{"id":"https://openalex.org/W2166516661","doi":"https://doi.org/10.1093/database/bas017","title":"How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience","display_name":"How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience","publication_year":2012,"publication_date":"2012-03-21","ids":{"openalex":"https://openalex.org/W2166516661","doi":"https://doi.org/10.1093/database/bas017","mag":"2166516661","pmid":"https://pubmed.ncbi.nlm.nih.gov/22438567"},"language":"en","primary_location":{"id":"doi:10.1093/database/bas017","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bas017","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","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/database/bas017","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007203127","display_name":"Martin Krallinger","orcid":"https://orcid.org/0000-0002-2646-8782"},"institutions":[{"id":"https://openalex.org/I4210089594","display_name":"Spanish National Cancer Research Centre","ror":"https://ror.org/00bvhmc43","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210089594"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"M. Krallinger","raw_affiliation_strings":["Structural and Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Spain","Structural and Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Spain,"],"affiliations":[{"raw_affiliation_string":"Structural and Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Spain","institution_ids":[]},{"raw_affiliation_string":"Structural and Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Spain,","institution_ids":["https://openalex.org/I4210089594"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018678007","display_name":"Florian Leitner","orcid":"https://orcid.org/0000-0003-4458-504X"},"institutions":[{"id":"https://openalex.org/I4210089594","display_name":"Spanish National Cancer Research Centre","ror":"https://ror.org/00bvhmc43","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210089594"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"F. Leitner","raw_affiliation_strings":["Structural and Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Spain,"],"affiliations":[{"raw_affiliation_string":"Structural and Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Spain,","institution_ids":["https://openalex.org/I4210089594"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008971014","display_name":"Migu\u00e9l V\u00e1zquez","orcid":"https://orcid.org/0000-0002-5713-1058"},"institutions":[{"id":"https://openalex.org/I4210089594","display_name":"Spanish National Cancer Research Centre","ror":"https://ror.org/00bvhmc43","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210089594"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"M. Vazquez","raw_affiliation_strings":["Structural and Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Spain,"],"affiliations":[{"raw_affiliation_string":"Structural and Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Spain,","institution_ids":["https://openalex.org/I4210089594"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063600106","display_name":"David Salgado","orcid":"https://orcid.org/0000-0002-5905-3591"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"D. Salgado","raw_affiliation_strings":["Australian Regenerative Medicine Institute, Monash University, Australia,"],"affiliations":[{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Australia,","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045468870","display_name":"Christophe Marcelle","orcid":"https://orcid.org/0000-0002-9612-7609"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"C. Marcelle","raw_affiliation_strings":["Australian Regenerative Medicine Institute, Monash University, Australia,"],"affiliations":[{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Australia,","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004507461","display_name":"Michael Tyers","orcid":null},"institutions":[{"id":"https://openalex.org/I4210096154","display_name":"Institute for Research in Immunology and Cancer","ror":"https://ror.org/00wj6x496","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210096154"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["CA","GB"],"is_corresponding":false,"raw_author_name":"M. Tyers","raw_affiliation_strings":["Institute for Research in Immunology and Cancer, Universite \u00b4de Montre \u00b4al, Montre \u00b4al, QC, Canada H3C 3J7","School of Biological Sciences, University of Edinburgh, Edinburgh, UK and"],"affiliations":[{"raw_affiliation_string":"Institute for Research in Immunology and Cancer, Universite \u00b4de Montre \u00b4al, Montre \u00b4al, QC, Canada H3C 3J7","institution_ids":["https://openalex.org/I4210096154"]},{"raw_affiliation_string":"School of Biological Sciences, University of Edinburgh, Edinburgh, UK and","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111986966","display_name":"Alfonso Valencia","orcid":null},"institutions":[{"id":"https://openalex.org/I4210089594","display_name":"Spanish National Cancer Research Centre","ror":"https://ror.org/00bvhmc43","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210089594"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"A. Valencia","raw_affiliation_strings":["Structural and Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Spain,"],"affiliations":[{"raw_affiliation_string":"Structural and Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Spain,","institution_ids":["https://openalex.org/I4210089594"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066701646","display_name":"A. Chatr-aryamontri","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]},{"id":"https://openalex.org/I4210096154","display_name":"Institute for Research in Immunology and Cancer","ror":"https://ror.org/00wj6x496","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210096154"]}],"countries":["CA","GB"],"is_corresponding":true,"raw_author_name":"A. Chatr-aryamontri","raw_affiliation_strings":["Institute for Research in Immunology and Cancer, Universite \u00b4de Montre \u00b4al, Montre \u00b4al, QC, Canada H3C 3J7","School of Biological Sciences, University of Edinburgh, Edinburgh, UK and"],"affiliations":[{"raw_affiliation_string":"Institute for Research in Immunology and Cancer, Universite \u00b4de Montre \u00b4al, Montre \u00b4al, QC, Canada H3C 3J7","institution_ids":["https://openalex.org/I4210096154"]},{"raw_affiliation_string":"School of Biological Sciences, University of Edinburgh, Edinburgh, UK and","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5066701646"],"corresponding_institution_ids":["https://openalex.org/I4210096154","https://openalex.org/I98677209"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":2.5549,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.90106337,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2012","issue":"0","first_page":"bas017","last_page":"bas017"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9914000034332275,"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":0.9818000197410583,"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":0.8268337249755859},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.7333475947380066},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6424642205238342},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6085777282714844},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5934306979179382},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.5589710474014282},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.520438015460968},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.5081310272216797},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.47898316383361816},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.46918678283691406},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.45048025250434875},{"id":"https://openalex.org/keywords/controlled-vocabulary","display_name":"Controlled vocabulary","score":0.4451253116130829},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4400201439857483},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.41948699951171875},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.4152508080005646},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3883516192436218},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.3408988416194916},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.32605934143066406},{"id":"https://openalex.org/keywords/suggested-upper-merged-ontology","display_name":"Suggested Upper Merged Ontology","score":0.2789454758167267},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2773376703262329},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.2576224207878113},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.25527602434158325},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.13671132922172546}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8268337249755859},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7333475947380066},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6424642205238342},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6085777282714844},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5934306979179382},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.5589710474014282},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.520438015460968},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5081310272216797},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.47898316383361816},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.46918678283691406},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.45048025250434875},{"id":"https://openalex.org/C110615152","wikidata":"https://www.wikidata.org/wiki/Q1469824","display_name":"Controlled