AIMC Topic: Biological Ontologies

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DermO; an ontology for the description of dermatologic disease.

Journal of biomedical semantics
BACKGROUND: There have been repeated initiatives to produce standard nosologies and terminologies for cutaneous disease, some dedicated to the domain and some part of bigger terminologies such as ICD-10. Recently, formally structured terminologies, o...

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

Journal of biomedical semantics
BACKGROUND: Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that descr...

Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications.

Journal of biomedical semantics
BACKGROUND: Clinical practice guidelines (CPGs) recommend pharmacologic treatments for clinical conditions, and drug structured product labels (SPLs) summarize approved treatment indications. Both resources are intended to promote evidence-based medi...

Generation of open biomedical datasets through ontology-driven transformation and integration processes.

Journal of biomedical semantics
BACKGROUND: Biomedical research usually requires combining large volumes of data from multiple heterogeneous sources, which makes difficult the integrated exploitation of such data. The Semantic Web paradigm offers a natural technological space for d...

Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events.

Journal of biomedical semantics
BACKGROUND: Neuropathy often occurs following drug treatment such as chemotherapy. Severe instances of neuropathy can result in cessation of life-saving chemotherapy treatment.

The cellular microscopy phenotype ontology.

Journal of biomedical semantics
BACKGROUND: Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and ...

An ontological model of the practice transformation process.

Journal of biomedical informatics
Patient-centered medical home is defined as an approach for providing comprehensive primary care that facilitates partnerships between individual patients and their personal providers. The current state of the practice transformation process is ad ho...

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

Journal of biomedical semantics
BACKGROUND: The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII fo...

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.

Journal of biomedical semantics
In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of informat...

OBIB-a novel ontology for biobanking.

Journal of biomedical semantics
BACKGROUND: Biobanking necessitates extensive integration of data to allow data analysis and specimen sharing. Ontologies have been demonstrated to be a promising approach in fostering better semantic integration of biobank-related data. Hitherto no ...