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Comparative Study
. 2007;8(10):R229.
doi: 10.1186/gb-2007-8-10-r229.

Simplified Ontologies Allowing Comparison of Developmental Mammalian Gene Expression

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Free PMC article
Comparative Study

Simplified Ontologies Allowing Comparison of Developmental Mammalian Gene Expression

Adele Kruger et al. Genome Biol. .
Free PMC article

Abstract

Model organisms represent an important resource for understanding the fundamental aspects of mammalian biology. Mapping of biological phenomena between model organisms is complex and if it is to be meaningful, a simplified representation can be a powerful means for comparison. The Developmental eVOC ontologies presented here are simplified orthogonal ontologies describing the temporal and spatial distribution of developmental human and mouse anatomy. We demonstrate the ontologies by identifying genes showing a bias for developmental brain expression in human and mouse.

Figures

Figure 1
Figure 1
Venn diagram illustrating the integration of mouse and human ontologies represented by the eVOC system. The total number of terms in each ontology is in parentheses. The numbers in each set are the number of terms in the intersection represented by that set. 'Mouse eVOC' represents the 28 individual mouse ontologies and 'Human eVOC' represents the 23 individual human and adult ontologies; therefore, the numbers in parentheses refer to the total number of terms in all the eVOC ontologies for each species. The intersection of the Mouse eVOC with the EMAP and MA ontologies represents the number of terms in Mouse eVOC that have database cross-references to EMAP and MA. Similarly, the intersection of the Human eVOC and HUMAT sets represents the number of Human eVOC terms that map to HUMAT terms. The number within the arrows represents the number of mapped human and mouse eVOC terms.
Figure 2
Figure 2
Screenshot of the Mouse Development ontology, visualized in COBrA. The left panel shows the hierarchy of the ontology, with 'brain' as the highlighted term. The right panel lists the 12 database cross-references mapped to 'brain', representing the accession of 'brain' in each of the 12 individual ontologies.
Figure 3
Figure 3
Screenshot of the individual Theiler Stage 13 ontology, visualized in COBrA The left panel displays the ontology with terms of anatomical structures occurring only in Theiler stage 13 of mouse development. The right panel lists the accession of the equivalent term in the external ontology as a database cross-reference.

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