{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T04:32:07Z","timestamp":1783139527493,"version":"3.54.6"},"reference-count":84,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2022,7,1]],"date-time":"2022-07-01T00:00:00Z","timestamp":1656633600000},"content-version":"vor","delay-in-days":181,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>During infection, the pathogen\u2019s entry into the host organism, breaching the host immune defense, spread and multiplication are frequently mediated by multiple interactions between the host and pathogen proteins. Systematic studying of host\u2013pathogen interactions (HPIs) is a challenging task for both experimental and computational approaches and is critically dependent on the previously obtained knowledge about these interactions found in the biomedical literature. While several HPI databases exist that manually filter HPI protein\u2013protein interactions from the generic databases and curated experimental interactomic studies, no comprehensive database on HPIs obtained from the biomedical literature is currently available. Here, we introduce a high-throughput literature-mining platform for extracting HPI data that includes the most comprehensive to date collection of HPIs obtained from the PubMed abstracts. Our HPI data portal, PHILM2Web (Pathogen\u2013Host Interactions by Literature Mining on the Web), integrates an automatically generated database of interactions extracted by PHILM, our high-precision HPI literature-mining algorithm. Currently, the database contains 23\u2009581 generic HPIs between 157 host and 403 pathogen organisms from 11\u2009609 abstracts. The interactions were obtained from processing 608\u2009972 PubMed abstracts, each containing mentions of at least one host and one pathogen organisms. In response to the coronavirus disease 2019 (COVID-19) pandemic, we also utilized PHILM to process 25\u2009796 PubMed abstracts obtained by the same query as the COVID-19 Open Research Dataset. This COVID-19 processing batch resulted in 257 HPIs between 19 host and 31 pathogen organisms from 167 abstracts. The access to the entire HPI dataset is available via a searchable PHILM2Web interface; scientists can also download the entire database in bulk for offline processing.<\/jats:p>\n               <jats:p>Database URL: http:\/\/philm2web.live<\/jats:p>","DOI":"10.1093\/database\/baac042","type":"journal-article","created":{"date-parts":[[2022,7,1]],"date-time":"2022-07-01T14:58:56Z","timestamp":1656687536000},"source":"Crossref","is-referenced-by-count":4,"title":["PHILM2Web: A high-throughput database of macromolecular host\u2013pathogen interactions on the Web"],"prefix":"10.1093","volume":"2022","author":[{"given":"Tuan-Dung","family":"Le","sequence":"first","affiliation":[{"name":"Department of Computer Science, Oklahoma State University , Stillwater, OK, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phuong D","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Oklahoma State University , Stillwater, OK, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitry","family":"Korkin","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute , Worcester, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4926-9292","authenticated-orcid":false,"given":"Thanh","family":"Thieu","sequence":"additional","affiliation":[{"name":"Machine Learning Department, Moffitt Cancer Center and Research Institute , Tampa, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,6,30]]},"reference":[{"key":"2022070114584823300_R1","first-page":"pp. 224","article-title":"Identifying protein-protein interaction using tree lstm and structured attention","author":"Ahmed","year":"2019"},{"key":"2022070114584823300_R2","doi-asserted-by":"publisher","first-page":"D566","DOI":"10.1093\/nar\/gku1126","article-title":"HIV-1, human interaction database: current status and new features","volume":"43","author":"Ako-Adjei","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2022070114584823300_R3","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baw103","article-title":"HPIDB 2.0: a curated database for host\u2013pathogen interactions","volume":"2016","author":"Ammari","year":"2016","journal-title":"Database"},{"key":"2022070114584823300_R4","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1038\/280361a0","article-title":"Population biology of infectious diseases: Part I","volume":"280","author":"Anderson","year":"1979","journal-title":"Nature"},{"key":"2022070114584823300_R5","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-019-3317-0","article-title":"Identification of infectious disease-associated host genes using machine learning techniques","volume":"736","author":"Barman","year":"2019","journal-title":"BMC Bioinform."},{"key":"2022070114584823300_R6","first-page":"D506","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"Bateman","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022070114584823300_R7","doi-asserted-by":"publisher","first-page":"D671","DOI":"10.1093\/nar\/gkt925","article-title":"HoPaCI-DB: host-pseudomonas and coxiella interaction database","volume":"42","author":"Bleves","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2022070114584823300_R8","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2017.00128","article-title":"Computational Analysis of Host\u2013Pathogen Protein Interactions between Humans and Different Strains of Enterohemorrhagic Escherichia coli","volume":"7","author":"Bose","year":"2017","journal-title":"Front. 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