{"corpus_id":3736055,"paper_sha":"fd8ba9431c2a1780e27b6f5e1e4947db9c85801c","doi":"10.1093/nar/gkr900","arxiv_id":null,"pmid":22070882,"pmcid":"3245043","mag_id":2102940758,"dblp_id":"journals/nar/GrazulisDMCLQSMDB12","acl_id":null,"title":"Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration","year":2011,"publication_date":"2011-11-08","venue":"Nucleic Acids Res.","journal":{"name":"Nucleic Acids Research","pages":"D420 - D427","volume":"40"},"journal_issn":null,"journal_title":null,"publication_types":["JournalArticle"],"pubmed_pub_types":["Journal Article","Research Support, Non-U.S. Gov't"],"s2_fields_of_study":["Biology","Medicine","Materials Science","Computer Science"],"reference_count":20,"citation_count":1096,"influential_citation_count":37,"is_open_access":true,"arxiv_categories":null,"arxiv_license":null,"arxiv_journal_ref":null,"mesh_headings":[{"d":"Cooperative Behavior","mj":false,"ui":"D003299"},{"d":"Crystallography","mj":true,"ui":"D003461"},{"d":"Databases, Factual","mj":true,"ui":"D016208"},{"d":"Models, Molecular","mj":false,"ui":"D008958"},{"d":"User-Computer Interface","mj":false,"ui":"D014584"}],"chemicals":null,"comments_corrections":null,"source_flags":5,"s2_open_access_pdf_url":"https://academic.oup.com/nar/article-pdf/40/D1/D420/16956726/gkr900.pdf","s2_open_access_landing_url":"https://www.semanticscholar.org/paper/fd8ba9431c2a1780e27b6f5e1e4947db9c85801c","s2_open_access_license":"CCBYNC","s2_open_access_status":"GOLD","pmc_open_access_pdf_url":null,"pmc_open_access_landing_url":null,"pmc_open_access_license":null,"pmc_open_access_status":null,"unpaywall_open_access_pdf_url":null,"unpaywall_open_access_landing_url":null,"unpaywall_open_access_license":null,"unpaywall_open_access_status":null,"abstract":"Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.","claims":[{"public_id":"cl_f10524419bcd9cb42cd6a59c188453b1","status":"active","text":"A newly developed website lets registered users deposit published and unpublished structures as personal communications or pre-publication depositions.","confidence":0.95,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_f10524419bcd9cb42cd6a59c188453b1"},{"public_id":"cl_03bf6a5c618822ab722715cbba753729","status":"active","text":"Allowing many users to deposit structures simultaneously is intended to extend the database and is presented as an initial step toward a worldwide Internet-based collaborative platform for collecting and curating structural knowledge.","confidence":0.9,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_03bf6a5c618822ab722715cbba753729"},{"public_id":"cl_348492de2e05ecea0258f1b88be2a20d","status":"active","text":"The Crystallography Open Database collects known small-molecule and small- to medium-cell crystal structures and makes them freely available on the Internet.","confidence":0.99,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_348492de2e05ecea0258f1b88be2a20d"},{"public_id":"cl_c7ab412d01cd22f835f015e4068f1c31","status":"active","text":"The database has aggregated approximately 150,000 crystal structures and provides basic search plus full or partial download access through standard open communication protocols.","confidence":0.95,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_c7ab412d01cd22f835f015e4068f1c31"}],"concepts":[{"public_id":"co_29660f3fdaa803f5b8e86208bf6bda12","status":"active","name":"basic search capabilities","description":"Search functions provided for querying the database contents.","types":["feature"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_29660f3fdaa803f5b8e86208bf6bda12"},{"public_id":"co_3826a77964dba38ee8baa877d8d76fee","status":"active","name":"pre-publication depositions","description":"Deposits of crystal structures made before formal publication.","types":["submission type"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_3826a77964dba38ee8baa877d8d76fee"},{"public_id":"co_6500860e762e8ae02454607da8fbdc36","status":"active","name":"open-access distribution model","description":"A distribution approach that makes the database freely accessible online.","types":["distribution