{"id":"https://openalex.org/W2031218556","doi":"https://doi.org/10.1093/database/bau126","title":"Comparison of human cell signaling pathway databases\u2014evolution, drawbacks and challenges","display_name":"Comparison of human cell signaling pathway databases\u2014evolution, drawbacks and challenges","publication_year":2015,"publication_date":"2015-01-01","ids":{"openalex":"https://openalex.org/W2031218556","doi":"https://doi.org/10.1093/database/bau126","mag":"2031218556","pmid":"https://pubmed.ncbi.nlm.nih.gov/25632107"},"language":"en","primary_location":{"id":"doi:10.1093/database/bau126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau126","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau126/16975831/bau126.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau126/16975831/bau126.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023247552","display_name":"Saikat Chowdhury","orcid":"https://orcid.org/0000-0002-0783-3959"},"institutions":[{"id":"https://openalex.org/I3125981224","display_name":"National Chemical Laboratory","ror":"https://ror.org/057mn3690","country_code":"IN","type":"facility","lineage":["https://openalex.org/I2799351866","https://openalex.org/I3125981224","https://openalex.org/I4210134808","https://openalex.org/I66760702"]},{"id":"https://openalex.org/I99364266","display_name":"Academy of Scientific and Innovative Research","ror":"https://ror.org/053rcsq61","country_code":"IN","type":"education","lineage":["https://openalex.org/I99364266"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Saikat Chowdhury","raw_affiliation_strings":["Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune, Maharashtra 411008, India and 2 Academy of Scientific & Innovative Research (AcSIR), New Delhi 110 001, India"],"affiliations":[{"raw_affiliation_string":"Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune, Maharashtra 411008, India and 2 Academy of Scientific & Innovative Research (AcSIR), New Delhi 110 001, India","institution_ids":["https://openalex.org/I99364266","https://openalex.org/I3125981224"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091792722","display_name":"Ram Rup Sarkar","orcid":"https://orcid.org/0000-0001-7115-163X"},"institutions":[{"id":"https://openalex.org/I3125981224","display_name":"National Chemical Laboratory","ror":"https://ror.org/057mn3690","country_code":"IN","type":"facility","lineage":["https://openalex.org/I2799351866","https://openalex.org/I3125981224","https://openalex.org/I4210134808","https://openalex.org/I66760702"]},{"id":"https://openalex.org/I99364266","display_name":"Academy of Scientific and Innovative Research","ror":"https://ror.org/053rcsq61","country_code":"IN","type":"education","lineage":["https://openalex.org/I99364266"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Ram Rup Sarkar","raw_affiliation_strings":["Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune, Maharashtra 411008, India and 2 Academy of Scientific & Innovative Research (AcSIR), New Delhi 110 001, India"],"affiliations":[{"raw_affiliation_string":"Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune, Maharashtra 411008, India and 2 Academy of Scientific & Innovative Research (AcSIR), New Delhi 110 001, India","institution_ids":["https://openalex.org/I99364266","https://openalex.org/I3125981224"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5023247552"],"corresponding_institution_ids":["https://openalex.org/I3125981224","https://openalex.org/I99364266"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":7.3956,"has_fulltext":true,"cited_by_count":113,"citation_normalized_percentile":{"value":0.97858059,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"2015","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":0.9997000098228455,"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":0.9997000098228455,"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":0.9973999857902527,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9958000183105469,"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/annotation","display_name":"Annotation","score":0.6663229465484619},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5875782370567322},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5379586219787598},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5174599289894104},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32080262899398804},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24214178323745728},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