{"id":"https://openalex.org/W2153490111","doi":"https://doi.org/10.1186/1756-0381-1-12","title":"A survey of visualization tools for biological network analysis","display_name":"A survey of visualization tools for biological network analysis","publication_year":2008,"publication_date":"2008-11-28","ids":{"openalex":"https://openalex.org/W2153490111","doi":"https://doi.org/10.1186/1756-0381-1-12","mag":"2153490111","pmid":"https://pubmed.ncbi.nlm.nih.gov/19040716"},"language":"en","primary_location":{"id":"doi:10.1186/1756-0381-1-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-1-12","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-1-12","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-1-12","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088991393","display_name":"Georgios A. Pavlopoulos","orcid":"https://orcid.org/0000-0002-4577-8276"},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]},{"id":"https://openalex.org/I1303691731","display_name":"European Molecular Biology Organization","ror":"https://ror.org/04wfr2810","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I1303691731"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Georgios A Pavlopoulos","raw_affiliation_strings":["Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, Heidelberg, Germany. pavlopou@embl.de","Structural and Computational Biology Unit, EMBL, Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, Heidelberg, Germany. pavlopou@embl.de","institution_ids":["https://openalex.org/I1303691731","https://openalex.org/I4210153543"]},{"raw_affiliation_string":"Structural and Computational Biology Unit, EMBL, Heidelberg, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005880914","display_name":"Anna-Lynn Wegener","orcid":null},"institutions":[{"id":"https://openalex.org/I1303691731","display_name":"European Molecular Biology Organization","ror":"https://ror.org/04wfr2810","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I1303691731"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Anna-Lynn Wegener","raw_affiliation_strings":["Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, Heidelberg, Germany","Structural and Computational Biology Unit, EMBL, Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, Heidelberg, Germany","institution_ids":["https://openalex.org/I1303691731"]},{"raw_affiliation_string":"Structural and Computational Biology Unit, EMBL, Heidelberg, Germany","institution_ids":[]}]},{"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/I1303691731","display_name":"European Molecular Biology Organization","ror":"https://ror.org/04wfr2810","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I1303691731"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Reinhard Schneider","raw_affiliation_strings":["Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, Heidelberg, Germany","Structural and Computational Biology Unit, EMBL, Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, Heidelberg, Germany","institution_ids":["https://openalex.org/I1303691731"]},{"raw_affiliation_string":"Structural and Computational Biology Unit, EMBL, Heidelberg, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5088991393"],"corresponding_institution_ids":["https://openalex.org/I1303691731","https://openalex.org/I4210153543"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":5.1007,"has_fulltext":true,"cited_by_count":227,"citation_normalized_percentile":{"value":0.96225296,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"1","issue":"1","first_page":"12","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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":0.9993000030517578,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.9850999712944031,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.9803000092506409,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.8137425184249878},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7907975316047668},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.7279458045959473},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6806653141975403},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.6402713060379028},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.6114904880523682},{"id":"https://openalex.org/keywords/graph-drawing","display_name":"Graph drawing","score":0.5788355469703674},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.5106173157691956},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4993472099304199},{"id":"https://openalex.org/keywords/information-visualization","display_name":"Information visualization","score":0.4698594808578491},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37799373269081116},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1485731303691864},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.13127440214157104}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.8137425184249878},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7907975316047668},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.7279458045959473},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6806653141975403},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.6402713060379028},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.6114904880523682},{"id":"https://openalex.org/C112953755","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph drawing","level":3,"score":0.5788355469703674},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.5106173157691956},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4993472099304199},{"id":"https://openalex.org/C185578843","wikidata":"https://www.wikidata.org/wiki/Q10609775","display_name":"Information visualization","level":3,"score":0.4698594808578491},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37799373269081116},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1485731303691864},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.13127440214157104},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1756-0381-1-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-1-12","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-1-12","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:19040716","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19040716","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":"BioData