{"id":"https://openalex.org/W4394642183","doi":"https://doi.org/10.1093/bioinformatics/btae194","title":"NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph","display_name":"NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph","publication_year":2024,"publication_date":"2024-04-08","ids":{"openalex":"https://openalex.org/W4394642183","doi":"https://doi.org/10.1093/bioinformatics/btae194","pmid":"https://pubmed.ncbi.nlm.nih.gov/38597890"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae194","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae194","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btae194","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075784411","display_name":"Antonio Di Maria","orcid":"https://orcid.org/0009-0008-9300-2297"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Antonio Di Maria","raw_affiliation_strings":["Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy","institution_ids":["https://openalex.org/I39063666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003102386","display_name":"Lorenzo Bellomo","orcid":"https://orcid.org/0009-0001-3138-3097"},"institutions":[{"id":"https://openalex.org/I157210198","display_name":"Scuola Normale Superiore","ror":"https://ror.org/03aydme10","country_code":"IT","type":"education","lineage":["https://openalex.org/I157210198"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Lorenzo Bellomo","raw_affiliation_strings":["Scuola Normale Superiore , Pisa, 56126 , Italy"],"affiliations":[{"raw_affiliation_string":"Scuola Normale Superiore , Pisa, 56126 , Italy","institution_ids":["https://openalex.org/I157210198"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039361341","display_name":"Fabrizio Billeci","orcid":null},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Fabrizio Billeci","raw_affiliation_strings":["Department of Computer Science, University of Catania , Catania, 95125, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Catania , Catania, 95125, Italy","institution_ids":["https://openalex.org/I39063666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5095368011","display_name":"Alfio Cardillo","orcid":null},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alfio Cardillo","raw_affiliation_strings":["Department of Computer Science, University of Catania , Catania, 95125, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Catania , Catania, 95125, Italy","institution_ids":["https://openalex.org/I39063666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023263135","display_name":"Salvatore Alaimo","orcid":"https://orcid.org/0000-0003-4825-7617"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Salvatore Alaimo","raw_affiliation_strings":["Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy","institution_ids":["https://openalex.org/I39063666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046786328","display_name":"Paolo Ferragina","orcid":"https://orcid.org/0000-0003-1353-360X"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paolo Ferragina","raw_affiliation_strings":["Department of Computer Science, University of Pisa , Pisa, 56126 , Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Pisa , Pisa, 56126 , Italy","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000272110","display_name":"Alfredo Ferro","orcid":"https://orcid.org/0000-0002-9431-5788"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alfredo Ferro","raw_affiliation_strings":["Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy","institution_ids":["https://openalex.org/I39063666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057481978","display_name":"Alfredo Pulvirenti","orcid":"https://orcid.org/0000-0002-9764-0295"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alfredo Pulvirenti","raw_affiliation_strings":["Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy","institution_ids":["https://openalex.org/I39063666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5075784411"],"corresponding_institution_ids":["https://openalex.org/I39063666"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.3833,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.79842415,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"40","issue":"5","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":0.9998999834060669,"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":0.9998999834060669,"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":0.9900000095367432,"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":0.9764999747276306,"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/computer-science","display_name":"Computer science","score":0.706181526184082},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5563691854476929},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.5190408825874329},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.497684508562088},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.46575528383255005},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.39938995242118835},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.27299293875694275}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.706181526184082},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5563691854476929},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.5190408825874329},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.497684508562088},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.46575528383255005},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.39938995242118835},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.27299293875694275}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btae194","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae194","pdf_url":null,"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:38597890","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38597890","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:pubmedcentral.nih.gov:11074003","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11074003","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11074003/pdf/btae194.pdf","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"},{"id":"pmh:oai:www.iris.sssup.it:11382/566933","is_oa":true,"landing_page_url":"https://hdl.handle.net/11382/566933","pdf_url":"https://www.iris.sssup.it/bitstream/11382/566933/1/btae194.pdf","source":{"id":"https://openalex.org/S4377196376","display_name":"CINECA IRIS Institutional Research Information System (Sant'Anna School of Advanced Studies)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I162290304","host_organization_name":"Scuola Superiore Sant'Anna","host_organization_lineage":["https://openalex.org/I162290304"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:ricerca.sns.it:11384/155423","is_oa":true,"landing_page_url":"https://hdl.handle.net/11384/155423","pdf_url":null,"source":{"id":"https://openalex.org/S7407050981","display_name":"Scuola Normale Superiore di Pisa","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":"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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae194","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae194","pdf_url":null,"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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1964670939","https://openalex.org/W2132773777","https://openalex.org/W2154142897","https://openalex.org/W2169099542","https://openalex.org/W2187413858","https://openalex.org/W2761714433","https://openalex.org/W2786016794","https://openalex.org/W2899915536","https://openalex.org/W2930950231","https://openalex.org/W2946690328","https://openalex.org/W2983166786","https://openalex.org/W3010336026","https://openalex.org/W3176163250","https://openalex.org/W4220958910","https://openalex.org/W4221081166","https://openalex.org/W4221142212","https://openalex.org/W4226055728","https://openalex.org/W4286008391","https://openalex.org/W4295736374","https://openalex.org/W4306353191","https://openalex.org/W4311459687","https://openalex.org/W4319813194","https://openalex.org/W4320525813","https://openalex.org/W4327617998","https://openalex.org/W4327898717","https://openalex.org/W4378574344","https://openalex.org/W4380853828","https://openalex.org/W4382599418","https://openalex.org/W6839421619","https://openalex.org/W6847729896"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4213212078","https://openalex.org/W4379210901","https://openalex.org/W2187227032","https://openalex.org/W2112788825","https://openalex.org/W1963735073","https://openalex.org/W4233129888","https://openalex.org/W106707639","https://openalex.org/W2146247781","https://openalex.org/W2054026175"],"abstract_inverted_index":{"https://netme.click/.":[0]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-07T14:57:38.498316","created_date":"2025-10-10T00:00:00"}
