{"id":"https://openalex.org/W1980783875","doi":"https://doi.org/10.1186/1471-2105-10-s10-s9","title":"Structuring and extracting knowledge for the support of hypothesis generation in molecular biology","display_name":"Structuring and extracting knowledge for the support of hypothesis generation in molecular biology","publication_year":2009,"publication_date":"2009-10-01","ids":{"openalex":"https://openalex.org/W1980783875","doi":"https://doi.org/10.1186/1471-2105-10-s10-s9","mag":"1980783875","pmid":"https://pubmed.ncbi.nlm.nih.gov/19796406"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-s10-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s10-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S10-S9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S10-S9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021179422","display_name":"Marco Roos","orcid":"https://orcid.org/0000-0002-8691-772X"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Marco Roos","raw_affiliation_strings":["Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands. roos@science.uva.nl","Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands. roos@science.uva.nl","institution_ids":["https://openalex.org/I887064364"]},{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075308601","display_name":"Michael S. Marshall","orcid":"https://orcid.org/0000-0002-5742-2031"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"M Scott Marshall","raw_affiliation_strings":["Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands","Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands","institution_ids":["https://openalex.org/I887064364"]},{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104091226","display_name":"Andrew P. Gibson","orcid":null},"institutions":[{"id":"https://openalex.org/I1295801184","display_name":"Netherlands Institute for Neuroscience","ror":"https://ror.org/05csn2x06","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1295801184","https://openalex.org/I1322597698"]},{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Andrew P Gibson","raw_affiliation_strings":["Swammerdam Institute for Life Science, University of Amsterdam, Amsterdam, 1018 WB, The Netherlands","Swammerdam Institute for Life Science, University of Amsterdam, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Swammerdam Institute for Life Science, University of Amsterdam, Amsterdam, 1018 WB, The Netherlands","institution_ids":["https://openalex.org/I1295801184","https://openalex.org/I887064364"]},{"raw_affiliation_string":"Swammerdam Institute for Life Science, University of Amsterdam, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1295801184","https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077586396","display_name":"Martijn J. Schuemie","orcid":"https://orcid.org/0000-0002-0817-5361"},"institutions":[{"id":"https://openalex.org/I913958620","display_name":"Erasmus University Rotterdam","ror":"https://ror.org/057w15z03","country_code":"NL","type":"education","lineage":["https://openalex.org/I913958620"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Martijn Schuemie","raw_affiliation_strings":["BioSemantics group, Erasmus University of Rotterdam, Rotterdam, 3000 DR, The Netherlands","BioSemantics group, Erasmus University of Rotterdam, Rotterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioSemantics group, Erasmus University of Rotterdam, Rotterdam, 3000 DR, The Netherlands","institution_ids":["https://openalex.org/I913958620"]},{"raw_affiliation_string":"BioSemantics group, Erasmus University of Rotterdam, Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I913958620"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031940626","display_name":"Edgar Meij","orcid":"https://orcid.org/0000-0003-0516-3688"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Edgar Meij","raw_affiliation_strings":["Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands","Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands","institution_ids":["https://openalex.org/I887064364"]},{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016907452","display_name":"Sophia Katrenko","orcid":"https://orcid.org/0000-0001-6618-2175"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Sophia Katrenko","raw_affiliation_strings":["Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands","Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands","institution_ids":["https://openalex.org/I887064364"]},{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085349960","display_name":"Willem Robert van Hage","orcid":null},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Willem Robert van Hage","raw_affiliation_strings":["Business Informatics, Faculty of Sciences, Vrije Universiteit, Amsterdam, 1081 HV, The Netherlands","Business Informatics, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Business Informatics, Faculty of Sciences, Vrije Universiteit, Amsterdam, 1081 HV, The Netherlands","institution_ids":["https://openalex.org/I865915315"]},{"raw_affiliation_string":"Business Informatics, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046157402","display_name":"Konstantinos