UniProt

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). 

Species variants in Uniprot, e.g., CSF2 HUMAN, CSF2 MOUSE, CSF2 RAT... 

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/...

UniProt (http //www.expasy.uniprot.org), Universal Protein Resource. Created by joining the Swiss-Prot information, TrEMBL and PIR contains protein sequence and function. 

Shaker residue numbers from http //www.expasy.org/uniprot/P08510... 

Bairoch A, Apweiler R, Wu G, et al. (2005) The universal protein resource (UniProt). Nucl. Acids Res. 33 D154—D159. 

Receptors are labeled according to their UniProt entry names. For cluster definition, see Ref. 30. 

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. 

Fig. 1 Blocks of multiple sequence alignment of protein sequences of carboxypeptidases from B. taurus, Mus musculus, Rattus norvegicus, Neurospora crassa, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens along with protein sequence from H. pylori (Uniprot accession code HPAG1 0372 from strain HPAG1). Numbers on the top correspond to amino acid residue number of the carboxypeptidase enzyme from B. taurus. Gray vertical columns indicate conserved residues. Amino acid residues corresponding to Glu-182 and His-306, which coordinate to zinc, are conserved, whereas another Zn-coordinating amino acid residue corresponding to His-179 is substituted by Gin in the Helicobacter sequence. Functionally important residues corresponding to Arg-237 are also conserved...

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... 

More members of the dysbindin protein family are known in humans than in any other species at present. In articular, there are eight human proteins with dysbindin domains listed by the National Center for Biotechnology Information (NCBI http //www.ncbi.nlm.nih.gov/) and/or by the Universal Protein Resource (UniProt http //www.pir.uniprot.org/index.shtml). They are schematically shown in Figure 2.2-1, which... 

Members of the dysblndin protein family based on NCBI and UniProt databases9... 

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... 

Lopez, R., Magrane, M., etal. (2005). The Universal Protein Resource (UniProt). Nucleic Acids Res. 33,154-159. 

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