AI Medical Compendium Topic:
Semantics

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Natural language processing in text mining for structural modeling of protein complexes.

BMC bioinformatics
BACKGROUND: Structural modeling of protein-protein interactions produces a large number of putative configurations of the protein complexes. Identification of the near-native models among them is a serious challenge. Publicly available results of bio...

Gene function prediction based on Gene Ontology Hierarchy Preserving Hashing.

Genomics
Gene Ontology (GO) uses structured vocabularies (or terms) to describe the molecular functions, biological roles, and cellular locations of gene products in a hierarchical ontology. GO annotations associate genes with GO terms and indicate the given ...

Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.

Journal of biomedical informatics
With the proliferation of heterogeneous health care data in the last three decades, biomedical ontologies and controlled biomedical terminologies play a more and more important role in knowledge representation and management, data integration, natura...

DMTO: a realistic ontology for standard diabetes mellitus treatment.

Journal of biomedical semantics
BACKGROUND: Treatment of type 2 diabetes mellitus (T2DM) is a complex problem. A clinical decision support system (CDSS) based on massive and distributed electronic health record data can facilitate the automation of this process and enhance its accu...

Distant supervision for neural relation extraction integrated with word attention and property features.

Neural networks : the official journal of the International Neural Network Society
Distant supervision for neural relation extraction is an efficient approach to extracting massive relations with reference to plain texts. However, the existing neural methods fail to capture the critical words in sentence encoding and meanwhile lack...

OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system.

Journal of biomedical semantics
BACKGROUND: The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowled...

Tackling the challenges of matching biomedical ontologies.

Journal of biomedical semantics
BACKGROUND: Biomedical ontologies pose several challenges to ontology matching due both to the complexity of the biomedical domain and to the characteristics of the ontologies themselves. The biomedical tracks in the Ontology Matching Evaluation Init...

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.

Journal of biomedical semantics
Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ...

Gene ontology concept recognition using named concept: understanding the various presentations of the gene functions in biomedical literature.

Database : the journal of biological databases and curation
OBJECTIVE: A major challenge in precision medicine is the development of patient-specific genetic biomarkers or drug targets. The firsthand information of the genes associated with the pathologic pathways of interest is buried in the ocean of biomedi...

Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism.

BMC systems biology
BACKGROUND: Rheumatism represents any disease condition marked with inflammation and pain in the joints, muscles, or connective tissues. Many traditional Chinese drugs have been used for a long time to treat rheumatism. However, a comprehensive infor...