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… Expand
Embracing Semantic Technology for Better Metadata Authoring in Biomedicine
TLDR
The architecture of the CEDAR Workbench is presented and on the technology choices made to construct an easily usable, open system that allows users to create and publish semantically enriched metadata in standard Web formats are focused on. Expand
The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments
TLDR
The CEDAR Workbench provides a versatile, REST-based environment for authoring metadata that are enriched with terms from ontologies for easy integration in scientific applications and reusability on the Web. Expand
Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases
TLDR
A recommendation system for metadata that uses association rule mining to uncover hidden associations among metadata values and to represent them in the form of association rules to present users with real-time recommendations when authoring metadata. Expand
Using semantic technologies to enhance metadata submissions to public repositories in biomedicine
TLDR
This paper describes a system called CEDAR, which provides a flexi- ble, highly configurable solution for producing submission workflows with highly descriptive metadata support and outlines how these tools have been used to deliver robust metadata submission pipelines for several communities. Expand
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies
TLDR
Overall, the metadata in BioSample reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements, and the aberrancies in the metadata are likely to impede search and secondary use of the associated datasets. Expand
The variable quality of metadata about biological samples used in biomedical experiments
TLDR
Overall, the metadata the authors analyzed reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements, and significant aberrancies that are likely to impede search and secondary use of the associated datasets. Expand

References

SHOWING 1-10 OF 17 REFERENCES
Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations
TLDR
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. Expand
RightField: embedding ontology annotation in spreadsheets
TLDR
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'. Expand
The National Center for Biomedical Ontology
TLDR
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. Expand
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, andExpand
An Open Repository Model for Acquiring Knowledge About Scientific Experiments
TLDR
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. Expand
TermGenie – a web-application for pattern-based ontology class generation
TLDR
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. Expand
linkedISA: semantic representation of ISA-Tab experimental metadata
TLDR
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. Expand
BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse
TLDR
BioPortal is an open repository of biomedical ontologies that provides programmatic and web-based access to ontologies developed in OBO, OWL, Protege frames, and RDF. Expand
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 employingExpand
Annotare—a tool for annotating high-throughput biomedical investigations and resulting data
TLDR
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. Expand
...
1
2
...