{"id":"https://openalex.org/W4377091942","doi":"https://doi.org/10.3233/shti230343","title":"OmicSDK-Transcriptomics: A Web Platform for Transcriptomics Data Analysis","display_name":"OmicSDK-Transcriptomics: A Web Platform for Transcriptomics Data Analysis","publication_year":2023,"publication_date":"2023-05-18","ids":{"openalex":"https://openalex.org/W4377091942","doi":"https://doi.org/10.3233/shti230343","pmid":"https://pubmed.ncbi.nlm.nih.gov/37203577"},"language":"en","primary_location":{"id":"doi:10.3233/shti230343","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3233/shti230343","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI230343","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI230343","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004317311","display_name":"Aurora Sucre","orcid":"https://orcid.org/0000-0002-4078-9275"},"institutions":[{"id":"https://openalex.org/I4210092551","display_name":"Vicomtech","ror":"https://ror.org/0023sah13","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210092551"]},{"id":"https://openalex.org/I4210100188","display_name":"Biogipuzkoa Health Research Institute","ror":"https://ror.org/01a2wsa50","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210100188"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Aurora Sucre","raw_affiliation_strings":["Biodonostia Health Research Institute, Basque Research and Technology Alliance (BRTA), 20014 Donostia-San Sebasti\u00e1n, Spain","Fundaci\u00f3n Vicomtech, Basque Research and Technology Alliance (BRTA), 20009 Donostia-San Sebasti\u00e1n, Spain"],"raw_orcid":"https://orcid.org/0000-0002-4078-9275","affiliations":[{"raw_affiliation_string":"Biodonostia Health Research Institute, Basque Research and Technology Alliance (BRTA), 20014 Donostia-San Sebasti\u00e1n, Spain","institution_ids":["https://openalex.org/I4210100188"]},{"raw_affiliation_string":"Fundaci\u00f3n Vicomtech, Basque Research and Technology Alliance (BRTA), 20009 Donostia-San Sebasti\u00e1n, Spain","institution_ids":["https://openalex.org/I4210092551"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087504296","display_name":"Mar\u00eda Vanina Mart\u00ednez","orcid":"https://orcid.org/0000-0003-2819-4735"},"institutions":[{"id":"https://openalex.org/I4210092551","display_name":"Vicomtech","ror":"https://ror.org/0023sah13","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210092551"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Maria Martinez","raw_affiliation_strings":["Fundaci\u00f3n Vicomtech, Basque Research and Technology Alliance (BRTA), 20009 Donostia-San Sebasti\u00e1n, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fundaci\u00f3n Vicomtech, Basque Research and Technology Alliance (BRTA), 20009 Donostia-San Sebasti\u00e1n, Spain","institution_ids":["https://openalex.org/I4210092551"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077885679","display_name":"Alba Gar\u00edn-Muga","orcid":"https://orcid.org/0000-0002-7160-1191"},"institutions":[{"id":"https://openalex.org/I4210092551","display_name":"Vicomtech","ror":"https://ror.org/0023sah13","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210092551"]},{"id":"https://openalex.org/I4210100188","display_name":"Biogipuzkoa Health Research Institute","ror":"https://ror.org/01a2wsa50","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210100188"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alba Garin-Muga","raw_affiliation_strings":["Biodonostia Health Research Institute, Basque Research and Technology Alliance (BRTA), 20014 Donostia-San Sebasti\u00e1n, Spain","Fundaci\u00f3n Vicomtech, Basque Research and Technology Alliance (BRTA), 20009 Donostia-San Sebasti\u00e1n, Spain"],"raw_orcid":"https://orcid.org/0000-0002-7160-1191","affiliations":[{"raw_affiliation_string":"Biodonostia Health Research Institute, Basque Research and Technology Alliance (BRTA), 20014 Donostia-San Sebasti\u00e1n, Spain","institution_ids":["https://openalex.org/I4210100188"]},{"raw_affiliation_string":"Fundaci\u00f3n Vicomtech, Basque Research and Technology Alliance (BRTA), 20009 Donostia-San Sebasti\u00e1n, Spain","institution_ids":["https://openalex.org/I4210092551"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5004317311"],"corresponding_institution_ids":["https://openalex.org/I4210092551","https://openalex.org/I4210100188"],"apc_list":null,"apc_paid":null,"fwci":1.3998,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.80965935,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"302","issue":null,"first_page":"1042","last_page":"1046"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980999827384949,"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":0.9980999827384949,"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":0.9980000257492065,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9969000220298767,"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/annotation","display_name":"Annotation","score":0.6983461380004883},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6508227586746216},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.5509827733039856},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5284319519996643},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5105322599411011},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.42794013023376465},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4004022181034088},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.26264292001724243},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22781258821487427},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1467927098274231},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.08276230096817017}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6983461380004883},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6508227586746216},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.5509827733039856},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5284319519996643},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5105322599411011},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.42794013023376465},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4004022181034088},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26264292001724243},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22781258821487427},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1467927098274231},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.08276230096817017},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.3233/shti230343","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3233/shti230343","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI230343","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},{"id":"pmid:37203577","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37203577","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":"Studies in health technology and informatics","raw_type":null}],"best_oa_location":{"id":"doi:10.3233/shti230343","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3233/shti230343","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI230343","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4377091942.pdf","grobid_xml":"https://content.openalex.org/works/W4377091942.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2100305481","https://openalex.org/W2169456326","https://openalex.org/W2790849272","https://openalex.org/W2883831944","https://openalex.org/W3123661237","https://openalex.org/W6684826817"],"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/W2399513595","https://openalex.org/W2625833328","https://openalex.org/W4405124681","https://openalex.org/W1533177136"],"abstract_inverted_index":{"Omics":[0],"sciences,":[1],"especially":[2],"transcriptomics,":[3],"have":[4,18],"grown":[5],"exponentially":[6],"since":[7],"the":[8,22,26,50],"first":[9],"human":[10],"genome":[11],"was":[12],"sequenced":[13],"in":[14,21],"2003.":[15],"Different":[16],"tools":[17,68],"been":[19],"developed":[20],"past":[23],"years":[24],"for":[25,58],"analysis":[27,61],"of":[28,31,35,53,93],"this":[29,45],"kind":[30],"data,":[32],"but":[33],"many":[34],"them":[36],"require":[37],"specific":[38],"programming":[39],"knowledge":[40],"to":[41,69],"be":[42,70],"used.":[43],"In":[44],"paper,":[46],"we":[47],"present":[48],"omicSDK-transcriptomics,":[49],"transcriptomics":[51],"module":[52],"OmicSDK,":[54],"a":[55,77,81],"comprehensive":[56],"tool":[57,79],"omics":[59,73],"data":[60],"that":[62],"combines":[63],"pre-processing,":[64],"annotation":[65],"and":[66,80],"visualization":[67],"used":[71],"with":[72],"data.":[74],"OmicSDK":[75],"comprises":[76],"command-line":[78],"user-friendly":[82],"web":[83],"solution,":[84],"so":[85],"researchers":[86],"having":[87],"different":[88],"backgrounds":[89],"can":[90],"take":[91],"advantage":[92],"all":[94],"its":[95],"functionalities.":[96]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
