{"id":"https://openalex.org/W4283783202","doi":"https://doi.org/10.1093/database/baac042","title":"PHILM2Web: A high-throughput database of macromolecular host\u2013pathogen interactions on the Web","display_name":"PHILM2Web: A high-throughput database of macromolecular host\u2013pathogen interactions on the Web","publication_year":2022,"publication_date":"2022-01-01","ids":{"openalex":"https://openalex.org/W4283783202","doi":"https://doi.org/10.1093/database/baac042","pmid":"https://pubmed.ncbi.nlm.nih.gov/35776535"},"language":"en","primary_location":{"id":"doi:10.1093/database/baac042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baac042","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baac042/44372801/baac042.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":"article","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/baac042/44372801/baac042.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000029613","display_name":"Tuan-Dung Le","orcid":null},"institutions":[{"id":"https://openalex.org/I115475287","display_name":"Oklahoma State University","ror":"https://ror.org/01g9vbr38","country_code":"US","type":"education","lineage":["https://openalex.org/I115475287"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tuan-Dung Le","raw_affiliation_strings":["Department of Computer Science, Oklahoma State University , Stillwater, OK, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Oklahoma State University , Stillwater, OK, USA","institution_ids":["https://openalex.org/I115475287"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025755515","display_name":"Phuong D. Nguyen","orcid":"https://orcid.org/0000-0002-2116-902X"},"institutions":[{"id":"https://openalex.org/I115475287","display_name":"Oklahoma State University","ror":"https://ror.org/01g9vbr38","country_code":"US","type":"education","lineage":["https://openalex.org/I115475287"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Phuong D Nguyen","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Oklahoma State University , Stillwater, OK, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Oklahoma State University , Stillwater, OK, USA","institution_ids":["https://openalex.org/I115475287"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022192689","display_name":"Dmitry Korkin","orcid":"https://orcid.org/0000-0002-3875-9085"},"institutions":[{"id":"https://openalex.org/I107077323","display_name":"Worcester Polytechnic Institute","ror":"https://ror.org/05ejpqr48","country_code":"US","type":"education","lineage":["https://openalex.org/I107077323"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dmitry Korkin","raw_affiliation_strings":["Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute , Worcester, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute , Worcester, MA, USA","institution_ids":["https://openalex.org/I107077323"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010978700","display_name":"Thanh Thieu","orcid":"https://orcid.org/0000-0002-4926-9292"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Thanh Thieu","raw_affiliation_strings":["Machine Learning Department, Moffitt Cancer Center and Research Institute , Tampa, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-4926-9292","affiliations":[{"raw_affiliation_string":"Machine Learning Department, Moffitt Cancer Center and Research Institute , Tampa, FL, USA","institution_ids":["https://openalex.org/I3019308854"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5010978700"],"corresponding_institution_ids":["https://openalex.org/I3019308854"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.2352,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.46713837,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"2022","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":0.9994000196456909,"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":0.9994000196456909,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9884999990463257,"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":0.9858999848365784,"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/host","display_name":"Host (biology)","score":0.7538080215454102},{"id":"https://openalex.org/keywords/pathogen","display_name":"Pathogen","score":0.5929479002952576},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5618823766708374},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49112197756767273},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37717387080192566},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.34237140417099},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.09959200024604797},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09479376673698425}],"concepts":[{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.7538080215454102},{"id":"https://openalex.org/C2776460866","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogen","level":2,"score":0.5929479002952576},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5618823766708374},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49112197756767273},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37717387080192566},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.34237140417099},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.09959200024604797},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09479376673698425}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/baac042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baac042","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baac042/44372801/baac042.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:35776535","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35776535","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:pubmedcentral.nih.gov:9248916","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9248916","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baac042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baac042","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baac042/44372801/baac042.