{"id":"https://openalex.org/W2119485467","doi":"https://doi.org/10.2390/biecoll-jib-2004-2","title":"Visual Understanding of Metabolic Pathways Across Organisms Using Layout in Two and a Half Dimensions","display_name":"Visual Understanding of Metabolic Pathways Across Organisms Using Layout in Two and a Half Dimensions","publication_year":2007,"publication_date":"2007-01-01","ids":{"openalex":"https://openalex.org/W2119485467","doi":"https://doi.org/10.2390/biecoll-jib-2004-2","mag":"2119485467"},"language":"en","primary_location":{"id":"pmh:oai:CiteSeerX.psu:10.1.1.178.4325","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.178.4325","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bic-gh.ipk-gatersleben.de/%7Eschreibe/publications/BrandesDS04a.pdf","raw_type":"text"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-72132","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003377833","display_name":"Ulrik Brandes","orcid":"https://orcid.org/0000-0002-1520-0430"},"institutions":[{"id":"https://openalex.org/I186354981","display_name":"University of Passau","ror":"https://ror.org/05ydjnb78","country_code":"DE","type":"education","lineage":["https://openalex.org/I186354981"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Brandes, Ulrik","raw_affiliation_strings":["University Of Passau#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University Of Passau#TAB#","institution_ids":["https://openalex.org/I186354981"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008149778","display_name":"Tim Dwyer","orcid":"https://orcid.org/0000-0002-9076-9571"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Dwyer, Tim","raw_affiliation_strings":["University of Sydney"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Sydney","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003441276","display_name":"Falk Schreiber","orcid":"https://orcid.org/0000-0002-9307-3254"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Schreiber, Falk","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5003377833"],"corresponding_institution_ids":["https://openalex.org/I186354981"],"apc_list":null,"apc_paid":null,"fwci":4.2771,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.94580365,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12536","display_name":"Topological and Geometric Data Analysis","score":0.972100019454956,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9541000127792358,"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/graph-drawing","display_name":"Graph drawing","score":0.7024114727973938},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6933538913726807},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6811899542808533},{"id":"https://openalex.org/keywords/stacking","display_name":"Stacking","score":0.5934749245643616},{"id":"https://openalex.org/keywords/graph-layout","display_name":"Graph Layout","score":0.5911263823509216},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5702170133590698},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5347145199775696},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5212393403053284},{"id":"https://openalex.org/keywords/interdependence","display_name":"Interdependence","score":0.4837491512298584},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.28562507033348083},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10523927211761475},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08994010090827942}],"concepts":[{"id":"https://openalex.org/C112953755","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph drawing","level":3,"score":0.7024114727973938},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6933538913726807},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6811899542808533},{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.5934749245643616},{"id":"https://openalex.org/C2911174283","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph Layout","level":4,"score":0.5911263823509216},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5702170133590698},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5347145199775696},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5212393403053284},{"id":"https://openalex.org/C185874996","wikidata":"https://www.wikidata.org/wiki/Q269699","display_name":"Interdependence","level":2,"score":0.4837491512298584},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.28562507033348083},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10523927211761475},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08994010090827942},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"pmh:oai:CiteSeerX.psu:10.1.1.178.4325","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.178.4325","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bic-gh.ipk-gatersleben.de/%7Eschreibe/publications/BrandesDS04a.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.2.3007","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.2.3007","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://pgrc-16.ipk-gatersleben.de/~schreibe/publications/BrandesDS04a.