{"id":"https://openalex.org/W2085577304","doi":"https://doi.org/10.1145/1066677.1066722","title":"Optimizing syntax patterns for discovering protein-protein interactions","display_name":"Optimizing syntax patterns for discovering protein-protein interactions","publication_year":2005,"publication_date":"2005-03-13","ids":{"openalex":"https://openalex.org/W2085577304","doi":"https://doi.org/10.1145/1066677.1066722","mag":"2085577304"},"language":"en","primary_location":{"id":"doi:10.1145/1066677.1066722","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1066677.1066722","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2005 ACM symposium on Applied computing","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078605382","display_name":"Conrad Plake","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Conrad Plake","raw_affiliation_strings":["Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","[Humboldt Universitat zu Berlin, Berlin, Germany]"],"affiliations":[{"raw_affiliation_string":"Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"[Humboldt Universitat zu Berlin, Berlin, Germany]","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034893893","display_name":"J\u00f6rg Hakenberg","orcid":"https://orcid.org/0000-0001-8781-7766"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"J\u00f6rg Hakenberg","raw_affiliation_strings":["Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","[Humboldt Universitat zu Berlin, Berlin, Germany]"],"affiliations":[{"raw_affiliation_string":"Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"[Humboldt Universitat zu Berlin, Berlin, Germany]","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055236937","display_name":"Ulf Leser","orcid":"https://orcid.org/0000-0003-2166-9582"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ulf Leser","raw_affiliation_strings":["Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","[Humboldt Universitat zu Berlin, Berlin, Germany]"],"affiliations":[{"raw_affiliation_string":"Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"[Humboldt Universitat zu Berlin, Berlin, Germany]","institution_ids":["https://openalex.org/I39343248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5078605382"],"corresponding_institution_ids":["https://openalex.org/I39343248"],"apc_list":null,"apc_paid":null,"fwci":1.58682814,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.79925928,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"195","last_page":"201"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"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":0.9994000196456909,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9919000267982483,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9918000102043152,"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":0.7922160029411316},{"id":"https://openalex.org/keywords/syntax","display_name":"Syntax","score":0.7331457734107971},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.7154078483581543},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.7143506407737732},{"id":"https://openalex.org/keywords/regular-expression","display_name":"Regular expression","score":0.5549201369285583},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5546740293502808},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.5020701885223389},{"id":"https://openalex.org/keywords/recall","display_name":"Recall","score":0.4791540503501892},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.46872174739837646},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4523521065711975},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4046611487865448},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3337865173816681},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3291414976119995},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1293359100818634}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7922160029411316},{"id":"https://openalex.org/C60048249","wikidata":"https://www.wikidata.org/wiki/Q37437","display_name":"Syntax","level":2,"score":0.7331457734107971},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.7154078483581543},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.7143506407737732},{"id":"https://openalex.org/C121329065","wikidata":"https://www.wikidata.org/wiki/Q185612","display_name":"Regular expression","level":2,"score":0.5549201369285583},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5546740293502808},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.5020701885223389},{"id":"https://openalex.org/C100660578","wikidata":"https://www.wikidata.org/wiki/Q18733","display_name":"Recall","level":2,"score":0.4791540503501892},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.46872174739837646},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4523521065711975},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4046611487865448},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3337865173816681},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3291414976119995},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1293359100818634},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1066677.1066722","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1066677.1066722","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2005 ACM symposium on Applied computing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.46000000834465027}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1505057322","https://openalex.org/W1604959358","https://openalex.org/W1790194223","https://openalex.org/W2004620268","https://openalex.org/W2018874418","https://openalex.org/W2096525273","https://openalex.org/W2104768328","https://openalex.org/W2109070394","https://openalex.org/W2114049512","https://openalex.org/W2115880858","https://openalex.org/W2123280311","https://openalex.org/W2130687290","https://openalex.org/W2155320925","https://openalex.org/W2158256570","https://openalex.org/W2160238006","https://openalex.org/W4255855797","https://openalex.org/W4256647194","https://openalex.org/W6654860678","https://openalex.org/W6679248178"],"related_works":["https://openalex.org/W2563334590","https://openalex.org/W3094387502","https://openalex.org/W2922478741","https://openalex.org/W2119827098","https://openalex.org/W2101092231","https://openalex.org/W4388713123","https://openalex.org/W2358294942","https://openalex.org/W4367460280","https://openalex.org/W72959484","https://openalex.org/W2770860644"],"abstract_inverted_index":{"We":[0,24,120,160],"propose":[1],"a":[2,26,32,51,55,166],"method":[3,76],"for":[4],"automated":[5],"extraction":[6],"of":[7,28,36,96,101,143,157,165],"protein-protein":[8,84],"interactions":[9],"from":[10,129,135],"scientific":[11],"text.":[12],"Our":[13,75],"system":[14,86,113,123],"matches":[15],"sentences":[16],"against":[17],"syntax":[18,82],"patterns":[19,144],"typically":[20],"describing":[21],"protein":[22,168],"interactions.":[23],"define":[25],"set":[27,44,67],"22":[29],"patterns,":[30],"each":[31],"regular":[33],"expression":[34],"consisting":[35],"anchor":[37],"positions":[38],"and":[39,48,63,87,152,178],"parameterizable":[40],"constraints.":[41],"This":[42],"small":[43],"is":[45],"then":[46],"refined":[47],"optimized":[49],"using":[50],"genetic":[52],"algorithm":[53],"on":[54,92,124],"training":[56],"set.":[57],"No":[58],"heuristic":[59],"definitions":[60],"are":[61],"necessary,":[62],"the":[64,112,130,133,138,150,155,163],"final":[65],"pattern":[66],"can":[68,77],"be":[69,78],"generated":[70],"completely":[71],"without":[72],"manual":[73],"curation.":[74],"applied":[79],"to":[80,110,147,149,154],"any":[81],"pattern-based":[83],"interaction":[85],"thus":[88],"complements":[89],"related":[90],"work":[91],"building":[93],"comprehensive":[94],"sets":[95],"such":[97],"patterns.":[98],"The":[99,140],"application":[100],"different":[102],"fitness-functions":[103],"during":[104],"evolution":[105],"provides":[106],"an":[107],"easy":[108],"way":[109],"tune":[111],"either":[114],"toward":[115],"precision,":[116,151],"recall,":[117],"or":[118],"f-measure.":[119],"evaluate":[121],"our":[122,158],"two":[125],"samples,":[126],"one":[127],"derived":[128],"BioCreAtIvE":[131],"corpus,":[132],"other":[134],"references":[136],"in":[137],"DIP.":[139],"automatic":[141],"refinement":[142],"adds":[145],"up":[146],"16%":[148],"5%":[153],"recall":[156,179],"system.":[159],"additionally":[161],"study":[162],"impact":[164],"proper":[167],"name":[169],"recognition,":[170],"which":[171],"could":[172],"improve":[173],"precision":[174],"by":[175,180],"about":[176],"17%":[177],"12%.":[181]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
