{"id":"https://openalex.org/W2026200213","doi":"https://doi.org/10.1186/2041-1480-5-40","title":"Making species checklists understandable to machines \u2013 a shift from relational databases to ontologies","display_name":"Making species checklists understandable to machines \u2013 a shift from relational databases to ontologies","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2026200213","doi":"https://doi.org/10.1186/2041-1480-5-40","mag":"2026200213","pmid":"https://pubmed.ncbi.nlm.nih.gov/25937880"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-5-40","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-40","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-40","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-40","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025448588","display_name":"Nina Laurenne","orcid":null},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Nina Laurenne","raw_affiliation_strings":["Semantic Computing Research Group (SeCo), Department of Media Technology, Aalto University, P.O. Box 15500, 00076 Aalto, Espoo, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Semantic Computing Research Group (SeCo), Department of Media Technology, Aalto University, P.O. Box 15500, 00076 Aalto, Espoo, Finland","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021291777","display_name":"Jouni Tuominen","orcid":"https://orcid.org/0000-0003-4789-5676"},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jouni Tuominen","raw_affiliation_strings":["Semantic Computing Research Group (SeCo), Department of Media Technology, Aalto University, P.O. Box 15500, 00076 Aalto, Espoo, Finland","Semantic Computing Research Group (SeCo), Department of Media Technology, Aalto University, Aalto, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Semantic Computing Research Group (SeCo), Department of Media Technology, Aalto University, P.O. Box 15500, 00076 Aalto, Espoo, Finland","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Semantic Computing Research Group (SeCo), Department of Media Technology, Aalto University, Aalto, Finland","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045622371","display_name":"Hannu Saarenmaa","orcid":"https://orcid.org/0000-0003-3716-575X"},"institutions":[{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]},{"id":"https://openalex.org/I4210107997","display_name":"Finland University","ror":"https://ror.org/014rks409","country_code":"FI","type":"education","lineage":["https://openalex.org/I4210107997"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Hannu Saarenmaa","raw_affiliation_strings":["Digitarium, University of Eastern Finland, P.O. Box 111, 80101 Joensuu, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Digitarium, University of Eastern Finland, P.O. Box 111, 80101 Joensuu, Finland","institution_ids":["https://openalex.org/I175532246","https://openalex.org/I4210107997"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086685353","display_name":"Eero Hyv\u00f6nen","orcid":"https://orcid.org/0000-0003-1695-5840"},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Eero Hyv\u00f6nen","raw_affiliation_strings":["Semantic Computing Research Group (SeCo), Department of Media Technology, Aalto University, P.O. Box 15500, 00076 Aalto, Espoo, Finland","Semantic Computing Research Group (SeCo), Department of Media Technology, Aalto University, Aalto, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Semantic Computing Research Group (SeCo), Department of Media Technology, Aalto University, P.O. Box 15500, 00076 Aalto, Espoo, Finland","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Semantic Computing Research Group (SeCo), Department of Media Technology, Aalto University, Aalto, Finland","institution_ids":["https://openalex.org/I9927081"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5025448588"],"corresponding_institution_ids":["https://openalex.org/I9927081"],"apc_list":{"value":1340,"currency":"USD","value_usd":1340},"apc_paid":{"value":1340,"currency":"USD","value_usd":1340},"fwci":0.3899,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.60017487,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"5","issue":"1","first_page":"40","last_page":"40"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.3434000015258789,"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":0.3434000015258789,"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/T10895","display_name":"Species Distribution and Climate Change","score":0.3312000036239624,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.14110000431537628,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/identifier","display_name":"Identifier","score":0.8415753841400146},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.773330569267273},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6011068224906921},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5966720581054688},{"id":"https://openalex.org/keywords/taxon","display_name":"Taxon","score":0.5514689683914185},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5194489359855652},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.5126482844352722},{"id":"https://openalex.org/keywords/linked-data","display_name":"Linked data","score":0.5073360800743103},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.5009708404541016},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4309332072734833},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.12936681509017944}],"concepts":[{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.8415753841400146},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.773330569267273},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6011068224906921},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5966720581054688},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.5514689683914185},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5194489359855652},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.5126482844352722},{"id":"https://openalex.org/C69075417","wikidata":"https://www.wikidata.org/wiki/Q515701","display_name":"Linked