Modeling quantitative traits for COVID-19 case reports

Medical practitioners record the condition status of a patient through qualitative and quantitative observations. The measurement of vital signs and molecular parameters in the clinics gives a complementary description of abnormal phenotypes associated with the progression of a disease. The Clinical Measurement Ontology (CMO) is used to standardize annotations of these measurable traits. However, researchers have no way to describe how these quantitative traits relate to phenotype concepts in a machine-readable manner. Using the WHO clinical case report form standard for the COVID-19 pandemic, we modeled quantitative traits and developed OWL axioms to formally relate clinical measurement terms with anatomical, biomolecular entities and phenotypes annotated with the Uber-anatomy ontology (Uberon), Chemical Entities of Biological Interest (ChEBI) and the Phenotype and Trait Ontology (PATO) biomedical ontologies. The formal description of these relations allows interoperability between clinical and biological descriptions, and facilitates automated reasoning for analysis of patterns over quantitative and qualitative biomedical observations.

GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals

GWAS Atlas (https://bigd.big.ac.cn/gwas/) is a manually curated resource of genome-wide variant-trait associations for a wide range of species. Unlike existing related resources, it features comprehensive integration of a high-quality collection of 75 467 variant-trait associations for 614 traits across 7 cultivated plants (cotton, Japanese apricot, maize, rapeseed, rice, sorghum and soybean) and two domesticated animals (goat and pig), which were manually curated from 254 publications. We integrated these associations into GWAS Atlas and presented them in terms of variants, genes, traits, studies and publications. More importantly, all associations and traits were annotated and organized based on a suite of ontologies (Plant Trait Ontology, Animal Trait Ontology for Livestock, etc.). Taken together, GWAS Atlas integrates high-quality curated GWAS associations for animals and plants and provides user-friendly web interfaces for data browsing and downloading, accordingly serving as a valuable resource for genetic research of important traits and breeding application.

Progress in Construction of Animal Trait Ontologies

Extracting and formulating an animal trait ontology is the basis of building a trait database. The character selection from existing traditional biodiversity databases is limited and biased by the information already in a collection. With the increasing amount of character data and the advance of character information acquisition projects, the success of making animal trait ontologies or specifications of terms is imminent. According to the general workflow of our ontology project, after investigating a large number of biodiversity databases, we extracted relatively complete character terms from dictionaries, training handbooks, journals and classical textbooks, and then constructed relationships according to some rules to form a preliminary animal trait ontology. When formulating the domain ontology/specification, our process is as follows: Select the group and related materials; select the "specification" as the starting point of work; and then supplement with the teaching materials, journal citations and dictionaries of the relevant group for reference; Extract terms from multiple sources, so only a few additions and modifications are needed after the second time; Make structural adjustments to all terms according to the specification of description sequence; Invite experts to examine and approve the project and repeat steps 2 and 3 (sometimes beginning from step 1) according to their opinions until they are approved. Select the group and related materials; select the "specification" as the starting point of work; and then supplement with the teaching materials, journal citations and dictionaries of the relevant group for reference; Extract terms from multiple sources, so only a few additions and modifications are needed after the second time; Make structural adjustments to all terms according to the specification of description sequence; Invite experts to examine and approve the project and repeat steps 2 and 3 (sometimes beginning from step 1) according to their opinions until they are approved. At present, we have completed the construction of terms and their relationships for a morphological description of feature ontologies in birds, mammals, insects (only Lepidoptera), amphibians and reptiles. While constructing such morphology / taxonomy-based ontologies, we also formulated their attributes, which are supplemented by ontologies in various fields. All these terms are undergoing the second review by domain experts. Although the existing work is only one small tip of the iceberg of the whole zoological trait ontology project, it is of great public interest. Compared with existing ontologies such as OBA (ontology of biological attributes, for development researchers) and UBERON (for surgeons), our ontologies are more suitable for taxonomists and biodiversity researchers.

Un langage de référence pour le phénotypage des animaux d’élevage : l’ontologie ATOL

Les avancées technologiques récentes en biologie permettent la production de grandes quantités de données capables de décrire de plus en plus finement les phénotypes. Pour traiter en masse ces informations à l’aide de programmes informatiques et comparer les phénotypes provenant d’études différentes, il est indispensable de disposer d’un langage standardisé définissant sans ambiguïté les caractères phénotypiques auxquels pourront se référer des utilisateurs variés (généticiens, physiologistes, biochimistes, modélisateurs, producteurs…). L’absence d’un tel référentiel pour les animaux d’élevage a conduit l’Inra, en collaboration avec ses partenaires internationaux, à mettre en place une ontologie nommée ATOL (« Animal Trait Ontology for Livestock »). Celle-ci vise à définir les caractères phénotypiques des animaux d’élevage en les organisant en catégories, autour des performances (efficacité alimentaire, fertilité), des produits (production laitière, de viande, d’oeufs, de foie gras) et des préoccupations sociétales (bien-être animal) se rapportant aux productions animales. Cet article explique les motivations à l’origine du projet, les objectifs poursuivis, la démarche adoptée et son originalité, ses limites et ses performances. Notre ambition est que cette ontologie, actuellement en accès libre sur la toile, soit largement utilisée pour référencer les caractères utilisés dans les publications et les bases de données, et ce pour favoriser une fouille bibliographique précise, facilitant ainsi l’intégration des informations à des fins de biologie systémique et prédictive.