{"id":"https://openalex.org/W6949596182","doi":"https://doi.org/10.5281/zenodo.15284917","title":"BioPortal Software for NAR-00680-Web-S-2025.R1 Publication","display_name":"BioPortal Software for NAR-00680-Web-S-2025.R1 Publication","publication_year":2025,"publication_date":"2025-04-25","ids":{"openalex":"https://openalex.org/W6949596182","doi":"https://doi.org/10.5281/zenodo.15284917"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.15284917","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.15284917","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"type":"other","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.15284917","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Vendetti, Jennifer","orcid":"https://orcid.org/0009-0005-5085-6514"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Vendetti, Jennifer","raw_affiliation_strings":["Stanford University"],"raw_orcid":"https://orcid.org/0009-0005-5085-6514","affiliations":[{"raw_affiliation_string":"Stanford University","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Harris, Nomi","orcid":"https://orcid.org/0000-0001-6315-3707"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Harris, Nomi","raw_affiliation_strings":["Lawrence Berkeley National Laboratory"],"raw_orcid":"https://orcid.org/0000-0001-6315-3707","affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Dorf, Michael","orcid":"https://orcid.org/0009-0005-2374-6344"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dorf, Michael","raw_affiliation_strings":["Stanford University"],"raw_orcid":"https://orcid.org/0009-0005-2374-6344","affiliations":[{"raw_affiliation_string":"Stanford University","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Skrenchuk, Alex","orcid":"https://orcid.org/0000-0003-3541-3334"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Skrenchuk, Alex","raw_affiliation_strings":["Stanford University"],"raw_orcid":"https://orcid.org/0000-0003-3541-3334","affiliations":[{"raw_affiliation_string":"Stanford University","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Caufield, J. Harry","orcid":"https://orcid.org/0000-0001-5705-7831"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Caufield, J. Harry","raw_affiliation_strings":["Lawrence Berkeley National Laboratory"],"raw_orcid":"https://orcid.org/0000-0001-5705-7831","affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Gon\u00e7alves, Rafael S.","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gon\u00e7alves, Rafael S.","raw_affiliation_strings":["Stanford University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Graybeal, John","orcid":"https://orcid.org/0000-0001-6875-5360"},"institutions":[{"id":"https://openalex.org/I4210125269","display_name":"RED Consulting (Norway)","ror":"https://ror.org/038ny6229","country_code":"NO","type":"company","lineage":["https://openalex.org/I4210125269"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Graybeal, John","raw_affiliation_strings":["GraybealSKI Consulting"],"raw_orcid":"https://orcid.org/0000-0001-6875-5360","affiliations":[{"raw_affiliation_string":"GraybealSKI Consulting","institution_ids":["https://openalex.org/I4210125269"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hegde, Harshad","orcid":"https://orcid.org/0000-0002-2411-565X"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hegde, Harshad","raw_affiliation_strings":["Lawrence Berkeley National Laboratory"],"raw_orcid":"https://orcid.org/0000-0002-2411-565X","affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Redmond, Timothy","orcid":"https://orcid.org/0009-0006-2218-4789"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Redmond, Timothy","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0009-0006-2218-4789","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Mungall, Christopher","orcid":"https://orcid.org/0000-0002-6601-2165"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mungall, Christopher","raw_affiliation_strings":["Lawrence Berkeley National Laboratory"],"raw_orcid":"https://orcid.org/0000-0002-6601-2165","affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"last","author":{"id":null,"display_name":"Musen, Mark","orcid":"https://orcid.org/0000-0003-3325-793X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Musen, Mark","raw_affiliation_strings":["Stanford University"],"raw_orcid":"https://orcid.org/0000-0003-3325-793X","affiliations":[{"raw_affiliation_string":"Stanford University","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":11,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.7595000267028809},{"id":"https://openalex.org/keywords/prot\u00e9g\u00e9","display_name":"Prot\u00e9g\u00e9","score":0.6442999839782715},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.6090999841690063},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.570900022983551},{"id":"https://openalex.org/keywords/hypermedia","display_name":"Hypermedia","score":0.5644000172615051},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5317999720573425},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5109999775886536},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5005000233650208}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8029999732971191},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7595000267028809},{"id":"https://openalex.org/C2779247653","wikidata":"https://www.wikidata.org/wiki/Q2066865","display_name":"Prot\u00e9g\u00e9","level":3,"score":0.6442999839782715},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.6090999841690063},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.570900022983551},{"id":"https://openalex.org/C2780126544","wikidata":"https://www.wikidata.org/wiki/Q837900","display_name":"Hypermedia","level":2,"score":0.5644000172615051},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5317999720573425},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5286999940872192},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5109999775886536},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5005000233650208},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4339999854564667},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.4235999882221222},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.41339999437332153},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.3822000026702881},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.33000001311302185},{"id":"https://openalex.org/C118248724","wikidata":"https://www.wikidata.org/wiki/Q5969997","display_name":"IDEF5","level":4,"score":0.3255999982357025},{"id":"https://openalex.org/C154210476","wikidata":"https://www.wikidata.org/wiki/Q7095057","display_name":"Ontology components","level":5,"score":0.31690001487731934},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3068999946117401},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.2768000066280365},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.2671999931335449},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.2533000111579895}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5281/zenodo.15284917","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.15284917","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.5281/zenodo.15284917","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.15284917","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.6651520133018494,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"This":[0],"software":[1],"includes":[2],"components":[3],"of":[4,84],"the":[5,13,73,97,106],"BioPortal":[6,33,87,98],"application":[7],"that":[8,90,104,119],"implement":[9],"functionality":[10],"described":[11],"in":[12,32,65,96],"manuscript":[14],"accepted":[15],"to":[16,109,123],"Nucleic":[17],"Acids":[18],"Research":[19],"(Manuscript":[20],"ID:":[21],"NAR-00680-Web-S-2025.R1).":[22],"bioportal_web_ui:":[23],"User":[24],"interface":[25],"for":[26,38,46,56,78],"browsing":[27],"and":[28,50,54,58,113],"interacting":[29],"with":[30,125],"ontologies":[31,57,70,77,115],"ontologies_api_ruby_client:":[34],"A":[35],"Ruby":[36,117],"client":[37],"accessing":[39,47],"BioPortal's":[40],"hypermedia":[41],"API":[42,45],"ontologies_api:":[43],"Hypermedia":[44],"ontology":[48,63],"metadata":[49],"content":[51],"ontologies_linked_data:":[52],"Models":[53],"serializers":[55],"related":[59],"artifacts":[60],"ncbo_annotator:":[61],"Identifies":[62],"concepts":[64],"free":[66],"text":[67,81],"using":[68],"BioPortal\u2019s":[69],"ncbo_ontology_recommender:":[71],"Suggests":[72],"most":[74],"relevant":[75],"biomedical":[76],"a":[79,93],"given":[80],"or":[82],"set":[83],"keywords":[85],"via":[86],"ncbo_cron:":[88],"Jobs":[89],"run":[91],"on":[92],"regular":[94],"basis":[95],"infrastructure":[99],"owlapi_wrapper:":[100],"Command":[101],"line":[102],"utility":[103],"wraps":[105],"Java":[107],"OWL-API":[108],"parse":[110],"RDFS,":[111],"OWL":[112],"OBO":[114],"goo:":[116],"library":[118],"provides":[120],"ORM-like":[121],"capabilities":[122],"interact":[124],"RDF/SPARQL":[126],"backends":[127]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
