ImmPort use cases

Use cases for ImmPort/ScienceCommons - from Paula 2009-01-06

Mapping significant polymorphisms on the pdb (Protein Data Bank) structure
Highlight the residues on a known structure (in most cases structures will not have been solved for individual alleles of a particular molecule or even for each molecule under study, so the best we can do here is to map the amino acids of interest on a solved HLA class I or class II structure)

Thread the sequence through a known structure (like in SWISS‐MODEL or PredictProtein) to obtain a model of what the polymorphisms will look like in three dimensions

Identifying what others have found about the feature(s) from the literature
Incorporate the gene ontology identifier as a SF attribute to link our analysis to semantic search of the literature

Pull out information from abstracts with structured and positional vocabulary; capture structural vocabulary as positional

Identifying putative allele‐specific binding peptides (from databases like MHCPEP)
Formulating generalities about those peptides (e.g. aromatic residues at position 3, etc)

Relating those to known disease antigens (i.e. does the peptide of interest originate from a protein known to be associated with disease)

Determining if a particular SFVT is associated with another autoimmune disease
A literature search as in the second use case, but with a focus on whether the polymorphism(s) is/are also associated with other autoimmune diseases A search of SFVTs from other autoimmune disease association studies for the presence (or absence) of significant disease association as compared to the SFVTs identified in the first study