Curator data curation

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. 

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. 

Computational methods have been applied to determine the connections in systems that are not well-defined by canonical pathways. This is either done by semi-automated and/or curated literature causal modeling [1] or by statistical methods based on large-scale data from expression or proteomic studies (a mostly theoretical approach is given by reference [2] and a more applied approach is in reference [3]). Many methods, including clustering, Bayesian analysis and principal component analysis have been used to find relationships and "fingerprints" in gene expression data [4]. 

Figure 2.1 BioPrint approach the in vitro data are all measured in a consistent manner with full dose response for any activity >30% at 10pM the in vivo data are curated from available data, supplemented by custom measured data from collaborators.

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. 

SPTR has been produced weekly since its start in January 1998. At the 14.6.1999, SPTR contained 323,354 entries 79,449 SWISS-PROT entries, 201,065 TrEMBL entries, and 42,840 TrEMBLnew entries. As the rate of incoming data and the addition of value through manual curation and automatic annotation increase, the plan is to produce SPTR daily in the near future. 

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. 

MetaBase is a curated database of human protein-protein and protein-DNA interactions, transcriptional factors, signaling, metabolism and bioactive molecules. MetaCore provides intuitive tools for data visualization, mapping and exchange, multiple networking algorithms and data mining. 

Human Proteinpedia provides a list of phosphopeptides identified in mass spectrometry-based phosphoproteomic studies. In addition, phosphorylation and dephosphorylation data curated from the literature are mapped to corresponding site and residue of sequences provided in HPRD. Using PhosphoMotif Finder one can analyze the presence of phosphorylation-based motifs, which are derived from the literature, in any protein of interest. This is a valuable data for biomedical investigators in the development of phospho-spedfic antibodies and peptide arrays. Availability of many raw MS datasets deposited in Human Proteinpedia... 

DSSTox www.epa.gov/ncct/dsstox Collection of curated chemical structures linked to data in a form that can be used for computational analyses... 

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