The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability

Y He, Z **ang, J Zheng, Y Lin, JA Overton… - Journal of biomedical …, 2018 - Springer
Ontologies are critical to data/metadata and knowledge standardization, sharing, and
analysis. With hundreds of biological and biomedical ontologies developed, it has become …

Knowledge-based biomedical data science

TJ Callahan, IJ Tripodi… - Annual review of …, 2020 - annualreviews.org
Knowledge-based biomedical data science involves the design and implementation of
computer systems that act as if they knew about biomedicine. Such systems depend on …

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

CJ Mungall, JA McMurry, S Köhler… - Nucleic acids …, 2017 - academic.oup.com
The correlation of phenotypic outcomes with genetic variation and environmental factors is a
core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient …

The computer science ontology: a large-scale taxonomy of research areas

AA Salatino, T Thanapalasingam, A Mannocci… - The Semantic Web …, 2018 - Springer
Ontologies of research areas are important tools for characterising, exploring, and analysing
the research landscape. Some fields of research are comprehensively described by large …

Neuro-symbolic representation learning on biological knowledge graphs

M Alshahrani, MA Khan, O Maddouri, AR Kinjo… - …, 2017 - academic.oup.com
Motivation Biological data and knowledge bases increasingly rely on Semantic Web
technologies and the use of knowledge graphs for data integration, retrieval and federated …

An open source knowledge graph ecosystem for the life sciences

TJ Callahan, IJ Tripodi, AL Stefanski, L Cappelletti… - Scientific Data, 2024 - nature.com
Translational research requires data at multiple scales of biological organization.
Advancements in sequencing and multi-omics technologies have increased the availability …

An ontology-based knowledge graph for representing interactions involving RNA molecules

E Cavalleri, A Cabri, M Soto-Gomez, S Bonfitto… - Scientific Data, 2024 - nature.com
The “RNA world” represents a novel frontier for the study of fundamental biological
processes and human diseases and is paving the way for the development of new drugs …

The computer science ontology: A comprehensive automatically-generated taxonomy of research areas

AA Salatino, T Thanapalasingam, A Mannocci… - Data …, 2020 - direct.mit.edu
Ontologies of research areas are important tools for characterizing, exploring, and analyzing
the research landscape. Some fields of research are comprehensively described by large …

An ontology-guided semantic data integration framework to support integrative data analysis of cancer survival

H Zhang, Y Guo, Q Li, TJ George, E Shenkman… - BMC medical informatics …, 2018 - Springer
Background Cancer is the second leading cause of death in the United States, exceeded
only by heart disease. Extant cancer survival analyses have primarily focused on individual …

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

EC Wood, AK Glen, LG Kvarfordt, F Womack… - BMC …, 2022 - Springer
Background Biomedical translational science is increasingly using computational reasoning
on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome …