Biochimica et biophysica acta. Gene regulatory mechanisms
Aug 11, 2021
The Sequence Ontology (SO) is a structured, controlled vocabulary that provides terms and definitions for genomic annotation. The Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) initiative has gathered input from many groups of res...
Journal of biomedical semantics
Aug 9, 2021
BACKGROUND: The ontology authoring step in ontology development involves having to make choices about what subject domain knowledge to include. This may concern sorting out ontological differences and making choices between conflicting axioms due to ...
BMC bioinformatics
Jul 21, 2021
BACKGROUND: Data integration to build a biomedical knowledge graph is a challenging task. There are multiple disease ontologies used in data sources and publications, each having its hierarchy. A common task is to map between ontologies, find disease...
Journal of biomedical semantics
Jul 18, 2021
BACKGROUND: Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool, and this holds especially f...
Journal of biomedical informatics
Jul 2, 2021
The current intensive research on potential remedies and vaccinations for COVID-19 would greatly benefit from an ontology of standardized COVID terms. The Coronavirus Infectious Disease Ontology (CIDO) is the largest among several COVID ontologies, a...
Computers in biology and medicine
Jun 8, 2021
BACKGROUND: Unstructured text created by patients represents a rich, but relatively inaccessible resource for advancing patient-centred care. This study aimed to develop an ontology for ocular immune-mediated inflammatory diseases (OcIMIDo), as a too...
Cladistics : the international journal of the Willi Hennig Society
May 28, 2021
We recently published a method to infer ancestral landmark-based shape ontogenies that takes into account the possible existence of changes in developmental timing. Here we describe SPASOS, a software to perform that analysis. SPASOS is an open-sourc...
Journal of biomedical semantics
Apr 16, 2021
BACKGROUND: Iranian traditional medicine, also known as Persian Medicine, is a holistic school of medicine with a long prolific history. It describes numerous concepts and the relationships between them. However, no unified language system has been p...
Journal of biomedical semantics
Apr 12, 2021
BACKGROUND: Biomedical ontologies contain a wealth of metadata that constitutes a fundamental infrastructural resource for text mining. For several reasons, redundancies exist in the ontology ecosystem, which lead to the same entities being described...
Journal of biomedical semantics
Mar 24, 2021
BACKGROUND: The amount of available data, which can facilitate answering scientific research questions, is growing. However, the different formats of published data are expanding as well, creating a serious challenge when multiple datasets need to be...