{"id":"https://openalex.org/W1973661008","doi":"https://doi.org/10.1186/1471-2105-10-376","title":"Algorithms for effective querying of compound graph-based pathway databases","display_name":"Algorithms for effective querying of compound graph-based pathway databases","publication_year":2009,"publication_date":"2009-11-16","ids":{"openalex":"https://openalex.org/W1973661008","doi":"https://doi.org/10.1186/1471-2105-10-376","mag":"1973661008","pmid":"https://pubmed.ncbi.nlm.nih.gov/19917102"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-376","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-376","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-376","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/10.1186/1471-2105-10-376","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006798669","display_name":"U\u011fur Do\u011frus\u00f6z","orcid":"https://orcid.org/0000-0002-7153-0784"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Ugur Dogrusoz","raw_affiliation_strings":["Computer Engineering Dept, Bilkent University, Center for Bioinformatics, Ankara, Turkey. ugur@cs.bilkent.edu.tr","Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Dept, Bilkent University, Center for Bioinformatics, Ankara, Turkey. ugur@cs.bilkent.edu.tr","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011579419","display_name":"Ahmet \u00c7etinta\u015f","orcid":null},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ahmet Cetintas","raw_affiliation_strings":["Center for Bioinformatics and Computer Engineering Dept., Bilkent University, Ankara, Turkey","Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computer Engineering Dept., Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037803004","display_name":"Emek Demir","orcid":"https://orcid.org/0000-0002-3663-7113"},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emek Demir","raw_affiliation_strings":["Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA","Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006448195","display_name":"\u00d6zg\u00fcn Babur","orcid":"https://orcid.org/0000-0002-0239-5259"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ozgun Babur","raw_affiliation_strings":["Center for Bioinformatics and Computer Engineering Dept., Bilkent University, Ankara, Turkey","Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computer Engineering Dept., Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5006798669"],"corresponding_institution_ids":["https://openalex.org/I168864056"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6751,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.68066049,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"10","issue":"1","first_page":"376","last_page":"376"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8841999769210815,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8841999769210815,"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":0.024299999698996544,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.020600000396370888,"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":0.7928637266159058},{"id":"https://openalex.org/keywords/graph-database","display_name":"Graph database","score":0.7035289406776428},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5598701238632202},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5477688312530518},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5331441760063171},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33742356300354004},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.32428643107414246},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.18939441442489624}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7928637266159058},{"id":"https://openalex.org/C176225458","wikidata":"https://www.wikidata.org/wiki/Q595971","display_name":"Graph database","level":3,"score":0.7035289406776428},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5598701238632202},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5477688312530518},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5331441760063171},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33742356300354004},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.32428643107414246},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.18939441442489624},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","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":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D025941","descriptor_name":"Protein Interaction Mapping","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":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-10-376","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-376","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-376","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:19917102","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19917102","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:doaj.org/article:41426b8a25bd41169c1572bbb816690d","is_oa":false,"landing_page_url":"https://doaj.org/article/41426b8a25bd41169c1572bbb816690d","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 376 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2784781","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2784781","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"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/22570","is_oa":false,"landing_page_url":"http://hdl.handle.net/11693/22570","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-376","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-376","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-376","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":[],"awards":[{"id":"https://openalex.org/G807269317","display_name":"PAT\u0130KA: H\u0131zl\u0131 bilgi toplanmas\u0131, ila\u00e7 geli\u015ftirilmesi ve hastal\u0131k tan\u0131lar\u0131na yard\u0131m i\u00e7in bir biyolojik yolak modelleme ve analiz \u00e7al\u0131\u015fmas\u0131","funder_award_id":"104E049","funder_id":"https://openalex.org/F4320322626","funder_display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu"}],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1973661008.pdf","grobid_xml":"https://content.openalex.org/works/W1973661008.