{"id":"https://openalex.org/W4233004559","doi":"https://doi.org/10.12688/f1000research.14776.1","title":"Automation of ReactomeFIViz via CyREST API","display_name":"Automation of ReactomeFIViz via CyREST API","publication_year":2018,"publication_date":"2018-05-02","ids":{"openalex":"https://openalex.org/W4233004559","doi":"https://doi.org/10.12688/f1000research.14776.1"},"language":"en","primary_location":{"id":"doi:10.12688/f1000research.14776.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.14776.1","pdf_url":"https://f1000research.com/articles/7-531/v1/pdf","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://f1000research.com/articles/7-531/v1/pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036915193","display_name":"Fred Loney","orcid":"https://orcid.org/0000-0002-8828-0726"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fred Loney","raw_affiliation_strings":["Knight Cancer Institute, Oregon Health & Science University, Portland, OR"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Knight Cancer Institute, Oregon Health & Science University, Portland, OR","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006718188","display_name":"Guanming Wu","orcid":"https://orcid.org/0000-0001-8196-1177"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guanming Wu","raw_affiliation_strings":["Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR"],"raw_orcid":"https://orcid.org/0000-0001-8196-1177","affiliations":[{"raw_affiliation_string":"Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR","institution_ids":["https://openalex.org/I165690674"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5036915193"],"corresponding_institution_ids":["https://openalex.org/I165690674"],"apc_list":{"value":1350,"currency":"USD","value_usd":1350},"apc_paid":{"value":1350,"currency":"USD","value_usd":1350},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.23392409,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"7","issue":null,"first_page":"531","last_page":"531"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9962000250816345,"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":0.9872999787330627,"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/workflow","display_name":"Workflow","score":0.7751299142837524},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7328137159347534},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6285189390182495},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6278389096260071},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4763246476650238},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4717184901237488},{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.4633283019065857},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.42878666520118713},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4115704298019409},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.339081346988678},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3253985047340393},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32161813974380493},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3000148832798004},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2060529589653015},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14658907055854797},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14028987288475037},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08358651399612427}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7751299142837524},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7328137159347534},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6285189390182495},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6278389096260071},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4763246476650238},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4717184901237488},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.4633283019065857},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.42878666520118713},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4115704298019409},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.339081346988678},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3253985047340393},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32161813974380493},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3000148832798004},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2060529589653015},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14658907055854797},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14028987288475037},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08358651399612427},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.12688/f1000research.14776.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.14776.1","pdf_url":"https://f1000research.com/articles/7-531/v1/pdf","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.14776.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.14776.1","pdf_url":"https://f1000research.com/articles/7-531/v1/pdf","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":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G6462374740","display_name":null,"funder_award_id":"5U41HG003751","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4233004559.pdf","grobid_xml":"https://content.openalex.org/works/W4233004559.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1956024495","https://openalex.org/W2050200982","https://openalex.org/W2058539819","https://openalex.org/W2096283457","https://openalex.org/W2159675211","https://openalex.org/W2800379400","https://openalex.org/W2802098958","https://openalex.org/W4233698560"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W4287027380","https://openalex.org/W3193760048","https://openalex.org/W4285822516","https://openalex.org/W2505261959"],"abstract_inverted_index":{"<ns4:p>Pathway-":[0],"and":[1,13,27,39,55,59,67,84,118,129,135,139],"network-based":[2,56,136],"approaches":[3,29],"project":[4],"seemingly":[5],"unrelated":[6],"genes":[7],"onto":[8],"the":[9,16,100,109,120,125],"context":[10],"of":[11,77,111],"pathways":[12,66],"networks,":[14],"enhancing":[15],"analysis":[17,36,58,138],"power":[18],"that":[19],"cannot":[20],"be":[21],"achieved":[22],"via":[23],"gene-based":[24],"approaches.":[25],"Pathway":[26],"network":[28],"are":[30],"routinely":[31],"applied":[32],"in":[33,80,99,114,144],"large-scale":[34],"data":[35,57,137],"for":[37,50,92],"cancer":[38],"other":[40],"complicated":[41],"diseases.":[42],"ReactomeFIViz":[43,93],"is":[44],"a":[45,89,104,115,127],"Cytoscape":[46],"app,":[47],"providing":[48],"features":[49,98],"researchers":[51],"to":[52,107,132],"perform":[53,133],"pathway-":[54,134],"visualization":[60,140],"by":[61,94],"leveraging":[62],"manually":[63],"curated":[64],"Reactome":[65,70],"highly":[68],"reliable":[69],"functional":[71],"interaction":[72],"network.":[73],"To":[74],"facilitate":[75],"adoption":[76],"this":[78,112],"app":[79,143],"bioinformatics":[81],"software":[82],"pipeline":[83],"workflow":[85],"development,":[86],"we":[87],"develop":[88],"CyREST":[90],"API":[91,113,122],"exposing":[95],"some":[96],"major":[97],"app.":[101],"We":[102],"describe":[103],"use":[105,110],"case":[106],"demonstrate":[108],"Python-based":[116],"notebook,":[117],"believe":[119],"new":[121],"will":[123],"provide":[124],"community":[126],"convenient":[128],"powerful":[130],"tool":[131],"using":[141],"our":[142],"an":[145],"automatic":[146],"way.</ns4:p>":[147]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
