Dataset Information

Phenotype annotation with the ontology of microbial phenotypes (OMP).

ABSTRACT: BACKGROUND:Microbial genetics has formed a foundation for understanding many aspects of biology. Systematic annotation that supports computational data mining should reveal further insights for microbes, microbiomes, and conserved functions beyond microbes. The Ontology of Microbial Phenotypes (OMP) was created to support such annotation. RESULTS:We define standards for an OMP-based annotation framework that supports the capture of a variety of phenotypes and provides flexibility for different levels of detail based on a combination of pre- and post-composition using OMP and other Open Biomedical Ontology (OBO) projects. A system for entering and viewing OMP annotations has been added to our online, public, web-based data portal. CONCLUSIONS:The annotation framework described here is ready to support projects to capture phenotypes from the experimental literature for a variety of microbes. Defining the OMP annotation standard should support the development of new software tools for data mining and analysis in comparative phenomics.

SUBMITTER: Siegele DA

PROVIDER: S-EPMC6631659 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Phenotype annotation with the ontology of microbial phenotypes (OMP).

Siegele Deborah A DA LaBonte Sandra A SA Wu Peter I-Fan PI Chibucos Marcus C MC Nandendla Suvarna S Giglio Michelle G MG Hu James C JC

Journal of biomedical semantics 20190715 1

<h4>Background</h4>Microbial genetics has formed a foundation for understanding many aspects of biology. Systematic annotation that supports computational data mining should reveal further insights for microbes, microbiomes, and conserved functions beyond microbes. The Ontology of Microbial Phenotypes (OMP) was created to support such annotation.<h4>Results</h4>We define standards for an OMP-based annotation framework that supports the capture of a variety of phenotypes and provides flexibility ...[more]

PMID: 31307550

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Project description:Analysing the relationships between biomolecules and the genetic diseases is a highly active area of research, where the aim is to identify the genes and their products that cause a particular disease due to functional changes originated from mutations. Biological ontologies are frequently employed in these studies, which provides researchers with extensive opportunities for knowledge discovery through computational data analysis. In this study, a novel approach is proposed for the identification of relationships between biomedical entities by automatically mapping phenotypic abnormality defining HPO terms with biomolecular function defining GO terms, where each association indicates the occurrence of the abnormality due to the loss of the biomolecular function expressed by the corresponding GO term. The proposed HPO2GO mappings were extracted by calculating the frequency of the co-annotations of the terms on the same genes/proteins, using already existing curated HPO and GO annotation sets. This was followed by the filtering of the unreliable mappings that could be observed due to chance, by statistical resampling of the co-occurrence similarity distributions. Furthermore, the biological relevance of the finalized mappings were discussed over selected cases, using the literature. The resulting HPO2GO mappings can be employed in different settings to predict and to analyse novel gene/protein-ontology term-disease relations. As an application of the proposed approach, HPO term-protein associations (i.e., HPO2protein) were predicted. In order to test the predictive performance of the method on a quantitative basis, and to compare it with the state-of-the-art, CAFA2 challenge HPO prediction target protein set was employed. The results of the benchmark indicated the potential of the proposed approach, as HPO2GO performance was among the best (Fmax = 0.35). The automated cross ontology mapping approach developed in this work may be extended to other ontologies as well, to identify unexplored relation patterns at the systemic level. The datasets, results and the source code of HPO2GO are available for download at: https://github.com/cansyl/HPO2GO.

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:Background Pulmonary atresia (PA) is a heterogeneous congenital heart defect and ventricular septal defect (VSD) is the most vital factor for the conventional classification of PA patients. The simple dichotomy could not fully describe the cardiac morphologies and pathophysiology in such a complex disease. We utilized the Human Phenotype Ontology (HPO) database to explore the phenotypic patterns of PA and the phenotypic influence on prognosis. Methods We recruited 786 patients with diagnoses of PA between 2008 and 2016 at Fuwai Hospital. According to cardiovascular phenotypes of patients, we retrieved 52 HPO terms for further analyses. The patients were classified into three clusters based on unsupervised hierarchical clustering. We used Kaplan–Meier curves to estimate survival, the log-rank test to compare survival between clusters, and univariate and multivariate Cox proportional hazards regression modeling to investigate potential risk factors. Results According to HPO term distribution, we observed significant differences of morphological abnormalities in 3 clusters. We defined cluster 1 as being associated with Tetralogy of Fallot (TOF), VSD, right ventricular hypertrophy (RVH), and aortopulmonary collateral arteries (ACA). ACA was not included in the cluster classification because it was not an HPO term. Cluster 2 was associated with hypoplastic right heart (HRH), atrial septal defect (ASD) and tricuspid disease as the main morphological abnormalities. Cluster 3 presented higher frequency of single ventricle (SV), dextrocardia, and common atrium (CA). The mortality rate in cluster 1 was significantly lower than the rates in cluster 2 and 3 (p = 0.04). Multivariable analysis revealed that abnormal atrioventricular connection (AAC, p = 0.011) and persistent left superior vena cava (LSVC, p = 0.003) were associated with an increased risk of mortality. Conclusions Our study reported a large cohort with clinical phenotypic, surgical strategy and long time follow-up. In addition, we provided a precise classification and successfully risk stratification for patients with PA.

Project description:There is an urgent need to standardize the semantics of biomedical data values, such as phenotypes, to enable comparative and integrative analyses. However, it is unlikely that all studies will use the same data collection protocols. As a result, retrospective standardization is often required, which involves matching of original (unstructured or locally coded) data to widely used coding or ontology systems such as SNOMED CT (clinical terms), ICD-10 (International Classification of Disease) and HPO (Human Phenotype Ontology). This data curation process is usually a time-consuming process performed by a human expert. To help mechanize this process, we have developed SORTA, a computer-aided system for rapidly encoding free text or locally coded values to a formal coding system or ontology. SORTA matches original data values (uploaded in semicolon delimited format) to a target coding system (uploaded in Excel spreadsheet, OWL ontology web language or OBO open biomedical ontologies format). It then semi- automatically shortlists candidate codes for each data value using Lucene and n-gram based matching algorithms, and can also learn from matches chosen by human experts. We evaluated SORTA's applicability in two use cases. For the LifeLines biobank, we used SORTA to recode 90?000 free text values (including 5211 unique values) about physical exercise to MET (Metabolic Equivalent of Task) codes. For the CINEAS clinical symptom coding system, we used SORTA to map to HPO, enriching HPO when necessary (315 terms matched so far). Out of the shortlists at rank 1, we found a precision/recall of 0.97/0.98 in LifeLines and of 0.58/0.45 in CINEAS. More importantly, users found the tool both a major time saver and a quality improvement because SORTA reduced the chances of human mistakes. Thus, SORTA can dramatically ease data (re)coding tasks and we believe it will prove useful for many more projects. Database URL: http://molgenis.org/sorta or as an open source download from http://www.molgenis.org/wiki/SORTA.

Dataset Information

Phenotype annotation with the ontology of microbial phenotypes (OMP).

Publications

Phenotype annotation with the ontology of microbial phenotypes (OMP).

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