{"id":"https://openalex.org/W4411735319","doi":"https://doi.org/10.1093/bioinformatics/btaf376","title":"CSpace: a concept embedding space for biomedical applications","display_name":"CSpace: a concept embedding space for biomedical applications","publication_year":2025,"publication_date":"2025-06-27","ids":{"openalex":"https://openalex.org/W4411735319","doi":"https://doi.org/10.1093/bioinformatics/btaf376","pmid":"https://pubmed.ncbi.nlm.nih.gov/40576218"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf376","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf376/63606578/btaf376.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf376/63606578/btaf376.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039373850","display_name":"Danilo Tomasoni","orcid":"https://orcid.org/0000-0002-8427-4230"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Danilo Tomasoni","raw_affiliation_strings":["Fondazione The Microsoft Research\u2014University of Trento Centre for Computational and Systems Biology (COSBI) , 38068 Rovereto (TN),","Fondazione the Microsoft Research\u2014University of Trento Centre for Computational and Systems Biology (COSBI) , Rovereto, Trento"],"affiliations":[{"raw_affiliation_string":"Fondazione The Microsoft Research\u2014University of Trento Centre for Computational and Systems Biology (COSBI) , 38068 Rovereto (TN),","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]},{"raw_affiliation_string":"Fondazione the Microsoft Research\u2014University of Trento Centre for Computational and Systems Biology (COSBI) , Rovereto, Trento","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052320095","display_name":"Luca Marchetti","orcid":"https://orcid.org/0000-0001-9043-7705"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Luca Marchetti","raw_affiliation_strings":["Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento , 38123 Povo (TN),","Fondazione The Microsoft Research\u2014University of Trento Centre for Computational and Systems Biology (COSBI) , 38068 Rovereto (TN),","Fondazione the Microsoft Research\u2014University of Trento Centre for Computational and Systems Biology (COSBI) , Rovereto, Trento","University of Trento Department of Cellular, Computational and Integrative Biology (CIBIO), , Povo, Trento"],"affiliations":[{"raw_affiliation_string":"Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento , 38123 Povo (TN),","institution_ids":["https://openalex.org/I193223587"]},{"raw_affiliation_string":"Fondazione The Microsoft Research\u2014University of Trento Centre for Computational and Systems Biology (COSBI) , 38068 Rovereto (TN),","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]},{"raw_affiliation_string":"Fondazione the Microsoft Research\u2014University of Trento Centre for Computational and Systems Biology (COSBI) , Rovereto, Trento","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]},{"raw_affiliation_string":"University of Trento Department of Cellular, Computational and Integrative Biology (CIBIO), , Povo, Trento","institution_ids":["https://openalex.org/I193223587"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5039373850"],"corresponding_institution_ids":["https://openalex.org/I193223587","https://openalex.org/I2802934434"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13765429,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9969000220298767,"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":0.9969000220298767,"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/T10028","display_name":"Topic Modeling","score":0.9921000003814697,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9768999814987183,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.7110967636108398},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.6958572268486023},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6611887216567993},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3649417757987976},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3107908368110657},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.07046407461166382}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.7110967636108398},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.6958572268486023},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6611887216567993},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3649417757987976},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3107908368110657},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.07046407461166382}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf376","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf376/63606578/btaf376.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40576218","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40576218","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:iris.unitn.it:11572/462591","is_oa":true,"landing_page_url":"https://hdl.handle.net/11572/462591","pdf_url":null,"source":{"id":"https://openalex.org/S4306401913","display_name":"Institutional Research Information System (Universit\u00e0 degli Studi di Trento)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193223587","host_organization_name":"University of Trento","host_organization_lineage":["https://openalex.org/I193223587"],"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":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12275461","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12275461","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf376","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf376/63606578/btaf376.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8199999928474426,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411735319.pdf","grobid_xml":"https://content.openalex.org/works/W4411735319.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W168564468","https://openalex.org/W202767273","https://openalex.org/W1614298861","https://openalex.org/W2084377579","https://openalex.org/W2493916176","https://openalex.org/W2735784619","https://openalex.org/W2882319491","https://openalex.org/W2944400536","https://openalex.org/W2946690328","https://openalex.org/W3116317633","https://openalex.org/W4225576545","https://openalex.org/W4287245321","https://openalex.org/W4393936594","https://openalex.org/W4403532961","https://openalex.org/W4403746919","https://openalex.org/W6795007937"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2081900870","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2932872266"],"abstract_inverted_index":{"Full":[0],"and":[1,16,22],"compressed":[2],"models":[3],"are":[4,18],"available":[5,19],"on":[6,23],"Zenodo":[7],"at":[8,20],"https://doi.org/10.5281/zenodo.14781672,":[9],"while":[10],"training":[11],"code,":[12],"examples,":[13],"interactive":[14],"visualizations":[15],"experiments":[17],"https://doi.org/10.5281/zenodo.15125706":[21],"the":[24],"GitHub":[25],"repository.":[26]},"counts_by_year":[],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
