{"id":"https://openalex.org/W2127997067","doi":"https://doi.org/10.1145/2506583.2506651","title":"Measuring Relatedness Between Scientific Entities in Annotation Datasets","display_name":"Measuring Relatedness Between Scientific Entities in Annotation Datasets","publication_year":2013,"publication_date":"2013-09-22","ids":{"openalex":"https://openalex.org/W2127997067","doi":"https://doi.org/10.1145/2506583.2506651","mag":"2127997067"},"language":"en","primary_location":{"id":"doi:10.1145/2506583.2506651","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506651","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069520441","display_name":"Guillermo Palma","orcid":"https://orcid.org/0000-0002-8111-2439"},"institutions":[{"id":"https://openalex.org/I629287","display_name":"Sim\u00f3n Bol\u00edvar University","ror":"https://ror.org/01ak5cj98","country_code":"VE","type":"education","lineage":["https://openalex.org/I629287"]}],"countries":["VE"],"is_corresponding":true,"raw_author_name":"Guillermo Palma","raw_affiliation_strings":["Universidad Sim\u00f3n Bol\u00edvar, Caracas, Venezuela","Universidad Simon-Bolivar, Caracas, Venezuela"],"affiliations":[{"raw_affiliation_string":"Universidad Sim\u00f3n Bol\u00edvar, Caracas, Venezuela","institution_ids":["https://openalex.org/I629287"]},{"raw_affiliation_string":"Universidad Simon-Bolivar, Caracas, Venezuela","institution_ids":["https://openalex.org/I629287"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055433807","display_name":"Mar\u00eda-Esther Vidal","orcid":"https://orcid.org/0000-0003-1160-8727"},"institutions":[{"id":"https://openalex.org/I629287","display_name":"Sim\u00f3n Bol\u00edvar University","ror":"https://ror.org/01ak5cj98","country_code":"VE","type":"education","lineage":["https://openalex.org/I629287"]}],"countries":["VE"],"is_corresponding":false,"raw_author_name":"Maria-Esther Vidal","raw_affiliation_strings":["Universidad Sim\u00f3n Bol\u00edvar, Caracas, Venezuela","Universidad Simon-Bolivar, Caracas, Venezuela"],"affiliations":[{"raw_affiliation_string":"Universidad Sim\u00f3n Bol\u00edvar, Caracas, Venezuela","institution_ids":["https://openalex.org/I629287"]},{"raw_affiliation_string":"Universidad Simon-Bolivar, Caracas, Venezuela","institution_ids":["https://openalex.org/I629287"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048814221","display_name":"Eric S. Haag","orcid":"https://orcid.org/0000-0002-6102-3498"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Haag","raw_affiliation_strings":["University of Maryland, College Park, USA"],"affiliations":[{"raw_affiliation_string":"University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054150982","display_name":"Louiqa Raschid","orcid":"https://orcid.org/0000-0002-0630-6049"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Louiqa Raschid","raw_affiliation_strings":["University of Maryland, College Park, USA"],"affiliations":[{"raw_affiliation_string":"University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015557906","display_name":"Andreas Thor","orcid":"https://orcid.org/0000-0003-2575-2893"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Thor","raw_affiliation_strings":["University of Leipzig, Germany"],"affiliations":[{"raw_affiliation_string":"University of Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5069520441"],"corresponding_institution_ids":["https://openalex.org/I629287"],"apc_list":null,"apc_paid":null,"fwci":2.0962,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.87264458,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"367","last_page":"376"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987999796867371,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987999796867371,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.998199999332428,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9976999759674072,"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/computer-science","display_name":"Computer science","score":0.7255852222442627},{"id":"https://openalex.org/keywords/semantic-similarity","display_name":"Semantic similarity","score":0.6704835295677185},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6211071610450745},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5854694247245789},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5705745816230774},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.48738962411880493},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.4518144726753235},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.4450336694717407},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4438638389110565},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.42566144466400146},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.41601887345314026},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38236236572265625},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30291038751602173},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.20187300443649292}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7255852222442627},{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.6704835295677185},