Dataset Information

ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases.

ABSTRACT: There is an urgent need for a unified resource that integrates trans-disciplinary annotations of emerging and reemerging animal infectious and zoonotic diseases. Such data integration will provide wonderful opportunity for epidemiologists, researchers and health policy makers to make data-driven decisions designed to improve animal health. Integrating emerging and reemerging animal infectious and zoonotic disease data from a large variety of sources into a unified open-access resource provides more plausible arguments to achieve better understanding of infectious and zoonotic diseases. We have developed a model for interlinking annotations of these diseases. These diseases are of particular interest because of the threats they pose to animal health, human health and global health security. We demonstrated the application of this model using brucellosis, an infectious and zoonotic disease. Preliminary annotations were deposited into VetBioBase database (http://vetbiobase.igbb.msstate.edu). This database is associated with user-friendly tools to facilitate searching, retrieving and downloading of disease-related information. Database URL: http://vetbiobase.igbb.msstate.edu.

SUBMITTER: Buza TM

PROVIDER: S-EPMC4651161 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases.

Buza Teresia M TM Jack Sherman W SW Kirunda Halid H Khaitsa Margaret L ML Lawrence Mark L ML Pruett Stephen S Peterson Daniel G DG

Database : the journal of biological databases and curation 20151118

There is an urgent need for a unified resource that integrates trans-disciplinary annotations of emerging and reemerging animal infectious and zoonotic diseases. Such data integration will provide wonderful opportunity for epidemiologists, researchers and health policy makers to make data-driven decisions designed to improve animal health. Integrating emerging and reemerging animal infectious and zoonotic disease data from a large variety of sources into a unified open-access resource provides m ...[more]

PMID: 26581408

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Project description:Scientists and clinicians who study genetic alterations and disease have traditionally described phenotypes in natural language. The considerable variation in these free-text descriptions has posed a hindrance to the important task of identifying candidate genes and models for human diseases and indicates the need for a computationally tractable method to mine data resources for mutant phenotypes. In this study, we tested the hypothesis that ontological annotation of disease phenotypes will facilitate the discovery of new genotype-phenotype relationships within and across species. To describe phenotypes using ontologies, we used an Entity-Quality (EQ) methodology, wherein the affected entity (E) and how it is affected (Q) are recorded using terms from a variety of ontologies. Using this EQ method, we annotated the phenotypes of 11 gene-linked human diseases described in Online Mendelian Inheritance in Man (OMIM). These human annotations were loaded into our Ontology-Based Database (OBD) along with other ontology-based phenotype descriptions of mutants from various model organism databases. Phenotypes recorded with this EQ method can be computationally compared based on the hierarchy of terms in the ontologies and the frequency of annotation. We utilized four similarity metrics to compare phenotypes and developed an ontology of homologous and analogous anatomical structures to compare phenotypes between species. Using these tools, we demonstrate that we can identify, through the similarity of the recorded phenotypes, other alleles of the same gene, other members of a signaling pathway, and orthologous genes and pathway members across species. We conclude that EQ-based annotation of phenotypes, in conjunction with a cross-species ontology, and a variety of similarity metrics can identify biologically meaningful similarities between genes by comparing phenotypes alone. This annotation and search method provides a novel and efficient means to identify gene candidates and animal models of human disease, which may shorten the lengthy path to identification and understanding of the genetic basis of human disease.

Project description:The present study assessed dairy cow welfare through the application of the Italian National Animal Welfare Reference Center (CReNBA) checklist in 36 dairy farms located in Ragusa (Italy) subjected to two different management conditions, housing with free access to pasture (Group 1, farms n = 17) and indoor housing (Group 2, farms n = 19). Five areas of investigation were considered: Area A, "Farm management and personnel"; Area B, "Facilities and equipment"; Area C, "Animal-based measures"; Area D, "Inspection of microclimatic environmental conditions and alarm systems"; and Area E, "Biosecurity". Blood samples were collected by coccygeal venipuncture from all animals (4081 cows). The specific antibodies against Mycobacterium avium subsp. paratuberculosis, Chlamydiophila abortus, Neospora caninum, bovine viral diarrhea virus, and the bovine herpesvirus were assessed by enzyme linked immunosorbent assay (ELISA) serological test. Group 1 (access to pasture) showed a lower value of percentage score recorded in Area A (p = 0.02) and E (p = 0.01) than Group 2 (indoor housing). Herpesvirus (Infectious bovine rhinotracheitis - IBR - detection of gB antibodies/IBR-gB) blood concentrations were higher in the cows housed indoor versus those with access to pasture (p = 0.01). Farm management and personnel (score A) was correlated with the level of bovine viral diarrhea virus (τ = 0.3754) and bovine-herpesvirus-specific antibodies (IBR-gB) (τ = 0.4159). "Biosecurity" percentage score showed a significant correlation with Chlamydiophila abortus (τ = -0.4621) in the cows with access to pasture and IBR-gB (τ = 0.3435) in the cows housed fully indoors. Group 2 showed a significantly reduced level of antibodies against Neospora caninum. In conclusion, differences in the welfare assessment score were observed in the "Farm management and personnel" and "Biosecurity" between the two management conditions. It had an effect on the prevalence of herpesvirus, which occurred more in cattle with access to pasture. Therefore, an accurate application of the checklist could be an instrument to prevent and control the spread of infections in farms.

Dataset Information

ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases.

Publications

ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases.

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