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1484040084","https://openalex.org/W1489285575","https://openalex.org/W1514415888","https://openalex.org/W1563476066","https://openalex.org/W1783384641","https://openalex.org/W1877439477","https://openalex.org/W1984249061","https://openalex.org/W1992009195","https://openalex.org/W1998971866","https://openalex.org/W1999895438","https://openalex.org/W2025183726","https://openalex.org/W2037718952","https://openalex.org/W2038264484","https://openalex.org/W2058451329","https://openalex.org/W2069157810","https://openalex.org/W2099007946","https://openalex.org/W2103599442","https://openalex.org/W2104009289","https://openalex.org/W2111823238","https://openalex.org/W2112200469","https://openalex.org/W2117604571","https://openalex.org/W2122863289","https://openalex.org/W2126434857","https://openalex.org/W2128601422","https://openalex.org/W2133319394","https://openalex.org/W2135435176","https://openalex.org/W2136523220","https://openalex.org/W2139483589","https://openalex.org/W2141297641","https://openalex.org/W2143969914","https://openalex.org/W2144063122","https://openalex.org/W2160540739","https://openalex.org/W2163480486","https://openalex.org/W2169804422","https://openalex.org/W2752885492","https://openalex.org/W3027688856","https://openalex.org/W3133279294","https://openalex.org/W3145128584","https://openalex.org/W4230392683","https://openalex.org/W4255852734","https://openalex.org/W4298203020"],"related_works":["https://openalex.org/W2003932708","https://openalex.org/W2284877871","https://openalex.org/W4283723149","https://openalex.org/W2560036845","https://openalex.org/W3115442681","https://openalex.org/W2007838763","https://openalex.org/W2391000461","https://openalex.org/W4386112722","https://openalex.org/W2972311463","https://openalex.org/W31445736"],"abstract_inverted_index":{"BACKGROUND:":[0],"Graph-based":[1],"pathway":[2,162,193,278],"ontologies":[3],"and":[4,25,42,125,170,187,207,210,260,263],"databases":[5],"are":[6],"widely":[7],"used":[8],"to":[9,20,26,38,105,113,148,151,157,168,202,233],"represent":[10],"data":[11],"about":[12],"cellular":[13,23],"processes.":[14],"This":[15],"representation":[16],"makes":[17],"it":[18,102,179],"possible":[19],"programmatically":[21],"integrate":[22],"networks":[24,112],"investigate":[27],"them":[28],"using":[29],"the":[30,115,120,192,197,220,243,251],"well-understood":[31],"concepts":[32],"of":[33,47,61,70,76,85,90,117,122,141,160,222,246,250,271],"graph":[34,49],"theory":[35],"in":[36,57,177,191,218],"order":[37],"predict":[39],"their":[40],"structural":[41],"dynamic":[43],"properties.":[44],"An":[45],"extension":[46],"this":[48,100,130],"representation,":[50],"namely":[51],"hierarchically":[52],"structured":[53],"or":[54,97,184],"compound":[55,111,183],"graphs,":[56],"which":[58,219],"a":[59,62,68,71,134,139,216,227,247,269],"member":[60],"biological":[63,77,86],"network":[64],"may":[65,199],"recursively":[66,213],"contain":[67],"sub-network":[69],"somehow":[72],"logically":[73],"similar":[74],"group":[75],"objects,":[78],"provides":[79],"many":[80],"additional":[81],"benefits":[82],"for":[83,182,231,258,267,275],"analysis":[84],"pathways,":[87],"including":[88],"reduction":[89],"complexity":[91],"by":[92],"decomposition":[93],"into":[94,215],"distinct":[95],"components":[96],"modules.":[98],"In":[99,195],"regard,":[101],"is":[103,155,175,286,291],"essential":[104],"effectively":[106],"query":[107,224],"such":[108],"integrated":[109],"large":[110,276],"extract":[114],"sub-networks":[116],"interest":[118],"with":[119,138],"help":[121],"efficient":[123],"algorithms":[124,143,239],"software":[126,252],"tools.":[127],"RESULTS:":[128],"Towards":[129],"goal,":[131],"we":[132],"developed":[133],"querying":[135,244],"framework,":[136],"along":[137],"number":[140,270],"graph-theoretic":[142],"from":[144,164],"simple":[145],"neighborhood":[146],"queries":[147,198],"shortest":[149],"paths":[150],"feedback":[152],"loops,":[153],"that":[154,178],"applicable":[156],"all":[158],"sorts":[159],"graph-based":[161,277],"databases,":[163],"PPIs":[165],"(protein-protein":[166],"interactions)":[167],"metabolic":[169],"signaling":[171],"pathways.":[172],"The":[173,238,281],"framework":[174],"unique":[176],"can":[180,211],"account":[181],"nested":[185],"structures":[186],"ubiquitous":[188],"entities":[189],"present":[190],"data.":[194],"addition,":[196],"be":[200,212,226],"related":[201],"each":[203],"other":[204],"through":[205],"\"AND\"":[206],"\"OR\"":[208],"operators,":[209],"organized":[214],"tree,":[217],"result":[221],"one":[223],"might":[225],"source":[228],"and/or":[229],"target":[230],"another,":[232],"form":[234],"more":[235],"complex":[236],"queries.":[237],"were":[240],"implemented":[241],"within":[242],"component":[245],"new":[248],"version":[249,289],"tool":[253],"PATIKAweb":[254,288],"(Pathway":[255],"Analysis":[256],"Tool":[257],"Integration":[259],"Knowledge":[261],"Acquisition)":[262],"have":[264],"proven":[265],"useful":[266],"answering":[268],"biologically":[272],"significant":[273],"questions":[274],"databases.":[279],"CONCLUSION:":[280],"PATIKA":[282],"Project":[283],"Web":[284],"site":[285],"http://www.patika.org.":[287],"2.1":[290],"available":[292],"at":[293],"http://web.patika.org.":[294]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