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.5.3732","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.5.3732","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.inf.uni-konstanz.de/algo/publications/bds-vumpa-04.pdf","raw_type":"text"},{"id":"pmh:oai:biecoll.ub.uni-bielefeld.de:183","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2007/183/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/index.php?paper_id=2","raw_type":"Journal Article"},{"id":"pmh:oai:kops.uni-konstanz.de:123456789/5694","is_oa":true,"landing_page_url":"http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-72132","pdf_url":null,"source":{"id":"https://openalex.org/S4306401487","display_name":"KOPS (University of Konstanz)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189712700","host_organization_name":"University of Konstanz","host_organization_lineage":["https://openalex.org/I189712700"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics. 2004, 1(1), 2. Available under: doi: 10.2390/biecoll-jib-2004-2","raw_type":"doc-type:Text"},{"id":"doi:10.2390/biecoll-jib-2004-2","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2004-2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:kops.uni-konstanz.de:123456789/5694","is_oa":true,"landing_page_url":"http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-72132","pdf_url":null,"source":{"id":"https://openalex.org/S4306401487","display_name":"KOPS (University of Konstanz)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189712700","host_organization_name":"University of Konstanz","host_organization_lineage":["https://openalex.org/I189712700"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics. 2004, 1(1), 2. Available under: doi: 10.2390/biecoll-jib-2004-2","raw_type":"doc-type:Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8158436435","display_name":null,"funder_award_id":"0312706A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W115293203","https://openalex.org/W1485323191","https://openalex.org/W1498322085","https://openalex.org/W1542351418","https://openalex.org/W1572701995","https://openalex.org/W1602198681","https://openalex.org/W1899261287","https://openalex.org/W1972246827","https://openalex.org/W1978132986","https://openalex.org/W2024491681","https://openalex.org/W2026790375","https://openalex.org/W2029230311","https://openalex.org/W2034694694","https://openalex.org/W2044013641","https://openalex.org/W2049670817","https://openalex.org/W2071353749","https://openalex.org/W2081622831","https://openalex.org/W2086475944","https://openalex.org/W2097747452","https://openalex.org/W2100438221","https://openalex.org/W2108036176","https://openalex.org/W2126415191","https://openalex.org/W2126536832","https://openalex.org/W2133850057","https://openalex.org/W2137439611","https://openalex.org/W2143740704","https://openalex.org/W2149107096","https://openalex.org/W2156966633","https://openalex.org/W2159482845","https://openalex.org/W2169804422"],"related_works":["https://openalex.org/W2167482691","https://openalex.org/W2159675211","https://openalex.org/W2075220720","https://openalex.org/W2013378906","https://openalex.org/W2462052167","https://openalex.org/W2102664288","https://openalex.org/W1946371345","https://openalex.org/W2160248492","https://openalex.org/W2147468287","https://openalex.org/W2108036176","https://openalex.org/W1572701995","https://openalex.org/W1524145331","https://openalex.org/W1522840240","https://openalex.org/W1968648267","https://openalex.org/W2323448541","https://openalex.org/W2280771347","https://openalex.org/W2022627391","https://openalex.org/W1518205410","https://openalex.org/W2779146784","https://openalex.org/W2220436833"],"abstract_inverted_index":{"We":[0],"propose":[1],"a":[2,6,37,67,77,88],"method":[3],"for":[4,70,95],"visualizing":[5],"set":[7],"of":[8,23,30,40,58,80,83,90],"related":[9],"metabolic":[10],"pathways":[11,51],"across":[12],"organisms":[13],"using":[14,87],"2":[15],"1/2":[16],"dimensional":[17],"graph":[18,97],"visualization.":[19],"Interdependent,":[20],"two-dimensional":[21],"layouts":[22],"each":[24,31],"pathway":[25,85],"are":[26,52,63,74],"stacked":[27],"on":[28],"top":[29],"other":[32],"so":[33],"that":[34],"biologists":[35],"get":[36],"full":[38],"picture":[39],"subtle":[41],"and":[42],"significant":[43],"differences":[44],"among":[45],"the":[46,55,59,71,81,91],"pathways.":[47,72],"The":[48],"(dis)similarities":[49],"between":[50],"expressed":[53],"by":[54,76],"Hamming":[56],"distances":[57],"underlying":[60],"graphs":[61,86],"which":[62],"used":[64],"to":[65,105],"compute":[66],"stacking":[68],"order":[69],"Layouts":[73],"determined":[75],"global":[78],"layout":[79,101],"union":[82],"all":[84],"variant":[89,100],"proven":[92],"Sugiyama":[93],"approach":[94,102],"layered":[96],"drawing.":[98],"Our":[99],"allows":[103],"edges":[104],"cross":[106],"if":[107],"they":[108],"appear":[109],"in":[110],"different":[111],"graphs.":[112]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-05-21T09:19:25.381259","created_date":"2025-10-10T00:00:00"}
