{"id":"https://openalex.org/W4220956629","doi":"https://doi.org/10.1007/s10115-022-01668-7","title":"Context mining and graph queries on giant biomedical knowledge graphs","display_name":"Context mining and graph queries on giant biomedical knowledge graphs","publication_year":2022,"publication_date":"2022-03-29","ids":{"openalex":"https://openalex.org/W4220956629","doi":"https://doi.org/10.1007/s10115-022-01668-7"},"language":"en","primary_location":{"id":"doi:10.1007/s10115-022-01668-7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10115-022-01668-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10115-022-01668-7.pdf","source":{"id":"https://openalex.org/S81770430","display_name":"Knowledge and Information Systems","issn_l":"0219-1377","issn":["0219-1377","0219-3116"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Knowledge and Information Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10115-022-01668-7.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047464344","display_name":"Jens D\u00f6rpinghaus","orcid":"https://orcid.org/0000-0003-0245-7752"},"institutions":[{"id":"https://openalex.org/I2801533059","display_name":"German Center for Neurodegenerative Diseases","ror":"https://ror.org/043j0f473","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I2801533059","https://openalex.org/I4405256427"]},{"id":"https://openalex.org/I4210134559","display_name":"Federal Institute for Vocational Education and Training","ror":"https://ror.org/0420tmj11","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210134559"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jens D\u00f6rpinghaus","raw_affiliation_strings":["Federal Institute for Vocational Education and Training (BIBB), Bonn, Germany","German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany"],"raw_orcid":"https://orcid.org/0000-0003-0245-7752","affiliations":[{"raw_affiliation_string":"Federal Institute for Vocational Education and Training (BIBB), Bonn, Germany","institution_ids":["https://openalex.org/I4210134559"]},{"raw_affiliation_string":"German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany","institution_ids":["https://openalex.org/I2801533059"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045759801","display_name":"Andreas Stefan","orcid":null},"institutions":[{"id":"https://openalex.org/I155417937","display_name":"Hochschule Bonn-Rhein-Sieg","ror":"https://ror.org/04m2anh63","country_code":"DE","type":"education","lineage":["https://openalex.org/I155417937"]},{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Stefan","raw_affiliation_strings":["Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany","Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Sankt Augustin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany","institution_ids":["https://openalex.org/I155417937"]},{"raw_affiliation_string":"Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091508214","display_name":"Bruce Schultz","orcid":"https://orcid.org/0000-0003-4492-9463"},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bruce Schultz","raw_affiliation_strings":["Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Sankt Augustin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016675379","display_name":"Marc Jacobs","orcid":"https://orcid.org/0000-0003-4153-3930"},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marc Jacobs","raw_affiliation_strings":["Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Sankt Augustin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5047464344"],"corresponding_institution_ids":["https://openalex.org/I2801533059","https://openalex.org/I4210134559"],"apc_list":{"value":2290,"currency":"EUR","value_usd":2890},"apc_paid":{"value":2290,"currency":"EUR","value_usd":2890},"fwci":4.6439,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.9500782,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"64","issue":"5","first_page":"1239","last_page":"1262"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9984999895095825,"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"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9984999895095825,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.9950000047683716,"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"}},{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.9894000291824341,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7832614183425903},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.6329479813575745},{"id":"https://openalex.org/keywords/polyglot","display_name":"Polyglot","score":0.5090105533599854},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4728783965110779},{"id":"https://openalex.org/keywords/graph-database","display_name":"Graph