The DOI matches its Crossref record; 42 of the 42 references it cites were found in a registry or an index.
The Proteomics Identifications database: 2010 update
Open accessAbstract
The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass spectrometry-derived proteomics data. For the last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5 million peptides and over 50 million spectra by September 2009. We here describe several new and improved features in PRIDE, including the revised submission process, which now includes direct submission of fragment ion annotations. Correspondingly, it is now possible to visualize spectrum fragmentation annotations on tandem mass spectra, a key feature for compliance with journal data submission requirements. We also describe recent developments in the PRIDE BioMart interface, which now allows integrative queries that can join PRIDE data to a growing number of biological resources such as Reactome, Ensembl, InterPro and UniProt. This ability to perform extremely powerful across-domain queries will certainly be a cornerstone of future bioinformatics analyses. Finally, we highlight the importance of data sharing in the proteomics field, and the corresponding integration of PRIDE with other databases in the ProteomExchange consortium.
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Cites
The Universal Protein Resource (UniProt)
Bairoch, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki070 · Cited by 3,774
InterPro: the integrative protein signature database
Hunter, S., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn785 · Cited by 2,107
Current Protocols in Bioinformatics
(2002) · John Wiley & Sons, Inc. eBooks · doi:10.1002/0471250953 · Cited by 1,207
BioMart – biological queries made easy
Smedley, D., Haider, S., Ballester, B., Holland, R., London, D., Thorisson, G., & Kasprzyk, A. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-22 · Cited by 1,111
The proteome of Saccharomyces cerevisiae mitochondria
Sickmann, A., Reinders, J., Wagner, Y., Joppich, C., Zahedi, R., Meyer, H. E., Schönfisch, B., Perschil, I., Chacinska, A., Guiard, B., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2135385100 · Cited by 895
Reactome knowledgebase of human biological pathways and processes
Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn863 · Cited by 873
Self-citationOpen Source System for Analyzing, Validating, and Storing Protein Identification Data
Craig, R., Cortens, J. P., & Beavis, R. C. (2004) · Journal of Proteome Research · doi:10.1021/pr049882h · Cited by 694
The International Protein Index: An integrated database for proteomics experiments
Kersey, P. J., Duarte, J., Williams, A., Karavidopoulou, Y., Birney, E., & Apweiler, R. (2004) · PROTEOMICS · doi:10.1002/pmic.200300721 · Cited by 693
Hubbard, T. J. P., Aken, B. L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn828 · Cited by 670
PRIDE: The proteomics identifications database
Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J., & Apweiler, R. (2005) · PROTEOMICS · doi:10.1002/pmic.200401303 · Cited by 594
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The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1262 · Cited by 1,918
Self-citationPaxdb, a database of protein abundance averages across all three domains of life
Wang, M., Weiss, M., Simonovic, M., Haertinger, G., Schrimpf, S. P., Hengartner, M. O., & von Mering, C. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.014704 · Cited by 466
“The necessity to systematically annotate the meta-information describing each sample is a unique challenge for the database repositories, although the infrastructure for this has much improved recently (notably by introducing standards and controlled vocabularies at the Pro-teomics Standards Initiative (18), and at PR…”
BackgroundMethodInfluentialToward interoperable bioscience data
Sansone, S.-A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L., et al. (2012) · Nature Genetics · doi:10.1038/ng.1054 · Cited by 475
Self-citationA High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas
Farrah, T., Deutsch, E. W., Omenn, G. S., Campbell, D. S., Sun, Z., Bletz, J. A., Mallick, P., Katz, J. E., Malmström, J., Ossola, R., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.006353 · Cited by 451
An Expanded Oct4 Interaction Network: Implications for Stem Cell Biology, Development, and Disease
Pardo, M., Lang, B., Yu, L., Prosser, H., Bradley, A., Babu, M. M., & Choudhary, J. (2010) · Cell Stem Cell · doi:10.1016/j.stem.2010.03.004 · Cited by 379
Metadata
- Authors
- Vizcaíno, J. A., Côté, R., Reisinger, F., Barsnes, H., Foster, J. M., Rameseder, J., Hermjakob, H., & Martens, L.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-11-10
- Volume
- 38
- Issue
- suppl_1
- Pages
- D736-D742
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2138563170
- Cited by
- 286
- References
- 42
- FWCI
- 19.88
- Type
- journal article
- Language
- en
- Open access
- gold
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- Vizcaíno, J. A., Côté, R., Reisinger, F., Barsnes, H., Foster, J. M., Rameseder, J., Hermjakob, H., & Martens, L. (2010). The Proteomics Identifications database: 2010 update. Nucleic Acids Research. https://doi.org/10.1093/nar/gkp964
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