713622</pmid><doi>10.1093/nar/gkz1062</doi><orcidid>https://orcid.org/0000-0001-6948-2042</orcidid><orcidid>https://orcid.org/0000-0001-5094-282X</orcidid><orcidid>https://orcid.org/0000-0001-5025-5886</orcidid><orcidid>https://orcid.org/0000-0002-8649-6611</orcidid><orcidid>https://orcid.org/0000-0003-3361-3594</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animals Database Issue Databases, Genetic DNA - genetics Genome, Human Genomics Humans Mice Software |
| title | New developments on the Encyclopedia of DNA Elements (ENCODE) data portal |
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