{"id":"https://openalex.org/W2986157475","doi":"https://doi.org/10.1109/mcse.2019.2952838","title":"Comparing the Use of Research Resource Identifiers and Natural Language Processing for Citation of Databases, Software, and Other Digital Artifacts","display_name":"Comparing the Use of Research Resource Identifiers and Natural Language Processing for Citation of Databases, Software, and Other Digital Artifacts","publication_year":2019,"publication_date":"2019-11-12","ids":{"openalex":"https://openalex.org/W2986157475","doi":"https://doi.org/10.1109/mcse.2019.2952838","mag":"2986157475","pmid":"https://pubmed.ncbi.nlm.nih.gov/40791297"},"language":"en","primary_location":{"id":"doi:10.1109/mcse.2019.2952838","is_oa":false,"landing_page_url":"https://doi.org/10.1109/mcse.2019.2952838","pdf_url":null,"source":{"id":"https://openalex.org/S107923245","display_name":"Computing in Science & Engineering","issn_l":"1521-9615","issn":["1521-9615","1558-366X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320061","host_organization_name":"AIP Publishing","host_organization_lineage":["https://openalex.org/P4310320061","https://openalex.org/P4310320257"],"host_organization_lineage_names":["AIP Publishing","American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computing in Science & Engineering","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://escholarship.org/content/qt9kh7h8zr/qt9kh7h8zr.pdf?t=q6l0af","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040580626","display_name":"Chun\u2010Nan Hsu","orcid":"https://orcid.org/0000-0002-5240-4707"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chun-Nan Hsu","raw_affiliation_strings":["University of California San Diego"],"affiliations":[{"raw_affiliation_string":"University of California San Diego","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058460697","display_name":"Anita Bandrowski","orcid":"https://orcid.org/0000-0002-5497-0243"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Anita E. Bandrowski","raw_affiliation_strings":["University of California San DiegoSciCrunch, Inc"],"affiliations":[{"raw_affiliation_string":"University of California San DiegoSciCrunch, Inc","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080810417","display_name":"Tom Gillespie","orcid":"https://orcid.org/0000-0002-7509-4801"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas H. Gillespie","raw_affiliation_strings":["University of California San Diego"],"affiliations":[{"raw_affiliation_string":"University of California San Diego","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077608769","display_name":"Jon Udell","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jon Udell","raw_affiliation_strings":["Hypothes.is"],"affiliations":[{"raw_affiliation_string":"Hypothes.is","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043562937","display_name":"Ko\u2010Wei Lin","orcid":"https://orcid.org/0000-0001-6645-2091"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ko-Wei Lin","raw_affiliation_strings":["University of California San Diego"],"affiliations":[{"raw_affiliation_string":"University of California San Diego","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024882547","display_name":"\u0130brahim Burak \u00d6zyurt","orcid":"https://orcid.org/0000-0003-3944-1893"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ibrahim Burak Ozyurt","raw_affiliation_strings":["University of California San Diego"],"affiliations":[{"raw_affiliation_string":"University of California San Diego","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076014872","display_name":"Jeffrey S. Grethe","orcid":"https://orcid.org/0000-0001-5212-7052"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey S. Grethe","raw_affiliation_strings":["University of California San Diego"],"affiliations":[{"raw_affiliation_string":"University of California San Diego","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061037631","display_name":"Maryann E. Martone","orcid":"https://orcid.org/0000-0002-8406-3871"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Maryann E. Martone","raw_affiliation_strings":["University of California San DiegoSciCrunch, Inc"],"affiliations":[{"raw_affiliation_string":"University of California San DiegoSciCrunch, Inc","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5040580626"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":null,"apc_paid":null,"fwci":0.4295,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.63056142,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"22","issue":"2","first_page":"22","last_page":"32"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11937","display_name":"Research Data Management Practices","score":0.9915000200271606,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8030503988265991},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.7994884848594666},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6967679262161255},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.6599868535995483},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5966684222221375},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5590603351593018},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5554350018501282},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5420111417770386},{"id":"https://openalex.org/keywords/citation","display_name":"Citation","score":0.5110691785812378},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.485638290643692},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.47485068440437317},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4721108675003052},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.45341333746910095}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8030503988265991},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.7994884848594666},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