Antimicrobial Peptides and Autoimmune Disease
The Sjögren’s Syndrome Knowledge Base (SSKB) is a resource for Sjögren’s syndrome research. The foundation for SSKB is a database of genes and proteins associated with Sjögren’s syndrome extracted from PubMed. The foundational database was established using the text-mining program EBIMed to query the Pubmed database, using the search term "Sjogren's Syndrome" restricted to "MeshHeadingsList."
The initial search in 2007 resulted in a selection of 7,733 abstracts and 1,293 potential genes/proteins. The abstracts were manually evaluated to remove duplicates and false-positives, resulting in a preliminary database of about 900 protein names and associated genes. In the case of older publications, where gene names were not readily identifiable, gene names were assigned based on in depth evaluation of the protein name context and available gene data in public databases, including Entrez and Uniprot. The data is continually updated and manually annotated to include new publications and data relating to the genes in the SSKB.
In a second project, microbiome data are collected by 16S rRNA sequencing of microbial samples from mouse and human anatomical sites. Data storage is requested for large data sets. Analysis is conducted in collaboration with the laboratory of Dan Knights (Computer Science and Engineering).
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