HPVdb: a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology
Identifieur interne : 000092 ( Main/Exploration ); précédent : 000091; suivant : 000093HPVdb: a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology
Auteurs : Guang Lan Zhang [États-Unis] ; Angelika B. Riemer [Allemagne] ; Derin B. Keskin [États-Unis] ; Lou Chitkushev [États-Unis] ; Ellis L. Reinherz [États-Unis] ; Vladimir Brusic [États-Unis]Source :
- Database: The Journal of Biological Databases and Curation [ 1758-0463 ] ; 2014.
Abstract
High-risk human papillomaviruses (HPVs) are the causes of many cancers, including cervical, anal, vulvar, vaginal, penile and oropharyngeal. To facilitate diagnosis, prognosis and characterization of these cancers, it is necessary to make full use of the immunological data on HPV available through publications, technical reports and databases. These data vary in granularity, quality and complexity. The extraction of knowledge from the vast amount of immunological data using data mining techniques remains a challenging task. To support integration of data and knowledge in virology and vaccinology, we developed a framework called KB-builder to streamline the development and deployment of web-accessible immunological knowledge systems. The framework consists of seven major functional modules, each facilitating a specific aspect of the knowledgebase construction process. Using KB-builder, we constructed the Human Papillomavirus T cell Antigen Database (HPVdb). It contains 2781 curated antigen entries of antigenic proteins derived from 18 genotypes of high-risk HPV and 18 genotypes of low-risk HPV. The HPVdb also catalogs 191 verified T cell epitopes and 45 verified human leukocyte antigen (HLA) ligands. Primary amino acid sequences of HPV antigens were collected and annotated from the UniProtKB. T cell epitopes and HLA ligands were collected from data mining of scientific literature and databases. The data were subject to extensive quality control (redundancy elimination, error detection and vocabulary consolidation). A set of computational tools for an in-depth analysis, such as sequence comparison using BLAST search, multiple alignments of antigens, classification of HPV types based on cancer risk, T cell epitope/HLA ligand visualization, T cell epitope/HLA ligand conservation analysis and sequence variability analysis, has been integrated within the HPVdb. Predicted Class I and Class II HLA binding peptides for 15 common HLA alleles are included in this database as putative targets. HPVdb is a knowledge-based system that integrates curated data and information with tailored analysis tools to facilitate data mining for HPV vaccinology and immunology. To our best knowledge, HPVdb is a unique data source providing a comprehensive list of HPV antigens and peptides.
Url:
DOI: 10.1093/database/bau031
PubMed: 24705205
PubMed Central: 3975992
Affiliations:
Links toward previous steps (curation, corpus...)
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- to stream Main, to step Curation: 000092
Le document en format XML
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type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Riemer, Angelika B" sort="Riemer, Angelika B" uniqKey="Riemer A" first="Angelika B." last="Riemer">Angelika B. 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Keskin</name><affiliation wicri:level="2"><nlm:aff id="bau031-AFF1">Cancer Vaccine Center, Dana-Farber Cancer Institute, 77 Ave Louis Pasteur, Boston, MA 02115, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cancer Vaccine Center, Dana-Farber Cancer Institute, 77 Ave Louis Pasteur, Boston, MA 02115</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="bau031-AFF1">Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Chitkushev, Lou" sort="Chitkushev, Lou" uniqKey="Chitkushev L" first="Lou" last="Chitkushev">Lou Chitkushev</name><affiliation wicri:level="2"><nlm:aff id="bau031-AFF1">Department of Computer Science, Metropolitan College, Boston University, 808 Commonwealth Ave, Boston, MA 02215, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Metropolitan College, Boston University, 808 Commonwealth Ave, Boston, MA 02215</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Reinherz, Ellis L" sort="Reinherz, Ellis L" uniqKey="Reinherz E" first="Ellis L." last="Reinherz">Ellis L. Reinherz</name><affiliation wicri:level="2"><nlm:aff id="bau031-AFF1">Cancer Vaccine Center, Dana-Farber Cancer Institute, 77 Ave Louis Pasteur, Boston, MA 02115, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cancer Vaccine Center, Dana-Farber Cancer Institute, 77 Ave Louis Pasteur, Boston, MA 02115</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="bau031-AFF1">Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Brusic, Vladimir" sort="Brusic, Vladimir" uniqKey="Brusic V" first="Vladimir" last="Brusic">Vladimir Brusic</name><affiliation wicri:level="2"><nlm:aff id="bau031-AFF1">Cancer Vaccine Center, Dana-Farber Cancer Institute, 77 Ave Louis Pasteur, Boston, MA 02115, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cancer Vaccine Center, Dana-Farber Cancer Institute, 77 Ave Louis Pasteur, Boston, MA 02115</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="bau031-AFF1">Department of Computer Science, Metropolitan College, Boston