13534051179885864}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6663229465484619},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5875782370567322},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5379586219787598},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5174599289894104},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32080262899398804},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24214178323745728},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13534051179885864}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/bau126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau126","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau126/16975831/bau126.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:25632107","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25632107","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:3302193","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4309023","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bau126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau126","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau126/16975831/bau126.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4000000059604645,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G5599793009","display_name":null,"funder_award_id":"BSC0121","funder_id":"https://openalex.org/F4320320721","funder_display_name":"Council of Scientific and Industrial Research, India"}],"funders":[{"id":"https://openalex.org/F4320320719","display_name":"Department of Science and Technology, Ministry of Science and Technology, India","ror":"https://ror.org/0101xrq71"},{"id":"https://openalex.org/F4320320721","display_name":"Council of Scientific and Industrial Research, India","ror":"https://ror.org/021wm7p51"},{"id":"https://openalex.org/F4320336761","display_name":"National Chemical Laboratory","ror":"https://ror.org/057mn3690"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2031218556.pdf","grobid_xml":"https://content.openalex.org/works/W2031218556.grobid-xml"},"referenced_works_count":119,"referenced_works":["https://openalex.org/W141889398","https://openalex.org/W172445582","https://openalex.org/W180513472","https://openalex.org/W1482515444","https://openalex.org/W1489982428","https://openalex.org/W1500827124","https://openalex.org/W1564861448","https://openalex.org/W1600040944","https://openalex.org/W1616421194","https://openalex.org/W1943053564","https://openalex.org/W1965853004","https://openalex.org/W1965917470","https://openalex.org/W1967582843","https://openalex.org/W1969325859","https://openalex.org/W1969709265","https://openalex.org/W1978007328","https://openalex.org/W1980578041","https://openalex.org/W1981721404","https://openalex.org/W1984566373","https://openalex.org/W1984852348","https://openalex.org/W1985166156","https://openalex.org/W1988689793","https://openalex.org/W1994458586","https://openalex.org/W2008195525","https://openalex.org/W2010502047","https://openalex.org/W2016060560","https://openalex.org/W2017218687","https://openalex.org/W2021842892","https://openalex.org/W2022472106","https://openalex.org/W2023292217","https://openalex.org/W2028184340","https://openalex.org/W2032802725","https://openalex.org/W2035680235","https://openalex.org/W2038264484","https://openalex.org/W2041769207","https://openalex.org/W2042301222","https://openalex.org/W2044267206","https://openalex.org/W2046434400","https://openalex.org/W2051614902","https://openalex.org/W2052685738","https://openalex.org/W2055488354","https://openalex.org/W2058594499","https://openalex.org/W2061751549","https://openalex.org/W2065807795","https://openalex.org/W2068209123","https://openalex.org/W2070575998","https://openalex.org/W2074906123","https://openalex.org/W2079048673","https://openalex.org/W2081010896","https://openalex.org/W2083990676","https://openalex.org/W2093431157","https://openalex.org/W2095304455","https://openalex.org/W2096766502","https://openalex.org/W2099131261","https://openalex.org/W2099526830","https://openalex.org/W2100673036","https://openalex.org/W2100980426","https://openalex.org/W2102653059","https://openalex.org/W2102899487","https://openalex.org/W2103031848","https://openalex.org/W2103085707","https://openalex.org/W2105284546","https://openalex.org/W2105325784","https://openalex.org/W2107062718","https://openalex.org/W2117513900","https://openalex.org/W2122302420","https://openalex.org/W2122863289","https://openalex.org/W2124419