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Description:

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BEL (Biological Expression Language) is a language for representing scientific findings in the life sciences in a computable form. These scientific findings can have a context which they are observed in. For instance the following BEL statement was observed in a Mouse (specifically Mus musculus species) within the Cell Nucleus. BEL would state this as a Species and CellStructure annotation before the statement:

Code Block
languagejs
titleBEL Script syntax
SET Species = Mouse
SET CellStructure = "Cell Nucleus"

abundance(CHEBI:"calcium(2+)") directlyIncreases kinaseActivity(proteinAbundance(SFAM:"CAMK2 Family"))

This project's goal is to create rules to develop RDF-based rules to expand and standardize statement annotations on BEL statements. Given what information we have about the species' biology we can validate annotation usage and even normalize across the entire biological network.

This project will involve the use of RDF (Semantic Web) and SPARQL query technology. Furthermore research will be needed to determine the best approach to encode these rules.

Results:

A program to execute queries against the create and apply annotation rules over an BEL RDF model.

Prerequisites:

RDF, SPARQL, programming language with RDF tool support (e.g. C, Java, Python, Ruby, etc.)

Mentor:

Natalie Catlett (email: ncatlett@selventa.com)