vocabulary","level":2,"score":0.4451253116130829},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4400201439857483},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.41948699951171875},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.4152508080005646},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3883516192436218},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.3408988416194916},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.32605934143066406},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.2789454758167267},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2773376703262329},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.2576224207878113},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.25527602434158325},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.13671132922172546},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","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":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/database/bas017","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bas017","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:22438567","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22438567","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:monash.edu:publications/6584d9c7-ac28-4ab7-abbe-a209f82be234","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3309177","pdf_url":null,"source":{"id":"https://openalex.org/S4306402625","display_name":"Monash University Research Portal (Monash University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I56590836","host_organization_name":"Monash University","host_organization_lineage":["https://openalex.org/I56590836"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Krallinger, M, Leitner, F, Vazquez, M, Salgado, D, Marcelle, C, Tyers, M, Valencia, A & Chatr-aryamontri, A 2012, 'How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience', Database: the Journal of Biological Databases and Curation, vol. 2012, bas017, pp. 1 - 12. https://doi.org/10.1093/database/bas017","raw_type":"article"},{"id":"pmh:oai:monash.edu:publications/6584d9c7-ac28-4ab7-abbe-a209f82be234","is_oa":true,"landing_page_url":"https://research.monash.edu/en/publications/6584d9c7-ac28-4ab7-abbe-a209f82be234","pdf_url":null,"source":{"id":"https://openalex.org/S4306402625","display_name":"Monash University Research Portal (Monash University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I56590836","host_organization_name":"Monash University","host_organization_lineage":["https://openalex.org/I56590836"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Krallinger , M , Leitner , F , Vazquez , M , Salgado , D , Marcelle , C , Tyers , M , Valencia , A &amp; Chatr-aryamontri , A 2012 , ' How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience ' , Database: the Journal of Biological Databases and Curation , vol. 2012 , bas017 , pp. 1 - 12 . https://doi.org/10.1093/database/bas017","raw_type":"article"},{"id":"pmh:oai:monash.edu:Publications/6584d9c7-ac28-4ab7-abbe-a209f82be234","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402625","display_name":"Monash University Research Portal (Monash University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I56590836","host_organization_name":"Monash University","host_organization_lineage":["https://openalex.org/I56590836"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1093/database/bas017","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bas017","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8100000023841858,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G1534840870","display_name":null,"funder_award_id":"22341","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G3497591915","display_name":null,"funder_award_id":"(NIH)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G42022835","display_name":null,"funder_award_id":"R01RR024031","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G426441180","display_name":null,"funder_award_id":"82940","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G4389354971","display_name":null,"funder_award_id":"Research","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G6282788884","display_name":null,"funder_award_id":"Canadian Institutes of Health","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G7257051450","display_name":"The Microme Project: A Knowledge-Based Bioinformatics Framework for Microbial Pathway Genomics","funder_award_id":"222886","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7273380189","display_name":null,"funder_award_id":"BB/F010486/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G793586166","display_name":"Proteomics Standards International Molecular Exchange - Systematic Capture of Published Molecular Interaction Data","funder_award_id":"223411","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8051717526","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G944173245","display_name":"The BioGRID Database: An Open International Resource for Biological Interactions","funder_award_id":"BB/F010486/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"},{"id":"https://openalex.org/F4320337901","display_name":"Office of Research Infrastructure Programs, National Institutes of