AIMC Topic: Semantics

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The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes.

Journal of biomedical semantics
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...

Using semantics for representing experimental protocols.

Journal of biomedical semantics
BACKGROUND: An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references t...

False memory for orthographically versus semantically similar words in adolescents with dyslexia: a fuzzy-trace theory perspective.

Annals of dyslexia
The presented research was conducted in order to investigate the connections between developmental dyslexia and the functioning of verbatim and gist memory traces-assumed in the fuzzy-trace theory. The participants were 71 high school students (33 wi...

Drug target ontology to classify and integrate drug discovery data.

Journal of biomedical semantics
BACKGROUND: One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research...

Entity recognition in the biomedical domain using a hybrid approach.

Journal of biomedical semantics
BACKGROUND: This article describes a high-recall, high-precision approach for the extraction of biomedical entities from scientific articles.

Artificial Intelligence Learning Semantics via External Resources for Classifying Diagnosis Codes in Discharge Notes.

Journal of medical Internet research
BACKGROUND: Automated disease code classification using free-text medical information is important for public health surveillance. However, traditional natural language processing (NLP) pipelines are limited, so we propose a method combining word emb...

Semantic biclustering for finding local, interpretable and predictive expression patterns.

BMC genomics
BACKGROUND: One of the major challenges in the analysis of gene expression data is to identify local patterns composed of genes showing coherent expression across subsets of experimental conditions. Such patterns may provide an understanding of under...

A new synonym-substitution method to enrich the human phenotype ontology.

BMC bioinformatics
BACKGROUND: Named entity recognition is critical for biomedical text mining, where it is not unusual to find entities labeled by a wide range of different terms. Nowadays, ontologies are one of the crucial enabling technologies in bioinformatics, pro...

Querying clinical data in HL7 RIM based relational model with morph-RDB.

Journal of biomedical semantics
BACKGROUND: Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to heterogeneous data sources. One p...

Towards refactoring the Molecular Function Ontology with a UML profile for function modeling.

Journal of biomedical semantics
BACKGROUND: Gene Ontology (GO) is the largest resource for cataloging gene products. This resource grows steadily and, naturally, this growth raises issues regarding the structure of the ontology. Moreover, modeling and refactoring large ontologies s...