Dizeez: an online game for human gene-disease annotation

on October 23, 2012 by Phillip Lord in 2012, Comments (0)

Abstract Structured gene annotations are a foundation upon which many bioinformatics and statistical analyses are built. However the structured annotations available in public databases are a sparse representation of […]

Read more...

A Task-Based Approach For Gene Ontology Evaluation

on October 15, 2012 by Phillip Lord in 2012, Comments (0)

Abstract The Gene Ontology annotations are important tools for interpreting gene sets. Here, we introduce a method for evaluating Gene Ontology annotations based on the impact they have on […]

Read more...

Ontology-driven visualisation of NHGRI GWAS data

on October 4, 2012 by Phillip Lord in 2012, Comments (0)

Abstract Motivation: We present a novel visualisation approach to generate a karyotype-variation dataset derived from the NHGRI GWAS catalogue diagram using an OWL knowledge base. Use of OWL allows […]

Read more...

Query Enhancement through the Practical Application of Ontology: The IEDB and OBI

on by Phillip Lord in 2012, Comments (0)

Abstract Ontologies categorize entities, provide standardized definitions, and enforce specific relationships between the entities that the specific ontology describes. Previously, we described how the Immune Epitope Database and Analysis […]

Read more...

Continuous Integration of Open Biological Ontology Libraries

on by Phillip Lord in 2012, Comments (0)

Abstract Ontologies within the OBO library are becoming less monolithic and more interlinked. This gives rise to a need for continuous integration tests, in which an ontology is checked […]

Read more...

Using Entropy Estimates for DAG-Based Ontologies

on by Phillip Lord in 2012, Comments (0)

Abstract Motivation: Entropy measurements on hierarchical structures have been used in methods for information retrieval and natural language modeling. Here we explore its application to semantic similarity. By finding […]

Read more...

Increased Expressivity of Gene Ontology Annotations

on by Phillip Lord in 2012, Comments (0)

1 Introduction Gene Ontology (GO) annotations can be modeled as pairwise associations between a gene or gene product G and a pre-coordinated class C from the ontology, augmented with […]

Read more...

The Human Studies Database Project Uses the Ontology of Clinical Research to Federate Human Studies Information

on by Phillip Lord in 2012, Comments (0)

1 Introduction Human studies are one of the most important sources of evidence for the advancement of medicine. Human studies data and metadata are dispersed in institutional review board […]

Read more...

Automated Annotation of Abstracts for Cognitive Experiments

on by Phillip Lord in 2012, Comments (0)

1 Motivation This work explores automatic annotation of fMRI studies based on standard terms from the Cognitive Paradigm Ontology (CogPO). We are using text-mining and stochastic modeling approaches on […]

Read more...

A data-driven approach to automatic discovery of prescription drugs in cardiovascular risk management

on by Phillip Lord in 2011, Comments (0)

Abstract Objectives: To evaluate a data-driven approach for automatically identifying medications used in the treatment of cardiovascular disease, and consider how these learned rules might be applied to ontology […]

Read more...