{"id":"https://openalex.org/W2121873490","doi":"https://doi.org/10.1093/bioinformatics/bts431","title":"A sequence comparison and gene expression data integration add-on for the Pathway Tools software","display_name":"A sequence comparison and gene expression data integration add-on for the Pathway Tools software","publication_year":2012,"publication_date":"2012-07-05","ids":{"openalex":"https://openalex.org/W2121873490","doi":"https://doi.org/10.1093/bioinformatics/bts431","mag":"2121873490","pmid":"https://pubmed.ncbi.nlm.nih.gov/22772948"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts431","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts431","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/17/2283/48872893/bioinformatics_28_17_2283.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/28/17/2283/48872893/bioinformatics_28_17_2283.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065889931","display_name":"Peter M. Krempl","orcid":null},"institutions":[{"id":"https://openalex.org/I4092182","display_name":"Graz University of Technology","ror":"https://ror.org/00d7xrm67","country_code":"AT","type":"education","lineage":["https://openalex.org/I4092182"]},{"id":"https://openalex.org/I92869138","display_name":"BOKU University","ror":"https://ror.org/057ff4y42","country_code":"AT","type":"education","lineage":["https://openalex.org/I92869138"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Peter M. Krempl","raw_affiliation_strings":["1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria","institution_ids":["https://openalex.org/I4092182","https://openalex.org/I92869138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016123662","display_name":"Juergen Mairhofer","orcid":"https://orcid.org/0000-0002-2686-1971"},"institutions":[{"id":"https://openalex.org/I4092182","display_name":"Graz University of Technology","ror":"https://ror.org/00d7xrm67","country_code":"AT","type":"education","lineage":["https://openalex.org/I4092182"]},{"id":"https://openalex.org/I92869138","display_name":"BOKU University","ror":"https://ror.org/057ff4y42","country_code":"AT","type":"education","lineage":["https://openalex.org/I92869138"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Juergen Mairhofer","raw_affiliation_strings":["1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria","institution_ids":["https://openalex.org/I4092182","https://openalex.org/I92869138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023494068","display_name":"Gerald Striedner","orcid":"https://orcid.org/0000-0001-8366-5195"},"institutions":[{"id":"https://openalex.org/I4092182","display_name":"Graz University of Technology","ror":"https://ror.org/00d7xrm67","country_code":"AT","type":"education","lineage":["https://openalex.org/I4092182"]},{"id":"https://openalex.org/I92869138","display_name":"BOKU University","ror":"https://ror.org/057ff4y42","country_code":"AT","type":"education","lineage":["https://openalex.org/I92869138"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Gerald Striedner","raw_affiliation_strings":["1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria","institution_ids":["https://openalex.org/I4092182","https://openalex.org/I92869138"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037209090","display_name":"Gerhard Thallinger","orcid":"https://orcid.org/0000-0002-2864-5404"},"institutions":[{"id":"https://openalex.org/I4092182","display_name":"Graz University of Technology","ror":"https://ror.org/00d7xrm67","country_code":"AT","type":"education","lineage":["https://openalex.org/I4092182"]},{"id":"https://openalex.org/I92869138","display_name":"BOKU University","ror":"https://ror.org/057ff4y42","country_code":"AT","type":"education","lineage":["https://openalex.org/I92869138"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Gerhard G. Thallinger","raw_affiliation_strings":["1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria","institution_ids":["https://openalex.org/I4092182","https://openalex.org/I92869138"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5037209090"],"corresponding_institution_ids":["https://openalex.org/I4092182","https://openalex.org/I92869138"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11753878,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"28","issue":"17","first_page":"2283","last_page":"2284"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.2508000135421753,"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":0.2508000135421753,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.13809999823570251,"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":0.09380000084638596,"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/plug-in","display_name":"Plug-in","score":0.6811907887458801},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6530832648277283},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6513110995292664},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6493521332740784},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5653024911880493},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4718570411205292},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43604153394699097},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4342794716358185},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4318656623363495},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4196609854698181},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3284217119216919},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.28452128171920776},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23313161730766296},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21079739928245544},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13983780145645142},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1377682387828827}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.6811907887458801},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6530832648277283},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6513110995292664},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6493521332740784},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5653024911880493},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4718570411205292},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43604153394699097},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4342794716358185},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4318656623363495},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4196609854698181},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3284217119216919},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28452128171920776},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23313161730766296},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21079739928245544},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13983780145645142},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1377682387828827},{"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/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","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":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"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":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bts431","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts431","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/17/2283/48872893/bioinformatics_28_17_2283.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:22772948","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22772948","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/bts431","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts431","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/17/2283/48872893/bioinformatics_28_17_2283.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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2121873490.pdf"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1983075974","https://openalex.org/W2085966004","https://openalex.org/W2118700972","https://openalex.org/W2128601422","https://openalex.org/W2137015675","https://openalex.org/W2139915240","https://openalex.org/W2144056254","https://openalex.org/W2149452073","https://openalex.org/W2158541664","https://openalex.org/W2158714788","https://openalex.org/W2168465568","https://openalex.org/W4233060585"],"related_works":["https://openalex.org/W4287378204","https://openalex.org/W2981957539","https://openalex.org/W47352601","https://openalex.org/W2545422590","https://openalex.org/W4240705470","https://openalex.org/W2945311252","https://openalex.org/W631546281","https://openalex.org/W4213354039","https://openalex.org/W2266220644","https://openalex.org/W2022968056"],"abstract_inverted_index":{"UNLABELLED:":[0],"We":[1],"present":[2],"a":[3],"plug-in":[4,30,92],"for":[5,112],"Pathway":[6,89,104,126],"Tools,":[7],"an":[8],"integrated":[9,21],"systems":[10],"biology":[11],"software":[12],"to":[13,38,63,80,97],"create,":[14],"maintain":[15],"and":[16,27,49,66,117],"query":[17],"Pathway/Genome":[18],"Databases.":[19],"Fully":[20],"into":[22,76,102],"the":[23,32,36,84,103],"graphical":[24],"user":[25,129],"interface":[26],"menu,":[28],"this":[29],"extends":[31],"application's":[33],"functionality":[34],"by":[35,53,125],"ability":[37],"create":[39],"multiple":[40],"sequence":[41,46],"alignments,":[42],"systematically":[43],"annotate":[44],"insertion":[45],"(IS)":[47],"elements":[48],"analyse":[50],"their":[51,99],"activity":[52],"cross-species":[54],"comparison":[55],"tools.":[56],"Microarray":[57],"probes":[58],"can":[59,73,118],"be":[60,74,119],"automatically":[61],"mapped":[62],"target":[64],"genes,":[65],"expression":[67],"data":[68],"obtained":[69],"with":[70],"these":[71],"arrays":[72],"transformed":[75],"input":[77],"formats":[78],"needed":[79],"visualize":[81],"them":[82],"in":[83],"various":[85],"omics":[86],"viewers":[87],"of":[88],"Tools.":[90,127],"The":[91],"API":[93],"itself":[94],"allows":[95],"developers":[96],"integrate":[98],"own":[100],"functions":[101],"Tools":[105],"menu.":[106],"AVAILABILITY:":[107],"Binaries":[108],"are":[109],"freely":[110,132],"available":[111,133],"non-commercial":[113],"users":[114],"at":[115],"http://genome.tugraz.at/PGDBToolbox/":[116],"used":[120],"on":[121],"all":[122],"platforms":[123],"supported":[124],"A":[128],"guide":[130],"is":[131],"at:":[134],"http://genome.tugraz.at/PGDBToolbox/documentation.shtml.":[135]},"counts_by_year":[],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
