{"id":"https://openalex.org/W4392899655","doi":"https://doi.org/10.23919/fusion59988.2024.10706497","title":"Reproducible Mapping of Tabular Data into Semantic Knowledge Graphs with OntoWeaver and BioCypher","display_name":"Reproducible Mapping of Tabular Data into Semantic Knowledge Graphs with OntoWeaver and BioCypher","publication_year":2024,"publication_date":"2024-07-08","ids":{"openalex":"https://openalex.org/W4392899655","doi":"https://doi.org/10.23919/fusion59988.2024.10706497"},"language":"en","primary_location":{"id":"doi:10.23919/fusion59988.2024.10706497","is_oa":false,"landing_page_url":"https://doi.org/10.23919/fusion59988.2024.10706497","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 27th International Conference on Information Fusion (FUSION)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal.science/hal-04509632/document","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023434001","display_name":"Johann Dr\u00e9o","orcid":"https://orcid.org/0000-0003-2727-9569"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Johann Dreo","raw_affiliation_strings":["Institut Pasteur, Universit&#x00E9; Paris Cit&#x00E9;,Computational Systems Biomedicine,Computational Biology Dept. Bioinformatics and Biostatistics Hub.,Paris,France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Pasteur, Universit&#x00E9; Paris Cit&#x00E9;,Computational Systems Biomedicine,Computational Biology Dept. Bioinformatics and Biostatistics Hub.,Paris,France","institution_ids":["https://openalex.org/I157536573"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022272004","display_name":"Claire Laudy","orcid":"https://orcid.org/0009-0009-3039-3224"},"institutions":[{"id":"https://openalex.org/I4210120156","display_name":"Laboratoire Albert Fert","ror":"https://ror.org/02erddr56","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I277688954","https://openalex.org/I4210120156","https://openalex.org/I4210140930"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Claire Laudy","raw_affiliation_strings":["Thales,Palaiseau,France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Thales,Palaiseau,France","institution_ids":["https://openalex.org/I4210120156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021965999","display_name":"Sebastian Lobentanzer","orcid":"https://orcid.org/0000-0003-3399-6695"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sebastian Lobentanzer","raw_affiliation_strings":["Institute for Computational Biomedicine Heidelberg University, Faculty of Medicine and Heidelberg University Hospital,Heidelberg,Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Biomedicine Heidelberg University, Faculty of Medicine and Heidelberg University Hospital,Heidelberg,Germany","institution_ids":["https://openalex.org/I2802164966","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069488778","display_name":"Marko Bari\u0107","orcid":null},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Marko Baric","raw_affiliation_strings":["Institut Pasteur, Universit&#x00E9; Paris Cit&#x00E9;,Computational Systems Biomedicine,Computational Biology Dept.,Paris,France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Pasteur, Universit&#x00E9; Paris Cit&#x00E9;,Computational Systems Biomedicine,Computational Biology Dept.,Paris,France","institution_ids":["https://openalex.org/I157536573"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067810280","display_name":"E. Gaydukova","orcid":"https://orcid.org/0000-0001-9025-1214"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ekaterina Gaydukova","raw_affiliation_strings":["Institut Pasteur, Universit&#x00E9; Paris Cit&#x00E9;,Computational Systems Biomedicine,Computational Biology Dept.,Paris,France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Pasteur, Universit&#x00E9; Paris Cit&#x00E9;,Computational Systems Biomedicine,Computational Biology Dept.,Paris,France","institution_ids":["https://openalex.org/I157536573"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059640936","display_name":"Benno Schwikowski","orcid":"https://orcid.org/0000-0001-5127-5619"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Benno Schwikowski","raw_affiliation_strings":["Institut Pasteur, Universit&#x00E9; Paris Cit&#x00E9;,Computational Systems Biomedicine,Computational Biology Dept.,Paris,France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Pasteur, Universit&#x00E9; Paris Cit&#x00E9;,Computational Systems Biomedicine,Computational Biology Dept.,Paris,France","institution_ids":["https://openalex.org/I157536573"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.2219,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.814443,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9200000166893005,"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"}},"topics":[{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9200000166893005,"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":0.7498214244842529},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.6127186417579651},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.49603161215782166},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3642403185367584},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.36387357115745544}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7498214244842529},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.6127186417579651},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.49603161215782166},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3642403185367584},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.36387357115745544}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.23919/fusion59988.2024.10706497","is_oa":false,"landing_page_url":"https://doi.org/10.23919/fusion59988.2024.10706497","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 27th International Conference on Information Fusion (FUSION)","raw_type":"proceedings-article"},{"id":"pmh:oai:HAL:hal-04509632v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04509632","pdf_url":"https://hal.science/hal-04509632/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"2024","raw_type":"Preprints, Working Papers, ..."}],"best_oa_location":{"id":"pmh:oai:HAL:hal-04509632v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04509632","pdf_url":"https://hal.science/hal-04509632/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"2024","raw_type":"Preprints, Working Papers, ..."},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4392899655.pdf"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1865476398","https://openalex.org/W2302501749","https://openalex.org/W2342249984","https://openalex.org/W2614443510","https://openalex.org/W2949492942","https://openalex.org/W4224307004","https://openalex.org/W4281704579","https://openalex.org/W4381190112","https://openalex.org/W4387335700","https://openalex.org/W4387728976","https://openalex.org/W6639334739","https://openalex.org/W6862335472"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W4402327032","https://openalex.org/W2382290278"],"abstract_inverted_index":{"Large-scale":[0],"high-level":[1,118],"information":[2,119],"fusion":[3,120],"and":[4,34,82,94,102,106,117],"data":[5,54,70],"integration":[6,93],"is":[7,84],"a":[8,21,32,43,59,74],"pressing":[9],"need":[10],"in":[11,31,86],"several":[12,111],"scientific":[13,112],"domains.":[14],"Recently,":[15],"the":[16],"biomedical":[17],"community":[18],"established":[19],"BioCypher,":[20,103],"tool":[22,45],"to":[23,46,50,71],"help":[24,110],"create":[25],"large":[26],"Semantic":[27],"Knowledge":[28],"Graphs":[29],"(SKGs)":[30],"simple":[33,60,75],"reproducible":[35,66],"way.":[36],"In":[37],"this":[38],"article,":[39],"we":[40],"introduce":[41],"OntoWeaver,":[42],"companion":[44],"BioCypher":[47,83],"that":[48,100],"allows":[49,64],"easily":[51],"extract":[52],"tabular":[53,69],"into":[55],"SKGs":[56,72,116],"by":[57],"using":[58],"declarative":[61,76],"mapping.":[62],"OntoWeaver":[63,81,101],"implementing":[65],"mappings":[67],"from":[68],"with":[73],"configuration.":[77],"The":[78],"use":[79,89],"of":[80],"demonstrated":[85],"two":[87],"different":[88],"cases:":[90],"cancer":[91],"database":[92],"invasive":[95],"species":[96],"monitoring.":[97],"We":[98],"believe":[99],"both":[104],"free":[105],"open-source":[107],"software,":[108],"can":[109],"communities":[113],"working":[114],"on":[115],"problems.":[121]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
