PMID- 21063943
OWN - NLM
STAT- MEDLINE
DCOM- 20110215
LR  - 20101110
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 696
DP  - 2011
TI  - PRIDE and "Database on Demand" as valuable tools for computational proteomics.
PG  - 93-105
LID - 10.1007/978-1-60761-987-1_6 [doi]
AB  - The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride ) 
      provides users with the ability to explore and compare mass spectrometry-based 
      proteomics experiments that reveal details of the protein expression found in a 
      broad range of taxonomic groups, tissues, and disease states. A PRIDE experiment 
      typically includes identifications of proteins, peptides, and protein 
      modifications. Additionally, many of the submitted experiments also include the 
      mass spectra that provide the evidence for these identifications. Finally, one of 
      the strongest advantages of PRIDE in comparison with other proteomics 
      repositories is the amount of metadata it contains, a key point to put the 
      above-mentioned data in biological and/or technical context. Several informatics 
      tools have been developed in support of the PRIDE database. The most recent one 
      is called "Database on Demand" (DoD), which allows custom sequence databases to 
      be built in order to optimize the results from search engines. We describe the 
      use of DoD in this chapter. Additionally, in order to show the potential of PRIDE 
      as a source for data mining, we also explore complex queries using federated 
      BioMart queries to integrate PRIDE data with other resources, such as Ensembl, 
      Reactome, or UniProt.
FAU - Vizcaino, Juan Antonio
AU  - Vizcaino JA
AD  - European Molecular Biology Laboratory, European Bioinformatics Institute, 
      Cambridge, UK.
FAU - Reisinger, Florian
AU  - Reisinger F
FAU - Cote, Richard
AU  - Cote R
FAU - Martens, Lennart
AU  - Martens L
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
SB  - IM
MH  - *Databases, Protein
MH  - Internet
MH  - Proteomics/*methods
MH  - Software
EDAT- 2010/11/11 06:00
MHDA- 2011/02/16 06:00
CRDT- 2010/11/11 06:00
PHST- 2010/11/11 06:00 [entrez]
PHST- 2010/11/11 06:00 [pubmed]
PHST- 2011/02/16 06:00 [medline]
AID - 10.1007/978-1-60761-987-1_6 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2011;696:93-105. doi: 10.1007/978-1-60761-987-1_6.