AIMC Topic: Biological Ontologies
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Cell ontology in an age of data-driven cell classification.
BMC bioinformatics
Dec 21, 2017
BACKGROUND: Data-driven cell classification is becoming common and is now being implemented on a massive scale by projects such as the Human Cell Atlas. The scale of these efforts poses a challenge. How can the results be made searchable and accessib...
Cell type discovery and representation in the era of high-content single cell phenotyping.
BMC bioinformatics
Dec 21, 2017
BACKGROUND: A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs a...
Auditing SNOMED CT hierarchical relations based on lexical features of concepts in non-lattice subgraphs.
Journal of biomedical informatics
Dec 20, 2017
OBJECTIVE: We introduce a structural-lexical approach for auditing SNOMED CT using a combination of non-lattice subgraphs of the underlying hierarchical relations and enriched lexical attributes of fully specified concept names. Our goal is to develo...
Integrating phenotype ontologies with PhenomeNET.
Journal of biomedical semantics
Dec 19, 2017
BACKGROUND: Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomical details being captured in c...
A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes.
Scientific reports
Dec 18, 2017
Whole cell responses arise from coordinated interactions between diverse human gene products functioning within various pathways underlying sub-cellular processes (SCP). Lower level SCPs interact to form higher level SCPs, often in a context specific...
Identifying genotype-phenotype relationships in biomedical text.
Journal of biomedical semantics
Dec 6, 2017
BACKGROUND: One important type of information contained in biomedical research literature is the newly discovered relationships between phenotypes and genotypes. Because of the large quantity of literature, a reliable automatic system to identify thi...
Experiences from the anatomy track in the ontology alignment evaluation initiative.
Journal of biomedical semantics
Dec 4, 2017
BACKGROUND: One of the longest running tracks in the Ontology Alignment Evaluation Initiative is the Anatomy track which focuses on aligning two anatomy ontologies. The Anatomy track was started in 2005. In 2005 and 2006 the task in this track was to...
Matching disease and phenotype ontologies in the ontology alignment evaluation initiative.
Journal of biomedical semantics
Dec 2, 2017
BACKGROUND: The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data ...
A document-centric approach for developing the tolAPC ontology.
Journal of biomedical semantics
Nov 28, 2017
BACKGROUND: There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometime...
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes.
Journal of biomedical semantics
Nov 23, 2017
BACKGROUND: High-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these data together with biological knowledge is a critical issue in biology and requires integrative tools and methods...
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