PMID- 19811689
OWN - NLM
STAT- MEDLINE
DCOM- 20100212
LR  - 20220318
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 10 Suppl 11
IP  - Suppl 11
DP  - 2009 Oct 8
TI  - HPD: an online integrated human pathway database enabling systems biology 
      studies.
PG  - S5
LID - 10.1186/1471-2105-10-S11-S5 [doi]
AB  - BACKGROUND: Pathway-oriented experimental and computational studies have led to a 
      significant accumulation of biological knowledge concerning three major types of 
      biological pathway events: molecular signaling events, gene regulation events, 
      and metabolic reaction events. A pathway consists of a series of molecular 
      pathway events that link molecular entities such as proteins, genes, and 
      metabolites. There are approximately 300 biological pathway resources as of April 
      2009 according to the Pathguide database; however, these pathway databases 
      generally have poor coverage or poor quality, and are difficult to integrate, due 
      to syntactic-level and semantic-level data incompatibilities. RESULTS: We 
      developed the Human Pathway Database (HPD) by integrating heterogeneous human 
      pathway data that are either curated at the NCI Pathway Interaction Database 
      (PID), Reactome, BioCarta, KEGG or indexed from the Protein Lounge Web sites. 
      Integration of pathway data at syntactic, semantic, and schematic levels was 
      based on a unified pathway data model and data warehousing-based integration 
      techniques. HPD provides a comprehensive online view that connects human 
      proteins, genes, RNA transcripts, enzymes, signaling events, metabolic reaction 
      events, and gene regulatory events. At the time of this writing HPD includes 999 
      human pathways and more than 59,341 human molecular entities. The HPD software 
      provides both a user-friendly Web interface for online use and a robust 
      relational database backend for advanced pathway querying. This pathway tool 
      enables users to 1) search for human pathways from different resources by simply 
      entering genes/proteins involved in pathways or words appearing in pathway names, 
      2) analyze pathway-protein association, 3) study pathway-pathway similarity, and 
      4) build integrated pathway networks. We demonstrated the usage and 
      characteristics of the new HPD through three breast cancer case studies. 
      CONCLUSION: HPD http://bio.informatics.iupui.edu/HPD is a new resource for 
      searching, managing, and studying human biological pathways. Users of HPD can 
      search against large collections of human biological pathways, compare related 
      pathways and their molecular entity compositions, and build high-quality, 
      expanded-scope disease pathway models. The current HPD software can help users 
      address a wide range of pathway-related questions in human disease biology 
      studies.
FAU - Chowbina, Sudhir R
AU  - Chowbina SR
AD  - Indiana University School of Informatics, Indianapolis, IN 46202, USA.
FAU - Wu, Xiaogang
AU  - Wu X
FAU - Zhang, Fan
AU  - Zhang F
FAU - Li, Peter M
AU  - Li PM
FAU - Pandey, Ragini
AU  - Pandey R
FAU - Kasamsetty, Harini N
AU  - Kasamsetty HN
FAU - Chen, Jake Y
AU  - Chen JY
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20091008
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
RN  - 0 (Proteins)
SB  - IM
MH  - Computational Biology/methods
MH  - *Databases, Factual
MH  - Databases, Protein
MH  - Humans
MH  - Internet
MH  - Proteins/chemistry
MH  - *Software
MH  - Systems Biology/*methods
PMC - PMC3226194
EDAT- 2009/10/14 06:00
MHDA- 2010/02/13 06:00
PMCR- 2009/10/08
CRDT- 2009/10/09 06:00
PHST- 2009/10/09 06:00 [entrez]
PHST- 2009/10/14 06:00 [pubmed]
PHST- 2010/02/13 06:00 [medline]
PHST- 2009/10/08 00:00 [pmc-release]
AID - 1471-2105-10-S11-S5 [pii]
AID - 10.1186/1471-2105-10-S11-S5 [doi]
PST - epublish
SO  - BMC Bioinformatics. 2009 Oct 8;10 Suppl 11(Suppl 11):S5. doi: 
      10.1186/1471-2105-10-S11-S5.