Health","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W102787101","https://openalex.org/W819451571","https://openalex.org/W1600759516","https://openalex.org/W1818881584","https://openalex.org/W1871852719","https://openalex.org/W1969271108","https://openalex.org/W1989626479","https://openalex.org/W1992742383","https://openalex.org/W2018874418","https://openalex.org/W2020336239","https://openalex.org/W2032445314","https://openalex.org/W2037442572","https://openalex.org/W2040610660","https://openalex.org/W2053673723","https://openalex.org/W2056119436","https://openalex.org/W2058987494","https://openalex.org/W2061166439","https://openalex.org/W2064030835","https://openalex.org/W2065455422","https://openalex.org/W2078478843","https://openalex.org/W2084168100","https://openalex.org/W2086482792","https://openalex.org/W2086878776","https://openalex.org/W2096601934","https://openalex.org/W2097424033","https://openalex.org/W2098383595","https://openalex.org/W2100751507","https://openalex.org/W2102162073","https://openalex.org/W2102304447","https://openalex.org/W2103017472","https://openalex.org/W2103308144","https://openalex.org/W2103897355","https://openalex.org/W2105612251","https://openalex.org/W2110183893","https://openalex.org/W2112543617","https://openalex.org/W2113142309","https://openalex.org/W2114368272","https://openalex.org/W2115950489","https://openalex.org/W2117805756","https://openalex.org/W2118877284","https://openalex.org/W2126276057","https://openalex.org/W2127554948","https://openalex.org/W2129129117","https://openalex.org/W2129708744","https://openalex.org/W2130253098","https://openalex.org/W2130687290","https://openalex.org/W2137881949","https://openalex.org/W2148130205","https://openalex.org/W2148362397","https://openalex.org/W2152398020","https://openalex.org/W2156467546","https://openalex.org/W2156997379","https://openalex.org/W2158439765","https://openalex.org/W2163107094","https://openalex.org/W2167304222","https://openalex.org/W2295692079","https://openalex.org/W2915108429","https://openalex.org/W2915827701","https://openalex.org/W2916767477","https://openalex.org/W2917375902","https://openalex.org/W4234895322"],"related_works":["https://openalex.org/W72173000","https://openalex.org/W2084805105","https://openalex.org/W1506177826","https://openalex.org/W26549824","https://openalex.org/W991275336","https://openalex.org/W2021890938","https://openalex.org/W2726617685","https://openalex.org/W2137937634","https://openalex.org/W2075856122","https://openalex.org/W2185688944"],"abstract_inverted_index":{"There":[0],"is":[1,98,135,140,250],"an":[2,202],"increasing":[3],"interest":[4],"in":[5,105,120,127,165,180,190,233,245],"developing":[6],"ontologies":[7,37],"and":[8,15,28,57,122,183,229,256],"controlled":[9,211],"vocabularies":[10],"to":[11,21,30,77,95,143,147,163,223,252,260],"improve":[12,31],"the":[13,47,58,82,92,101,106,115,128,166,181,207,234,237],"efficiency":[14],"consistency":[16],"of":[17,33,54,72,84,89,100,156,169,219,227,236,241],"manual":[18,133],"literature":[19,94,182],"curation,":[20],"enable":[22],"more":[23],"formal":[24],"biocuration":[25],"workflow":[26],"results":[27],"ultimately":[29],"analysis":[32],"biological":[34,170],"data.":[35,171],"Two":[36],"that":[38,66,111,195],"have":[39],"been":[40,161],"successfully":[41],"used":[42,63,178],"for":[43,51,81,188,200],"this":[44],"purpose":[45],"are":[46],"Gene":[48],"Ontology":[49],"(GO)":[50],"annotating":[52,201],"aspects":[53],"gene":[55],"products":[56],"Molecular":[59],"Interaction":[60],"ontology":[61,129,203,231],"(PSI-MI)":[62],"by":[64],"databases":[65],"archive":[67],"protein-protein":[68,253],"interactions.":[69],"The":[70],"examination":[71],"protein":[73],"interactions":[74],"has":[75,160],"proven":[76],"be":[78],"extremely":[79],"promising":[80],"understanding":[83],"cellular":[85],"processes.":[86],"Manual":[87],"mapping":[88],"information":[90],"from":[91,151,206],"biomedical":[93],"bio-ontology":[96],"terms":[97,177,232,258],"one":[99],"most":[102],"challenging":[103],"components":[104],"curation":[107,134],"pipeline.":[108],"It":[109],"requires":[110],"expert":[112],"curators":[113],"interpret":[114],"natural":[116],"language":[117],"descriptions":[118],"contained":[119],"articles":[121],"infer":[123],"their":[124],"semantic":[125],"equivalents":[126],"(controlled":[130],"vocabulary).":[131],"Since":[132],"a":[136,216],"time-consuming":[137],"process,":[138],"there":[139],"strong":[141],"motivation":[142],"implement":[144],"text-mining":[145,221],"techniques":[146],"automatically":[148,224],"extract":[149,225],"annotations":[150,226],"free":[152],"text.":[153],"A":[154],"range":[155],"text":[157],"mining":[158],"strategies":[159,173],"devised":[162],"assist":[164],"automated":[167],"extraction":[168],"These":[172],"either":[174],"recognize":[175],"technical":[176],"recurrently":[179],"propose":[184],"them":[185],"as":[186,197],"candidates":[187],"inclusion":[189],"ontologies,":[191],"or":[192,209],"retrieve":[193],"passages":[194],"serve":[196],"evidential":[198],"support":[199],"term,":[204],"e.g.":[205],"PSI-MI":[208,230,257],"GO":[210,228],"vocabularies.":[212],"Here,":[213],"we":[214],"provide":[215],"general":[217],"overview":[218],"current":[220],"methods":[222],"context":[235],"BioCreative":[238],"(Critical":[239],"Assessment":[240],"Information":[242],"Extraction":[243],"Systems":[244],"Biology)":[246],"challenge.":[247],"Special":[248],"emphasis":[249],"given":[251],"interaction":[254,261],"data":[255],"referring":[259],"detection":[262],"methods.":[263]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":5}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
