Dataset Information

Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP.

ABSTRACT: BACKGROUND: Large-scale mutagenesis projects are ongoing to improve our understanding about the pathology and subsequently the treatment of diseases. Such projects do not only record the genotype but also report phenotype descriptions of the genetically modified organisms under investigation. Thus far, phenotype data is stored in species-specific databases that lack coherence and interoperability in their phenotype representations. One suggestion to overcome the lack of integration are Entity-Quality (EQ) statements. However, a reliable automated transformation of the phenotype annotations from the databases into EQ statements is still missing. RESULTS: Here, we report on our ongoing efforts to develop a method (called EQ-liser) for the automated generation of EQ representations from phenotype ontology concept labels. We implemented the suggested method in a prototype and applied it to a subset of Mammalian and Human Phenotype Ontology concepts. In the case of MP, we were able to identify the correct EQ representation in over 52% of structure and process phenotypes. However, applying the EQ-liser prototype to the Human Phenotype Ontology yields a correct EQ representation in only 13.3% of the investigated cases. CONCLUSIONS: With the application of the prototype to two phenotype ontologies, we were able to identify common patterns of mistakes when generating the EQ representation. Correcting these mistakes will pave the way to a species-independent solution to automatically derive EQ representations from phenotype ontology concept labels. Furthermore, we were able to identify inconsistencies in the existing manually defined EQ representations of current phenotype ontologies. Correcting these inconsistencies will improve the quality of the manually defined EQ statements.

SUBMITTER: Oellrich A

PROVIDER: S-EPMC4016257 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP.

Oellrich Anika A Grabmüller Christoph C Rebholz-Schuhmann Dietrich D

Journal of biomedical semantics 20131016 1

<h4>Background</h4>Large-scale mutagenesis projects are ongoing to improve our understanding about the pathology and subsequently the treatment of diseases. Such projects do not only record the genotype but also report phenotype descriptions of the genetically modified organisms under investigation. Thus far, phenotype data is stored in species-specific databases that lack coherence and interoperability in their phenotype representations. One suggestion to overcome the lack of integration are En ...[more]

PMID: 24131519

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Project description:BackgroundObesity has a strong genetic influence, with some variants showing stronger associations among women than men. Women are also more likely to distribute weight in the abdomen following menopause. We investigated whether genetic loci link with obesity-related phenotypes differently by menopausal status.MethodsWe performed univariate and bivariate linkage analysis for the phenotypes of body mass index (BMI), waist (W) and hip (H) circumferences (WC, HC), and WH ratio (WHR) separately among 172 pre-menopausal and 405 post-menopausal women from 90 multigenerational families using a genome scan with 403 microsatellite markers. Bivariate analysis used pair-wise combinations of obesity phenotypes to detect linkage at loci with pleiotropic effects for genetically correlated traits. BMI was adjusted in models of WC, HC and WHR.ResultsPre-menopausal women, compared to post-menopausal women, had higher heritability for BMI (h2 = 94% versus h2 = 39%, respectively) and for HC (h2 = 99% versus h2 = 43%, respectively), and lower heritability for WC (h2 = 29% versus h2 = 61%, respectively) and for WHR (h2 = 39% versus h2 = 57%, respectively). Among pre-menopausal women, the strongest evidence for linkage was for the combination of BMI and HC traits at 3p26 (bivariate LOD = 3.65) and at 13q13-q14 (bivariate LOD = 3.59). Among post-menopausal women, the highest level of evidence for genetic linkage was for HC at 4p15.3 (univariate LOD = 2.70) and 14q13 (univariate LOD = 2.51). WC was not clearly linked to any locus.ConclusionsThese results support a genetic basis for fat deposition that differs by menopausal status, and suggest that the same loci encode genes that influence general obesity (BMI) and HC, specifically, among pre-menopausal women. However, lower heritability among pre-menopausal women for WC and WHR suggests that pre-menopausal waist girth may be influenced to a greater extent by controllable environmental factors than post-menopausal waist girth. Possibly, targeted interventions for weight control among pre-menopausal women may prevent or attenuate post-menopausal abdominal weight deposition.

Dataset Information

Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP.

Publications

Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP.

Similar Datasets

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