AIMC Topic: Biological Ontologies
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Reporting and connecting cell type names and gating definitions through ontologies.
BMC bioinformatics
Apr 25, 2019
BACKGROUND: Human immunology studies often rely on the isolation and quantification of cell populations from an input sample based on flow cytometry and related techniques. Such techniques classify cells into populations based on the detection of a p...
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation.
BMC bioinformatics
Apr 25, 2019
BACKGROUND: Stem cells and stem cell lines are widely used in biomedical research. The Cell Ontology (CL) and Cell Line Ontology (CLO) are two community-based OBO Foundry ontologies in the domains of in vivo cells and in vitro cell line cells, respec...
Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies.
BMC bioinformatics
Apr 25, 2019
Cell cultures and cell lines are widely used in life science experiments. In conjunction with the 2018 International Conference on Biomedical Ontology (ICBO-2018), the 2nd International Workshop on Cells in ExperimentaL Life Science (CELLS-2018) focu...
An ontology for representing hematologic malignancies: the cancer cell ontology.
BMC bioinformatics
Apr 25, 2019
BACKGROUND: Within the cancer domain, ontologies play an important role in the integration and annotation of data in order to support numerous biomedical tools and applications. This work seeks to leverage existing standards in immunophenotyping cell...
The cell line ontology-based representation, integration and analysis of cell lines used in China.
BMC bioinformatics
Apr 25, 2019
BACKGROUND: The Chinese National Infrastructure of Cell Line stores and distributes cell lines for biomedical research in China. This study aims to represent and integrate the information of NICR cell lines into the community-based Cell Line Ontology...
Concept embedding to measure semantic relatedness for biomedical information ontologies.
Journal of biomedical informatics
Apr 19, 2019
There have been many attempts to identify relationships among concepts corresponding to terms from biomedical information ontologies such as the Unified Medical Language System (UMLS). In particular, vector representation of such concepts using infor...
Interactive biomedical ontology matching.
PloS one
Apr 17, 2019
Due to continuous evolution of biomedical data, biomedical ontologies are becoming larger and more complex, which leads to the existence of many overlapping information. To support semantic inter-operability between ontology-based biomedical systems,...
Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO.
BMC systems biology
Apr 5, 2019
BACKGROUND: Improving efficiency of disease diagnosis based on phenotype ontology is a critical yet challenging research area. Recently, Human Phenotype Ontology (HPO)-based semantic similarity has been affectively and widely used to identify causati...
A mode-of-action ontology model for safety evaluation of chemicals: Outcome of a series of workshops on repeated dose toxicity.
Toxicology in vitro : an international journal published in association with BIBRA
Apr 4, 2019
Repeated dose toxicity evaluation aims at assessing the occurrence of adverse effects following chronic or repeated exposure to chemicals. Non-animal approaches have gained importance in the last decades because of ethical considerations as well as d...
DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.
Cell systems
Mar 13, 2019
Systems biology requires not only genome-scale data but also methods to integrate these data into interpretable models. Previously, we developed approaches that organize omics data into a structured hierarchy of cellular components and pathways, call...
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