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One of the main goals in proteomics is to extract and collect all the functional information available in existing databases in relation to a defined set of identified proteins. Due to the huge amount of data available, it is not possible to gather up this information by hand; we need to have automatic methods for addressing this task.
Protein information and knowledge extractor (PIKE) solves this problem by accessing several public information systems and databases automatically through the Internet and retrieving all functional information available on the different repositories, and then clustering this information according to the pre-selected criteria. The PIKE bioinformatics tool, accessible through http://proteo.cnb.uam.es:8080/pike, uses the Java and XML languages. Starting with a selected group of identified proteins, listed as NCBI nr, uniprot, and/or ipi (http://www.ebi.ac.uk/IPI/IPIhelp.html) accession codes, PIKE retrieves all relevant information stored in databases by choosing the correct pathway and/or the best information source.
Once the search is done, a typical PIKE output shows a report table with an entry for each protein containing all extracted information. The report contains a large amount of meaningful protein features, such as (1) function information, (2) sub-cellular location, (3) tissue specificity, (4) links with other repositories, such as Mendelian Inheritance in Man (OMIM) or Kyoto Encyclopaedia of Genes and Genomes (KEGG), and (5) gene ontology tree classification. The table is exportable in CSV and text file formats, and, more important, it is possible to export it in PRIDE XML (http://www.ebi.ac.uk/pride/) format for results integration into the information stored in other applications such as ProteinScape.