F. Krommydas","orcid":"https://orcid.org/0000-0002-3154-0363"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Konstantinos Krommydas","raw_affiliation_strings":["Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands","Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands","institution_ids":["https://openalex.org/I887064364"]},{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071446834","display_name":"Pieter Adriaans","orcid":"https://orcid.org/0000-0002-8473-7856"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Pieter W Adriaans","raw_affiliation_strings":["Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands","Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands","institution_ids":["https://openalex.org/I887064364"]},{"raw_affiliation_string":"Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands#TAB#","institution_ids":["https://openalex.org/I887064364"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5021179422"],"corresponding_institution_ids":["https://openalex.org/I887064364"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.5106,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.80845556,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"10","issue":"S10","first_page":"S9","last_page":"S9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.988099992275238,"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":0.988099992275238,"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":0.0034000000450760126,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.00279999990016222,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7996584177017212},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7145576477050781},{"id":"https://openalex.org/keywords/structuring","display_name":"Structuring","score":0.5096518993377686},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5027086734771729},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.44881337881088257},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.44756004214286804},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.44193994998931885},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.44117119908332825},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.43216145038604736},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.42071861028671265},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.41626936197280884},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.41364413499832153},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.40341904759407043},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2805095314979553},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21515870094299316},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1426510214805603}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7996584177017212},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7145576477050781},{"id":"https://openalex.org/C2775945657","wikidata":"https://www.wikidata.org/wiki/Q381442","display_name":"Structuring","level":2,"score":0.5096518993377686},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5027086734771729},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.44881337881088257},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.44756004214286804},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.44193994998931885},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.44117119908332825},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.43216145038604736},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.42071861028671265},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.41626936197280884},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.41364413499832153},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.40341904759407043},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2805095314979553},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21515870094299316},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1426510214805603},{"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","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/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","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":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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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}],"locations_count":10,"locations":[{"id":"doi:10.1186/1471-2105-10-s10-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s10-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S10-S9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19796406","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19796406","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:dare.uva.nl:openaire_cris_publications/a529d04f-1424-44b3-adeb-b8c94fcee67b","is_oa":true,"landing_page_url":"https://handle.uba.uva.nl/personal/pure/en/publications/structuring-and-extracting-knowledge-for-the-support-of-hypothesis-generation-in-molecular-biology(a529d04f-1424-44b3-adeb-b8c94fcee67b).