Mining Association Rules from Gene Ontology and Protein Networks: Promises and Challenges.

Using GO-WAR for mining cross-ontology weighted association rules

“…Existing approaches span from the use of AR to improve the annotation consistency, as presented in [8], to the use of AR to analyze microarray data [9][10][11][12][13][14], (see [15] for a detailed review). As we pointed out in a previous work [5], the use of AR presents two main issues due to the Number and the Nature of Annotations [16]. The number of annotation is for each protein or gene is highly variable within the same GO taxonomy and over different species as we depict in Fig.…”

“…The whole set of annotated data represents a valuable resource for the existing approach of analysis. From those, the use of association rules (AR) [4][5][6] is less popular with respect to other techniques, such as statistical methods or semantic similarities [7]. Existing approaches span from the use of AR to improve the annotation consistency, as presented in [8], to the use of AR to analyze microarray data [9][10][11][12][13][14], (see [15] for a detailed review).…”

“…An inconsistent annotation is defined following the true path rule: a rule contains an inconsistent annotation when it contains both a term t and its ancestors [8,5]. For these reasons, Faria et al [8] proposed the manual filtering of ancestors and low specific terms using a definition of specificity in terms of descendants and ancestors.…”

Comparison of Standard Discretization with a New Method for Quantitative Association Rules

“…valor = confianza · 1E6 + soporte · 1E2 + lift (5) valor = confianza · 1E6 + cobertura · 1E2 + lift (6)…”

Representation of Concept Hierarchy using an Efficient Encoding Scheme

“…Data mining with its unlimited diversity of techniques and approaches may be applicable to retrieve knowledge at any kind of information repositories [1] like sensor network data mining [2], gene ontology mining [3], cloud computing [4], spatial data mining [5,6], network intrusion detection [7,8] and many more. The information retrieval from the transactional database is becoming very tedious because it may include large number of concept hierarchies.…”