Database for Annotation

In the biosciences, a database is a curated repository of raw data containing annotations, further analysis, and links to other databases. Examples of databases are the SWISSPROT database for annotated protein sequences or the FlyBase database of genetic and molecular data for Drosophila melanogaster. 

Dennis, G., Sherman, B., Hosack, D., Yang, J., et al. (2003) DAVID database for annotation, visualization, and integrated discovery. Genome Biology, 4, P3. 

Cahan, R, Ahmad, A.M., Burke, H., Fu, S., Lai, Y, Florea, L., Dharker, N., Kobrinski, T., Kale, R, and McCaffrey, T.A. 2005. List of lists-annotated (LOLA) A database for annotation and comparison of published microarray gene lists. Gene 360 78-82. 

In recent years, both the electronic access to public documentation sources and the increase in the number of data generated and reported have facilitated the construction of pharmacologically annotated chemical databases. For example, the MDL Drug Data Report (MDDR)... 

Information of our chemical and siRNA libraries is stored in a PostgreSQL database. We annotate our validated hits using a DatabaseReader and a Joiner node to obtain either chemical structures for chemical screens or GenelD for RNAi screens. KNIME has many tools for cheminformatics, can visualize the molecule structures, and has tools to retrieve data from external public databases via Web queries to further annotate hits, allowing clustering either by chemical substructures or GO terms. 

The number of records in total, as well as the number of unique compounds and targets, is highly relevant. Both the diversity of target classes and the big target families need to be taken into account. This breadth and depth comes specifically from the scope and number of scientific journals and patents that are covered within the database. For these sources, the age of the annotation needs to be taken into account. It is also very important that especially human targets are covered. 

Much of the value of databases, assuming the provision of accurate sequence data, arises from the quality of the annotation that is available. This normally includes at least a brief description of the function of the sequence and essential references to the literature. Many databases include a lot more than this. In particular, SWISS-PROT (8)is viewed as the most reliable source for annotation information. SWISS-PROT emerged in the 1980s out of a need to have high quality, robust annotations for the protein sequences that made up its core content. However, the process of annotation is labor intensive and not one that is easily automated. Although the content of SWISS-PROT is well regarded, it lacks the completeness of the source DNA databases because of the necessary delay in incorporating newly annotated sequences. Indeed, a team of annotators is employed at the... 

Sigrist CJA, Cerutti L, de Castro E et al (2010) PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res 38 D161-D166... 

CE amol-fmol Separation, profiling Rapid separation, isomeric resolution, small sample volume Limited databases for CE, standards required for structural annotation, limited compatibility with MS... 

MS fmol-pmol Composition, profiling Potential for automation, databases for assisted or automated annotation Isomers indistinguishable, separation/ derivatization required to prevent ion suppression... 

Besides MassTRIX, several other solutions for annotation of mass spectromet-ric data exist. Two examples are the Pathos Web server (http //motif.gla.ac.uk/ Pathos/pathos.html) (41) and Paintomics (www.paintomics.org) (42). Pathos principally is based on the same functionality as MassTRIX and is written in Java and uses an underlying MySQL database. It annotates possible metabolites within an error range to experimental masses. Additionally, for this... 

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