mining","raw_type":null},{"id":"pmh:oai:doaj.org/article:7311acd9f16f4258b1d6722fc866a008","is_oa":true,"landing_page_url":"https://doaj.org/article/7311acd9f16f4258b1d6722fc866a008","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 1, Iss 1, p 12 (2008)","raw_type":"article"},{"id":"pmh:oai:orbilu.uni.lu:10993/17189","is_oa":true,"landing_page_url":"http://orbilu.uni.lu/handle/10993/17189","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":"BioData Mining (2008)","raw_type":"peer reviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:2636684","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2636684","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1756-0381-1-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-1-12","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-1-12","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2153490111.pdf","grobid_xml":"https://content.openalex.org/works/W2153490111.grobid-xml"},"referenced_works_count":79,"referenced_works":["https://openalex.org/W188275245","https://openalex.org/W839878123","https://openalex.org/W1503013560","https://openalex.org/W1581109488","https://openalex.org/W1606933656","https://openalex.org/W1916339519","https://openalex.org/W1946371345","https://openalex.org/W1986662234","https://openalex.org/W1988393300","https://openalex.org/W1992673035","https://openalex.org/W2006933206","https://openalex.org/W2022381538","https://openalex.org/W2033377040","https://openalex.org/W2042880070","https://openalex.org/W2047600440","https://openalex.org/W2058673890","https://openalex.org/W2059361536","https://openalex.org/W2059942088","https://openalex.org/W2061806063","https://openalex.org/W2069162648","https://openalex.org/W2075220720","https://openalex.org/W2082621456","https://openalex.org/W2095436325","https://openalex.org/W2096525273","https://openalex.org/W2096969035","https://openalex.org/W2096975829","https://openalex.org/W2099396594","https://openalex.org/W2100966644","https://openalex.org/W2103017472","https://openalex.org/W2105769812","https://openalex.org/W2105893525","https://openalex.org/W2107580398","https://openalex.org/W2108078368","https://openalex.org/W2109278577","https://openalex.org/W2109745408","https://openalex.org/W2110280725","https://openalex.org/W2111627817","https://openalex.org/W2111973517","https://openalex.org/W2112809329","https://openalex.org/W2115590900","https://openalex.org/W2120607558","https://openalex.org/W2121388578","https://openalex.org/W2121905803","https://openalex.org/W2130863229","https://openalex.org/W2131347449","https://openalex.org/W2132992030","https://openalex.org/W2133298156","https://openalex.org/W2134672568","https://openalex.org/W2135805255","https://openalex.org/W2137522673","https://openalex.org/W2138844251","https://openalex.org/W2138872556","https://openalex.org/W2140635350","https://openalex.org/W2140812562","https://openalex.org/W2142237411","https://openalex.org/W2142643607","https://openalex.org/W2142890842","https://openalex.org/W2145889895","https://openalex.org/W2147714160","https://openalex.org/W2149194035","https://openalex.org/W2150908245","https://openalex.org/W2152339547","https://openalex.org/W2154687603","https://openalex.org/W2155723007","https://openalex.org/W2157727556","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W2161062388","https://openalex.org/W2162270048","https://openalex.org/W2166898290","https://openalex.org/W2167482691","https://openalex.org/W2167609496","https://openalex.org/W2315135172","https://openalex.org/W2387046089","https://openalex.org/W4211054902","https://openalex.org/W4213060373","https://openalex.org/W4213317598","https://openalex.org/W4230903726","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2155492529","https://openalex.org/W4252504573","https://openalex.org/W4385510321","https://openalex.org/W2101315668","https://openalex.org/W15348386","https://openalex.org/W2171298469","https://openalex.org/W2098027521","https://openalex.org/W4214598766","https://openalex.org/W2082199132","https://openalex.org/W1561795279"],"abstract_inverted_index":{"The":[0],"analysis":[1],"and":[2,10,27,87,93,126,133,147],"interpretation":[3],"of":[4,25,36,44,69,73,80,85,109,130,144],"relationships":[5],"between":[6],"biological":[7,59,110],"molecules,":[8],"networks":[9,111],"concepts":[11],"is":[12],"becoming":[13],"a":[14,31,41,66,76],"major":[15],"bottleneck":[16],"in":[17,78,114,141],"systems":[18],"biology.":[19],"Very":[20],"often":[21,50],"the":[22,34,37,52,115,122,124,127,142],"pure":[23],"amount":[24],"data":[26,53,145],"their":[28],"heterogeneity":[29],"provides":[30],"challenge":[32],"for":[33,107],"visualization":[35,101,108],"data.":[38],"There":[39],"are":[40,63,99,104],"wide":[42,67],"variety":[43],"graph":[45],"representations":[46],"available,":[47],"which":[48],"most":[49],"map":[51],"on":[54,121],"2D":[55],"graphs":[56],"to":[57,65,90],"visualize":[58],"interactions.":[60],"These":[61],"methods":[62],"applicable":[64],"range":[68],"problems,":[70],"nevertheless":[71],"many":[72],"them":[74],"reach":[75],"limit":[77],"terms":[79],"user":[81],"friendliness":[82],"when":[83],"thousands":[84],"nodes":[86],"connections":[88],"have":[89],"be":[91,138],"analyzed":[92],"visualized.":[94],"In":[95],"this":[96],"study":[97],"we":[98],"reviewing":[100],"tools":[102,136],"that":[103],"currently":[105],"available":[106],"mainly":[112],"invented":[113],"latest":[116],"past":[117],"years.":[118],"We":[119],"comment":[120],"functionality,":[123],"limitations":[125],"specific":[128],"strengths":[129],"these":[131,135],"tools,":[132],"how":[134],"could":[137],"further":[139],"developed":[140],"direction":[143],"integration":[146],"information":[148],"sharing.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":17},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":19},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":16},{"year":2013,"cited_by_count":19},{"year":2012,"cited_by_count":22}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
