Curating information

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a data repository providing curated information on microbial catabolic enzymes and their organization into metabolic pathways 54. At present, the UM-BBD stores information on approximately 100 pathways with 700 reactions, 600 compounds and 400 enzymes. The database does not try to cover every known enzyme but rather focuses on those used for the biodegradation of xenobiotics. UM-BBD is linked to the ENZYME, BRENDA and KEGG/LIGAND databases mentioned above. 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

Swiss-Prot ia a curated databank of information on protein sequence, structure and function. It can be found under http //www.ebi.ac.uk/swissprot/. 

Screening brings back a rich variety of information, not just what the curator put in the database. Suddenly a chemist can read everything about a molecule ever printed, not just what someone decided to associate it with. Distant associations -A related to B and B related to C might mean A related to C- will become apparent. 

The reluctance of museum curators and collectors to allow permanent damage to antiquities was, until not long ago, the main reason for the small amount of analytical work done on ancient coins. This was understandable since performing chemical analysis required removing a sample from the coin or damaging its surface, which meant either the destruction or defacement of, at least, a portion of a coin. More recently, however, a number of nondestructive methods of analysis such as neutron activation, X-ray fluorescence, and some techniques of surface analysis have been successfully applied to obtain information about ancient coins and the people and societies involved in their production (Carter 1993 Barrandon et al. 1977). 

Information gathering As you report your results to the museum curator, she decides that there is nothing terribly unique about naphthalene dissolved in kerosene. She asks you to dispose of the sample according to your university protocols and she will display the empty bottle in the museum. 

If the museum curator wanted to display the bottle and its contents, would you have enough information to make a recommendation on display conditions ... 

Another major source are the amino acid sequences direcdy derived from protein sequencing. Thousands of such sequences have been detected by the SWISS-PROT curators in publications (or have been directly submitted by researchers to SWISS-PROT) and entered into the database. Protein sequences detected by the NCBI journal scan have also been included. For some proteins the Brookhaven Protein Data Bank (PDB) (Abola et al., 1996) is the only source for the sequence information. The PDB entries are checked regularly, and new SWISS-PROT entries were created whenever necessary. 

AntiBase 2005 is a comprehensive database of 31 022 natural compounds from micro-organisms and higher fungi based on curated literature reports. In addition to descriptive chemical data, biological data (e.g. pharmacological activity, toxicity) and information on origin and isolation are included. 

The SCOP database is curated manually, with the objective of placing proteins in the correct evolutionary framework based on conserved structural features. Two similar enterprises, the CATH (class, architecture, topology, and homologous superfamily) and FSSP (/old classification based on structure-structure alignment of proteins) databases, make use of more automated methods and can provide additional information. 

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