Abstract
BackgroundKeyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database.ResultsWe have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions.ConclusionRepresenting the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology.
Highlights
Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions
We developed a new representation of the Gene Ontology (GO) and a search engine that finds all the semantically relevant interactions of a query protein using the representation
When the user specifies a GO term or protein superfamily [15] for the query protein, the search engine returns all interactions that involve the protein annotated with the GO term or superfamily as well as the proteins annotated with more specific terms than the specified GO term
Summary
Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Most of the databases allow the user to retrieve protein-protein interactions that satisfy a condition specified in a query. Keyword matching or ID matching is one of the most commonly used searching methods This type of search retrieves all of the records in the database which contain a keyword or ID specified in a query. The user can alter retrieval results using Boolean operators such as AND, OR and NOT
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