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Roos, M, Marshall, M S, Gibson, A P, Schuemie, M, Meij, E, Katrenko, S, van Hage, W R, Krommydas, K & Adriaans, P W 2009, 'Structuring and extracting knowledge for the support of hypothesis generation in molecular biology', BMC Bioinformatics, vol. 10, no. S10, pp. S9. https://doi.org/10.1186/1471-2105-10-S10-S9","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pure.eur.nl:openaire_cris_publications/7f9b9237-bd3a-43c0-94f5-5f4aece84d95","is_oa":false,"landing_page_url":"https://pure.eur.nl/en/publications/7f9b9237-bd3a-43c0-94f5-5f4aece84d95","pdf_url":null,"source":{"id":"https://openalex.org/S4306401266","display_name":"EUR Research Repository (Erasmus University Rotterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I913958620","host_organization_name":"Erasmus University Rotterdam","host_organization_lineage":["https://openalex.org/I913958620"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Roos, M, Marshall, MS, Gibson, AP, Schuemie, M, Meij, E, Katrenko, S, van Hage, WR, Krommydas, K & Adriaans, PW 2009, 'Structuring and extracting knowledge for the support of hypothesis generation in molecular biology', BMC Bioinformatics, vol. 10.","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:research.vu.nl:publications/f224d258-f55b-4c04-a325-5e192a44debb","is_oa":true,"landing_page_url":"https://research.vu.nl/en/publications/f224d258-f55b-4c04-a325-5e192a44debb","pdf_url":"https://research.vu.nl/en/publications/f224d258-f55b-4c04-a325-5e192a44debb","source":{"id":"https://openalex.org/S4306401107","display_name":"VU Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I865915315","host_organization_name":"Vrije Universiteit Amsterdam","host_organization_lineage":["https://openalex.org/I865915315"],"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":"Roos, M, Scott, M S, Gibson, A P, Schuemie, M, Meij, E, Katrenko, S, van Hage, W R, Krommydas, K & Adriaans, P W 2009, 'Structuring and extracting knowledge for the support of hypothesis generation in molecular biology', BMC Bioinformatics. https://doi.org/10.1186/1471-2105-10-S10-S9","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:uvapub:oai:dare.uva.nl:publications/a529d04f-1424-44b3-adeb-b8c94fcee67b","is_oa":true,"landing_page_url":"https://dare.uva.nl/personal/pure/en/publications/structuring-and-extracting-knowledge-for-the-support-of-hypothesis-generation-in-molecular-biology(a529d04f-1424-44b3-adeb-b8c94fcee67b).html","pdf_url":"https://dare.uva.nl/personal/pure/en/publications/structuring-and-extracting-knowledge-for-the-support-of-hypothesis-generation-in-molecular-biology(a529d04f-1424-44b3-adeb-b8c94fcee67b).html","source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"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":"BMC Bioinformatics, 10(S10). BioMed Central","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:dare.ubvu.vu.nl:1871/20415","is_oa":false,"landing_page_url":"http://hdl.handle.net/1871/20415","pdf_url":null,"source":{"id":"https://openalex.org/S4306400546","display_name":"Digital Academic REpository of VU University Amsterdam (Vrije Universiteit Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I865915315","host_organization_name":"Vrije Universiteit Amsterdam","host_organization_lineage":["https://openalex.org/I865915315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Article / Letter to editor"},{"id":"pmh:oai:dare.uva.nl:publications/a529d04f-1424-44b3-adeb-b8c94fcee67b","is_oa":false,"landing_page_url":"http://dare.uva.nl/personal/pure/en/publications/structuring-and-extracting-knowledge-for-the-support-of-hypothesis-generation-in-molecular-biology(a529d04f-1424-44b3-adeb-b8c94fcee67b).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:doaj.org/article:ccbf67801fd04ae68b99f354806d0e6c","is_oa":true,"landing_page_url":"https://doaj.org/article/ccbf67801fd04ae68b99f354806d0e6c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss Suppl 10, p S9 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2755830","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2755830","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-s10-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s10-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S10-S9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.4300000071525574,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1980783875.pdf","grobid_xml":"https://content.openalex.org/works/W1980783875.