{"id":"https://openalex.org/W4321372967","doi":"https://doi.org/10.3390/data8020041","title":"VPAgs-Dataset4ML: A Dataset to Predict Viral Protective Antigens for Machine Learning-Based Reverse Vaccinology","display_name":"VPAgs-Dataset4ML: A Dataset to Predict Viral Protective Antigens for Machine Learning-Based Reverse Vaccinology","publication_year":2023,"publication_date":"2023-02-17","ids":{"openalex":"https://openalex.org/W4321372967","doi":"https://doi.org/10.3390/data8020041"},"language":"en","primary_location":{"id":"doi:10.3390/data8020041","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data8020041","pdf_url":"https://www.mdpi.com/2306-5729/8/2/41/pdf?version=1679648589","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2306-5729/8/2/41/pdf?version=1679648589","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033779408","display_name":"Zakia Salod","orcid":"https://orcid.org/0000-0001-7774-1104"},"institutions":[{"id":"https://openalex.org/I95023434","display_name":"University of KwaZulu-Natal","ror":"https://ror.org/04qzfn040","country_code":"ZA","type":"education","lineage":["https://openalex.org/I95023434"]}],"countries":["ZA"],"is_corresponding":true,"raw_author_name":"Zakia Salod","raw_affiliation_strings":["Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa"],"raw_orcid":"https://orcid.org/0000-0001-7774-1104","affiliations":[{"raw_affiliation_string":"Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa","institution_ids":["https://openalex.org/I95023434"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048805720","display_name":"Ozayr Mahomed","orcid":"https://orcid.org/0000-0001-8076-0453"},"institutions":[{"id":"https://openalex.org/I4210165735","display_name":"Dasman Diabetes Institute","ror":"https://ror.org/05tppc012","country_code":"KW","type":"education","lineage":["https://openalex.org/I4210165735"]},{"id":"https://openalex.org/I95023434","display_name":"University of KwaZulu-Natal","ror":"https://ror.org/04qzfn040","country_code":"ZA","type":"education","lineage":["https://openalex.org/I95023434"]}],"countries":["KW","ZA"],"is_corresponding":false,"raw_author_name":"Ozayr Mahomed","raw_affiliation_strings":["Dasman Diabetes Institute, P.O. Box 1180, Dasman 15462, Kuwait City, Kuwait","Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa"],"raw_orcid":"https://orcid.org/0000-0001-8076-0453","affiliations":[{"raw_affiliation_string":"Dasman Diabetes Institute, P.O. Box 1180, Dasman 15462, Kuwait City, Kuwait","institution_ids":["https://openalex.org/I4210165735"]},{"raw_affiliation_string":"Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa","institution_ids":["https://openalex.org/I95023434"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5033779408"],"corresponding_institution_ids":["https://openalex.org/I95023434"],"apc_list":{"value":1600,"currency":"CHF","value_usd":1732},"apc_paid":{"value":1600,"currency":"CHF","value_usd":1732},"fwci":0.2999,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.61819833,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"8","issue":"2","first_page":"41","last_page":"41"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9998999834060669,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9998999834060669,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9957000017166138,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.7194380760192871},{"id":"https://openalex.org/keywords/reverse-vaccinology","display_name":"Reverse vaccinology","score":0.670810878276825},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4881077706813812},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45650702714920044},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.45224320888519287},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.4330378770828247},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36969834566116333},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3069949448108673},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.17076832056045532},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.14594808220863342},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0799264907836914}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.7194380760192871},{"id":"https://openalex.org/C2781152039","wikidata":"https://www.wikidata.org/wiki/Q7318278","display_name":"Reverse vaccinology","level":4,"score":0.670810878276825},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4881077706813812},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45650702714920044},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.45224320888519287},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.4330378770828247},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36969834566116333},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3069949448108673},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.17076832056045532},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.14594808220863342},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0799264907836914},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3390/data8020041","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data8020041","pdf_url":"https://www.mdpi.com/2306-5729/8/2/41/pdf?version=1679648589","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},{"id":"pmh:oai:RePEc:gam:jdataj:v:8:y:2023:i:2:p:41-:d:1072576","is_oa":false,"landing_page_url":"https://www.mdpi.com/2306-5729/8/2/41/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:7b16fb8bd91d454585cf83a98e8e92a6","is_oa":true,"landing_page_url":"https://doaj.org/article/7b16fb8bd91d454585cf83a98e8e92a6","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Data, Vol 8, Iss 2, p 41 (2023)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2306-5729/8/2/41/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/data8020041","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Data","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/data8020041","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data8020041","pdf_url":"https://www.mdpi.com/2306-5729/8/2/41/pdf?version=1679648589","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4321372967.pdf"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W71547456","https://openalex.org/W1680392829","https://openalex.org/W1831050183","https://openalex.org/W1850527962","https://openalex.org/W1873332500","https://openalex.org/W1979900513","https://openalex.org/W1996746577","https://openalex.org/W2005095482","https://openalex.org/W2018214960","https://openalex.org/W2046498003","https://openalex.org/W2055043387","https://openalex.org/W2067761505","https://openalex.org/W2089873422","https://openalex.org/W2101234009","https://openalex.org/W2102367710","https://openalex.org/W2104933073","https://openalex.org/W2114850508","https://openalex.org/W2119611042","https://openalex.org/W2124672930","https://openalex.org/W2127435093","https://openalex.org/W2130203599","https://openalex.org/W2131850886","https://openalex.org/W2139212933","https://openalex.org/W2148143831","https://openalex.org/W2156039063","https://openalex.org/W2156909104","https://openalex.org/W2161984798","https://openalex.org/W2166637863","https://openalex.org/W2171295581","https://openalex.org/W2181616869","https://openalex.org/W2303521084","https://openalex.org/W2342249984","https://openalex.org/W2413168313","https://openalex.org/W2582743722","https://openalex.org/W2585805431","https://openalex.org/W2588466226","https://openalex.org/W2612634114","https://openalex.org/W2800958454","https://openalex.org/W2906828558","https://openalex.org/W2914586483","https://openalex.org/W2950954328","https://openalex.org/W3006708056","https://openalex.org/W3092849554","https://openalex.org/W3115663295","https://openalex.org/W3158218142","https://openalex.org/W3162421907","https://openalex.org/W4211054902","https://openalex.org/W4234971943","https://openalex.org/W4235859326","https://openalex.org/W4242679723","https://openalex.org/W4292550103","https://openalex.org/W4399570526","https://openalex.org/W6639048329","https://openalex.org/W6639175750","https://openalex.org/W6675011870","https://openalex.org/W6675354045","https://openalex.org/W6685764666","https://openalex.org/W6715088133","https://openalex.org/W6751464957","https://openalex.org/W6756040250","https://openalex.org/W6787745904","https://openalex.org/W6794605398","https://openalex.org/W6869345919","https://openalex.org/W7053126446"],"related_works":["https://openalex.org/W24553703","https://openalex.org/W4211000692","https://openalex.org/W4212920271","https://openalex.org/W1262800261","https://openalex.org/W2612240612","https://openalex.org/W4324018414","https://openalex.org/W4211208250","https://openalex.org/W4211054902","https://openalex.org/W4313471342","https://openalex.org/W3084019278"],"abstract_inverted_index":{"Reverse":[0],"vaccinology":[1],"(RV)":[2],"is":[3,29],"a":[4,12,33],"computer-aided":[5],"approach":[6],"for":[7,164],"vaccine":[8,23],"development":[9],"that":[10],"identifies":[11],"subset":[13],"of":[14,35,171],"pathogen":[15],"proteins":[16],"as":[17,130],"protective":[18],"antigens":[19,163],"(PAgs)":[20],"or":[21],"potential":[22],"candidates.":[24],"Machine":[25],"learning":[26],"(ML)-based":[27],"RV":[28],"promising,":[30],"but":[31],"requires":[32],"dataset":[34,153],"PAgs":[36,55,58,68,88,95,142],"(positives)":[37],"and":[38,73,105,112,118,145],"non-protective":[39,74,127,147],"protein":[40,75,128,138,148],"sequences":[41,76,129,149],"(negatives).":[42],"This":[43,152],"study":[44],"aimed":[45],"to":[46,52,66,116,123,157,161],"create":[47],"an":[48],"ML":[49,159],"dataset,":[50],"VPAgs-Dataset4ML,":[51],"predict":[53,162],"viral":[54,87,137,166],"based":[56],"on":[57,94,109,126],"obtained":[59],"from":[60,69,77,89,132],"Protegen.":[61],"We":[62],"performed":[63],"seven":[64,83],"steps":[65,84,107],"identify":[67],"the":[70,97,113,124,169],"Protegen":[71],"website":[72],"Universal":[78],"Protein":[79],"Resource":[80],"(UniProt).":[81],"The":[82],"included":[85],"downloading":[86],"Protegen,":[90],"performing":[91],"quality":[92,120],"checks":[93,121],"using":[96],"standard":[98],"BLASTp":[99],"identity":[100],"check":[101],"\u226430%":[102],"via":[103],"MMseqs2,":[104],"computational":[106],"running":[108],"Google":[110],"Colaboratory":[111],"Ubuntu":[114],"terminal":[115],"retrieve":[117],"perform":[119],"(similar":[122],"PAgs)":[125],"negatives":[131],"UniProt.":[133],"VPAgs-Dataset4ML":[134],"contains":[135],"2145":[136],"sequences,":[139],"with":[140,168],"210":[141],"in":[143,150],"positive.fasta":[144],"1935":[146],"negative.fasta.":[151],"can":[154],"be":[155],"used":[156],"train":[158],"models":[160],"various":[165],"pathogens":[167],"aim":[170],"developing":[172],"effective":[173],"vaccines.":[174]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-01-25T23:04:38.658462","created_date":"2025-10-10T00:00:00"}
