{"id":"https://openalex.org/W2104408775","doi":"https://doi.org/10.1093/bioinformatics/btg056","title":"ASAP: automated sequence annotation pipeline forweb-based updating of sequence information with a local dynamicdatabase","display_name":"ASAP: automated sequence annotation pipeline forweb-based updating of sequence information with a local dynamicdatabase","publication_year":2003,"publication_date":"2003-03-21","ids":{"openalex":"https://openalex.org/W2104408775","doi":"https://doi.org/10.1093/bioinformatics/btg056","mag":"2104408775","pmid":"https://pubmed.ncbi.nlm.nih.gov/12651736"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg056","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg056","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/5/675/48904204/bioinformatics_19_5_675.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/19/5/675/48904204/bioinformatics_19_5_675.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015347383","display_name":"Andrew V. Kossenkov","orcid":"https://orcid.org/0000-0002-1536-0418"},"institutions":[{"id":"https://openalex.org/I4210104529","display_name":"Moscow Research Institute for Cybernetic Medicine","ror":"https://ror.org/01kjj2h97","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210104529"]},{"id":"https://openalex.org/I887846188","display_name":"National Research Nuclear University MEPhI","ror":"https://ror.org/04w8z7f34","country_code":"RU","type":"education","lineage":["https://openalex.org/I887846188"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Andrew Kossenkov","raw_affiliation_strings":["Cybernetics Department, Moscow Engineering Physics Institute, Moscow, Russian Federation. av_kossenkov@fccc.edu","Cybernetics Department, Moscow Engineering Physics Institute, Moscow, Russian Federation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cybernetics Department, Moscow Engineering Physics Institute, Moscow, Russian Federation. av_kossenkov@fccc.edu","institution_ids":["https://openalex.org/I887846188"]},{"raw_affiliation_string":"Cybernetics Department, Moscow Engineering Physics Institute, Moscow, Russian Federation","institution_ids":["https://openalex.org/I4210104529"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066605872","display_name":"Frank J. Manion","orcid":"https://orcid.org/0000-0003-1030-6348"},"institutions":[{"id":"https://openalex.org/I1289437631","display_name":"Fox Chase Cancer Center","ror":"https://ror.org/0567t7073","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1289437631","https://openalex.org/I4210122924"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Frank J. Manion","raw_affiliation_strings":["Fox Chase Cancer Center"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fox Chase Cancer Center","institution_ids":["https://openalex.org/I1289437631"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001201157","display_name":"Eugene Korotkov","orcid":"https://orcid.org/0000-0003-2960-8936"},"institutions":[{"id":"https://openalex.org/I1313323035","display_name":"Russian Academy of Sciences","ror":"https://ror.org/05qrfxd25","country_code":"RU","type":"government","lineage":["https://openalex.org/I1313323035"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Eugene Korotkov","raw_affiliation_strings":["Russian Academy of Sciences"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Russian Academy of Sciences","institution_ids":["https://openalex.org/I1313323035"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056819227","display_name":"Thomas D. Moloshok","orcid":null},"institutions":[{"id":"https://openalex.org/I1289437631","display_name":"Fox Chase Cancer Center","ror":"https://ror.org/0567t7073","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1289437631","https://openalex.org/I4210122924"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas D. Moloshok","raw_affiliation_strings":["Fox Chase Cancer Center"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fox Chase Cancer Center","institution_ids":["https://openalex.org/I1289437631"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014591184","display_name":"Michael F. Ochs","orcid":null},"institutions":[{"id":"https://openalex.org/I1289437631","display_name":"Fox Chase Cancer Center","ror":"https://ror.org/0567t7073","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1289437631","https://openalex.org/I4210122924"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael F. Ochs","raw_affiliation_strings":["Fox Chase Cancer Center"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fox Chase Cancer Center","institution_ids":["https://openalex.org/I1289437631"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9122,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.7246042,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"19","issue":"5","first_page":"675","last_page":"676"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9968000054359436,"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":0.9968000054359436,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9211000204086304,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9132000207901001,"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":0.8428595066070557},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7721023559570312},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7469602227210999},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.6370396018028259},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5927858352661133},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5774290561676025},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5773103833198547},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.4588189423084259},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.43063366413116455},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.400410920381546},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.34321272373199463},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.2845371961593628},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14954179525375366},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12097972631454468}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8428595066070557},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7721023559570312},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7469602227210999},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.6370396018028259},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5927858352661133},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5774290561676025},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5773103833198547},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.4588189423084259},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.43063366413116455},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.400410920381546},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.34321272373199463},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.2845371961593628},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14954179525375366},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12097972631454468},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"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":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btg056","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg056","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/5/675/48904204/bioinformatics_19_5_675.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:12651736","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12651736","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg056","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg056","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/5/675/48904204/bioinformatics_19_5_675.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7031966244","display_name":null,"funder_award_id":"P30 CA006927","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G921727105","display_name":null,"funder_award_id":"CA06927","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2104408775.pdf"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1986891966","https://openalex.org/W2027229725","https://openalex.org/W2112724335","https://openalex.org/W2144975794","https://openalex.org/W2150934173","https://openalex.org/W2158304452","https://openalex.org/W2162993740"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W3046984657","https://openalex.org/W2053943328","https://openalex.org/W2105364679"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"The":[2,38,63,80],"automated":[3],"sequence":[4,24],"annotation":[5],"pipeline":[6],"(ASAP)":[7],"is":[8,65,106],"designed":[9],"to":[10,67],"ease":[11],"routine":[12],"investigation":[13],"of":[14,29,34,43,61,85,94,98],"new":[15,54],"functional":[16],"annotations":[17],"on":[18],"unknown":[19],"sequences,":[20],"such":[21],"as":[22,49,56,58],"expressed":[23],"tags":[25],"(ESTs),":[26],"through":[27],"querying":[28],"web-accessible":[30],"resources":[31],"and":[32,70,72],"maintenance":[33],"a":[35,53,89,95,99],"local":[36],"database.":[37],"system":[39],"allows":[40],"easy":[41,83],"use":[42],"the":[44,50,59,92,109],"output":[45],"from":[46,77],"one":[47],"search":[48],"input":[51],"for":[52,74],"search,":[55],"well":[57],"filtering":[60],"results.":[62],"database":[64,81],"used":[66],"store":[68],"formats":[69],"parameters":[71],"information":[73,87],"parsing":[75],"data":[76],"web":[78,101],"sites.":[79],"permits":[82],"updating":[84],"format":[86,93],"should":[88,121],"site":[90],"modify":[91],"query":[96],"or":[97],"returned":[100],"page.":[102],"Availability:":[103],"Source":[104],"code":[105],"available":[107],"under":[108],"GNU":[110],"public":[111],"license":[112],"at":[113],"http://bioinformatics.fccc.edu/":[114],"Contact:":[115],"av_kossenkov@fccc.edufj_manion@fccc.edukatrin22@mtu-net.rutd_moloshok@fccc.edum_ochs@fccc.edu":[116],"*":[117],"To":[118],"whom":[119],"correspondence":[120],"be":[122],"addressed.":[123]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2025-10-10T00:00:00"}
