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SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes
BackgroundDespite a wide adoption of English in science, a significant amount of biomedical data are produced in other languages, such as French. Yet...
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CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata
BackgroundPublic biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these interfaces...
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Identifying diseases-related metabolites using random walk
BackgroundMetabolites disrupted by abnormal state of human body are deemed as the effect of diseases. In comparison with the cause of diseases like...
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An online tool for measuring and visualizing phenotype similarities using HPO
BackgroundThe Human Phenotype Ontology (HPO) is one of the most popular bioinformatics resources. Recently, HPO-based phenotype semantic similarity...
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A new synonym-substitution method to enrich the human phenotype ontology
BackgroundNamed entity recognition is critical for biomedical text mining, where it is not unusual to find entities labeled by a wide range of...
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Semantic Technologies and Bio-Ontologies
As information available through data repositories constantly grows, the need for automated mechanisms for linking, querying, and sharing data has...
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NOBLE – Flexible concept recognition for large-scale biomedical natural language processing
BackgroundNatural language processing (NLP) applications are increasingly important in biomedical data analysis, knowledge engineering, and decision...
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The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature
BackgroundThe Interaction Network Ontology (INO) logically represents biological interactions, pathways, and networks. INO has been demonstrated to...
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Text Mining for Precision Medicine: Bringing Structure to EHRs and Biomedical Literature to Understand Genes and Health
The key question of precision medicine is whether it is possible to find clinically actionable granularity in diagnosing disease and classifying...
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Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters
BackgroundOntological concepts are useful for many different biomedical tasks. Concepts are difficult to recognize in text due to a disconnect...
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USI: a fast and accurate approach for conceptual document annotation
BackgroundSemantic approaches such as concept-based information retrieval rely on a corpus in which resources are indexed by concepts belonging to a...
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Map** of Biomedical Text to Concepts of Lexicons, Terminologies, and Ontologies
Concept map** is a fundamental task in biomedical text mining in which textual mentions of concepts of interest are...
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KaBOB: ontology-based semantic integration of biomedical databases
BackgroundThe ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration...
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Map** biological entities using the longest approximately common prefix method
BackgroundThe significant growth in the volume of electronic biomedical data in recent decades has pointed to the need for approximate string...
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Toward knowledge support for analysis and interpretation of complex traits
The systematic description of complex traits, from the organism to the cellular level, is important for hypothesis generation about underlying...
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Role of Text Mining in Early Identification of Potential Drug Safety Issues
Drugs are an important part of today’s medicine, designed to treat, control, and prevent diseases; however, besides their therapeutic effects, drugs...
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STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation
BackgroundGene Ontology (GO) enrichment analysis remains one of the most common methods for hypothesis generation from high throughput datasets....
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