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W98346458","https://openalex.org/W1510720609","https://openalex.org/W1532325895","https://openalex.org/W1535786933","https://openalex.org/W1542026696","https://openalex.org/W1553005811","https://openalex.org/W1570448133","https://openalex.org/W1580184797","https://openalex.org/W1646048262","https://openalex.org/W1692535048","https://openalex.org/W1812636409","https://openalex.org/W1967176062","https://openalex.org/W1974833742","https://openalex.org/W2027398710","https://openalex.org/W2042377056","https://openalex.org/W2066003039","https://openalex.org/W2071108800","https://openalex.org/W2087383805","https://openalex.org/W2091729411","https://openalex.org/W2098098151","https://openalex.org/W2098538932","https://openalex.org/W2112723752","https://openalex.org/W2113142309","https://openalex.org/W2115007282","https://openalex.org/W2118208190","https://openalex.org/W2121588207","https://openalex.org/W2122435612","https://openalex.org/W2134418889","https://openalex.org/W2137653635","https://openalex.org/W2144949988","https://openalex.org/W2150424267","https://openalex.org/W2152590979","https://openalex.org/W2155232871","https://openalex.org/W2156222477","https://openalex.org/W2156470649","https://openalex.org/W2156576948","https://openalex.org/W2156622158","https://openalex.org/W2259172389","https://openalex.org/W2792952625","https://openalex.org/W4213009331","https://openalex.org/W4241509948"],"related_works":["https://openalex.org/W4251394462","https://openalex.org/W1580673008","https://openalex.org/W1510936208","https://openalex.org/W2016355461","https://openalex.org/W2386938185","https://openalex.org/W1986386500","https://openalex.org/W2068844411","https://openalex.org/W2793744252","https://openalex.org/W2072284316","https://openalex.org/W1516746680"],"abstract_inverted_index":{"BACKGROUND:":[0],"Hypothesis":[1],"generation":[2,121],"in":[3,12,43,146,244,283,342],"molecular":[4],"and":[5,62,80,95,132,161,165,186,241,336,347],"cellular":[6],"biology":[7],"is":[8,19,30,197,217],"an":[9],"empirical":[10],"process":[11],"which":[13],"knowledge":[14,75,139,191,243,271,294,304,322],"derived":[15],"from":[16,49,69,140,192,201],"prior":[17,57,74],"experiments":[18,278],"distilled":[20],"into":[21],"a":[22,100,136,153,171,180,212,218,236,291,340],"comprehensible":[23],"model.":[24],"The":[25,168,215,253],"requirement":[26],"of":[27,35,46,122,152,179,189,199,247,262,270,293],"automated":[28,117],"support":[29,118],"exemplified":[31],"by":[32,105],"the":[33,44,90,93,106,120,157,177,202,230,245,260,268,343],"difficulty":[34],"considering":[36],"all":[37],"relevant":[38],"facts":[39],"that":[40,88,102,173,295],"are":[41,128],"contained":[42],"millions":[45],"documents":[47],"available":[48,76],"PubMed.":[50],"Semantic":[51,125],"Web":[52,126,314],"provides":[53],"tools":[54,84],"for":[55,77,119,148,239],"sharing":[56],"knowledge,":[58,134],"while":[59,135,183],"information":[60,63],"retrieval":[61],"extraction":[64,68,96,272,323],"techniques":[65],"enable":[66],"its":[67],"literature.":[70],"Their":[71],"combination":[72],"makes":[73],"computational":[78],"analysis":[79,188],"inference.":[81],"While":[82],"some":[83],"provide":[85],"complete":[86],"solutions":[87],"limit":[89],"control":[91,104],"over":[92,108],"modeling":[94],"processes,":[97],"we":[98,329],"seek":[99],"methodology":[101,172,254],"supports":[103],"experimenter":[107],"these":[109],"critical":[110],"processes.":[111,273],"RESULTS:":[112],"We":[113,142,234],"describe":[114],"progress":[115],"towards":[116],"biomolecular":[123,251],"hypotheses.":[124],"technologies":[127],"used":[129,257,318],"to":[130,229,258,276,302,319],"structure":[131],"store":[133],"workflow":[137,166,196],"extracts":[138],"text.":[141],"designed":[143],"minimal":[144],"proto-ontologies":[145],"OWL":[147],"capturing":[149],"different":[150],"aspects":[151],"text":[154,160,163],"mining":[155],"experiment:":[156],"biological":[158,223,265],"hypothesis,":[159],"documents,":[162],"mining,":[164],"provenance.":[167],"models":[169,266],"fit":[170],"allows":[174],"focus":[175],"on":[176,250],"requirements":[178],"single":[181],"experiment":[182],"supporting":[184],"reuse":[185],"posterior":[187],"extracted":[190],"multiple":[193],"experiments.":[194,297],"Our":[195],"composed":[198],"services":[200],"'Adaptive":[203],"Information":[204],"Disclosure":[205],"Application'":[206],"(AIDA)":[207],"toolkit":[208],"as":[209,211,307],"well":[210],"few":[213],"others.":[214],"output":[216],"semantic":[219,288],"model":[220],"with":[221,225,286],"putative":[222],"relations,":[224],"each":[226],"relation":[227],"linked":[228],"corresponding":[231],"evidence.":[232],"CONCLUSION:":[233],"demonstrated":[235],"'do-it-yourself'":[237],"approach":[238],"structuring":[240],"extracting":[242],"context":[246],"experimental":[248],"research":[249],"mechanisms.":[252],"can":[255,279,300,316],"be":[256,280,317],"bootstrap":[259],"construction":[261],"semantically":[263],"rich":[264],"using":[267],"results":[269],"Models":[274],"specific":[275],"particular":[277],"constructed":[281],"that,":[282],"turn,":[284],"link":[285,301],"other":[287,303],"models,":[289],"creating":[290],"web":[292],"spans":[296],"Mapping":[298],"mechanisms":[299],"resources":[305],"such":[306],"OBO":[308],"ontologies":[309],"or":[310],"SKOS":[311],"vocabularies.":[312],"AIDA":[313],"Services":[315],"design":[320],"personalized":[321],"procedures.":[324],"In":[325],"our":[326],"example":[327],"experiment,":[328],"found":[330],"three":[331],"proteins":[332],"(NF-Kappa":[333],"B,":[334],"p21,":[335],"Bax)":[337],"potentially":[338],"playing":[339],"role":[341],"interplay":[344],"between":[345],"nutrients":[346],"epigenetic":[348],"gene":[349],"regulation.":[350]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
