{"id":"https://openalex.org/W4231025004","doi":"https://doi.org/10.12688/f1000research.14613.1","title":"CyTargetLinker app update: A flexible solution for network extension in Cytoscape","display_name":"CyTargetLinker app update: A flexible solution for network extension in Cytoscape","publication_year":2018,"publication_date":"2018-06-14","ids":{"openalex":"https://openalex.org/W4231025004","doi":"https://doi.org/10.12688/f1000research.14613.1"},"language":"en","primary_location":{"id":"doi:10.12688/f1000research.14613.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.14613.1","pdf_url":null,"source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"type":"preprint","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.12688/f1000research.14613.1","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062841937","display_name":"Martina Kutmon","orcid":null},"institutions":[{"id":"https://openalex.org/I34352273","display_name":"Maastricht University","ror":"https://ror.org/02jz4aj89","country_code":"NL","type":"education","lineage":["https://openalex.org/I34352273"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Martina Kutmon","raw_affiliation_strings":["Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER","Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER","institution_ids":["https://openalex.org/I34352273"]},{"raw_affiliation_string":"Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER","institution_ids":["https://openalex.org/I34352273"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061353760","display_name":"Friederike Ehrhart","orcid":"https://orcid.org/0000-0002-7770-620X"},"institutions":[{"id":"https://openalex.org/I2800191616","display_name":"Maastricht University Medical Centre","ror":"https://ror.org/02d9ce178","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800191616"]},{"id":"https://openalex.org/I34352273","display_name":"Maastricht University","ror":"https://ror.org/02jz4aj89","country_code":"NL","type":"education","lineage":["https://openalex.org/I34352273"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Friederike Ehrhart","raw_affiliation_strings":["Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER","GKC-Rett Expertise Centre, Maastricht University Medical Center, Maastricht, 6200 MD"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER","institution_ids":["https://openalex.org/I34352273"]},{"raw_affiliation_string":"GKC-Rett Expertise Centre, Maastricht University Medical Center, Maastricht, 6200 MD","institution_ids":["https://openalex.org/I2800191616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060194743","display_name":"Egon Willighagen","orcid":"https://orcid.org/0000-0001-7542-0286"},"institutions":[{"id":"https://openalex.org/I34352273","display_name":"Maastricht University","ror":"https://ror.org/02jz4aj89","country_code":"NL","type":"education","lineage":["https://openalex.org/I34352273"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Egon L. Willighagen","raw_affiliation_strings":["Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER","institution_ids":["https://openalex.org/I34352273"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075750072","display_name":"Chris T. Evelo","orcid":"https://orcid.org/0000-0002-5301-3142"},"institutions":[{"id":"https://openalex.org/I34352273","display_name":"Maastricht University","ror":"https://ror.org/02jz4aj89","country_code":"NL","type":"education","lineage":["https://openalex.org/I34352273"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Chris T. Evelo","raw_affiliation_strings":["Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER","Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER","institution_ids":["https://openalex.org/I34352273"]},{"raw_affiliation_string":"Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER","institution_ids":["https://openalex.org/I34352273"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088503440","display_name":"Susan L. Coort","orcid":"https://orcid.org/0000-0003-1224-9690"},"institutions":[{"id":"https://openalex.org/I34352273","display_name":"Maastricht University","ror":"https://ror.org/02jz4aj89","country_code":"NL","type":"education","lineage":["https://openalex.org/I34352273"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Susan L. Coort","raw_affiliation_strings":["Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER","institution_ids":["https://openalex.org/I34352273"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5062841937"],"corresponding_institution_ids":["https://openalex.org/I34352273"],"apc_list":{"value":1350,"currency":"USD","value_usd":1350},"apc_paid":{"value":1350,"currency":"USD","value_usd":1350},"fwci":1.17815074,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.76491348,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"7","issue":null,"first_page":"743","last_page":"743"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9951000213623047,"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":0.9951000213623047,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.964900016784668,"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":0.9605000019073486,"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/open-peer-review","display_name":"Open peer review","score":0.930105984210968},{"id":"https://openalex.org/keywords/plant-biology","display_name":"Plant