{"id":"https://openalex.org/W2138545793","doi":"https://doi.org/10.1093/bioinformatics/bti488","title":"Fast parsers for Entrez Gene","display_name":"Fast parsers for Entrez Gene","publication_year":2005,"publication_date":"2005-05-06","ids":{"openalex":"https://openalex.org/W2138545793","doi":"https://doi.org/10.1093/bioinformatics/bti488","mag":"2138545793","pmid":"https://pubmed.ncbi.nlm.nih.gov/15879451"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti488","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/14/3189/48971510/bioinformatics_21_14_3189.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/14/3189/48971510/bioinformatics_21_14_3189.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000026020","display_name":"Mingyi Liu","orcid":"https://orcid.org/0000-0002-8101-8522"},"institutions":[{"id":"https://openalex.org/I4923324","display_name":"Fraunhofer-Gesellschaft","ror":"https://ror.org/05hkkdn48","country_code":"DE","type":"government","lineage":["https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"M. Liu","raw_affiliation_strings":["GPC Biotech AG Fraunhoferstrasse 20, 82152 Martinsried, Germany","GPC Biotech AG  Fraunhoferstrasse 20, 82152 Martinsried, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GPC Biotech AG Fraunhoferstrasse 20, 82152 Martinsried, Germany","institution_ids":["https://openalex.org/I4923324"]},{"raw_affiliation_string":"GPC Biotech AG  Fraunhoferstrasse 20, 82152 Martinsried, Germany","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083244522","display_name":"Andrey Grigoriev","orcid":"https://orcid.org/0000-0002-3227-532X"},"institutions":[{"id":"https://openalex.org/I4923324","display_name":"Fraunhofer-Gesellschaft","ror":"https://ror.org/05hkkdn48","country_code":"DE","type":"government","lineage":["https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"A. Grigoriev","raw_affiliation_strings":["GPC Biotech AG Fraunhoferstrasse 20, 82152 Martinsried, Germany","GPC Biotech AG  Fraunhoferstrasse 20, 82152 Martinsried, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GPC Biotech AG Fraunhoferstrasse 20, 82152 Martinsried, Germany","institution_ids":["https://openalex.org/I4923324"]},{"raw_affiliation_string":"GPC Biotech AG  Fraunhoferstrasse 20, 82152 Martinsried, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5000026020"],"corresponding_institution_ids":["https://openalex.org/I4923324"],"apc_list":null,"apc_paid":null,"fwci":0.5023,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.64174855,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"21","issue":"14","first_page":"3189","last_page":"3190"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9909999966621399,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9909999966621399,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9866999983787537,"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":0.9790999889373779,"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/perl","display_name":"Perl","score":0.9567670822143555},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.7436153292655945},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7211320400238037},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6959296464920044},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3469806909561157},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32663780450820923},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.30626440048217773},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2142367660999298}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.9567670822143555},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.7436153292655945},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7211320400238037},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6959296464920044},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3469806909561157},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32663780450820923},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.30626440048217773},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2142367660999298}],"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":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D030541","descriptor_name":"Databases, Genetic","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":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti488","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/14/3189/48971510/bioinformatics_21_14_3189.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15879451","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15879451","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.424.115","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.424.115","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2005/05/06/bioinformatics.bti488.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti488","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/14/3189/48971510/bioinformatics_21_14_3189.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4099999964237213},{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4099999964237213}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2138545793.pdf","grobid_xml":"https://content.openalex.org/works/W2138545793.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W2047017978","https://openalex.org/W2107580398","https://openalex.org/W2122232025","https://openalex.org/W2150934173","https://openalex.org/W2165270659"],"related_works":["https://openalex.org/W2480056510","https://openalex.org/W2412623563","https://openalex.org/W190299232","https://openalex.org/W1521481095","https://openalex.org/W594361471","https://openalex.org/W2604964690","https://openalex.org/W2417897055","https://openalex.org/W2613359208","https://openalex.org/W3046984657","https://openalex.org/W2053943328"],"abstract_inverted_index":{"NCBI":[0],"completed":[1],"the":[2,26,33,39,82,95,119,125],"transition":[3,126],"of":[4,36,41,86,116],"its":[5],"main":[6],"genome":[7],"annotation":[8,29,100],"database":[9],"from":[10,127],"Locuslink":[11,37,128],"to":[12,19,32,118,129],"Entrez":[13,27,52,98,130],"Gene":[14,28,53,99],"in":[15,45,55,102],"Spring":[16],"2005.":[17],"However,":[18],"this":[20],"date":[21],"few":[22],"parsers":[23,64],"exist":[24],"for":[25],"file.":[30],"Owing":[31],"widespread":[34],"use":[35],"and":[38,75,80,113,123],"popularity":[40],"Perl":[42,56,76,89],"programming":[43],"language":[44],"bioinformatics,":[46],"a":[47],"publicly":[48],"available":[49],"high":[50],"performance":[51],"parser":[54,93],"is":[57],"urgently":[58],"needed.":[59],"We":[60],"present":[61],"four":[62],"such":[63],"that":[65],"were":[66],"developed":[67],"using":[68],"several":[69],"parsing":[70],"approaches":[71],"(Parse::RecDescent,":[72],"Parse::Yapp,":[73],"Perl-byacc":[74],"5":[77],"regular":[78],"expressions)":[79],"provide":[81],"first":[83],"in-depth":[84],"comparison":[85],"these":[87],"sophisticated":[88],"tools.":[90],"Our":[91],"fastest":[92],"processes":[94],"entire":[96],"human":[97],"file":[101],"under":[103],"12":[104],"min":[105],"on":[106],"one":[107],"Intel":[108],"Xeon":[109],"2.4":[110],"GHz":[111],"CPU":[112],"can":[114],"be":[115],"help":[117],"bioinformatics":[120],"community":[121],"during":[122],"after":[124],"Gene.":[131]},"counts_by_year":[{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}