{"id":"https://openalex.org/W4416632077","doi":"https://doi.org/10.5256/f1000research.138369.r155717","title":"Peer Review Report For: Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App [version 2; peer review: 1 approved, 1 approved with reservations]","display_name":"Peer Review Report For: Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App [version 2; peer review: 1 approved, 1 approved with reservations]","publication_year":2022,"publication_date":"2022-12-01","ids":{"openalex":"https://openalex.org/W4416632077","doi":"https://doi.org/10.5256/f1000research.138369.r155717"},"language":null,"primary_location":{"id":"doi:10.5256/f1000research.138369.r155717","doi":"https://doi.org/10.5256/f1000research.138369.r155717","is_oa":true,"landing_page_url":"https://doi.org/10.5256/f1000research.138369.r155717","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"University of Toronto","raw_type":"peer-review"},"volume":null,"type":"peer-review","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.5256/f1000research.138369.r155717","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103222589","display_name":"Pritam Saha","orcid":"https://orcid.org/0000-0002-5935-4183","observed_orcids":["https://orcid.org/0000-0002-5935-4183"]},"institutions":[{"id":"https://openalex.org/I170979836","display_name":"Jadavpur University","ror":"https://ror.org/02af4h012","country_code":"IN","type":"education","lineage":["https://openalex.org/I170979836"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Pritam Saha","raw_affiliation_strings":["Electrical Engineering Department, Jadavpur University, Kolkata West Bengal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Electrical Engineering Department, Jadavpur University, Kolkata West Bengal","institution_ids":["https://openalex.org/I170979836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006448195","display_name":"\u00d6zg\u00fcn Babur","orcid":"https://orcid.org/0000-0002-0239-5259","observed_orcids":["https://orcid.org/0000-0002-0239-5259"]},"institutions":[{"id":"https://openalex.org/I33434090","display_name":"University of Massachusetts Boston","ror":"https://ror.org/04ydmy275","country_code":"US","type":"education","lineage":["https://openalex.org/I33434090"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"\u00d6zgun Babur","raw_affiliation_strings":["Computer Science Department, University of Massachusetts Boston, Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Massachusetts Boston, Boston, MA","institution_ids":["https://openalex.org/I33434090"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008166270","display_name":"Chris Sander","orcid":"https://orcid.org/0000-0001-6059-6270","observed_orcids":["https://orcid.org/0000-0001-6059-6270"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Sander","raw_affiliation_strings":["Broad Institute of Harvard and MIT, Cambridge, MA","Department of Cell Biology, Harvard Medical School, Boston, MA","Department of Data Science, Dana-Farber Cancer Institute, Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of Harvard and MIT, Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Cell Biology, Harvard Medical School, Boston, MA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Data Science, Dana-Farber Cancer Institute, Boston, MA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5147864827","display_name":"Augustin Luna","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Augustin Luna","raw_affiliation_strings":["Broad Institute of Harvard and MIT, Cambridge, MA","Department of Cell Biology, Harvard Medical School, Boston, MA","Department of Data Science, Dana-Farber Cancer Institute, Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of Harvard and MIT, Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Cell Biology, Harvard Medical School, Boston, MA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Data Science, Dana-Farber Cancer Institute, Boston, MA","institution_ids":["https://openalex.org/I4210117453"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5103222589"],"corresponding_institution_ids":["https://openalex.org/I170979836"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":1.0,"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":1.0,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.0,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cytoscape-app","display_name":"Cytoscape app","score":0.9200000166893005},{"id":"https://openalex.org/keywords/causal-inference","display_name":"causal inference","score":0.6029999852180481},{"id":"https://openalex.org/keywords/proteomic-profile","display_name":"proteomic profile","score":0.9010000228881836},{"id":"https://openalex.org/keywords/biological-pathways","display_name":"biological pathways","score":0.6600000262260437},{"id":"https://openalex.org/keywords/network-visualization","display_name":"network