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6211071610450745},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5854694247245789},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5705745816230774},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.48738962411880493},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.4518144726753235},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.4450336694717407},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4438638389110565},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.42566144466400146},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.41601887345314026},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38236236572265625},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30291038751602173},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.20187300443649292},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2506583.2506651","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506651","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.453.438","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.453.438","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://dbs.uni-leipzig.de/file/acmbcb2013_submission_123.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W30666142","https://openalex.org/W36021107","https://openalex.org/W103340358","https://openalex.org/W111988062","https://openalex.org/W186091728","https://openalex.org/W202767273","https://openalex.org/W1034019924","https://openalex.org/W1647729745","https://openalex.org/W1679882079","https://openalex.org/W1963838724","https://openalex.org/W1998982581","https://openalex.org/W2007038646","https://openalex.org/W2013093146","https://openalex.org/W2057175746","https://openalex.org/W2063999654","https://openalex.org/W2069870183","https://openalex.org/W2084168100","https://openalex.org/W2084377579","https://openalex.org/W2087064593","https://openalex.org/W2092317446","https://openalex.org/W2100935296","https://openalex.org/W2113364427","https://openalex.org/W2117805756","https://openalex.org/W2128049108","https://openalex.org/W2128600649","https://openalex.org/W2139736926","https://openalex.org/W2294408688","https://openalex.org/W2953332543","https://openalex.org/W6604582446","https://openalex.org/W6636975626"],"related_works":["https://openalex.org/W17155033","https://openalex.org/W3207760230","https://openalex.org/W1496222301","https://openalex.org/W4312814274","https://openalex.org/W1590307681","https://openalex.org/W2536018345","https://openalex.org/W4285370786","https://openalex.org/W2296488620","https://openalex.org/W2358353312","https://openalex.org/W2353836703"],"abstract_inverted_index":{"Linked":[0],"Open":[1],"Data":[2],"has":[3],"made":[4],"available":[5],"a":[6,59,108,118,143,180,191],"diversity":[7],"of":[8,75,133,136,153,166,171,194,197,204],"scientific":[9,31],"collections":[10],"where":[11],"scientists":[12],"have":[13,88],"annotated":[14],"entities":[15,57,130],"in":[16,36,91,107,131],"the":[17,52,73,76,92,126,134,164,195],"datasets":[18,43,170],"with":[19,82],"controlled":[20],"vocabulary":[21],"terms":[22,132],"(CV":[23],"terms)":[24],"from":[25],"ontologies.":[26],"These":[27],"semantic":[28],"annotations":[29],"encode":[30],"knowledge":[32],"which":[33],"is":[34],"captured":[35],"annotation":[37,120],"datasets.":[38],"One":[39],"can":[40,189,200],"mine":[41],"these":[42],"to":[44,156],"discover":[45],"relationships":[46,69],"and":[47,149,173,179,199],"patterns":[48],"between":[49,56,128],"entities.":[50],"Determining":[51],"relatedness":[53,106,127,196],"(or":[54],"similarity)":[55],"becomes":[58],"building":[60],"block":[61],"for":[62],"graph":[63],"pattern":[64],"mining,":[65],"e.g.,":[66,94],"identifying":[67],"drug-drug":[68],"could":[70],"depend":[71],"on":[72,168],"similarity":[74,86,121,135],"diseases":[77],"(conditions)":[78],"that":[79,124,187],"are":[80],"associated":[81],"each":[83],"drug.":[84],"Diverse":[85],"metrics":[87],"been":[89],"proposed":[90],"literature,":[93],"i)":[95],"string-similarity":[96],"metrics;":[97,100,103],"ii)":[98],"path-similarity":[99],"iii)":[101],"topological-similarity":[102],"all":[104],"measure":[105],"given":[109],"taxonomy":[110],"or":[111],"ontology.":[112],"In":[113],"this":[114],"paper,":[115],"we":[116,150],"consider":[117],"novel":[119,206],"metric":[122],"AnnSim":[123,141,167,188],"measures":[125],"two":[129],"their":[137,174],"annotations.":[138],"We":[139,161],"model":[140],"as":[142],"1-to-1":[144],"maximal":[145],"weighted":[146],"bipartite":[147],"match,":[148],"exploit":[151],"properties":[152],"existing":[154],"solvers":[155],"provide":[157,190,201],"an":[158,202],"efficient":[159],"solution.":[160],"empirically":[162],"study":[163],"effectiveness":[165],"real-world":[169],"genes":[172],"GO":[175],"annotations,":[176],"clinical":[177],"trials,":[178],"human":[181],"disease":[182],"benchmark.":[183],"Our":[184],"results":[185],"suggest":[186],"deeper":[192],"understanding":[193],"concepts":[198],"explanation":[203],"potential":[205],"patterns.":[207]},"counts_by_year":[{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
