{"id":"https://openalex.org/W1665355332","doi":"https://doi.org/10.1371/journal.pcbi.1004321","title":"Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways","display_name":"Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways","publication_year":2015,"publication_date":"2015-08-27","ids":{"openalex":"https://openalex.org/W1665355332","doi":"https://doi.org/10.1371/journal.pcbi.1004321","mag":"1665355332","pmid":"https://pubmed.ncbi.nlm.nih.gov/26313928"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004321","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004321","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004321&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004321&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075454403","display_name":"Zachary A. King","orcid":"https://orcid.org/0000-0003-1238-1499"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zachary A. King","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065854572","display_name":"Andreas Dr\u00e4ger","orcid":"https://orcid.org/0000-0002-1240-5553"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Andreas Dr\u00e4ger","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America; Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany","Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America; Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany","institution_ids":[]},{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101406018","display_name":"Ali Ebrahim","orcid":"https://orcid.org/0000-0002-4009-2128"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ali Ebrahim","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003812348","display_name":"Nikolaus Sonnenschein","orcid":"https://orcid.org/0000-0002-7581-4936"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Nikolaus Sonnenschein","raw_affiliation_strings":["Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074538839","display_name":"Nathan E. Lewis","orcid":"https://orcid.org/0000-0001-7700-3654"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan E. Lewis","raw_affiliation_strings":["Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051097609","display_name":"Bernhard \u00d8. Palsson","orcid":"https://orcid.org/0000-0003-2357-6785"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bernhard O. Palsson","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America; Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America","Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America","Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America; Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5051097609"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":11.7479,"has_fulltext":true,"cited_by_count":435,"citation_normalized_percentile":{"value":0.99020509,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"11","issue":"8","first_page":"e1004321","last_page":"e1004321"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9983999729156494,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9983999729156494,"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":0.9980000257492065,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9898999929428101,"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/escher","display_name":"Escher","score":0.7129166126251221},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.581501305103302},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5740755796432495},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.5100284218788147},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.46593302488327026},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.41133901476860046},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4107678234577179},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.3866980969905853},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24040713906288147},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2368772029876709},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14498740434646606},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.1424730122089386},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12848025560379028}],"concepts":[{"id":"https://openalex.org/C2779618335","wikidata":"https://www.wikidata.org/wiki/Q5397186","display_name":"Escher","level":2,"score":0.7129166126251221},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.581501305103302},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5740755796432495},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.5100284218788147},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.46593302488327026},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.41133901476860046},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4107678234577179},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.3866980969905853},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24040713906288147},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2368772029876709},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14498740434646606},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.1424730122089386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12848025560379028}],"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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1004321","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004321","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004321&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:26313928","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26313928","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:osti.gov:1455068","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1455068","pdf_url":"https://www.osti.gov/servlets/purl/1455068","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:ark:/13030/qt4932k5wp","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:6fe2f51436954778bc2cfe1fd2a53c2b","is_oa":true,"landing_page_url":"https://doaj.org/article/6fe2f51436954778bc2cfe1fd2a53c2b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 11, Iss 8, p e1004321 (2015)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt4932k5wp","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/4932k5wp","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS computational biology, vol 11, iss 8","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/1526019","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Escher_A_Web_Application_for_Building_Sharing_and_Embedding_Data_Rich_Visualizations_of_Biological_Pathways_/1526019","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:4552468","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4552468","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/4d5386e2-d59b-4a4e-9e01-3d7338595108","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/4d5386e2-d59b-4a4e-9e01-3d7338595108","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"King , Z A , Draeger , A , Ebrahim , A , Sonnenschein , N , Lewis , N &amp; Palsson , B O 2015 , ' Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways ' , PLoS Computational Biology , vol. 11 , no. 8 , e1004321 . https://doi.org/10.1371/journal.pcbi.1004321","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004321","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004321","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004321&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1823837441","display_name":null,"funder_award_id":"DE-SC0008701","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3005190885","display_name":null,"funder_award_id":"332020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4026863680","display_name":null,"funder_award_id":"1144086","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5558664217","display_name":null,"funder_award_id":"R21 HD080682","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7555623405","display_name":null,"funder_award_id":"DGE-1144086","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320323153","display_name":"Danmarks Tekniske Universitet","ror":"https://ror.org/04qtj9h94"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1665355332.pdf","grobid_xml":"https://content.openalex.org/works/W1665355332.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1916502439","https://openalex.org/W1965264154","https://openalex.org/W1999758530","https://openalex.org/W2016088798","https://openalex.org/W2020541351","https://openalex.org/W2038264484","https://openalex.org/W2040676413","https://openalex.org/W2043186257","https://openalex.org/W2044935306","https://openalex.org/W2045478141","https://openalex.org/W2048465561","https://openalex.org/W2068146784","https://openalex.org/W2068586234","https://openalex.org/W2075283200","https://openalex.org/W2078151980","https://openalex.org/W2080056257","https://openalex.org/W2084769889","https://openalex.org/W2090120515","https://openalex.org/W2096245011","https://openalex.org/W2100305481","https://openalex.org/W2121411279","https://openalex.org/W2122860350","https://openalex.org/W2124737787","https://openalex.org/W2124967403","https://openalex.org/W2126546123","https://openalex.org/W2128014041","https://openalex.org/W2132206153","https://openalex.org/W2134185611","https://openalex.org/W2135415614","https://openalex.org/W2144009916","https://openalex.org/W2150599425","https://openalex.org/W2150908245","https://openalex.org/W2150930786","https://openalex.org/W2152301430","https://openalex.org/W2155142785","https://openalex.org/W2159739447","https://openalex.org/W2160541874","https://openalex.org/W2163993275","https://openalex.org/W2167155938","https://openalex.org/W2169333371","https://openalex.org/W2170776520","https://openalex.org/W2558692177","https://openalex.org/W2941307081"],"related_works":["https://openalex.org/W2013728941","https://openalex.org/W4225274103","https://openalex.org/W2154046714","https://openalex.org/W2189613078","https://openalex.org/W2579659702","https://openalex.org/W2923661510","https://openalex.org/W1574055964","https://openalex.org/W1965329638","https://openalex.org/W2542318691","https://openalex.org/W3160708108"],"abstract_inverted_index":{"Escher":[0,15,31,101,140],"is":[1],"a":[2,16,48],"web":[3,106],"application":[4],"for":[5,20,139],"visualizing":[6],"data":[7,38,55,84,95],"on":[8,36,61],"biological":[9],"pathways.":[10],"Three":[11],"key":[12],"features":[13,131],"make":[14],"uniquely":[17],"effective":[18],"tool":[19],"pathway":[21,29,33],"visualization.":[22],"First,":[23],"users":[24,43,52,77],"can":[25,44,53,78,115,141],"rapidly":[26,117],"design":[27],"new":[28],"maps.":[30],"provides":[32,125],"suggestions":[34],"based":[35],"user":[37],"and":[39,65,93,121,132],"genome-scale":[40],"models,":[41],"so":[42,112],"draw":[45],"pathways":[46],"in":[47,81],"semi-automated":[49],"way.":[50],"Second,":[51],"visualize":[54],"related":[56],"to":[57,144],"genes":[58],"or":[59],"proteins":[60],"the":[62,103,135,146],"associated":[63],"reactions":[64],"pathways,":[66],"using":[67],"rules":[68],"that":[69,113],"define":[70],"which":[71],"enzymes":[72],"catalyze":[73],"each":[74,128],"reaction.":[75],"Thus,":[76],"identify":[79],"trends":[80],"common":[82],"genomic":[83],"types":[85,96],"(e.g.":[86,97],"RNA-Seq,":[87],"proteomics,":[88],"ChIP)--in":[89],"conjunction":[90],"with":[91],"metabolite-":[92],"reaction-oriented":[94],"metabolomics,":[98],"fluxomics).":[99],"Third,":[100],"harnesses":[102],"strengths":[104],"of":[105,127,129,148],"technologies":[107],"(SVG,":[108],"D3,":[109],"developer":[110],"tools)":[111],"visualizations":[114],"be":[116,142],"adapted,":[118],"extended,":[119],"shared,":[120],"embedded.":[122],"This":[123],"paper":[124],"examples":[126],"these":[130],"explains":[133],"how":[134],"development":[136,147],"approach":[137],"used":[138,143],"guide":[145],"future":[149],"visualization":[150],"tools.":[151]},"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":40},{"year":2024,"cited_by_count":60},{"year":2023,"cited_by_count":52},{"year":2022,"cited_by_count":40},{"year":2021,"cited_by_count":52},{"year":2020,"cited_by_count":57},{"year":2019,"cited_by_count":41},{"year":2018,"cited_by_count":37},{"year":2017,"cited_by_count":21},{"year":2016,"cited_by_count":18},{"year":2015,"cited_by_count":2}],"updated_date":"2026-06-13T07:54:00.901334","created_date":"2025-10-10T00:00:00"}
