Uniprot database

To create our terminology containing both internal terms and external terms we semiautomatically extract terms from available external resources (e.g., MeSH, EMTREE, UniProt). Then we fit the extracted terms to our data structure and preserve the reference to the source system because sometimes terms are very specific to certain databases. We refer to the terms specific to a database as local terms. These local terms are stored in a dedicated data structure, the Metastore. It must be noted that we refer to accession codes and identifiers used in databases such as UniProt, RefSeq, and GO as local terms (see Tables 31.1 and 31.2). 

Figure 2.4 Sample entry for human insulin as present in the Swiss-Prot database. Refer to text for further details. Reproduced from the Swiss-Prot database on the Uniprot website htt //www.ebi.uniprot.org/...

The lower part shows information ofselected protein sequence. The small table shows the results of sequence search against UNIPROT(Swiss-prot/TrEMBL), nr.aa, and UniGene database see Subheading 2, items 2 and 4) using BLAST. 

Other very useful databases (mainly in terms of amino acid sequences in allergens) are the ones which characterize proteins (e.g., The UniProt Knowledgebase— http //expasy.org/sprot/. This database consists of... 

Compare allergenic sequences within the Allergome database and outside in Uniprot... 

The characterization as a target protein might become possible through the combination of textual information with entries from databases such as UniProt,14 PubChem,15 or DrugBank.16 At ChEBI,17 the European Bioinformatics Institute s database on bioactive small molecules, this integration of chemical information with biological entities is realized through expert curation of entries and introduction to referential links to databases such as UniProt and PDB. 

BioRDF (Ruttenberg et al. 2007) supports a variety of neurochemical databases, has RDF-ified gene records, databases of receptor-ligand and protein-protein interactions, a directory of commercially available antibodies, Reactome, KEGG, the NCI metathesaurus, and UniProt (which is a collaboration between the SIB in Zurich and the EBI in Hinxton, UK), hence providing a Semantic Web representation of protein sequences. 

The UniProt KB is an automatically and manually annotated protein database drawn from translation of DDBJ/EMBL-Bank/GenBank coding sequences and directly sequenced proteins. Each sequence receives a imique, stable identifier allowing unambiguous identification of any protein across datasets. The KB also provides cross-references to external data collections such as the underlying DNA sequence entries in the DDBJ/EMBL-Bank/GenBank nucleotide sequence databases, 2D PAGE and 3D protein structure databases, various protein domain... 

The method used by the pathway hole Hlling program PH-Filler (8) is as follows. Given a reaction that is a pathway hole, the program Hrst queries the UniProt database to find all known sequences for enzymes that catalyze that same reaction in other... 

For those who want to query PGDB data through a relational database system, the attribute-value files exported by Pathway Tools can be loaded into SRFs BioWarehouse system (14). BioWarehouse is an Oracle or MySQL-based system for integration of multiple public bioinformatics databases. PGDB data can be queried through BioWarehouse alone or in combination with other bioinformatics databases such as UniProt, Genbank, NCBI Taxonomy, ENZYME, and KEGG. 

Introduction to Molecular Biology Databases. 1994-2004. R. Apweiler, R. Lopez, B. Marx, UniProt, SWISS-PROT, Switzerland. URL http //www.ebi.ac.uk/swissprot/Publications/ mbdl.html. Contents include bibliographic, taxonomy, nucleotide sequence, genetic, and protein sequence databases PIR, SWISS-PROT, and TrEMBL, and specialized protein, protein sequence, secondary protein, and structme databases. 

Links to external databases (taken from UniProt) + +... 

UniProt is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProt is comprised of three components, each optimized for different uses. The UniProt Knowledgebase (UniProt) is the central access point for extensive curated protein information, including function, classification, and cross-reference. The UniProt Non-redundant Reference (UniRef) databases combine closely related sequences into a single record to speed searches. The UniProt Archive (UniParc) is a comprehensive repository, reflecting the history of all protein sequences. 

Bairoch, A., R. Apweiler, C. H. Wu, W. C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, et al. 2005. The Universal Protein Resource (UniProt). Nucleic Acids Res 33, Database Issue D154-9. 

Field/value-based flat files have been very commonly used in bioinformatics. Examples are the flat file libraries from GenBank, European Molecular Biology Laboratory Nucleotide Sequence Database (EMBL), DNA Data Bank of Japan, or Universal Protein Resource (UniProt). These file types are a very limited solution because they lack referencing, vocabulary control, and constraints. In addition, on the file level, there is no inherent locking mechanism that detects when a file is being used or modified. However, these file types are primarily used for reading purposes. 

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