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August 01, 2006
Other Databases for Omics Researchers (Omics Series, 17)
The premiere source of omics databases is of course the collection available from NIH-NLM-NCBI (Blast, OMIM, etc). These were highlighted in a previous blog entry in this series (#9). For the current blog entry, we have selected examples of omics databases made available from various research centers, institutes and organizations around the world. We included only collections of databases, or specific databases that were free and openly available at the time of writing. There are many more that require subscription. As you can see, there are also many that do not.
* OMICS DATABASE COLLECTIONS
Kyoto University Bioinformatics Center: Genome Databases in Japan: http://www.genome.jp/genome_db/
NIH: Computational Molecular Biology: Databases: http://molbio.info.nih.gov/molbio/db.html
Proteomic World: Databases: http://www.proteomicworld.org/DatabasePage.html
* DATABASES FROM SPECIFIC PROJECTS
Baylor College of Medicine: Department of Pharmacology: Small RNA database: http://condor.bcm.tmc.edu/smallRNA/smallrna.html
BioGRID: A General Repository for Interaction Datasets: http://www.thebiogrid.org/
Bioinformatics.org, Open-Source Bioinformatics for Researchers: Online Databases: http://bioinformatics.org/
- Online Databases EST Clusters: http://bioinformatics.org/zest/
- Immigrant Genes: http://bioinformatics.org/immigrant/
- Leukemia Genes: http://bioinformatics.org/legend/
- p53 Tumor Protein Gene: http://bioinformatics.org/p53/
- Pancreatic Cancer Genes: http://bioinformatics.org/pcgdb/
- TB Drug Targets: http://bioinformatics.org/tbdtdb/
- T2K Acronym Finder: http://bioinformatics.org/textknowledge/
European Bioinformatics Institute (EMBL-EBI): IntAct Interaction Database: http://www.ebi.ac.uk/intact/index.jsp
"IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available."
European Bioinformatics Institute (EMBL-EBI): PRIDE (PRoteomics IDEntifications database): http://www.ebi.ac.uk/pride/
Georgetown University Medical Center: Protein Information Resource (Integrated Protein Informatics Resource for Genomic and Proteomic Research): http://pir.georgetown.edu/pirwww/index.shtml
Georgetown University Medical Center: Protein Information Resource: Search & Analysis Tools: http://pir.georgetown.edu/pirwww/search/
Harvard University: Dana Farber Cancer Institute: WorfDB, The C. elegans ORFeome cloning project: http://worfdb.dfci.harvard.edu/
Harvard University: Harvard Institute of Proteomics: FlexGene Database: http://kotel.harvard.edu:8080/FLEX/welcome.jsp
Kyoto University Bioinformatics Center: DBGET: Web of Molecular Biology Databases: http://www.genome.jp/dbget/
MedicalComputing.net: Search Human Gene Information Database: http://www.medicalcomputing.net/cgi-bin/query_human_gene_info
MHCPEP [A database of MHC binding peptides (v. 1.3)]: http://wehih.wehi.edu.au/mhcpep/
Entries include: " ... the peptide sequence, its MHC specificity and, when available, experimental method, observed activity, binding affinity, source protein, anchor positions, and publication references."
NanoWerk: NanoBank: Nanomaterials Database: http://www.nanowerk.com/phpscripts/n_dbsearch.php
Real Time Primers, validated primer sets for quantitative real time PCR: http://www.realtimeprimers.org/
RNA Interference, database of siRNA sequences and RNA inhibition studies: http://www.rnainterference.org/
Rutgers State University of New Jersey: The Nucleic Acid Database Project:
Nucleic Acid Database (NDB): http://ndbserver.rutgers.edu/
University of Texas: Bioinformatics, Proteomics, and Functional Genomics: Open Proteomics Database: http://apropos.icmb.utexas.edu/OPD/
"OPD is a public database for storing and disseminating mass spectrometry based proteomics data. The database currently contains roughly 3,000,000 spectra representing experiments from 5 different organisms."
Weizmann Institute of Science: GeneCards: http://www.genecards.org/index.shtml
"GeneCards is an integrated database of human genes that includes automatically-mined genomic, proteomic and transcriptomic information, as well as orthologies, disease relationships, SNPs, gene expression, gene function, and service links for ordering assays and antibodies."
World Health Organization (WHO): International Database on Craniofacial Anomalies (IDCFA): http://www.who.int/genomics/anomalies/idcfa/en/
WormBase: http://www.wormbase.org/
* WANT MORE?
Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (database OR dataset OR search)
Posted by pfa at August 1, 2006 04:42 PM