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Knowledge Bases

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A curated knowledgebase on endocrine disrupting chemicals and their biological systems-level perturbations.

The Science of the total environment
Human well-being can be affected by exposure to several chemicals in the environment. One such group is endocrine disrupting chemicals (EDCs) that can perturb the hormonal homeostasis leading to adverse health effects. In this work, we have developed...

Dual CNN for Relation Extraction with Knowledge-Based Attention and Word Embeddings.

Computational intelligence and neuroscience
Relation extraction is the underlying critical task of textual understanding. However, the existing methods currently have defects in instance selection and lack background knowledge for entity recognition. In this paper, we propose a knowledge-based...

Enhancing ontology-driven diagnostic reasoning with a symptom-dependency-aware Naïve Bayes classifier.

BMC bioinformatics
BACKGROUND: Ontology has attracted substantial attention from both academia and industry. Handling uncertainty reasoning is important in researching ontology. For example, when a patient is suffering from cirrhosis, the appearance of abdominal vein v...

SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.

Neuron
Synapses are fundamental information-processing units of the brain, and synaptic dysregulation is central to many brain disorders ("synaptopathies"). However, systematic annotation of synaptic genes and ontology of synaptic processes are currently la...

Uncovering the structure of self-regulation through data-driven ontology discovery.

Nature communications
Psychological sciences have identified a wealth of cognitive processes and behavioral phenomena, yet struggle to produce cumulative knowledge. Progress is hamstrung by siloed scientific traditions and a focus on explanation over prediction, two issue...

MCRDR Knowledge-Based 3D Dialogue Simulation in Clinical Training and Assessment.

Journal of medical systems
Dialogue-based simulation is a real-world practice technique for medical and clinical education that provides students with an opportunity to train using hands-on experiences without putting actual patients being put at risk. In this paper, a 3D inte...

Knowledge-guided convolutional networks for chemical-disease relation extraction.

BMC bioinformatics
BACKGROUND: Automatic extraction of chemical-disease relations (CDR) from unstructured text is of essential importance for disease treatment and drug development. Meanwhile, biomedical experts have built many highly-structured knowledge bases (KBs), ...

Discrimination power of knowledge-based potential dictated by the dominant energies in native protein structures.

Amino acids
Extracting a well-designed energy function is important for protein structure evaluation. Knowledge-based potential functions are one type of the energy functions which can be obtained from known protein structures. The pairwise potential between ato...

Integrating Bonded and Nonbonded Potentials in the Knowledge-Based Scoring Function for Protein Structure Prediction.

Journal of chemical information and modeling
An accurate energy scoring function is crucial for protein structure prediction. Given the increasing number of experimentally determined structures, knowledge-based approaches have been widely used to develop scoring functions for protein structure ...