{"id":"https://openalex.org/W2120451336","doi":"https://doi.org/10.1093/nar/gku629","title":"Editorial: Nucleic Acids Research annual Web Server Issue in 2014","display_name":"Editorial: Nucleic Acids Research annual Web Server Issue in 2014","publication_year":2014,"publication_date":"2014-07-01","ids":{"openalex":"https://openalex.org/W2120451336","doi":"https://doi.org/10.1093/nar/gku629","mag":"2120451336"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gku629","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku629","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W1/7448483/gku629.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"editorial","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/42/W1/W1/7448483/gku629.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065328235","display_name":"Gary Benson","orcid":"https://orcid.org/0000-0003-2374-5462"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Gary Benson","raw_affiliation_strings":["Executive Editor, Web Server Issue, Nucleic Acids Research"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Executive Editor, Web Server Issue, Nucleic Acids Research","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5065328235"],"corresponding_institution_ids":[],"apc_list":{"value":3992,"currency":"USD","value_usd":3992},"apc_paid":{"value":3992,"currency":"USD","value_usd":3992},"fwci":null,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"W1","first_page":"W1","last_page":"W2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9778000116348267,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9778000116348267,"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/biology","display_name":"Biology","score":0.932368278503418},{"id":"https://openalex.org/keywords/nucleic-acid","display_name":"Nucleic acid","score":0.704421877861023},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42352765798568726},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4092922806739807},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3298895061016083},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27416402101516724},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.12070173025131226}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.932368278503418},{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.704421877861023},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42352765798568726},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4092922806739807},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3298895061016083},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27416402101516724},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.12070173025131226}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/nar/gku629","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku629","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W1/7448483/gku629.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:3176814","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4086090","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/nar/gku629","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku629","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W1/7448483/gku629.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.5400000214576721,"id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320290","display_name":"University of Oxford","ror":"https://ror.org/052gg0110"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2120451336.pdf","grobid_xml":"https://content.openalex.org/works/W2120451336.