University, 808 Commonwealth Ave, Boston, MA 02215, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Metropolitan College, Boston University, 808 Commonwealth Ave, Boston, MA 02215</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="bau031-AFF1">Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author></analytic><series><title level="j">Database: The Journal of Biological Databases and Curation</title><idno type="eISSN">1758-0463</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>High-risk human papillomaviruses (HPVs) are the causes of many cancers, including cervical, anal, vulvar, vaginal, penile and oropharyngeal. To facilitate diagnosis, prognosis and characterization of these cancers, it is necessary to make full use of the immunological data on HPV available through publications, technical reports and databases. These data vary in granularity, quality and complexity. The extraction of knowledge from the vast amount of immunological data using data mining techniques remains a challenging task. To support integration of data and knowledge in virology and vaccinology, we developed a framework called KB-builder to streamline the development and deployment of web-accessible immunological knowledge systems. The framework consists of seven major functional modules, each facilitating a specific aspect of the knowledgebase construction process. Using KB-builder, we constructed the Human Papillomavirus T cell Antigen Database (HPVdb). It contains 2781 curated antigen entries of antigenic proteins derived from 18 genotypes of high-risk HPV and 18 genotypes of low-risk HPV. The HPVdb also catalogs 191 verified T cell epitopes and 45 verified human leukocyte antigen (HLA) ligands. Primary amino acid sequences of HPV antigens were collected and annotated from the UniProtKB. T cell epitopes and HLA ligands were collected from data mining of scientific literature and databases. The data were subject to extensive quality control (redundancy elimination, error detection and vocabulary consolidation). A set of computational tools for an in-depth analysis, such as sequence comparison using BLAST search, multiple alignments of antigens, classification of HPV types based on cancer risk, T cell epitope/HLA ligand visualization, T cell epitope/HLA ligand conservation analysis and sequence variability analysis, has been integrated within the HPVdb. Predicted Class I and Class II HLA binding peptides for 15 common HLA alleles are included in this database as putative targets. HPVdb is a knowledge-based system that integrates curated data and information with tailored analysis tools to facilitate data mining for HPV vaccinology and immunology. To our best knowledge, HPVdb is a unique data source providing a comprehensive list of HPV antigens and peptides.</p><p><bold>Database URL:</bold><ext-link ext-link-type="uri" xlink:href="http://cvc.dfci.harvard.edu/hpv/">http://cvc.dfci.harvard.edu/hpv/</ext-link></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zur Hausen, H" uniqKey="Zur Hausen H">H. zur Hausen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ganguly, N" uniqKey="Ganguly N">N. Ganguly</name></author><author><name sortKey="Parihar, S P" uniqKey="Parihar S">S.P. 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Daf</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>États-Unis</li></country><region><li>Bade-Wurtemberg</li><li>District de Karlsruhe</li><li>Massachusetts</li></region><settlement><li>Heidelberg</li></settlement></list><tree><country name="États-Unis"><region name="Massachusetts"><name sortKey="Zhang, Guang Lan" sort="Zhang, Guang Lan" uniqKey="Zhang G" first="Guang Lan" last="Zhang">Guang Lan Zhang</name></region><name sortKey="Brusic, Vladimir" sort="Brusic, Vladimir" uniqKey="Brusic V" first="Vladimir" last="Brusic">Vladimir Brusic</name><name sortKey="Brusic, Vladimir" sort="Brusic, Vladimir" uniqKey="Brusic V" first="Vladimir" last="Brusic">Vladimir Brusic</name><name sortKey="Brusic, Vladimir" sort="Brusic, Vladimir" uniqKey="Brusic V" first="Vladimir" last="Brusic">Vladimir Brusic</name><name sortKey="Chitkushev, Lou" sort="Chitkushev, Lou" uniqKey="Chitkushev L" first="Lou" last="Chitkushev">Lou Chitkushev</name><name sortKey="Keskin, Derin B" sort="Keskin, Derin B" uniqKey="Keskin D" first="Derin B." last="Keskin">Derin B. Keskin</name><name sortKey="Keskin, Derin B" sort="Keskin, Derin B" uniqKey="Keskin D" first="Derin B." last="Keskin">Derin B. Keskin</name><name sortKey="Reinherz, Ellis L" sort="Reinherz, Ellis L" uniqKey="Reinherz E" first="Ellis L." last="Reinherz">Ellis L. Reinherz</name><name sortKey="Reinherz, Ellis L" sort="Reinherz, Ellis L" uniqKey="Reinherz E" first="Ellis L." last="Reinherz">Ellis L. Reinherz</name><name sortKey="Zhang, Guang Lan" sort="Zhang, Guang Lan" uniqKey="Zhang G" first="Guang Lan" last="Zhang">Guang Lan Zhang</name><name sortKey="Zhang, Guang Lan" sort="Zhang, Guang Lan" uniqKey="Zhang G" first="Guang Lan" last="Zhang">Guang Lan Zhang</name></country><country name="Allemagne"><region name="Bade-Wurtemberg"><name sortKey="Riemer, Angelika B" sort="Riemer, Angelika B" uniqKey="Riemer A" first="Angelika B." last="Riemer">Angelika B. Riemer</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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