{"id":"https://openalex.org/W2953632535","doi":"https://doi.org/10.1093/bib/bbz067","title":"Closing the gap between formats for storing layout information in systems biology","display_name":"Closing the gap between formats for storing layout information in systems biology","publication_year":2019,"publication_date":"2019-05-15","ids":{"openalex":"https://openalex.org/W2953632535","doi":"https://doi.org/10.1093/bib/bbz067","mag":"2953632535","pmid":"https://pubmed.ncbi.nlm.nih.gov/31273380"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbz067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz067","pdf_url":"https://academic.oup.com/bib/article-pdf/21/4/1249/33583794/bbz067.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/21/4/1249/33583794/bbz067.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049617942","display_name":"David Hoksza","orcid":"https://orcid.org/0000-0003-4679-0557"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]},{"id":"https://openalex.org/I21250087","display_name":"Charles University","ror":"https://ror.org/024d6js02","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21250087"]}],"countries":["CZ","LU"],"is_corresponding":true,"raw_author_name":"David Hoksza","raw_affiliation_strings":["Faculty of Mathematics and Physics, Charles University, Malostransk\u00e9 n\u00e1m. 25, 118 00 Prague, Czech Republic","Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg"],"raw_orcid":"https://orcid.org/0000-0003-4679-0557","affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Physics, Charles University, Malostransk\u00e9 n\u00e1m. 25, 118 00 Prague, Czech Republic","institution_ids":["https://openalex.org/I21250087"]},{"raw_affiliation_string":"Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg","institution_ids":["https://openalex.org/I186903577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042744881","display_name":"Piotr Gawron","orcid":"https://orcid.org/0000-0002-9328-8052"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Piotr Gawron","raw_affiliation_strings":["Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg","institution_ids":["https://openalex.org/I186903577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022319056","display_name":"Marek Ostaszewski","orcid":"https://orcid.org/0000-0003-1473-370X"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Marek Ostaszewski","raw_affiliation_strings":["Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg"],"raw_orcid":"https://orcid.org/0000-0003-1473-370X","affiliations":[{"raw_affiliation_string":"Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg","institution_ids":["https://openalex.org/I186903577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063254041","display_name":"Jan Hasenauer","orcid":"https://orcid.org/0000-0002-4935-3312"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jan Hasenauer","raw_affiliation_strings":["Department of Mathematics, Technische Universit\u00e4t M\u00fcnchen, M\u00fcnchen, Germany","Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen - German Research Center for Environmental Health, Ingolst\u00e4dter Landstr. 1, 85764, Neuherberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Technische Universit\u00e4t M\u00fcnchen, M\u00fcnchen, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen - German Research Center for Environmental Health, Ingolst\u00e4dter Landstr. 1, 85764, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079833473","display_name":"Reinhard Schneider","orcid":"https://orcid.org/0000-0002-8278-1618"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Reinhard Schneider","raw_affiliation_strings":["Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg","institution_ids":["https://openalex.org/I186903577"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5049617942"],"corresponding_institution_ids":["https://openalex.org/I186903577","https://openalex.org/I21250087"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.7088,"has_fulltext":true,"cited_by_count":37,"citation_normalized_percentile":{"value":0.84797185,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"21","issue":"4","first_page":"1249","last_page":"1260"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987999796867371,"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":0.9987999796867371,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9987999796867371,"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":0.9983999729156494,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.77286297082901},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6442939639091492},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.636884331703186},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.6165194511413574},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5723514556884766},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.39237433671951294},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33771464228630066},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.15593600273132324},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.139815092086792},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13615649938583374},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1273587942123413}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.77286297082901},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6442939639091492},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.636884331703186},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.6165194511413574},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5723514556884766},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.39237433671951294},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33771464228630066},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.15593600273132324},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.139815092086792},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13615649938583374},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1273587942123413},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1093/bib/bbz067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz067","pdf_url":"https://academic.oup.com/bib/article-pdf/21/4/1249/33583794/bbz067.