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1503756910","https://openalex.org/W2617507009","https://openalex.org/W2063208150","https://openalex.org/W2605962812","https://openalex.org/W2072950538","https://openalex.org/W2010795951","https://openalex.org/W4288064360","https://openalex.org/W2164015999","https://openalex.org/W3176053661","https://openalex.org/W2309544048"],"abstract_inverted_index":{"The":[0,42,85,118,176,361,459,673,1040],"2014":[1,119,319],"Web":[2,120,177,402,573,883,951,997],"Server":[3,121,178,403,884,952,998],"Issue":[4,860],"of":[5,15,28,63,78,126,149,187,207,210,222,252,300,346,351,357,418,483,550,561,612,636,659,706,757,781,787,795,809,845,849,897,944,965,976,1011,1044,1072],"Nucleic":[6],"Acids":[7],"Research":[8,246,938],"is":[9,33,55,393,462,627,750,1046],"the":[10,124,185,188,204,219,238,249,261,278,289,305,318,352,372,401,416,432,434,469,489,493,539,590,610,616,634,637,657,687,690,704,707,711,725,782,843,857,866,882,915,929,941,950,960,963,995,1008,1012,1038,1057,1073,1092],"12th":[11],"in":[12,172,237,248,259,400,424,471,502,509,566,764,837,928,940,1037],"a":[13,166,297,347,381,394,419,448,484,551,555,559,584,606,624,645,746,838,862,873,909,1083],"series":[14,560],"annual":[16],"special":[17,53,128,966],"issues":[18],"dedicated":[19],"to":[20,229,268,295,304,314,374,431,513,563,589,716,721,818,829,906,991,1016,1065,1069,1078],"web-based":[21],"software":[22],"resources":[23],"for":[24,58,131,146,152,255,285,311,331,343,364,405,438,451,479,586,661,745,807,833,881,917,957,971,987,994,1042,1051,1056,1087],"analysis":[25,62,91,660,875,975],"and":[26,69,72,94,106,112,144,191,203,232,243,274,277,325,354,380,386,455,500,524,530,621,656,667,699,701,728,779,789,792,801,820,893,923,935,981,983,1024,1082],"visualization":[27,532],"molecular":[29],"biology":[30,60,912,973],"data.":[31],"It":[32,440],"freely":[34,199],"available":[35,200],"online":[36],"under":[37],"NAR's":[38],"open":[39],"access":[40,622],"policy.":[41],"present":[43],"issue":[44,122,179,404,885,999,1059],"reports":[45],"on":[46,56,377,755],"80":[47],"web":[48,150,167,201,302,358,406,411,607,747],"servers.":[49],"Topics.":[50],"This":[51,629,827,1030],"year's":[52],"emphasis":[54,967],"tools":[57,533,970],"synthetic":[59,972],"design,":[61,974],"high":[64,140,367,977],"throughput":[65,141,978],"sequencing":[66,142,979],"data,":[67,137,143,379,980],"network":[68,982],"pathway":[70,984],"analysis,":[71],"biological":[73],"text":[74],"mining.":[75],"A":[76],"total":[77],"19":[79],"papers":[80,170],"deal":[81],"with":[82,165,197,447,948,1007],"these":[83,173,1089],"topics.":[84],"other":[86,426,567,671],"major":[87],"topic":[88],"categories":[89],"include":[90,753,777,1066],"involving":[92],"DNA":[93],"RNA":[95],"(12":[96],"papers);":[97,101,105],"gene":[98],"prioritization":[99],"(5":[100,104],"drug-target":[102],"interactions":[103],"proteins,":[107],"including":[108,422,798,1076],"structure,":[109],"ligand":[110],"binding,":[111],"functional":[113,388,1014],"site":[114],"prediction":[115,811],"(24":[116],"papers).":[117],"continues":[123],"presentation":[125],"two":[127],"categories,":[129],"one":[130,145,1003],"stand-alone":[132],"programs":[133,568],"that":[134,155,391,413,467,534,546,575,604,643,653,685,749,851,871],"analyze":[135,821],"high-throughput":[136],"such":[138,898],"as":[139,598,861,908],"large":[147],"collections":[148],"services":[151],"automated":[153],"analyses":[154],"can":[156,618],"be":[157,182,475,498,520,528,543,564,571,596,650,665,676,772,825,969,1033],"utilized":[158],"programmatically":[159],"rather":[160,732],"than":[161,427,733],"through":[162,689],"manual":[163],"interaction":[164],"browser.":[168],"Six":[169],"fall":[171],"categories.":[174],"Acknowledgements.":[175],"would":[180],"not":[181,570,577,649,668,762,771,815,879],"possible":[183,863],"without":[184],"work":[186,213],"many":[189],"scientists":[190],"programmers":[192],"who":[193],"have":[194,414,442],"provided":[195,597,723],"us":[196],"outstanding,":[198],"resources,":[202],"conscientious":[205],"efforts":[206],"literally":[208],"hundreds":[209],"reviewers.":[211],"My":[212],"was":[214],"made":[215],"possible,":[216,505,710],"first,":[217],"by":[218,593,670,678,724,1018],"editorial":[220],"assistance":[221,258],"Fay":[223],"Oppenheim.":[224],"Thank":[225],"you.":[226],"Thanks":[227],"also":[228],"Allyson":[230,921],"Byrd":[231,922],"Joe":[233,924],"Perez-Rogers,":[234,925],"PhD":[235,926],"students":[236,927],"Boston":[239,930],"University":[240,282,931],"Bioinformatics":[241,932],"Program,":[242,934],"Artem":[244,936],"Mamonov,":[245,937],"Associate":[247,939],"BU":[250,942],"department":[251],"Biomedical":[253,945],"Engineering,":[254,946],"their":[256,301,579,904,1002,1062],"outstanding":[257],"evaluating":[260],"proposal":[262,353,744,953,1005],"websites":[263,850],"(Figure":[264],"1).":[265],"Additional":[266,465],"thanks":[267],"Martine":[269],"Bernardes-Silva,":[270],"Editorial":[271],"Manager,":[272],"NAR,":[273],"Jennifer":[275],"Boyd":[276],"staff":[279],"at":[280,609,623,868,919,1028,1096],"Oxford":[281],"Press.":[283],"Instructions":[284,1086],"Submissions.":[286],"To":[287],"streamline":[288],"review":[290],"process,":[291,692],"authors":[292,918],"are":[293,366,436,736,804,877,1026,1094],"required":[294],"send":[296],"one-page":[298],"summary":[299,348],"server":[303,359,748],"editor,":[306],"Dr.":[307],"Gary":[308],"Benson":[309],"(narwbsrv@bu.edu),":[310],"pre-approval":[312,365],"prior":[313],"manuscript":[315,332,905,1093],"submission.":[316,333],"For":[317,959],"issue,":[320,962],"269":[321],"summaries":[322],"were":[323,329,340],"submitted":[324,1055],"106,":[326],"or":[327,338,408,537,558,683,835,841],"39%,":[328],"approved":[330],"Of":[334],"those":[335,722,830],"approved,":[336],"80,":[337],"75%,":[339],"ultimately":[341],"accepted":[342],"publication.":[344],"Review":[345],"includes":[349],"evaluation":[350],"extensive":[355,680],"testing":[356,949],"functionality.":[360],"key":[362],"criteria":[363],"scientific":[368],"quality,":[369],"wide":[370],"interest,":[371],"ability":[373],"do":[375,576],"computations":[376],"user-submitted":[378,822],"well":[382,384],"designed,":[383],"implemented,":[385],"fully":[387,1013],"website.":[389,726],"Note":[390,545,652],"there":[392],"minimum":[395],"two-year":[396],"interval":[397],"before":[398,1035],"publication":[399,423],"servers,":[407,412],"essentially":[409],"similar":[410,720],"been":[415],"subject":[417],"previous":[420],"publication,":[421],"journals":[425],"NAR.":[428],"With":[429],"respect":[430],"website,":[433],"following":[435],"guidelines":[437],"approval.":[439],"should":[441,474,497,519,527,542,631,675,714,776,855,1032],"an":[443,599,602,679],"easy-to-find":[444],"submission":[445,691,1043],"page":[446,1004],"simple":[449],"mechanism":[450,585],"loading":[452],"test":[453,457],"data":[454,473,613,655,761,784,823,839,854],"setting":[456],"parameters.":[458],"preferred":[460,737],"method":[461,876,891],"one-click":[463],"loading.":[464],"mechanisms":[466],"assist":[468],"user":[470,490,617,663,688],"submitting":[472],"implemented":[476],"where":[477],"appropriate,":[478],"example,":[480],"automatic":[481],"download":[482],"pdb":[485],"structure":[486],"file":[487,697],"once":[488],"has":[491],"entered":[492],"appropriate":[494,880],"identifier.":[495],"Output":[496],"dynamic":[499,717],"rich":[501],"detail.":[503],"Wherever":[504],"supporting":[506],"evidence":[507],"used":[508,763],"calculations":[510,580],"and/or":[511],"links":[512,1068,1077,1090],"external":[514],"databases":[515],"containing":[516],"additional":[517],"information":[518,536,1031],"provided.":[521],"Numerical,":[522],"textual,":[523],"visual":[525],"output":[526,547,718],"mixed":[529],"any":[531],"add":[535],"increase":[538],