visualization","score":0.703000009059906},{"id":"https://openalex.org/keywords/cancer-proteomics","display_name":"cancer proteomics","score":0.5450000166893005},{"id":"https://openalex.org/keywords/module-detection","display_name":"module detection","score":0.6940000057220459},{"id":"https://openalex.org/keywords/protein-protein-interaction","display_name":"protein-protein interaction","score":0.6439999938011169}],"concepts":[{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.7480999827384949},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6376000046730042},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5562999844551086},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4611000120639801},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.45579999685287476},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4375},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.43050000071525574},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.36410000920295715},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3612000048160553},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.35850000381469727},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3483999967575073},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.337799996137619},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.3025999963283539},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.2973000109195709},{"id":"https://openalex.org/C112953755","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph drawing","level":3,"score":0.2924000024795532},{"id":"https://openalex.org/C2779230013","wikidata":"https://www.wikidata.org/wiki/Q25303877","display_name":"Pathway analysis","level":4,"score":0.29100000858306885},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.28949999809265137},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.28630000352859497},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.28369998931884766},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.2736000120639801},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.25999999046325684},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.2572000026702881}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5256/f1000research.138369.r155717","doi":"https://doi.org/10.5256/f1000research.138369.r155717","is_oa":true,"landing_page_url":"https://doi.org/10.5256/f1000research.138369.r155717","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"University of Toronto","raw_type":"peer-review"}],"best_oa_location":{"id":"doi:10.5256/f1000research.138369.r155717","doi":"https://doi.org/10.5256/f1000research.138369.r155717","is_oa":true,"landing_page_url":"https://doi.org/10.5256/f1000research.138369.r155717","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"University of Toronto","raw_type":"peer-review"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.8199999928474426}],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Introduction:":[0],"CausalPath":[1,37,49,80,95,113,118,137],"compares":[2],"experimentally":[3],"measured":[4,19],"changes":[5,17],"in":[6,18,71,124,146],"molecular":[7,108],"profiles":[8],"against":[9],"curated":[10],"biological":[11],"pathways":[12],"and":[13,58,119],"infers":[14],"causality":[15],"between":[16],"features":[20,144],"from":[21,28,47,84,136],"profiling":[22,109],"experiments":[23],"(e.g.,":[24,128],"RNA-seq":[25],"or":[26,30],"proteomics":[27],"total":[29],"phospho-protein":[31],"levels).":[32],"Methods:":[33],"We":[34],"developed":[35],"the":[36,48,52,77,87,99,112,132,141,147],"Cytoscape":[38,53,96,120,148],"App,":[39],"an":[40],"app":[41],"(i.e.,":[42],"plugin)":[43],"for":[44],"visualizing":[45],"results":[46,82],"method":[50],"within":[51],"Java-based":[54],"desktop":[55],"network":[56],"analysis":[57,81,138],"visualization":[59,78],"platform.":[60],"Use":[61],"Cases:":[62],"Users":[63],"are":[64,105],"given":[65],"instruction":[66],"that":[67,104,134],"represents":[68],"use":[69],"cases":[70],"multiple":[72],"cancer":[73],"research":[74],"areas":[75],"through":[76],"of":[79,101,117],"generated":[83],"data":[85,110],"by":[86,107,139],"Clinical":[88],"Proteomic":[89],"Tumor":[90],"Analysis":[91],"Consortium.":[92],"Discussion:":[93],"The":[94],"App":[97],"visualizes":[98],"set":[100],"known":[102],"interactions":[103],"supported":[106],"via":[111],"method.":[114],"This":[115],"integration":[116],"benefits":[121],"users":[122],"interested":[123],"performing":[125],"secondary":[126],"analyses":[127],"module":[129],"detection)":[130],"on":[131],"sub-networks":[133],"result":[135],"utilizing":[140],"many":[142],"analytical":[143],"available":[145],"software":[149],"ecosystem.":[150]},"counts_by_year":[],"updated_date":"2026-10-12T09:40:04.860316","created_date":"2025-11-25T00:00:00"}
