{"id":"https://openalex.org/W2138675401","doi":"https://doi.org/10.1093/bib/bbl037","title":"Mining literature for systems biology","display_name":"Mining literature for systems biology","publication_year":2006,"publication_date":"2006-09-26","ids":{"openalex":"https://openalex.org/W2138675401","doi":"https://doi.org/10.1093/bib/bbl037","mag":"2138675401","pmid":"https://pubmed.ncbi.nlm.nih.gov/17032698"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbl037","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbl037","pdf_url":"https://academic.oup.com/bib/article-pdf/7/4/399/448480/bbl037.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/7/4/399/448480/bbl037.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102723391","display_name":"Patricia Roberts\u2010Miller","orcid":"https://orcid.org/0009-0002-9995-6282"},"institutions":[{"id":"https://openalex.org/I1297540436","display_name":"Biogen (United States)","ror":"https://ror.org/02jqkb192","country_code":"US","type":"company","lineage":["https://openalex.org/I1297540436"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"P. M. Roberts","raw_affiliation_strings":["Biogen Idec Inc., 14 Cambridge Center, Cambridge MA 02142, USA. Phoebe.Roberts@biogenidec.com"],"affiliations":[{"raw_affiliation_string":"Biogen Idec Inc., 14 Cambridge Center, Cambridge MA 02142, USA. Phoebe.Roberts@biogenidec.com","institution_ids":["https://openalex.org/I1297540436"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5102723391"],"corresponding_institution_ids":["https://openalex.org/I1297540436"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.8606,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.90646362,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"7","issue":"4","first_page":"399","last_page":"406"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9984999895095825,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9771999716758728,"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":0.7311757206916809},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5935340523719788},{"id":"https://openalex.org/keywords/subject","display_name":"Subject (documents)","score":0.5475538372993469},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4956933259963989},{"id":"https://openalex.org/keywords/analytics","display_name":"Analytics","score":0.46482259035110474},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4452435374259949},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3496379256248474},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2582477927207947},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1750563383102417}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7311757206916809},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5935340523719788},{"id":"https://openalex.org/C2777855551","wikidata":"https://www.wikidata.org/wiki/Q12310021","display_name":"Subject (documents)","level":2,"score":0.5475538372993469},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4956933259963989},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.46482259035110474},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4452435374259949},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3496379256248474},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2582477927207947},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1750563383102417}],"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":"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":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbl037","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbl037","pdf_url":"https://academic.oup.com/bib/article-pdf/7/4/399/448480/bbl037.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17032698","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17032698","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.579.8729","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.579.8729","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bib.oxfordjournals.org/content/7/4/399.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbl037","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbl037","pdf_url":"https://academic.oup.com/bib/article-pdf/7/4/399/448480/bbl037.