Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

DR Unni, SAT Moxon, M Bada, M Brush… - Clinical and …, 2022 - Wiley Online Library
Within clinical, biomedical, and translational science, an increasing number of projects are
adopting graphs for knowledge representation. Graph‐based data models elucidate the …

PomBase: a Global Core Biodata Resource—growth, collaboration, and sustainability

KM Rutherford, M Lera-Ramírez, V Wood - Genetics, 2024 - academic.oup.com
Abstract PomBase (https://www. pombase. org), the model organism database (MOD) for
fission yeast, was recently awarded Global Core Biodata Resource (GCBR) status by the …

Generalisable long COVID subtypes: findings from the NIH N3C and RECOVER programmes

JT Reese, H Blau, E Casiraghi, T Bergquist… - …, 2023 - thelancet.com
Background Stratification of patients with post-acute sequelae of SARS-CoV-2 infection
(PASC, or long COVID) would allow precision clinical management strategies. However …

A simple standard for sharing ontological map**s (SSSOM)

N Matentzoglu, JP Balhoff, SM Bello, C Bizon… - Database, 2022 - academic.oup.com
Despite progress in the development of standards for describing and exchanging scientific
information, the lack of easy-to-use standards for map** between different representations …

Dynamic retrieval augmented generation of ontologies using artificial intelligence (DRAGON-AI)

S Toro, AV Anagnostopoulos, SM Bello… - Journal of Biomedical …, 2024 - Springer
Background Ontologies are fundamental components of informatics infrastructure in
domains such as biomedical, environmental, and food sciences, representing consensus …

DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms

M Kulmanov, R Hoehndorf - Bioinformatics, 2022 - academic.oup.com
Motivation Protein functions are often described using the Gene Ontology (GO) which is an
ontology consisting of over 50 000 classes and a large set of formal axioms. Predicting the …

2022 updates to the Rat Genome Database: a findable, accessible, interoperable, and reusable (FAIR) resource

M Vedi, JR Smith, G Thomas Hayman, M Tutaj… - Genetics, 2023 - academic.oup.com
Abstract The Rat Genome Database (RGD, https://rgd. mcw. edu) has evolved from simply a
resource for rat genetic markers, maps, and genes, by adding multiple genomic data types …

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies

N Matentzoglu, D Goutte-Gattat, SZK Tan, JP Balhoff… - Database, 2022 - academic.oup.com
Similar to managing software packages, managing the ontology life cycle involves multiple
complex workflows such as preparing releases, continuous quality control checking and …

The use of ontologies to accelerate the behavioral sciences: Promises and challenges

C Sharp, RM Kaplan… - Current Directions in …, 2023 - journals.sagepub.com
Behavioral scientists produce a vast amount of research every year yet struggle to produce
cumulative knowledge that is easily translated in applied settings. This article summarizes a …

Unifying the identification of biomedical entities with the Bioregistry

CT Hoyt, M Balk, TJ Callahan, D Domingo-Fernández… - Scientific data, 2022 - nature.com
The standardized identification of biomedical entities is a cornerstone of interoperability,
reuse, and data integration in the life sciences. Several registries have been developed to …