• Corpus ID: 26194364

Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench

@inproceedings{Romero2017SupportingOS,
  title={Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench},
  author={Marcos Mart{\'i}nez Romero and Martin J. O'Connor and Michael Dorf and Jennifer Vendetti and Debra Willrett and Attila Levente Egyedi and John Graybeal and Mark A. Musen},
  booktitle={ICBO},
  year={2017}
}
The availability of associated descriptive metadata for scientific datasets is important for discovering and reproducing scientific experiments. The use of ontologies has become a key focus for increasing the quality of these metadata. Despite the wide availability of biomedical ontologies, scientists wishing to use these ontologies when developing metadata descriptions face a number of practical difficulties. A core difficulty is the lack of tools for developing ontology-linked metadata… 

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References

SHOWING 1-10 OF 17 REFERENCES

Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations

A core component of this approach is a value recommendation framework that uses analysis of previously entered metadata and ontology-based metadata specifications to help users rapidly and accurately enter their metadata.

RightField: embedding ontology annotation in spreadsheets

RightField is an open source application that provides a mechanism for embedding ontology annotation support for Life Science data in Excel spreadsheets, enabling scientists to consistently annotate their data with 'semantic annotation by stealth'.

The National Center for Biomedical Ontology

The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal, which makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data.

The center for expanded data annotation and retrieval

The Center for Expanded Data Annotation and Retrieval is studying the creation of comprehensive and expressive metadata for biomedical datasets to facilitate data discovery, data interpretation, and

BioPortal: ontologies and integrated data resources at the click of a mouse

BioPortal not only provides investigators, clinicians, and developers ‘one-stop shopping’ to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.

An Open Repository Model for Acquiring Knowledge About Scientific Experiments

A pressing need for a metadata representation format that provides strong interoperation capabilities together with robust semantic underpinnings is described, together with open-source Web-based tools that support the acquisition, search, and management of metadata.

TermGenie – a web-application for pattern-based ontology class generation

TermGenie is a web-based class-generation system that complements traditional ontology development tools and is simple and intuitive and can be used by most biocurators without extensive training.

linkedISA: semantic representation of ISA-Tab experimental metadata

This work introduces the linkedISA conversion tool from ISA-Tab to the Resource Description Framework (RDF), supporting mappings from the ISA syntax to multiple community-defined, open ontologies and capitalising on user-provided ontology annotations in the experimental metadata.

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

Summary: The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing

Annotare—a tool for annotating high-throughput biomedical investigations and resulting data

Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis.