CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata

BMC Bioinformatics
Syed Ahmad Chan BukhariSteven H Kleinstein

Abstract

Public biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these interfaces typically reflect the ad hoc metadata specification practices of the associated repositories, leading to a lack of standardization in the collected metadata. This lack of standardization limits the ability of the source datasets to be broadly discovered, reused, and integrated with other datasets. To increase reuse, discoverability, and reproducibility of the described experiments, datasets should be appropriately annotated by using agreed-upon terms, ideally from ontologies or other controlled term sources. This work presents "CEDAR OnDemand", a browser extension powered by the NCBO (National Center for Biomedical Ontology) BioPortal that enables users to seamlessly enter ontology-based metadata through existing web forms native to individual repositories. CEDAR OnDemand analyzes the web page contents to identify the text input fields and associate them with relevant ontologies which are recommended automatically based upon input fields' labels (using the NCBO ontology recommender) and a pre-defined list of ontologies. These field-specific ontologies are used for controlling metadata entry. CEDAR O...Continue Reading

References

Dec 19, 2003·Nucleic Acids Research·Todd W HarrisLincoln D Stein
Oct 13, 2007·Nucleic Acids Research·Kirill DegtyarenkoMichael Ashburner
Dec 6, 2007·BMC Bioinformatics·Darren A NataleCathy H Wu
Jun 2, 2009·Nucleic Acids Research·Natalya F NoyMark A Musen
Jan 7, 2011·BMC Bioinformatics·Terrence F MeehanAlexander D Diehl
Feb 10, 2011·Standards in Genomic Sciences·Carsten KettnerPatricia L Whetzel
Nov 15, 2011·Nucleic Acids Research·Lynn Marie SchrimlWarren Alden Kibbe
Dec 6, 2011·Nucleic Acids Research·Scott Federhen
Dec 6, 2011·Nucleic Acids Research·Tanya BarrettJames Ostell
Feb 2, 2012·Genome Biology·Christopher J MungallMelissa A Haendel
Jun 6, 2013·Journal of Biomedical Semantics·Randi VitaBjoern Peters
Jun 6, 2013·Journal of Biomedical Semantics·Patricia L Whetzel, UNKNOWN NCBO Team
Jan 1, 2014·Journal of Biomedical Semantics·Sirarat SarntivijaiYongqun He
Mar 16, 2016·Scientific Data·Mark D WilkinsonBarend Mons
Mar 3, 2017·Plant Methods·Timothy M Beissinger, Gota Morota
Jun 9, 2017·Journal of Biomedical Semantics·Marcos Martínez-RomeroMark A Musen
Nov 23, 2017·Frontiers in Immunology·Felix BredenThomas B Kepler

❮ Previous
Next ❯

Methods Mentioned

BETA
BioSample

Software Mentioned

Windows
Linux
Recommender
Uber Anatomy Ontology ( UBERON )
CEDAR OnDemand
MiAIRR
Ontology Lookup Service ( OLS )
Google Chrome
NCBO
Firefox

Related Concepts

Related Feeds

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.

Related Papers

Summit on Translational Bioinformatics
Clement JonquetMark Musen
Journal of Biomedical Semantics
Patricia L Whetzel, NCBO team
Journal of the American Medical Informatics Association : JAMIA
Mark MusenNCBO team
© 2022 Meta ULC. All rights reserved