model"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_6500860e762e8ae02454607da8fbdc36"},{"public_id":"co_660e1cdcb0a8e9629051e319add1fc8d","status":"active","name":"structural knowledge","description":"Curated information about crystal structures and related structural data.","types":["knowledge domain"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_660e1cdcb0a8e9629051e319add1fc8d"},{"public_id":"co_6b3b69847eeb57b5dc2f447a24ac2ec8","status":"active","name":"newly developed website","description":"A website interface created for depositing crystal structures into the database.","types":["web platform"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_6b3b69847eeb57b5dc2f447a24ac2ec8"},{"public_id":"co_8047d11c2604254032843b5717d1e43f","status":"active","name":"small molecule / small to medium sized unit cell crystal structures","description":"Crystal structures of small molecules with small to medium unit cells that are included in the database.","types":["dataset content"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_8047d11c2604254032843b5717d1e43f"},{"public_id":"co_8eaf878026dc71d6f05e2b44c71123be","status":"active","name":"registered users","description":"Users who have accounts enabling them to submit structures through the website.","types":["user group"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_8eaf878026dc71d6f05e2b44c71123be"},{"public_id":"co_bb803a6e97606c91daa2856a5bc40cf8","status":"active","name":"open communication protocols","description":"Standard internet protocols used for downloading all or parts of the database.","types":["protocol"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_bb803a6e97606c91daa2856a5bc40cf8"},{"public_id":"co_dddff6cc69dd633225080ee4b577e730","status":"active","name":"Crystallography Open Database","description":"An open-access database of crystal structures hosted at crystallography.net.","types":["database"],"aliases":["COD"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_dddff6cc69dd633225080ee4b577e730"},{"public_id":"co_f78519449de7cff8805d161d538fad0e","status":"active","name":"world-wide collaboration","description":"A global collaborative model for shared collection and curation of structural knowledge.","types":["collaboration platform"],"aliases":["world wide Internet-based collaborative platform"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_f78519449de7cff8805d161d538fad0e"}],"external_ids":{"DOI":"10.1093/nar/gkr900","ArXiv":null,"PubMed":22070882,"PubMedCentral":"3245043","MAG":2102940758,"DBLP":"journals/nar/GrazulisDMCLQSMDB12","ACL":null},"open_access":{"is_open_access":true,"pdf_url":"https://academic.oup.com/nar/article-pdf/40/D1/D420/16956726/gkr900.pdf","landing_url":"https://www.semanticscholar.org/paper/fd8ba9431c2a1780e27b6f5e1e4947db9c85801c","source":"semantic_scholar","pdf_url_source":"semantic_scholar_open_access_pdf","license":"CCBYNC","status":"GOLD","reason":null},"reference_availability":{"status":"available","references_indexed":true,"full_text_available":false,"full_text_source":null,"count_basis":"semantic_scholar_metadata","extraction_status":"not_applicable","reason":null},"source":{"provider":"episteme2","base_corpus":"semantic_scholar_dump","freshness_mode":"unknown","basis":["semantic_scholar_metadata","postgres_metadata"],"limits":["paper metadata is based on indexed upstream scholarly datasets","claims and concepts are available only for extracted papers","absence of claims or concepts means no extracted graph data is available in this response"],"status":"available","degraded":false,"degraded_reasons":[],"diagnostics":{"status":"available","degraded":false,"degraded_reasons":[],"metadata_status":"available","graph_status":"available","abstract_status":"available"},"source_flags":5},"paper_id":634319,"paper_uid":"1049dfd2-c5aa-445c-adfd-1184088dea4b","canonical_identity":{"paper_id":634319,"paper_uid":"1049dfd2-c5aa-445c-adfd-1184088dea4b","identity_status":"available","lookup_basis":"semantic_scholar_external_id","compatibility_path":"corpus_id"},"url":"https://sah.borca.ai/papers/3736055"}