6967679262161255},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.6599868535995483},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5966684222221375},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5590603351593018},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5554350018501282},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5420111417770386},{"id":"https://openalex.org/C2778805511","wikidata":"https://www.wikidata.org/wiki/Q1713","display_name":"Citation","level":2,"score":0.5110691785812378},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.485638290643692},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.47485068440437317},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4721108675003052},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.45341333746910095},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1109/mcse.2019.2952838","is_oa":false,"landing_page_url":"https://doi.org/10.1109/mcse.2019.2952838","pdf_url":null,"source":{"id":"https://openalex.org/S107923245","display_name":"Computing in Science & Engineering","issn_l":"1521-9615","issn":["1521-9615","1558-366X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320061","host_organization_name":"AIP Publishing","host_organization_lineage":["https://openalex.org/P4310320061","https://openalex.org/P4310320257"],"host_organization_lineage_names":["AIP Publishing","American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computing in Science & Engineering","raw_type":"journal-article"},{"id":"pmid:40791297","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40791297","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computing in science & engineering","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt9kh7h8zr","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/9kh7h8zr","pdf_url":"https://escholarship.org/content/qt9kh7h8zr/qt9kh7h8zr.pdf?t=q6l0af","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computing in Science & Engineering, vol 22, iss 2","raw_type":"article"},{"id":"pmh:ark:/13030/qt9kh7h8zr","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12338378","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12338378","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Comput Sci Eng","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:escholarship.org:ark:/13030/qt9kh7h8zr","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/9kh7h8zr","pdf_url":"https://escholarship.org/content/qt9kh7h8zr/qt9kh7h8zr.pdf?t=q6l0af","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computing in Science & Engineering, vol 22, iss 2","raw_type":"article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1131467706","display_name":null,"funder_award_id":"U24DK097771","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G197008112","display_name":null,"funder_award_id":"NIDDK","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6312945067","display_name":null,"funder_award_id":"DK097771","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G7089866635","display_name":null,"funder_award_id":"DA039832","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8169943893","display_name":null,"funder_award_id":"DK097771","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2986157475.pdf","grobid_xml":"https://content.openalex.org/works/W2986157475.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1938986183","https://openalex.org/W2077509789","https://openalex.org/W2114224807","https://openalex.org/W2190273774","https://openalex.org/W2226221146","https://openalex.org/W2266909730","https://openalex.org/W2286236870","https://openalex.org/W2346015361","https://openalex.org/W2418022613","https://openalex.org/W2470289662","https://openalex.org/W2914605960","https://openalex.org/W2915039166","https://openalex.org/W2950860947","https://openalex.org/W6638793922","https://openalex.org/W6764079558"],"related_works":["https://openalex.org/W4378651134","https://openalex.org/W4252684102","https://openalex.org/W2608983118","https://openalex.org/W2352307597","https://openalex.org/W1979633005","https://openalex.org/W2163724607","https://openalex.org/W3135403405","https://openalex.org/W2023227762","https://openalex.org/W1980092392","https://openalex.org/W1981780420"],"abstract_inverted_index":{"The":[0,83],"Research":[1],"Resource":[2],"Identifier":[3],"(RRID)":[4],"was":[5,102],"introduced":[6],"in":[7,81],"2014":[8],"to":[9,77,104,131,136],"better":[10],"identify":[11,78,105],"biomedical":[12],"research":[13],"resources":[14,25,110],"and":[15,29,50,93,124],"track":[16],"their":[17,52],"use":[18,53],"across":[19],"the":[20,36,61,69,109],"literature,":[21],"including":[22],"key":[23],"digital":[24,55,137],"such":[26],"as":[27,114,116],"databases":[28],"software.":[30],"Authors":[31],"include":[32],"an":[33,46],"RRID":[34,65,89],"after":[35],"first":[37],"mention":[38],"of":[39,48,63,71,108],"any":[40],"resource":[41,56,79,138],"used.":[42],"Here,":[43],"we":[44,120],"provide":[45,132],"overview":[47],"RRIDs":[49,113,123],"analyze":[51],"for":[54],"identification.":[57],"We":[58],"quantitatively":[59],"compare":[60],"output":[62],"our":[64,95],"curation":[66],"workflow":[67],"with":[68],"outputs":[70],"automated":[72],"text":[73,100,125],"mining":[74,101,126],"systems":[75],"used":[76],"mentions":[80],"text.":[82],"results":[84],"show":[85],"that":[86,94],"authors":[87],"follow":[88],"reporting":[90],"guidelines":[91],"well,":[92],"natural":[96],"language":[97],"processing":[98],"based":[99],"able":[103],"nearly":[106],"all":[107],"identified":[111],"by":[112],"well":[115],"thousands":[117],"more.":[118],"Finally,":[119],"demonstrate":[121],"how":[122],"can":[127],"complement":[128],"each":[129],"other":[130],"a":[133],"scalable":[134],"solution":[135],"citation.":[139]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}