{"id":"https://openalex.org/W2050667238","doi":"https://doi.org/10.1093/nar/gki450","title":"ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics","display_name":"ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics","publication_year":2005,"publication_date":"2005-06-26","ids":{"openalex":"https://openalex.org/W2050667238","doi":"https://doi.org/10.1093/nar/gki450","mag":"2050667238","pmid":"https://pubmed.ncbi.nlm.nih.gov/15980549"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki450","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki450","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W621/7623308/gki450.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/33/suppl_2/W621/7623308/gki450.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103556767","display_name":"H.-J. Chung","orcid":null},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"H.-J. Chung","raw_affiliation_strings":["Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul 110-799, Korea","Seoul National University Biomedical Informatics (SNUBI),Seoul National University College of Medicine,Seoul 110-799,Korea"],"affiliations":[{"raw_affiliation_string":"Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul 110-799, Korea","institution_ids":["https://openalex.org/I139264467"]},{"raw_affiliation_string":"Seoul National University Biomedical Informatics (SNUBI),Seoul National University College of Medicine,Seoul 110-799,Korea","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113645980","display_name":"C. H. Park","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"C. H. Park","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103822027","display_name":"Man-Seok Han","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. R. Han","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100753386","display_name":"Soo\u2010Youn Lee","orcid":"https://orcid.org/0000-0001-7595-4042"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S. Lee","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007730800","display_name":"Jungyoon Ohn","orcid":"https://orcid.org/0000-0002-9254-2047"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. H. Ohn","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101570101","display_name":"Jihoon Kim","orcid":"https://orcid.org/0000-0002-5107-390X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. Kim","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101570101","display_name":"Jihoon Kim","orcid":"https://orcid.org/0000-0002-5107-390X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. Kim","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5026578909","display_name":"Junil Kim","orcid":"https://orcid.org/0000-0002-1202-1808"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. H. Kim","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5103556767"],"corresponding_institution_ids":["https://openalex.org/I139264467"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.7727,"has_fulltext":false,"cited_by_count":52,"citation_normalized_percentile":{"value":0.9033968,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"33","issue":"Web Server","first_page":"W621","last_page":"W626"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9987000226974487,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9962000250816345,"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/scalable-vector-graphics","display_name":"Scalable Vector Graphics","score":0.6583036184310913},{"id":"https://openalex.org/keywords/microarray-databases","display_name":"Microarray databases","score":0.6344597339630127},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6081227660179138},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5048907399177551},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.45146799087524414},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.3837915062904358},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3495739698410034},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3347485065460205},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3001024127006531},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.27804750204086304},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26406192779541016},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.21303772926330566},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16868945956230164}],"concepts":[{"id":"https://openalex.org/C202629362","wikidata":"https://www.wikidata.org/wiki/Q2078","display_name":"Scalable Vector Graphics","level":2,"score":0.6583036184310913},{"id":"https://openalex.org/C548314002","wikidata":"https://www.wikidata.org/wiki/Q6839218","display_name":"Microarray databases","level":5,"score":0.6344597339630127},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6081227660179138},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5048907399177551},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.45146799087524414},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.3837915062904358},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3495739698410034},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3347485065460205},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3001024127006531},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.27804750204086304},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26406192779541016},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.21303772926330566},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16868945956230164}],"mesh":[{"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":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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","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":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","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":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gki450","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki450","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W621/7623308/gki450.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:15980549","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15980549","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:oai:europepmc.org:155226","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1160211","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:s-space.snu.ac.kr:10371/46957","is_oa":false,"landing_page_url":"https://hdl.handle.net/10371/46957","pdf_url":null,"source":{"id":"https://openalex.org/S4306401345","display_name":"Seoul National University Open Repository (Seoul National University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139264467","host_organization_name":"Seoul National University","host_organization_lineage":["https://openalex.org/I139264467"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/nar/gki450","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki450","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W621/7623308/gki450.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":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2050667238.pdf","grobid_xml":"https://content.openalex.org/works/W2050667238.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1964895626","https://openalex.org/W2095321122","https://openalex.org/W2103017472","https://openalex.org/W2105126547","https://openalex.org/W2111360319","https://openalex.org/W2122683221","https://openalex.org/W2127069089","https://openalex.org/W2132206153","https://openalex.org/W2135000328","https://openalex.org/W2137786672","https://openalex.org/W2139703939","https://openalex.org/W2166760188","https://openalex.org/W2167190345","https://openalex.org/W4236956086"],"related_works":["https://openalex.org/W2358969090","https://openalex.org/W3183425535","https://openalex.org/W2354624479","https://openalex.org/W2394137533","https://openalex.org/W2362190996","https://openalex.org/W2385461408","https://openalex.org/W2026517560","https://openalex.org/W2183420549","https://openalex.org/W1980329767","https://openalex.org/W1971278063"],"abstract_inverted_index":{"ArrayXPath":[0,42,81],"(http://www.snubi.org/software/ArrayXPath/)":[1],"is":[2,43],"a":[3],"web-based":[4],"service":[5],"for":[6,85],"mapping":[7],"and":[8,28,32,50,60,70],"visualizing":[9],"microarray":[10,40],"gene-expression":[11,90],"data":[12],"with":[13,53,93],"integrated":[14,54,92],"biological":[15,37],"pathway":[16],"resources":[17],"using":[18],"Scalable":[19],"Vector":[20],"Graphics":[21],"(SVG).":[22],"Deciphering":[23],"the":[24,75,79],"crosstalk":[25],"among":[26],"pathways":[27],"integrating":[29,46],"biomedical":[30,98],"ontologies":[31],"knowledge":[33],"bases":[34],"may":[35],"help":[36],"interpretation":[38],"of":[39,78,89],"data.":[41],"empowered":[44],"by":[45,97],"gene-pathway,":[47],"disease-pathway,":[48],"drug-pathway":[49],"pathway-pathway":[51],"correlations":[52],"Gene":[55],"Ontology,":[56],"Medical":[57],"Subject":[58],"Headings":[59],"OMIM":[61],"Morbid":[62],"Map-based":[63],"annotations.":[64],"We":[65],"applied":[66],"Fisher's":[67],"exact":[68],"test":[69],"relative":[71],"risk":[72],"to":[73],"evaluate":[74],"statistical":[76],"significance":[77],"correlations.":[80],"produces":[82],"Javascript-enabled":[83],"SVGs":[84],"web-enabled":[86],"interactive":[87],"visualization":[88],"profiles":[91],"gene-pathway-disease":[94],"interactions":[95],"enriched":[96],"ontologies.":[99]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}