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REVIEW Accelerating Discovery for Complex Neurological and Behavioral Disorders Through Systems Genetics and Integrative Genomics in the Laboratory Mouse
, 2012
"... Abstract Recent advances in systems genetics and integra-tive functional genomics have greatly improved the study of complex neurological and behavioral traits. The methods developed for the integrated characterization of new, high-resolution mouse genetic reference populations and sys-tems genetics ..."
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Abstract Recent advances in systems genetics and integra-tive functional genomics have greatly improved the study of complex neurological and behavioral traits. The methods developed for the integrated characterization of new, high-resolution mouse genetic reference populations and sys-tems genetics enable behavioral geneticists an unprecedented opportunity to address questions of the molecular basis of neurological and psychiatric disorders and their comorbidities. Integrative genomics augment these strategies by enabling rapid informatics-assisted candidate gene prioritization, cross-species translation, and mechanistic comparison across related disorders from a wealth of existing data in mouse and other model organisms. Ultimately, through these comple-mentary approaches, finding the mechanisms and sources of genetic variation underlying complex neurobehavioral disease related traits is becoming tractable. Furthermore, these methods enable categorization of neurobehavioral disorders through their underlying biological basis. Together, these model organism-based approaches can lead to a refinement of diagnostic categories and targeted treatment of neurological and psychiatric disease.
Clinical Data Wrangling using Ontological Realism and Referent Tracking
"... Abstract — Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1 ..."
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Abstract — Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the
Annotating affective neuroscience data with the Emotion Ontology
"... The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in r ..."
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The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. Such annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in
INBIOMEDvision Promoting and Monitoring Biomedical Informatics in Europe Prospective analysis on
, 2013
"... enabling personalised medicine ..."
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Open Access Foundations for a realist ontology of mental disease
"... While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as ‘mental disorder’, ‘disease ’ and ‘illness’ might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the earl ..."
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While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as ‘mental disorder’, ‘disease ’ and ‘illness’ might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology (BFO) and in the application of BFO in the Ontology of General Medical Science (OGMS). We analyzed statements about what counts as a mental disease provided (1) in the research agenda for the DSM-V, and (2) in Pies ’ model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future.
Address for Correspondence:
"... D ow nloaded from DOI: 10.1161/CIRCULATIONAHA.114.014149 2 Nitrate accumulates in the plasma from oral intake of foods rich in nitrate, such as green leafy vegetables and root plants like beet root, or from the intravascular oxidation of NO, produced by the NO synthase enzymes, to nitrate by oxyhemo ..."
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D ow nloaded from DOI: 10.1161/CIRCULATIONAHA.114.014149 2 Nitrate accumulates in the plasma from oral intake of foods rich in nitrate, such as green leafy vegetables and root plants like beet root, or from the intravascular oxidation of NO, produced by the NO synthase enzymes, to nitrate by oxyhemoglobin. Nitrate is then concentrated in the saliva and reacts with oral commensal bacteria which contain nitrate reductase enzymes.1 Humans do not possess nitrate reductase enzymes so require these bacteria for conversion of nitrate to nitrite. Nitrite is then swallowed and systemically absorbed where it can be further reduced via one-electron transfer reactions with hemoglobin, myoglobin, neuroglobin and molybopterrin-containing enzymes (such as xanthine oxidase, aldehyde oxidase and mARC).2-7 This is now referred to as the nitrate-nitrite-NO pathway and involves a series of oxygen-independent and NO synthase independent single electron transfer reactions (Figure 1A).
Original article Construction of protein phosphorylation
"... networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint ..."
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networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint