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.7200000286102295}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2138675401.pdf","grobid_xml":"https://content.openalex.org/works/W2138675401.grobid-xml"},"referenced_works_count":75,"referenced_works":["https://openalex.org/W1499561015","https://openalex.org/W1510579866","https://openalex.org/W1525672751","https://openalex.org/W1553529581","https://openalex.org/W1600005654","https://openalex.org/W1972301305","https://openalex.org/W1976316416","https://openalex.org/W1982035848","https://openalex.org/W1990800680","https://openalex.org/W1994803330","https://openalex.org/W2014358138","https://openalex.org/W2021025020","https://openalex.org/W2030404924","https://openalex.org/W2048130697","https://openalex.org/W2049752727","https://openalex.org/W2050721857","https://openalex.org/W2054878850","https://openalex.org/W2056119436","https://openalex.org/W2072159031","https://openalex.org/W2077953882","https://openalex.org/W2081965566","https://openalex.org/W2083752219","https://openalex.org/W2085442947","https://openalex.org/W2096525273","https://openalex.org/W2099668895","https://openalex.org/W2103017472","https://openalex.org/W2107591926","https://openalex.org/W2109453886","https://openalex.org/W2115260641","https://openalex.org/W2116271446","https://openalex.org/W2118806902","https://openalex.org/W2119412782","https://openalex.org/W2128572161","https://openalex.org/W2131165643","https://openalex.org/W2134711219","https://openalex.org/W2137485088","https://openalex.org/W2138689719","https://openalex.org/W2138843474","https://openalex.org/W2139259976","https://openalex.org/W2139924741","https://openalex.org/W2140407633","https://openalex.org/W2143738293","https://openalex.org/W2144001613","https://openalex.org/W2145221987","https://openalex.org/W2147404343","https://openalex.org/W2148282068","https://openalex.org/W2149184178","https://openalex.org/W2150252713","https://openalex.org/W2155606054","https://openalex.org/W2157870551","https://openalex.org/W2158875454","https://openalex.org/W2159203162","https://openalex.org/W2159583324","https://openalex.org/W2161732286","https://openalex.org/W2164085997","https://openalex.org/W2167199696","https://openalex.org/W2168905447","https://openalex.org/W2183798833","https://openalex.org/W2315991549","https://openalex.org/W2768824252","https://openalex.org/W2944782266","https://openalex.org/W3186587728","https://openalex.org/W4230903726","https://openalex.org/W4231824804","https://openalex.org/W4239678514","https://openalex.org/W4240689716","https://openalex.org/W4248234957","https://openalex.org/W6633075837","https://openalex.org/W6664600091","https://openalex.org/W6675471023","https://openalex.org/W6681260644","https://openalex.org/W6681483942","https://openalex.org/W6683913575","https://openalex.org/W6685026573","https://openalex.org/W7073557482"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4388258507","https://openalex.org/W2392013855","https://openalex.org/W4318064328","https://openalex.org/W2357926602","https://openalex.org/W2374569605","https://openalex.org/W2386062718","https://openalex.org/W5284979","https://openalex.org/W4390482427","https://openalex.org/W4245853730"],"abstract_inverted_index":{"Currently,":[0],"literature":[1,23],"is":[2,24,98],"integrated":[3,78],"in":[4,8,19,27,50,70,121],"systems":[5,140],"biology":[6],"studies":[7],"three":[9],"ways.":[10],"Hand-curated":[11],"pathways":[12],"have":[13],"been":[14],"sufficient":[15],"for":[16,83,93],"assembling":[17],"models":[18],"numerous":[20],"studies.":[21],"Second,":[22],"frequently":[25],"accessed":[26],"a":[28],"derived":[29,118],"form,":[30],"such":[31],"as":[32,67,102,136],"the":[33,37,71,100],"concepts":[34,65,119],"represented":[35],"by":[36],"Medical":[38],"Subject":[39],"Headings":[40],"(MeSH)":[41],"and":[42,109,123,125,127],"Gene":[43],"Ontologies":[44],"(GO),":[45],"or":[46],"functional":[47],"relationships":[48],"captured":[49,120],"protein-protein":[51],"interaction":[52],"(PPI)":[53],"databases;":[54],"both":[55],"of":[56,62,96,113,130],"these":[57],"are":[58,76],"convenient,":[59],"consistent":[60],"reductions":[61],"more":[63,107],"complex":[64],"expressed":[66],"free":[68],"text":[69,91,103,131],"literature.":[72],"Moreover,":[73],"their":[74],"contents":[75],"easily":[77],"into":[79],"computational":[80],"processes":[81],"required":[82],"dealing":[84],"with":[85],"large":[86],"data":[87],"sets.":[88],"Last,":[89],"mining":[90],"directly":[92],"specific":[94],"types":[95],"information":[97],"on":[99],"rise":[101],"analytics":[104],"methods":[105],"become":[106],"accurate":[108],"accessible.":[110],"These":[111],"uses":[112],"literature,":[114],"specifically":[115],"manual":[116],"curation,":[117],"ontologies":[122],"databases,":[124],"indirect":[126],"direct":[128],"application":[129],"mining,":[132],"will":[133],"be":[134],"discussed":[135],"they":[137],"pertain":[138],"to":[139],"biology.":[141]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
