AIMC Topic: Knowledge Bases
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Patient and Graph Embeddings for Predictive Diagnosis of Drug Iatrogenesis.
Studies in health technology and informatics
May 27, 2021
In the context of the IA.TROMED project we intend to develop and evaluate original algorithmic methods that will rely on semantic enrichment of embeddings by combining new deep learning algorithms, such as models founded on transformers, and symbolic...
A representation model for biological entities by fusing structured axioms with unstructured texts.
Bioinformatics (Oxford, England)
May 23, 2021
MOTIVATION: Structured semantic resources, for example, biological knowledge bases and ontologies, formally define biological concepts, entities and their semantic relationships, manifested as structured axioms and unstructured texts (e.g. textual de...
Integrative biomarker detection on high-dimensional gene expression data sets: a survey on prior knowledge approaches.
Briefings in bioinformatics
May 20, 2021
Gene expression data provide the expression levels of tens of thousands of genes from several hundred samples. These data are analyzed to detect biomarkers that can be of prognostic or diagnostic use. Traditionally, biomarker detection for gene expre...
LBERT: Lexically aware Transformer-based Bidirectional Encoder Representation model for learning universal bio-entity relations.
Bioinformatics (Oxford, England)
Apr 20, 2021
MOTIVATION: Natural Language Processing techniques are constantly being advanced to accommodate the influx of data as well as to provide exhaustive and structured knowledge dissemination. Within the biomedical domain, relation detection between bio-e...
UniProt: the universal protein knowledgebase in 2021.
Nucleic acids research
Jan 8, 2021
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over ...
Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology.
Nucleic acids research
Jan 8, 2021
The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for the laboratory mouse, a widely used animal model for comparative studies of the genetic and genomic basis for human health and disease. ...
canSAR: update to the cancer translational research and drug discovery knowledgebase.
Nucleic acids research
Jan 8, 2021
canSAR (http://cansar.icr.ac.uk) is the largest, public, freely available, integrative translational research and drug discovery knowledgebase for oncology. canSAR integrates vast multidisciplinary data from across genomic, protein, pharmacological, ...
Open Targets Platform: supporting systematic drug-target identification and prioritisation.
Nucleic acids research
Jan 8, 2021
The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence. It is publicl...
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases.
Nucleic acids research
Jan 8, 2021
Kinases form the backbone of numerous cell signaling pathways, with their dysfunction similarly implicated in multiple pathologies. Further facilitated by their druggability, kinases are a major focus of therapeutic development efforts in diseases su...
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.
Nucleic acids research
Jan 8, 2021
Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons), inferring their activities across a range of conditions, and enabling their ass...
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