database","score":0.440863698720932},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.42494815587997437},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.4104686975479126},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.38252994418144226},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.3661367893218994},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.362693190574646},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.306938111782074}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7832614183425903},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.6329479813575745},{"id":"https://openalex.org/C2780239667","wikidata":"https://www.wikidata.org/wiki/Q2102850","display_name":"Polyglot","level":2,"score":0.5090105533599854},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4728783965110779},{"id":"https://openalex.org/C176225458","wikidata":"https://www.wikidata.org/wiki/Q595971","display_name":"Graph database","level":3,"score":0.440863698720932},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.42494815587997437},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.4104686975479126},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.38252994418144226},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.3661367893218994},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.362693190574646},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.306938111782074},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1007/s10115-022-01668-7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10115-022-01668-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10115-022-01668-7.pdf","source":{"id":"https://openalex.org/S81770430","display_name":"Knowledge and Information Systems","issn_l":"0219-1377","issn":["0219-1377","0219-3116"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Knowledge and Information Systems","raw_type":"journal-article"},{"id":"pmh:oai:DiVA.org:lnu-131820","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-131820","pdf_url":null,"source":{"id":"https://openalex.org/S4306401598","display_name":"DiVA (Linnaeus University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I223464139","host_organization_name":"Linnaeus University","host_organization_lineage":["https://openalex.org/I223464139"],"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":"","raw_type":"Article in journal"},{"id":"pmh:oai:null:publica/429044","is_oa":false,"landing_page_url":"https://publica.fraunhofer.de/handle/publica/429044","pdf_url":null,"source":{"id":"https://openalex.org/S4306400318","display_name":"Fraunhofer-Publica (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"},{"id":"pmh:oai:pub.dzne.de:163784","is_oa":true,"landing_page_url":"https://pub.dzne.de/search?p=id:%22DZNE-2022-00522%22","pdf_url":null,"source":{"id":"https://openalex.org/S7407051172","display_name":"DZNE Pub","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"Knowledge and information systems 64, 1239-1262 (2022). doi:10.1007/s10115-022-01668-7","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pub.h-brs.de:6148","is_oa":true,"landing_page_url":"https://pub.h-brs.de/frontdoor/index/index/docId/6148","pdf_url":null,"source":{"id":"https://openalex.org/S4306400385","display_name":"Publication Server of Bonn-Rhein-Sieg University of Applied Sciences (Bonn-Rhein-Sieg University of Applied Sciences)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I135140700","host_organization_name":"University of Bonn","host_organization_lineage":["https://openalex.org/I135140700"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Knowledge and Information Systems (2022) 64:1239\u20131262","raw_type":"publishedVersion"}],"best_oa_location":{"id":"doi:10.1007/s10115-022-01668-7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10115-022-01668-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10115-022-01668-7.pdf","source":{"id":"https://openalex.org/S81770430","display_name":"Knowledge and Information Systems","issn_l":"0219-1377","issn":["0219-1377","0219-3116"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Knowledge and Information Systems","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.44999998807907104,"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12"}],"awards":[{"id":"https://openalex.org/G6002116566","display_name":null,"funder_award_id":"115568","funder_id":"https://openalex.org/F4320314178","funder_display_name":"European Federation of Pharmaceutical Industries and Associations"}],"funders":[{"id":"https://openalex.org/F4320314178","display_name":"European Federation of Pharmaceutical Industries and Associations","ror":"https://ror.org/00g1x4v36"},{"id":"https://openalex.org/F4320321773","display_name":"Fraunhofer-Gesellschaft","ror":"https://ror.org/05hkkdn48"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4220956629.pdf","grobid_xml":"https://content.openalex.org/works/W4220956629.