PT  - JOURNAL ARTICLE
AU  - Chris J. Mungall
TI  - Formalization of Genome Interval Relations
AID  - 10.1101/006650
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 006650
4099  - http://biorxiv.org/content/early/2014/06/27/006650.short
4100  - http://biorxiv.org/content/early/2014/06/27/006650.full
AB  - In order to take full advantage of next generation genomics data, I need informatics methods to be based on agreed upon formally specified standards that can be implemented easily in a uniform fashion without ambiguity. These standards should be encoded as logical formulae, so that provably correct and efficient decision procedures can be used for query answering and validation.In this paper I present the core of such a standard for sequence data: a collection of definitions of relations that hold between genomic intervals, and an alegbra for performing operations upon these intervals. I show how these relations can be used to extend formalize concepts in the Sequence Ontology (SO).