Posts In Category Year

BioAssay Ontology: Modularization, Integration and Applications

on September 23, 2013 by Phillip Lord in 2013, Comments (0)

1 Introduction The lack of established and widely-used standards to describe and annotate biological assays and screening results in the domain of chemical probe and drug discovery is a […]

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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 […]

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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 […]

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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 […]

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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 […]

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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 […]

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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 […]

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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 […]

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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 […]

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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 […]

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