{"id":"https://openalex.org/W4408667057","doi":"https://doi.org/10.1186/s13326-025-00323-8","title":"New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern","display_name":"New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern","publication_year":2025,"publication_date":"2025-03-21","ids":{"openalex":"https://openalex.org/W4408667057","doi":"https://doi.org/10.1186/s13326-025-00323-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/40114175"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-025-00323-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00323-8","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-025-00323-8","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-025-00323-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080226175","display_name":"Gene D. Godbold","orcid":"https://orcid.org/0000-0002-5702-4690"},"institutions":[{"id":"https://openalex.org/I4210118524","display_name":"Universit\u00e9 Bourgogne Franche-Comt\u00e9","ror":"https://ror.org/02dn7x778","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210118524"]},{"id":"https://openalex.org/I4210154833","display_name":"Signature Research (United States)","ror":"https://ror.org/04djzj803","country_code":"US","type":"company","lineage":["https://openalex.org/I4210154833"]}],"countries":["FR","US"],"is_corresponding":true,"raw_author_name":"Gene Godbold","raw_affiliation_strings":["Signature Science, LLC, 1670 Discovery Drive, Charlottesville, VA, 22911, USA. ggodbold@signaturescience.com","Signature Science, LLC, 1670 Discovery Drive, Charlottesville, VA, 22911, USA"],"affiliations":[{"raw_affiliation_string":"Signature Science, LLC, 1670 Discovery Drive, Charlottesville, VA, 22911, USA. ggodbold@signaturescience.com","institution_ids":["https://openalex.org/I4210154833"]},{"raw_affiliation_string":"Signature Science, LLC, 1670 Discovery Drive, Charlottesville, VA, 22911, USA","institution_ids":["https://openalex.org/I4210154833","https://openalex.org/I4210118524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063162464","display_name":"Jody B. Proescher","orcid":"https://orcid.org/0000-0002-8100-7866"},"institutions":[{"id":"https://openalex.org/I2802946424","display_name":"Johns Hopkins University Applied Physics Laboratory","ror":"https://ror.org/029pp9z10","country_code":"US","type":"facility","lineage":["https://openalex.org/I145311948","https://openalex.org/I2802946424"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jody Proescher","raw_affiliation_strings":["Asymmetric Operations Sector, The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD, 20723, USA"],"affiliations":[{"raw_affiliation_string":"Asymmetric Operations Sector, The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD, 20723, USA","institution_ids":["https://openalex.org/I2802946424"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014365246","display_name":"Pascale Gaudet","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Pascale Gaudet","raw_affiliation_strings":["SIB Swiss Institute of Bioinformatics and GO Central, 4 rue Michel-Servet, Geneva, 1211, Switzerland. pascale.gaudet@sib.swiss","SIB Swiss Institute of Bioinformatics and GO Central, 4 rue Michel-Servet, Geneva, 1211, Switzerland"],"affiliations":[{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics and GO Central, 4 rue Michel-Servet, Geneva, 1211, Switzerland. pascale.gaudet@sib.swiss","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics and GO Central, 4 rue Michel-Servet, Geneva, 1211, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014365246","https://openalex.org/A5080226175"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210118524","https://openalex.org/I4210154833"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":3.8977,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.93009825,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"4","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9973999857902527,"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":0.9973999857902527,"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":0.9932000041007996,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9901000261306763,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6967977285385132},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6359186768531799},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5872825980186462},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.504297137260437},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45688918232917786},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4557083249092102},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2872923016548157},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2047521471977234},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.1758488416671753},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15832459926605225},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10295331478118896}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6967977285385132},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6359186768531799},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5872825980186462},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.504297137260437},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45688918232917786},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4557083249092102},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2872923016548157},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2047521471977234},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.1758488416671753},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15832459926605225},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10295331478118896},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s13326-025-00323-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00323-8","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-025-00323-8","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:40114175","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40114175","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":"Journal of biomedical semantics","raw_type":null},{"id":"pmh:oai:doaj.org/article:1341865129604a5e85f142206bfac260","is_oa":true,"landing_page_url":"https://doaj.org/article/1341865129604a5e85f142206bfac260","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Biomedical Semantics, Vol 16, Iss 1, Pp 1-9 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11927349","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11927349","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Biomed Semantics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13326-025-00323-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00323-8","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-025-00323-8","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Zero hunger","score":0.550000011920929,"id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G7891100991","display_name":null,"funder_award_id":"W911NF-17-2-0089","funder_id":"https://openalex.org/F4320333051","funder_display_name":"Intelligence Advanced Research Projects Activity"}],"funders":[{"id":"https://openalex.org/F4320333051","display_name":"Intelligence Advanced Research Projects Activity","ror":"https://ror.org/01v3fsc55"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408667057.pdf"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1970698656","https://openalex.org/W1974896839","https://openalex.org/W2018594744","https://openalex.org/W2065329772","https://openalex.org/W2076356824","https://openalex.org/W2102428625","https://openalex.org/W2103017472","https://openalex.org/W2114025920","https://openalex.org/W2172919339","https://openalex.org/W2218658383","https://openalex.org/W2261710818","https://openalex.org/W2949099357","https://openalex.org/W3012283572","https://openalex.org/W3173268502","https://openalex.org/W3212393265","https://openalex.org/W4225669898","https://openalex.org/W4283171645","https://openalex.org/W4303426886","https://openalex.org/W4319455753","https://openalex.org/W4323036511","https://openalex.org/W4393523089"],"related_works":["https://openalex.org/W2003333417","https://openalex.org/W2378862226","https://openalex.org/W118236634","https://openalex.org/W2355326633","https://openalex.org/W2804669904","https://openalex.org/W2149777447","https://openalex.org/W2347456287","https://openalex.org/W2121651557","https://openalex.org/W2782969047","https://openalex.org/W2794019507"],"abstract_inverted_index":{"The":[0],"enhanced":[1],"and":[2,8],"expanded":[3],"terms":[4],"enable":[5],"a":[6,12,17],"quick":[7],"pertinent":[9],"evaluation":[10],"of":[11,34],"sequence's":[13],"ability":[14],"to":[15,27,38],"endow":[16],"microbe":[18],"with":[19],"pathogenic":[20,47],"function":[21],"when":[22],"they":[23],"are":[24],"appropriately":[25],"applied":[26],"relevant":[28],"sequences.":[29],"This":[30,49],"will":[31,50],"allow":[32],"providers":[33],"synthetic":[35],"nucleic":[36],"acids":[37],"rapidly":[39],"assess":[40],"sequences":[41],"ordered":[42],"by":[43],"their":[44],"customers":[45],"for":[46],"capacity.":[48],"help":[51],"fulfill":[52],"the":[53],"new":[54],"US":[55],"government":[56],"guidance.":[57]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-06T07:47:59.780226","created_date":"2025-10-10T00:00:00"}