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W103049419","https://openalex.org/W1904543801","https://openalex.org/W1984761526","https://openalex.org/W2020278455","https://openalex.org/W2036265926","https://openalex.org/W2095848001","https://openalex.org/W2103017472","https://openalex.org/W2141869602","https://openalex.org/W2148544545","https://openalex.org/W2167868352","https://openalex.org/W2302501749","https://openalex.org/W2416840882","https://openalex.org/W2473206977","https://openalex.org/W2515964835","https://openalex.org/W2528662265","https://openalex.org/W2668736619","https://openalex.org/W2739381839","https://openalex.org/W2767891136","https://openalex.org/W2805947038","https://openalex.org/W2889506336","https://openalex.org/W2894360925","https://openalex.org/W2898784679","https://openalex.org/W2898912700","https://openalex.org/W2903428671","https://openalex.org/W2908264335","https://openalex.org/W2953216885","https://openalex.org/W2965573702","https://openalex.org/W2973652726"],"related_works":["https://openalex.org/W3021456553","https://openalex.org/W2776293731","https://openalex.org/W2965230088","https://openalex.org/W4293389049","https://openalex.org/W1534806717","https://openalex.org/W2550790379","https://openalex.org/W4389150935","https://openalex.org/W2610919777","https://openalex.org/W4243630814","https://openalex.org/W2951852920"],"abstract_inverted_index":{"Abstract":[0],"Contextual":[1],"information":[2,251],"is":[3,27,131,147,194,206],"widely":[4],"considered":[5],"for":[6,41,79,93],"NLP":[7],"and":[8,44,86,101,111,127,130,137,162,183,212,234],"knowledge":[9,63,84,119,187,228],"discovery":[10,45,85],"in":[11,246],"life":[12],"sciences":[13],"since":[14],"it":[15],"highly":[16],"influences":[17],"the":[18,90,123,167,210],"exact":[19],"meaning":[20],"of":[21,105,125,169,214,248],"natural":[22],"language.":[23],"The":[24],"scientific":[25],"challenge":[26],"not":[28],"only":[29],"to":[30,37,75,208],"extract":[31],"such":[32],"context":[33,77,80,96,146,247],"data,":[34],"but":[35],"also":[36],"store":[38],"this":[39,170],"data":[40,78,129,136,140,204,233],"further":[42],"query":[43],"approaches.":[46],"Classical":[47],"approaches":[48],"use":[49,176,221],"RDF":[50],"triple":[51],"stores,":[52],"which":[53],"have":[54],"serious":[55],"limitations.":[56],"Here,":[57,145,199],"we":[58,200,241],"propose":[59],"a":[60,94,103,118,148,185,190,196,243],"multiple":[61],"step":[62],"graph":[64,82,120,156,180,188,193,229],"approach":[65,172],"using":[66,141,252],"labeled":[67,191],"property":[68,192],"graphs":[69],"based":[70,107],"on":[71,108],"polyglot":[72],"persistence":[73],"systems":[74],"utilize":[76,224],"mining,":[81],"queries,":[83],"extraction.":[87],"We":[88,165,217],"introduce":[89],"graph-theoretic":[91],"foundation":[92],"general":[95,150],"concept":[97,106,151],"within":[98],"semantic":[99],"networks":[100],"show":[102,242],"proof":[104],"biomedical":[109,215],"literature":[110],"text":[112,134],"mining.":[113],"Our":[114],"test":[115],"system":[116],"contains":[117],"derived":[121,230],"from":[122,231],"entirety":[124],"PubMed":[126,232],"SCAIView":[128],"enriched":[132,235],"with":[133,173,236],"mining":[135],"domain-specific":[138],"language":[139],"Biological":[142],"Expression":[143],"Language.":[144],"more":[149,158],"than":[152,159],"annotations.":[153],"This":[154],"dense":[155],"has":[157],"71M":[160],"nodes":[161],"850M":[163],"relationships.":[164],"discuss":[166],"impact":[168],"novel":[171],"27":[174],"real-world":[175,220],"cases":[177,222],"represented":[178],"by":[179],"queries.":[181],"Storing":[182],"querying":[184],"giant":[186],"as":[189],"still":[195],"technological":[197],"challenge.":[198],"demonstrate":[201],"how":[202],"our":[203,225],"model":[205],"able":[207],"support":[209],"understanding":[211],"interpretation":[213],"data.":[216,239],"present":[218],"several":[219],"that":[223],"massive,":[226],"generated":[227],"additional":[237],"contextual":[238],"Finally,":[240],"working":[244],"example":[245],"biologically":[249],"relevant":[250],"SCAIView.":[253]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
