{"id":"https://openalex.org/W2141065858","doi":"https://doi.org/10.1093/nar/gkl194","title":"botXminer: mining biomedical literature with a new web-based application","display_name":"botXminer: mining biomedical literature with a new web-based application","publication_year":2006,"publication_date":"2006-07-01","ids":{"openalex":"https://openalex.org/W2141065858","doi":"https://doi.org/10.1093/nar/gkl194","mag":"2141065858","pmid":"https://pubmed.ncbi.nlm.nih.gov/16845112"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkl194","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl194","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W748/7623026/gkl194.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W748/7623026/gkl194.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006764467","display_name":"Uma Mudunuri","orcid":null},"institutions":[{"id":"https://openalex.org/I880747138","display_name":"Science Applications International Corporation (United States)","ror":"https://ror.org/00zv91802","country_code":"US","type":"company","lineage":["https://openalex.org/I880747138"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"U. Mudunuri","raw_affiliation_strings":["Science Applications International Corporation-Frederick, Advanced Biomedical Computing Center, SAIC-Frederick Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Science Applications International Corporation-Frederick, Advanced Biomedical Computing Center, SAIC-Frederick Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA","institution_ids":["https://openalex.org/I880747138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088311319","display_name":"R. Scott Stephens","orcid":"https://orcid.org/0000-0002-5472-7577"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"R. Stephens","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022873668","display_name":"David H. Bruining","orcid":"https://orcid.org/0000-0003-4320-8429"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"D. Bruining","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004057129","display_name":"Derong Liu","orcid":"https://orcid.org/0000-0003-3715-4778"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"D. Liu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5090131850","display_name":"Frank J. Lebeda","orcid":"https://orcid.org/0000-0002-6735-9312"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"F. J. Lebeda","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.9546,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.73694372,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"34","issue":"Web Server","first_page":"W748","last_page":"W752"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9757000207901001,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9750000238418579,"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/information-retrieval","display_name":"Information retrieval","score":0.6910699605941772},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6752777099609375},{"id":"https://openalex.org/keywords/oracle","display_name":"Oracle","score":0.624371349811554},{"id":"https://openalex.org/keywords/schema","display_name":"Schema (genetic algorithms)","score":0.6147120594978333},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.5808829069137573},{"id":"https://openalex.org/keywords/medline","display_name":"MEDLINE","score":0.46509993076324463},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4412344694137573},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4269470274448395},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3458477556705475},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20207509398460388},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06636011600494385}],"concepts":[{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6910699605941772},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6752777099609375},{"id":"https://openalex.org/C55166926","wikidata":"https://www.wikidata.org/wiki/Q2892946","display_name":"Oracle","level":2,"score":0.624371349811554},{"id":"https://openalex.org/C52146309","wikidata":"https://www.wikidata.org/wiki/Q7431116","display_name":"Schema (genetic algorithms)","level":2,"score":0.6147120594978333},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.5808829069137573},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.46509993076324463},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4412344694137573},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4269470274448395},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3458477556705475},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20207509398460388},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06636011600494385},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":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":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","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}],"locations_count":7,"locations":[{"id":"doi:10.1093/nar/gkl194","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl194","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W748/7623026/gkl194.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16845112","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16845112","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":"Nucleic acids research","raw_type":null},{"id":"pmh:ADA452715","is_oa":false,"landing_page_url":"http://oai.dtic.mil/oai/oai?&amp;verb=getRecord&amp;metadataPrefix=html&amp;identifier=ADA452715","pdf_url":null,"source":{"id":"https://openalex.org/S4406923043","display_name":"Defense Technical Information Center (DTIC)","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":"DTIC","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.277.893","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.277.893","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/13/87/Nucleic_Acids_Res_2006_Jul_1_34(Web_Server_issue)_W748-W752.tar.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.594.1137","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.594.1137","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/34/suppl_2/W748.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:1341258","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1538892","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1538892","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkl194","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkl194","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl194","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W748/7623026/gkl194.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320332186","display_name":"Defense Threat Reduction Agency","ror":"https://ror.org/04tz64554"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1566012138","https://openalex.org/W1623698862","https://openalex.org/W1840306201","https://openalex.org/W1977648090","https://openalex.org/W2053673723","https://openalex.org/W2103477204","https://openalex.org/W2109166752","https://openalex.org/W2132784310","https://openalex.org/W2159203162","https://openalex.org/W2162135725","https://openalex.org/W4240689716"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2474469336","https://openalex.org/W2391431582","https://openalex.org/W2374451721","https://openalex.org/W2366230866","https://openalex.org/W1788528807","https://openalex.org/W2361533086","https://openalex.org/W188567224","https://openalex.org/W2364059239","https://openalex.org/W2527040475"],"abstract_inverted_index":{"This":[0,85],"paper":[1],"outlines":[2],"botXminer,":[3],"a":[4,14,102],"publicly":[5],"available":[6],"application":[7],"to":[8],"search":[9,52],"XML-formatted":[10],"MEDLINE":[11,54],"data":[12],"in":[13,19],"complete,":[15],"object-relational":[16],"schema":[17],"implemented":[18],"Oracle":[20],"XML":[21],"DB.":[22],"An":[23],"advantage":[24],"offered":[25],"by":[26],"botXminer":[27,100],"is":[28],"that":[29,38,106],"it":[30],"can":[31,107],"generate":[32],"quantitative":[33],"results":[34],"with":[35,50,97],"certain":[36],"queries":[37],"are":[39,76],"not":[40],"feasible":[41],"through":[42],"the":[43],"Entrez-PubMed":[44],"interface.":[45],"After":[46],"retrieving":[47],"citations":[48,75,96],"associated":[49],"user-supplied":[51],"terms,":[53],"fields":[55],"(title,":[56],"abstract,":[57],"journal,":[58],"MeSH":[59],"and":[60,62,66,72,78],"chemical)":[61],"terms":[63],"(MeSH":[64],"qualifiers":[65],"descriptors,":[67],"keywords,":[68],"author,":[69],"gene":[70],"symbol":[71],"chemical),":[73],"these":[74,95],"grouped":[77],"displayed":[79],"as":[80],"tabulated":[81],"or":[82],"graphic":[83],"results.":[84],"work":[86],"represents":[87],"an":[88],"extension":[89],"of":[90],"previous":[91],"research":[92],"for":[93],"integrating":[94],"relational":[98],"systems.":[99],"has":[101],"user-friendly,":[103],"intuitive":[104],"interface":[105],"be":[108],"freely":[109],"accessed":[110],"at":[111],"http://botdb.abcc.ncifcrf.gov.":[112]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