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31273380","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31273380","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmid:32083642","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32083642","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7373180","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7373180","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:opus-zb.helmholtz-muenchen.de:56551","is_oa":true,"landing_page_url":"https://push-zb.helmholtz-muenchen.de/frontdoor.php?source_opus=56551","pdf_url":null,"source":{"id":"https://openalex.org/S4377196115","display_name":"Site cant be reached","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief. Bioinform. 21, 1249-1260 (2020)","raw_type":"Text"},{"id":"pmh:oai:orbilu.uni.lu:10993/40903","is_oa":true,"landing_page_url":"http://orbilu.uni.lu/handle/10993/40903","pdf_url":null,"source":{"id":"https://openalex.org/S4306401815","display_name":"Open Repository and Bibliography (University of Luxembourg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I186903577","host_organization_name":"University of Luxembourg","host_organization_lineage":["https://openalex.org/I186903577"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics (2019)","raw_type":"peer reviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:7820845","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7820845","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbz067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz067","pdf_url":"https://academic.oup.com/bib/article-pdf/21/4/1249/33583794/bbz067.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2953632535.pdf","grobid_xml":"https://content.openalex.org/works/W2953632535.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1665355332","https://openalex.org/W1969709265","https://openalex.org/W1970594207","https://openalex.org/W1973242626","https://openalex.org/W1978486653","https://openalex.org/W1989277387","https://openalex.org/W2023250031","https://openalex.org/W2048465561","https://openalex.org/W2049335983","https://openalex.org/W2068146784","https://openalex.org/W2069157810","https://openalex.org/W2095304455","https://openalex.org/W2096951208","https://openalex.org/W2102653059","https://openalex.org/W2103033592","https://openalex.org/W2117364474","https://openalex.org/W2126662515","https://openalex.org/W2126997165","https://openalex.org/W2134185611","https://openalex.org/W2134221731","https://openalex.org/W2138326194","https://openalex.org/W2145435867","https://openalex.org/W2146737319","https://openalex.org/W2146958900","https://openalex.org/W2147472054","https://openalex.org/W2150908245","https://openalex.org/W2159675211","https://openalex.org/W2159739447","https://openalex.org/W2160751597","https://openalex.org/W2163993275","https://openalex.org/W2164298117","https://openalex.org/W2170032647","https://openalex.org/W2185357718","https://openalex.org/W2202347610","https://openalex.org/W2339662749","https://openalex.org/W2411305692","https://openalex.org/W2523314419","https://openalex.org/W2559588208","https://openalex.org/W2792322849","https://openalex.org/W2795410052","https://openalex.org/W2800340189","https://openalex.org/W2802438470","https://openalex.org/W2807615161","https://openalex.org/W2809141626","https://openalex.org/W2895192159","https://openalex.org/W2916475656","https://openalex.org/W2962889697","https://openalex.org/W4233698560","https://openalex.org/W4234812893","https://openalex.org/W4237335579","https://openalex.org/W6647548779","https://openalex.org/W6678606060","https://openalex.org/W6684475696","https://openalex.org/W6686208936","https://openalex.org/W6749319540"],"related_works":["https://openalex.org/W2384475851","https://openalex.org/W2000444236","https://openalex.org/W2353602216","https://openalex.org/W2367078749","https://openalex.org/W2381798600","https://openalex.org/W1910583078","https://openalex.org/W2351618306","https://openalex.org/W2133117170","https://openalex.org/W2999162218","https://openalex.org/W1537443268"],"abstract_inverted_index":{"The":[0,95,124],"understanding":[1],"of":[2,37,43,61,128,134],"complex":[3],"biological":[4],"networks":[5,131],"often":[6],"relies":[7],"on":[8,69],"both":[9],"a":[10,14,58,87,100],"dedicated":[11],"layout":[12,63],"and":[13,47,51,72,82,84,103],"topology.":[15],"Currently,":[16],"there":[17,27],"are":[18,28],"three":[19],"major":[20],"competing":[21],"layout-aware":[22,111],"systems":[23,66,112,148],"biology":[24,113],"formats,":[25,114],"but":[26],"no":[29],"software":[30,33,79],"tools":[31],"or":[32,140],"libraries":[34,81],"supporting":[35],"all":[36],"them.":[38],"This":[39],"complicates":[40],"the":[41,62,92,106,115],"management":[42],"molecular":[44],"network":[45],"layouts":[46,119],"hinders":[48],"their":[49,70,75],"reuse":[50],"extension.":[52],"In":[53],"this":[54],"paper,":[55],"we":[56],"present":[57],"high-level":[59],"overview":[60],"formats":[64],"in":[65,77,147],"biology,":[67],"focusing":[68],"commonalities":[71],"differences,":[73],"review":[74],"support":[76],"existing":[78],"tools,":[80],"repositories":[83],"finally":[85],"introduce":[86],"new":[88],"conversion":[89,127],"module":[90,96,125],"within":[91],"MINERVA":[93],"platform.":[94],"is":[97],"available":[98],"via":[99],"REST":[101],"API":[102],"offers,":[104],"besides":[105],"ability":[107],"to":[108,117],"convert":[109],"between":[110],"possibility":[116],"export":[118],"into":[120],"several":[121],"graphical":[122],"formats.":[123],"enables":[126],"very":[129],"large":[130],"with":[132],"thousands":[133],"elements,":[135],"such":[136],"as":[137],"disease":[138],"maps":[139],"metabolic":[141],"reconstructions,":[142],"rendering":[143],"it":[144],"widely":[145],"applicable":[146],"biology.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
