{"id":"https://openalex.org/W2151871052","doi":"https://doi.org/10.2390/biecoll-jib-2008-100","title":"Subgraph Queries by Context-free Grammars","display_name":"Subgraph Queries by Context-free Grammars","publication_year":2008,"publication_date":"2008-01-01","ids":{"openalex":"https://openalex.org/W2151871052","doi":"https://doi.org/10.2390/biecoll-jib-2008-100","mag":"2151871052","pmid":"https://pubmed.ncbi.nlm.nih.gov/20134073"},"language":"en","primary_location":{"id":"pmid:20134073","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20134073","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":"Journal of integrative bioinformatics","raw_type":null},"type":"article","indexed_in":["datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.2390/biecoll-jib-2008-100","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034149799","display_name":"Petteri Sev\u00f3n","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Sevon, Petteri","raw_affiliation_strings":["Helsinki Institute for Information Technology, Department of Computer Science,PO Box 68, FI-00014 University of Helsinki, Finland"],"affiliations":[{"raw_affiliation_string":"Helsinki Institute for Information Technology, Department of Computer Science,PO Box 68, FI-00014 University of Helsinki, Finland","institution_ids":["https://openalex.org/I32943570","https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017516043","display_name":"Lauri Eronen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eronen, Lauri","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5034149799"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I32943570"],"apc_list":null,"apc_paid":null,"fwci":1.1732,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.85423871,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"5","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9957000017166138,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9803000092506409,"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":0.7499038577079773},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.722978949546814},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5438788533210754},{"id":"https://openalex.org/keywords/vertex","display_name":"Vertex (graph theory)","score":0.504186749458313},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4833762049674988},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4594079256057739},{"id":"https://openalex.org/keywords/context-free-grammar","display_name":"Context-free grammar","score":0.42244648933410645},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.4191173315048218},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3617984652519226},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.2406480610370636},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23807811737060547},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21023079752922058},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18228542804718018}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7499038577079773},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.722978949546814},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5438788533210754},{"id":"https://openalex.org/C80899671","wikidata":"https://www.wikidata.org/wiki/Q1304193","display_name":"Vertex (graph theory)","level":3,"score":0.504186749458313},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4833762049674988},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4594079256057739},{"id":"https://openalex.org/C97212296","wikidata":"https://www.wikidata.org/wiki/Q338047","display_name":"Context-free grammar","level":3,"score":0.42244648933410645},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.4191173315048218},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3617984652519226},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.2406480610370636},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23807811737060547},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21023079752922058},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18228542804718018},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"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/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":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","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":"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}],"locations_count":4,"locations":[{"id":"pmid:20134073","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20134073","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.485.7455","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.485.7455","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/articles/pdf/jib-100.pdf","raw_type":"text"},{"id":"pmh:oai:biecoll.ub.uni-bielefeld.de:294","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2008/294/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/index.php?paper_id=100","raw_type":"Journal Article"},{"id":"doi:10.2390/biecoll-jib-2008-100","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2008-100","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.2390/biecoll-jib-2008-100","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2008-100","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.6100000143051147,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1488882141","https://openalex.org/W1525196841","https://openalex.org/W1980622548","https://openalex.org/W1997520998","https://openalex.org/W2017102965","https://openalex.org/W2042853248","https://openalex.org/W2098571317","https://openalex.org/W2103599442","https://openalex.org/W2134495021","https://openalex.org/W2135282325"],"related_works":["https://openalex.org/W2167561219","https://openalex.org/W2604647807","https://openalex.org/W1966569037","https://openalex.org/W2026407613","https://openalex.org/W2609192861","https://openalex.org/W2306375758","https://openalex.org/W2131538679","https://openalex.org/W2940821404","https://openalex.org/W2381256431","https://openalex.org/W118648491"],"abstract_inverted_index":{"We":[0,20,58,73],"describe":[1],"a":[2,22,46,49,81,120,136],"method":[3],"for":[4,63,128],"querying":[5],"vertex-":[6],"and":[7,92],"edge-labeled":[8],"graphs":[9,85],"using":[10,119,135],"context-free":[11],"grammars":[12],"to":[13],"specify":[14],"the":[15,26,31,53,56,70,76,102],"class":[16],"of":[17,33,43,52,83],"interesting":[18],"paths.":[19,72],"introduce":[21],"novel":[23,61],"problem,":[24],"finding":[25],"connection":[27,103],"subgraph":[28,47,104],"induced":[29],"by":[30],"set":[32,82],"matching":[34],"paths":[35,113,133],"between":[36,55],"given":[37],"two":[38,41],"vertices":[39],"or":[40],"sets":[42],"vertices.":[44,57],"Such":[45],"provides":[48],"concise":[50],"summary":[51],"relationship":[54],"also":[59],"present":[60],"algorithms":[62,79],"parsing":[64,78,101,111,122],"subgraphs":[65],"directly":[66,105],"without":[67],"enumerating":[68],"all":[69],"individual":[71,112],"evaluate":[74],"experimentally":[75],"presented":[77],"on":[80,93],"real":[84],"derived":[86],"from":[87],"publicly":[88],"available":[89],"biomedical":[90],"databases":[91],"randomly":[94],"generated":[95],"graphs.":[96],"The":[97],"results":[98],"indicate":[99],"that":[100,118],"is":[106],"much":[107],"more":[108],"effective":[109],"than":[110],"separately.":[114],"Furthermore,":[115],"we":[116],"show":[117],"bidirectional":[121],"algorithm,":[123],"in":[124],"most":[125],"cases,":[126],"allows":[127],"searching":[129],"twice":[130],"as":[131,134],"long":[132],"unidirectional":[137],"search":[138],"strategy.":[139]},"counts_by_year":[{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
