AIMC Topic: Software

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Using natural language processing to extract mammographic findings.

Journal of biomedical informatics
OBJECTIVE: Structured data on mammographic findings are difficult to obtain without manual review. We developed and evaluated a rule-based natural language processing (NLP) system to extract mammographic findings from free-text mammography reports.

Describing the breakbone fever: IDODEN, an ontology for dengue fever.

PLoS neglected tropical diseases
BACKGROUND: Ontologies represent powerful tools in information technology because they enhance interoperability and facilitate, among other things, the construction of optimized search engines. To address the need to expand the toolbox available for ...

Aber-OWL: a framework for ontology-based data access in biology.

BMC bioinformatics
BACKGROUND: Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within t...

PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease.

Database : the journal of biological databases and curation
Rats have been used extensively as animal models to study physiological and pathological processes involved in human diseases. Numerous rat strains have been selectively bred for certain biological traits related to specific medical interests. Recent...

ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life.

Bioinformatics (Oxford, England)
UNLABELLED: The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centr...

Biomedical question answering using semantic relations.

BMC bioinformatics
BACKGROUND: The proliferation of the scientific literature in the field of biomedicine makes it difficult to keep abreast of current knowledge, even for domain experts. While general Web search engines and specialized information retrieval (IR) syste...

Ontology-based data integration between clinical and research systems.

PloS one
Data from the electronic medical record comprise numerous structured but uncoded elements, which are not linked to standard terminologies. Reuse of such data for secondary research purposes has gained in importance recently. However, the identificati...

Predicting fecal sources in waters with diverse pollution loads using general and molecular host-specific indicators and applying machine learning methods.

Journal of environmental management
In this study we use a machine learning software (Ichnaea) to generate predictive models for water samples with different concentrations of fecal contamination (point source, moderate and low). We applied several MST methods (host-specific Bacteroide...

Development of system using beam's eye view images to measure respiratory motion tracking errors in image-guided robotic radiosurgery system.

Journal of applied clinical medical physics
The accuracy of the CyberKnife Synchrony Respiratory Tracking System (SRTS) is considered to be patient-dependent because the SRTS relies on an individual correlation between the internal tumor position (ITP) and the external marker position (EMP), a...

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.

Bioinformatics (Oxford, England)
MOTIVATION: Glycosylation is a ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes (BPs) such as cellular communication, ligand recognition and subcellular reco...