"user's":[540],"understanding":[541],"utilized.":[544],"consisting":[548],"merely":[549],"few":[552],"numerical":[553],"values,":[554],"static":[556],"spreadsheet,":[557],"files":[562],"opened":[565],"will":[569,648,770,824,968],"approved.":[572,651],"servers":[574],"finish":[578],"immediately":[581],"must":[582,664,752,1000,1060],"implement":[583],"returning":[587],"results":[588,658],"user.":[591],"Notification":[592],"email":[594],"may":[595],"option,":[600],"but":[601],"alternative":[603],"returns":[605],"link":[608,630,715],"time":[611],"submission,":[614],"which":[615],"then":[619],"bookmark":[620],"later":[625],"time,":[626],"required.":[628],"ideally":[632],"report":[633],"status":[635],"job":[638],"(queued,":[639],"running,":[640],"finished).":[641],"Websites":[642,814],"require":[644],"guest":[646],"login":[647],"uploaded":[654],"each":[662],"private":[666],"viewable":[669],"users.":[672],"website":[674,1015],"supported":[677],"help":[681,712,730],"section":[682,1064],"tutorial":[684],"guides":[686],"contains":[693],"details":[694,754],"about":[695],"input":[696],"formats":[698],"parameters,":[700],"importantly,":[702],"explains":[703],"meaning":[705],"output.":[708],"Whenever":[709],"pages":[713],"examples":[719],"Text":[727],"figure":[729],"pages,":[731],"video":[734],"tutorials,":[735],"because":[738,886],"they":[739],"simplify":[740],"quick":[741],"look-up.":[742],"Any":[743],"predictive":[751,796],"validation":[756,768,783,812,894],"predictions":[758],"from":[759],"new":[760,874],"training.":[765],"N-fold":[766],"cross":[767],"methods":[769,899],"considered":[773],"sufficient.":[774],"Details":[775],"size":[778],"composition":[780],"set":[785],"(number":[786],"positive":[788],"negative":[790],"cases),":[791],"several":[793],"measures":[794],"performance,":[797],"sensitivity,":[799],"specificity,":[800],"precision.":[802],"Proposals":[803,870],"frequently":[805],"rejected":[806],"lack":[808],"adequate":[810,890],"information.":[813],"clearly":[816],"designed":[817],"accept":[819],"rejected.":[826],"applies":[828],"established":[831],"primarily":[832],"lookup":[834],"exploration":[836],"set,":[840],"serve":[842],"function":[844],"\u201cdata":[846],"aggregators.\u201d":[847],"Authors":[848,896,989],"provide":[852],"novel":[853],"consider":[856,902],"NAR":[858,907],"Database":[859],"venue":[864],"(see":[865,914],"instructions":[867,916,1023],"http://www.oxfordjournals.org/our_journals/nar/for_authors/msprep_database.html).":[869],"describe":[872],"generally":[878],"limited":[887],"space":[888],"makes":[889],"description":[892],"problematic.":[895],"might":[900],"instead":[901],"sending":[903,1036],"regular":[910],"computational":[911],"paper":[913],"http://www.oxfordjournals.org/our_journals/nar/for_authors/criteria_scope.html#Computational%20Biology).":[920],"Graduate":[933],"Department":[943],"helped":[947],"websites.":[954],"Special":[955],"Emphasis":[956],"2015.":[958,988,1049],"2015":[961,996,1058],"topics":[964],"analysis.":[985],"Deadlines":[986],"wishing":[990],"submit":[992,1001],"manuscripts":[993],"along":[1006],"URL":[1009],"address":[1010],"narwbsrv@bu.edu":[1017],"31":[1019,1047],"December":[1020],"2014.":[1021],"Detailed":[1022],"requirements":[1025],"presented":[1027,1095],"http://www.oxfordjournals.org/nar/for_authors/submission_webserver.html.":[1029,1097],"consulted":[1034],"summary.":[1039],"deadline":[1041],"articles":[1045],"January":[1048],"Requirement":[1050],"References":[1052,1063],"Links.":[1053],"Manuscripts":[1054],"format":[1061],"active":[1067],"electronic":[1070],"versions":[1071],"cited":[1074],"papers,":[1075],"PubMed,":[1079],"PubMed":[1080],"Central,":[1081],"DOI":[1084],"link.":[1085],"incorporating":[1088],"into":[1091]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