982","https://openalex.org/W2124662474","https://openalex.org/W2125637396","https://openalex.org/W2125984976","https://openalex.org/W2127020923","https://openalex.org/W2127863452","https://openalex.org/W2128601422","https://openalex.org/W2130687290","https://openalex.org/W2133579817","https://openalex.org/W2136178650","https://openalex.org/W2137518425","https://openalex.org/W2137575744","https://openalex.org/W2139254860","https://openalex.org/W2139328007","https://openalex.org/W2142302575","https://openalex.org/W2143969914","https://openalex.org/W2147714160","https://openalex.org/W2150908245","https://openalex.org/W2151014102","https://openalex.org/W2156907249","https://openalex.org/W2158691076","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W2161441225","https://openalex.org/W2163480486","https://openalex.org/W2163485494","https://openalex.org/W2164298117","https://openalex.org/W2165253681","https://openalex.org/W2171322586","https://openalex.org/W2171599819","https://openalex.org/W2172045503","https://openalex.org/W2175715045","https://openalex.org/W2239090104","https://openalex.org/W2312381546","https://openalex.org/W2314971636","https://openalex.org/W2317845988","https://openalex.org/W2406585419","https://openalex.org/W2492514793","https://openalex.org/W2502930843","https://openalex.org/W2510854709","https://openalex.org/W4237293127","https://openalex.org/W4243826908","https://openalex.org/W6605722572","https://openalex.org/W6646797311","https://openalex.org/W6647584156","https://openalex.org/W6660594790","https://openalex.org/W6664195865","https://openalex.org/W6673972711","https://openalex.org/W6676117026","https://openalex.org/W6680606729","https://openalex.org/W6684390987","https://openalex.org/W6685665237"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136"],"abstract_inverted_index":{"Elucidating":[0],"the":[1,56,170,181,193],"complexities":[2],"of":[3,8,21,35,62,169],"cell":[4,25,121],"signaling":[5,122],"pathways":[6],"is":[7],"immense":[9],"importance":[10],"to":[11,46,110,144,155,192],"gain":[12],"understanding":[13],"about":[14],"various":[15,48,80],"biological":[16],"phenomenon,":[17],"such":[18,95],"as":[19,96],"dynamics":[20],"gene/protein":[22],"expression":[23],"regulation,":[24],"fate":[26],"determination,":[27],"embryogenesis":[28],"and":[29,43,71,93,103,117,131,139,148,159,178],"disease":[30],"progression.":[31],"The":[32],"successful":[33],"completion":[34],"human":[36],"genome":[37],"project":[38],"has":[39],"also":[40,78,173],"helped":[41],"experimental":[42,66],"theoretical":[44],"biologists":[45],"analyze":[47],"important":[49],"pathways.":[50],"To":[51],"advance":[52],"this":[53],"study,":[54],"during":[55],"past":[57],"two":[58,126],"decades,":[59],"systematic":[60],"collections":[61],"pathway":[63,97,129],"data":[64,98,136],"from":[65,137],"studies":[67],"have":[68],"been":[69],"compiled":[70],"distributed":[72],"freely":[73,134],"by":[74],"several":[75,91],"databases,":[76],"which":[77,107,162,188],"integrate":[79],"computational":[81],"tools":[82],"for":[83,184],"further":[84],"analysis.":[85],"Despite":[86],"significant":[87],"advancements,":[88],"there":[89],"exist":[90],"drawbacks":[92],"challenges,":[94],"heterogeneity,":[99],"annotation,":[100],"regular":[101],"update":[102],"automated":[104],"image":[105],"reconstructions,":[106],"motivated":[108],"us":[109],"perform":[111],"a":[112],"thorough":[113],"review":[114,151],"on":[115,125],"popular":[116],"actively":[118],"functioning":[119],"24":[120],"databases.":[123],"Based":[124],"major":[127],"characteristics,":[128],"information":[130],"technical":[132],"details,":[133],"accessible":[135],"commercial":[138],"academic":[140],"databases":[141,171],"are":[142,163],"examined":[143],"understand":[145],"their":[146,175],"evolution":[147],"enrichment.":[149],"This":[150],"not":[152,164],"only":[153],"helps":[154],"identify":[156],"some":[157],"novel":[158],"useful":[160,191],"features,":[161],"yet":[165],"included":[166],"in":[167],"any":[168],"but":[172],"highlights":[174],"current":[176],"limitations":[177],"subsequently":[179],"propose":[180],"reasonable":[182],"solutions":[183],"future":[185],"database":[186],"development,":[187],"could":[189],"be":[190],"whole":[194],"scientific":[195],"community.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":21},{"year":2017,"cited_by_count":13},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":6}],"updated_date":"2026-04-22T08:38:42.863108","created_date":"2025-10-10T00:00:00"}