biology","score":0.8327603340148926},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.6419150829315186},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.5451154708862305},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4625588655471802},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4451938569545746},{"id":"https://openalex.org/keywords/physiology","display_name":"Physiology","score":0.3774714171886444},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3704417943954468},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09008032083511353}],"concepts":[{"id":"https://openalex.org/C2983643791","wikidata":"https://www.wikidata.org/wiki/Q1999993","display_name":"Open peer review","level":3,"score":0.930105984210968},{"id":"https://openalex.org/C2992936677","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Plant biology","level":2,"score":0.8327603340148926},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.6419150829315186},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.5451154708862305},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4625588655471802},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4451938569545746},{"id":"https://openalex.org/C42407357","wikidata":"https://www.wikidata.org/wiki/Q521","display_name":"Physiology","level":1,"score":0.3774714171886444},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3704417943954468},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09008032083511353},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.12688/f1000research.14613.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.14613.1","pdf_url":null,"source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.12688/f1000research.14613.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.14613.1","pdf_url":null,"source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1975875968","https://openalex.org/W1975934689","https://openalex.org/W1999758530","https://openalex.org/W2080133951","https://openalex.org/W2110838720","https://openalex.org/W2119412782","https://openalex.org/W2120680184","https://openalex.org/W2143392414","https://openalex.org/W2159675211","https://openalex.org/W2515221167","https://openalex.org/W2537623931","https://openalex.org/W2554401505","https://openalex.org/W2559812869","https://openalex.org/W2759579009","https://openalex.org/W2767914218","https://openalex.org/W2767995756","https://openalex.org/W2805923143","https://openalex.org/W2808385741","https://openalex.org/W4247844442","https://openalex.org/W6977061496"],"related_works":["https://openalex.org/W2248904208","https://openalex.org/W2240080159","https://openalex.org/W2624797522","https://openalex.org/W2247484637","https://openalex.org/W2078218631","https://openalex.org/W2061128535","https://openalex.org/W2734166346","https://openalex.org/W4391486731","https://openalex.org/W2219548690","https://openalex.org/W2912180145"],"abstract_inverted_index":{"<ns7:p>Here,":[0],"we":[1,130,150],"present":[2],"an":[3,140,152,163],"update":[4],"of":[5,170,199,205],"the":[6,42,62,117,126,155,167,184,195,200,203,211,220],"open-source":[7],"CyTargetLinker":[8,18,43,160,193],"app":[9,201],"for":[10,49,166],"Cytoscape":[11,66,102,106],"(http://apps.cytoscape.org/apps/cytargetlinker)":[12],"that":[13],"introduces":[14],"new":[15,54],"automation":[16,55],"features.":[17],"provides":[19],"a":[20,111,132,174],"simple":[21],"interface":[22],"to":[23,28,59,82,134,161],"extend":[24,110,144],"networks":[25],"with":[26,71,100,116,119,146],"links":[27],"relevant":[29],"data":[30],"and/or":[31],"knowledge":[32],"extracted":[33],"from":[34,139],"so-called":[35],"linksets.":[36],"The":[37,53],"linksets":[38],"are":[39],"provided":[40],"on":[41],"website":[44],"or":[45],"can":[46],"be":[47],"custom-made":[48],"specific":[50],"use":[51,94,128],"cases.":[52],"feature":[56],"enables":[57],"users":[58,81],"programmatically":[60],"execute":[61],"app\u2019s":[63],"functionality":[64],"in":[65,183,191,202,216,222],"(command":[67],"line":[68],"tool)":[69],"and":[70,87,91,104,122,143,158,187,197],"external":[72],"tools":[73],"(e.g.":[74],"R,":[75],"Jupyter,":[76],"Python,":[77],"etc).":[78],"This":[79],"allows":[80],"share":[83],"their":[84],"analysis":[85],"workflows":[86],"therefore":[88],"increase":[89],"repeatability":[90],"reproducibility.":[92],"Three":[93],"cases":[95],"demonstrate":[96],"automated":[97],"workflows,":[98],"combinations":[99],"other":[101],"apps":[103],"core":[105],"functionality.":[107],"We":[108],"first":[109],"protein-protein":[112],"interaction":[113],"network":[114,165,206],"created":[115,131],"stringApp,":[118],"compound-target":[120],"interactions":[121],"disease-gene":[123],"annotations.":[124],"In":[125,208],"second":[127],"case,":[129],"workflow":[133],"load":[135],"differentially":[136],"expressed":[137],"genes":[138],"experimental":[141],"dataset":[142],"it":[145],"gene-pathway":[147],"associations.":[148],"Lastly,":[149],"chose":[151],"example":[153],"outside":[154],"biological":[156],"domain":[157],"used":[159],"create":[162],"author-article-journal":[164],"five":[168],"authors":[169],"this":[171],"manuscript":[172],"using":[173],"two-step":[175],"extension":[176],"mechanism.":[177],"With":[178],"300":[179],"downloads":[180,190],"per":[181],"month":[182],"last":[185],"year":[186],"over":[188],"12,000":[189],"total,":[192],"shows":[194],"adoption":[196],"relevance":[198],"field":[204],"biology.":[207],"April":[209],"2018,":[210],"original":[212],"publication":[213],"was":[214],"cited":[215],"57":[217],"articles":[218],"demonstrating":[219],"applicability":[221],"biomedical":[223],"research.</ns7:p>":[224]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1}],"updated_date":"2026-02-13T15:27:49.765798","created_date":"2025-10-10T00:00:00"}