data","level":3,"score":0.5073360800743103},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.5009708404541016},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4309332072734833},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.12936681509017944},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/2041-1480-5-40","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-40","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-40","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:25937880","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25937880","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":"Journal of biomedical semantics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4417522","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4417522","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Biomed Semantics","raw_type":"Text"},{"id":"pmh:oai:helda.helsinki.fi:10138/155554","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/155554","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"http://purl.org/eprint/type/JournalArticle"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-5-40","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-40","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-40","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Responsible consumption and production","score":0.49000000953674316,"id":"https://metadata.un.org/sdg/12"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2026200213.pdf","grobid_xml":"https://content.openalex.org/works/W2026200213.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W51932600","https://openalex.org/W172637933","https://openalex.org/W188284870","https://openalex.org/W1519024891","https://openalex.org/W1519646691","https://openalex.org/W1530608603","https://openalex.org/W1623746512","https://openalex.org/W1774690403","https://openalex.org/W1857833304","https://openalex.org/W1990628530","https://openalex.org/W1993977866","https://openalex.org/W2030103067","https://openalex.org/W2044988198","https://openalex.org/W2046134920","https://openalex.org/W2052153382","https://openalex.org/W2055532234","https://openalex.org/W2079335886","https://openalex.org/W2092448465","https://openalex.org/W2095942334","https://openalex.org/W2106581684","https://openalex.org/W2128585367","https://openalex.org/W2139934466","https://openalex.org/W2139995546","https://openalex.org/W2140681832","https://openalex.org/W2142678031","https://openalex.org/W2158223995","https://openalex.org/W2159327312","https://openalex.org/W2161661053","https://openalex.org/W2184493668","https://openalex.org/W2249452089","https://openalex.org/W2281227730","https://openalex.org/W2286479539","https://openalex.org/W2339038263","https://openalex.org/W2416787743","https://openalex.org/W2611894836","https://openalex.org/W2731867995","https://openalex.org/W2991278699","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2776293731","https://openalex.org/W1723367271","https://openalex.org/W2206235183","https://openalex.org/W4211148702","https://openalex.org/W1780389289","https://openalex.org/W1607526536","https://openalex.org/W2127217276","https://openalex.org/W2130019778","https://openalex.org/W4239617640","https://openalex.org/W4293165842"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,25,82,99,208,271],"scientific":[2,23,55,200],"names":[3,29,56,72,201],"of":[4,76,92,144,171,210,220,251,268,285,292,306,309,318],"plants":[5],"and":[6,20,45,116,229,264,281,298,312,323],"animals":[7],"play":[8],"a":[9,156,167,227,232,276],"major":[10],"role":[11],"in":[12,79,113,141,155,163,199,313],"Life":[13,105],"Sciences":[14],"as":[15,183,231],"information":[16,80,140,219,238,269,280],"is":[17,30,85,213],"indexed,":[18],"integrated,":[19],"searched":[21],"using":[22,160,191,260],"names.":[24],"main":[26],"problem":[27],"with":[28],"their":[31],"ambiguous":[32],"nature,":[33],"because":[34],"more":[35,117,168,319],"than":[36],"one":[37],"name":[38,93],"may":[39,48],"point":[40],"to":[41,64,70,86,97,165,178,278],"the":[42,50,125,142,180,217,240,249,258,266,283,304,307,316],"same":[43,51,181],"taxon":[44,228,241],"multiple":[46],"taxa":[47,188],"share":[49],"name.":[52],"In":[53],"addition,":[54],"change":[57],"over":[58,205],"time,":[59],"which":[60,109,121,236],"makes":[61],"them":[62],"open":[63],"various":[65],"interpretations.":[66],"Applying":[67],"machine-understandable":[68],"semantics":[69,308],"these":[71],"enables":[73,248],"efficient":[74],"processing":[75],"biological":[77,252,310,321],"content":[78,182],"systems.":[81],"first":[83],"step":[84],"use":[87,209],"unique":[88],"persistent":[89],"identifiers":[90,103],"instead":[91],"strings":[94],"when":[95],"referring":[96],"taxa.":[98],"most":[100],"commonly":[101],"used":[102,112],"are":[104,110,122,153,189],"Science":[106],"Identifiers":[107],"(LSID),":[108],"traditionally":[111],"relational":[114,157],"databases,":[115],"recently":[118],"HTTP":[119,192,211,224,296],"URIs,":[120],"applied":[123],"on":[124,257,289],"Semantic":[126,184,299],"Web":[127,185,300],"by":[128],"Linked":[129,261,272],"Data":[130,262,273],"applications.":[131],"RESULTS:":[132],"We":[133,194],"introduce":[134,175],"two":[135],"models":[136],"for":[137,215],"expressing":[138],"taxonomic":[139,172,218,293],"form":[143],"species":[145,151,221],"checklists.":[146,222],"First,":[147],"we":[148,174],"show":[149],"how":[150,197],"checklists":[152],"presented":[154],"database":[158],"system":[159],"LSIDs.":[161],"Then,":[162],"order":[164],"gain":[166],"detailed":[169],"representation":[170,305],"information,":[173],"meta-ontology":[176],"TaxMeOn":[177],"model":[179],"ontologies":[186],"where":[187],"identified":[190],"URIs.":[193],"also":[195,302],"explore":[196],"changes":[198],"can":[202,242],"be":[203,243],"managed":[204],"time.":[206],"CONCLUSIONS:":[207],"URIs":[212,297],"preferable":[214],"presenting":[216],"An":[223],"URI":[225],"identifies":[226],"operates":[230],"web":[233,259],"address":[234],"from":[235,254],"additional":[237],"about":[239],"located,":[244],"unlike":[245],"LSID.":[246],"This":[247],"integration":[250],"data":[253,287],"different":[255],"sources":[256],"principles":[263],"prevents":[265],"formation":[267],"silos.":[270],"approach":[274],"allows":[275],"user":[277],"assemble":[279],"evaluate":[282],"complexity":[284],"taxonomical":[286],"based":[288],"conflicting":[290],"views":[291],"classifications.":[294],"Using":[295],"technologies":[301],"facilitate":[303],"data,":[311],"this":[314],"way,":[315],"creation":[317],"\"intelligent\"":[320],"applications":[322],"services.":[324]},"counts_by_year":[{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
