PMID- 24705205
OWN - NLM
STAT- MEDLINE
DCOM- 20140826
LR  - 20211021
IS  - 1758-0463 (Electronic)
IS  - 1758-0463 (Linking)
VI  - 2014
DP  - 2014
TI  - HPVdb: a data mining system for knowledge discovery in human papillomavirus with 
      applications in T cell immunology and vaccinology.
PG  - bau031
LID - 10.1093/database/bau031 [doi]
LID - bau031
AB  - 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. Database URL: 
      http://cvc.dfci.harvard.edu/hpv/.
FAU - Zhang, Guang Lan
AU  - Zhang GL
AD  - Cancer Vaccine Center, Dana-Farber Cancer Institute, 77 Ave Louis Pasteur, 
      Boston, MA 02115, USA, Department of Computer Science, Metropolitan College, 
      Boston University, 808 Commonwealth Ave, Boston, MA 02215, USA, Department of 
      Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA and 
      German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, 
      Germany.
FAU - Riemer, Angelika B
AU  - Riemer AB
FAU - Keskin, Derin B
AU  - Keskin DB
FAU - Chitkushev, Lou
AU  - Chitkushev L
FAU - Reinherz, Ellis L
AU  - Reinherz EL
FAU - Brusic, Vladimir
AU  - Brusic V
LA  - eng
GR  - U01 AI090043/AI/NIAID NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20140404
PL  - England
TA  - Database (Oxford)
JT  - Database : the journal of biological databases and curation
JID - 101517697
RN  - 0 (Antigens, Viral)
RN  - 0 (Epitopes, T-Lymphocyte)
RN  - 0 (Papillomavirus Vaccines)
SB  - IM
MH  - Amino Acid Sequence
MH  - Antigens, Viral/immunology
MH  - Conserved Sequence
MH  - Data Mining/*methods
MH  - *Databases, Genetic
MH  - Databases, Protein
MH  - Epitopes, T-Lymphocyte/chemistry/immunology
MH  - Genetic Variation
MH  - Humans
MH  - Knowledge Bases
MH  - Molecular Sequence Data
MH  - Papillomaviridae/classification/*immunology
MH  - Papillomavirus Vaccines/*immunology
MH  - *Software
MH  - T-Lymphocytes/*immunology
MH  - *Vaccination
PMC - PMC3975992
EDAT- 2014/04/08 06:00
MHDA- 2014/08/27 06:00
PMCR- 2014/04/04
CRDT- 2014/04/08 06:00
PHST- 2014/04/08 06:00 [entrez]
PHST- 2014/04/08 06:00 [pubmed]
PHST- 2014/08/27 06:00 [medline]
PHST- 2014/04/04 00:00 [pmc-release]
AID - bau031 [pii]
AID - 10.1093/database/bau031 [doi]
PST - epublish
SO  - Database (Oxford). 2014 Apr 4;2014:bau031. doi: 10.1093/database/bau031. Print 
      2014.