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":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.7799999713897705}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4283783202.pdf","grobid_xml":"https://content.openalex.org/works/W4283783202.grobid-xml"},"referenced_works_count":91,"referenced_works":["https://openalex.org/W138570049","https://openalex.org/W138910040","https://openalex.org/W165790511","https://openalex.org/W1986657538","https://openalex.org/W1986708244","https://openalex.org/W1995683190","https://openalex.org/W1996076856","https://openalex.org/W2006952608","https://openalex.org/W2016602975","https://openalex.org/W2022484638","https://openalex.org/W2022675863","https://openalex.org/W2030377680","https://openalex.org/W2032243072","https://openalex.org/W2033727482","https://openalex.org/W2035252561","https://openalex.org/W2039748234","https://openalex.org/W2040223842","https://openalex.org/W2043764521","https://openalex.org/W2052685738","https://openalex.org/W2055509168","https://openalex.org/W2059655508","https://openalex.org/W2071879021","https://openalex.org/W2077398039","https://openalex.org/W2092123736","https://openalex.org/W2095867585","https://openalex.org/W2100751507","https://openalex.org/W2101727078","https://openalex.org/W2105476170","https://openalex.org/W2107005506","https://openalex.org/W2109576136","https://openalex.org/W2112543617","https://openalex.org/W2113849888","https://openalex.org/W2115048111","https://openalex.org/W2118754867","https://openalex.org/W2124249167","https://openalex.org/W2132582966","https://openalex.org/W2133177319","https://openalex.org/W2140364813","https://openalex.org/W2142678031","https://openalex.org/W2144014661","https://openalex.org/W2147818576","https://openalex.org/W2147874847","https://openalex.org/W2147880316","https://openalex.org/W2159126118","https://openalex.org/W2160103276","https://openalex.org/W2163038531","https://openalex.org/W2163485494","https://openalex.org/W2165253681","https://openalex.org/W2166488856","https://openalex.org/W2168637722","https://openalex.org/W2193324235","https://openalex.org/W2283435117","https://openalex.org/W2465613542","https://openalex.org/W2556858158","https://openalex.org/W2605988327","https://openalex.org/W2740048509","https://openalex.org/W2807219321","https://openalex.org/W2884165257","https://openalex.org/W2893358487","https://openalex.org/W2896457183","https://openalex.org/W2900569176","https://openalex.org/W2904726360","https://openalex.org/W2914039052","https://openalex.org/W2914171828","https://openalex.org/W2916355958","https://openalex.org/W2921356981","https://openalex.org/W2951615992","https://openalex.org/W2951679282","https://openalex.org/W2963706121","https://openalex.org/W2964348125","https://openalex.org/W2991377209","https://openalex.org/W2997563016","https://openalex.org/W3022046398","https://openalex.org/W3070389369","https://openalex.org/W3136918052","https://openalex.org/W4235505822","https://openalex.org/W4255024766","https://openalex.org/W6605646921","https://openalex.org/W6606806286","https://openalex.org/W6669829439","https://openalex.org/W6679673443","https://openalex.org/W6683496858","https://openalex.org/W6739183500","https://openalex.org/W6742309098","https://openalex.org/W6754350045","https://openalex.org/W6755201987","https://openalex.org/W6755207826","https://openalex.org/W6760638759","https://openalex.org/W6776225533","https://openalex.org/W6781960150","https://openalex.org/W6783763832"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2091398531","https://openalex.org/W2343234619","https://openalex.org/W3173815060","https://openalex.org/W4286497165"],"abstract_inverted_index":{"During":[0],"infection,":[1],"the":[2,6,10,24,50,59,74,89,108,118,132,150,193,211,215,241,256],"pathogen's":[3],"entry":[4],"into":[5],"host":[7,11,25,159,185,230],"organism,":[8],"breaching":[9],"immune":[12],"defense,":[13],"spread":[14],"and":[15,26,42,45,77,160,186,231],"multiplication":[16],"are":[17],"frequently":[18],"mediated":[19],"by":[20,128,142,210],"multiple":[21],"interactions":[22,33,56,72,140,169],"between":[23,157,228],"pathogen":[27,162,188,233],"proteins.":[28],"Systematic":[29],"studying":[30],"of":[31,114,139,181],"host-pathogen":[32],"(HPIs)":[34],"is":[35,46,92,245],"a":[36,98,248],"challenging":[37],"task":[38],"for":[39,102,261],"both":[40],"experimental":[41,79],"computational":[43],"approaches":[44],"critically":[47],"dependent":[48],"on":[49,85,131],"previously":[51],"obtained":[52,87,116,171,209],"knowledge":[53],"about":[54],"these":[55],"found":[57],"in":[58,225,259],"biomedical":[60,90],"literature.":[61],"While":[62],"several":[63],"HPI":[64,70,104,122,146,243],"databases":[65,76],"exist":[66],"that":[67,106],"manually":[68],"filter":[69],"protein-protein":[71],"from":[73,88,117,164,172,235],"generic":[75,155],"curated":[78],"interactomic":[80],"studies,":[81],"no":[82],"comprehensive":[83,110],"database":[84,138,151,258],"HPIs":[86,115,156,227],"literature":[91],"currently":[93],"available.":[94],"Here,":[95],"we":[96,199],"introduce":[97],"high-throughput":[99],"literature-mining":[100,147],"platform":[101],"extracting":[103],"data":[105,123],"includes":[107],"most":[109],"to":[111,192,203,240],"date":[112],"collection":[113],"PubMed":[119,176,207],"abstracts.":[120,167,237],"Our":[121],"portal,":[124],"PHILM2Web":[125,250],"(Pathogen-Host":[126],"Interactions":[127],"Literature":[129],"Mining":[130],"Web),":[133],"integrates":[134],"an":[135],"automatically":[136],"generated":[137],"extracted":[141],"PHILM,":[143],"our":[144],"high-precision":[145],"algorithm.":[148],"Currently,":[149],"contains":[152],"23":[153],"581":[154],"157":[158],"403":[161],"organisms":[163,234],"11":[165],"609":[166],"The":[168,238],"were":[170],"processing":[173,222],"608":[174],"972":[175],"abstracts,":[177],"each":[178],"containing":[179],"mentions":[180],"at":[182],"least":[183],"one":[184,187],"organisms.":[189],"In":[190],"response":[191],"coronavirus":[194],"disease":[195],"2019":[196],"(COVID-19)":[197],"pandemic,":[198],"also":[200,254],"utilized":[201],"PHILM":[202],"process":[204],"25":[205],"796":[206],"abstracts":[208],"same":[212],"query":[213],"as":[214],"COVID-19":[216,221],"Open":[217],"Research":[218],"Dataset.":[219],"This":[220],"batch":[223],"resulted":[224],"257":[226],"19":[229],"31":[232],"167":[236],"access":[239],"entire":[242,257],"dataset":[244],"available":[246],"via":[247],"searchable":[249],"interface;":[251],"scientists":[252],"can":[253],"download":[255],"bulk":[260],"offline":[262],"processing.":[263],"Database":[264],"URL:":[265],"http://philm2web.live.":[266]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-09T07:27:16.801131","created_date":"2025-10-10T00:00:00"}
