CEDAR OnDemand is a Chrome browser extension that helps users create standardized metadata on web forms. It utilizes ontology web services from NCBO to provide controlled vocabularies for metadata fields. When activated on a web form, it analyzes the form and recommends relevant ontology terms based on field descriptions. This allows standardized metadata creation within existing repository interfaces without code changes. The goal is to facilitate high-quality FAIR metadata generation through public repository submission forms.

1. CEDAR
An intelligent browser extension to generate
ontology-based metadata.
OnDemand
Syed Ahmad Chan Bukhari, PhD
ahmad.chan@yale.edu

2. Importance of Scientific Metadata
● Scientific data are generated by experiments or observations.
● Datasets must be accompanied by auxiliary information in order to be
interpreted and accessed.
Metadata helps
● Datasets more understandable for humans and processable for the machines
● Scientific data analysis- often requires multiple datasets to be integrated
across multiple repositories.
● Discovery in the large variety of scientific datasets and support reproducibility.

3. What is the high-quality metadata?
● Datasets and their metadata should be identifiable globally, described using
standardized terminologies, and available in a standardized machine readable
format.

4. Challenges with the generation of high-quality
metadata
● The diversity of metadata representation formats and the poor support for
semantic markup typically result in metadata that are of poor quality.
Metadata Diversity in NCBI repositories

5. Current practices towards data standardization
● Scientific communities have developed templates incorporating detailed
checklists of the metadata needed to describe about the particular types of
experimental data sources.
● Minimum information standards such as
○ MIAME: Minimum information about a microarray experiment
○ MIAPE: Minimum Information About a Proteomics Experiment
● What is the minimum amount of information (metadata) needed for reporting
results in a reproducible and reusable fashion.

6. Metadata Standardization and availability
● A large number of public repositories use these community derived templates
to collect metadata from users
FAIRsharing provides a central catalog of existing standards
and data formats.

7. Metadata Standardization and availability

8. CEDAR helps to generate FAIR metadata

9. CEDAR Advantages over conventional
approaches
● Decrease authoring time
○ Suggest values
○ Pre-filling some of the fields
○ Extract metadata from unstructured sources
● Increase metadata quality (accurate, complete, standardized data)
○ No mistakes and inconsistencies
○ Validation (required values, format, data types)
○ Standardized metadata (ontologies)
○ Accurate, complete, standardized

10. CEDAR provides run-time recommendations

11. CEDAR can help editing metadata within its
environment
● CEDAR template designing and metadata approaches are centralized.
● Outside of the CEDAR workbench, there are a number of existing portals
providing conventional metadata submitting environments.

13. ● CEDAR OnDemand is a browser extension
○ An extension is essentially a small software program that can access
contents of a web page, modify it and can enhance the functionality of a web
browser.

14. Most of public data repositories provide web
interfaces
● The lack of standardization in the collected metadata limits the source datasets to
be broadly discovered and reused.
● The creation of standardized metadata can be facilitated using standard
vocabularies/ontologies.
● CEDAR have developed technologies to facilitate high-quality metadata authoring.
● While CEDAR has been working closely with several data providers to implement
such pipelines, there is a communication and implementation overhead.

15. ● To reach out to the maximum available public biomedical data repositories and
enable users to generate ontology linked standardised metadata within the
repository specific environment.
● This approach enables the user to seamlessly enter ontologically-controlled
metadata through existing web forms native to individual repositories.
● CEDAR OnDemand helps lower the barrier of incorporating ontologies into
standardized metadata entry for public data repositories.
The key advantage of this approach is that it facilitates the creation of
ontology-annotated metadata into existing web forms without requiring
the individual repositories to change any code.

16. A manifest file is the entry point for the chrome extension script to take
action

17. ● CEDAR OnDemand facilitates users to create standardised machine readable
metadata on web forms accessible through WWW.
● It can have its own interface to operate or can work seamlessly without providing
any graphical interface.
● CEDAR OnDemand utilizes the CEDAR terminology API server and the NCBO
web services to access ontologies available on bioportal and to predict relevant
metadata.

19. ● Upon activation, CEDAR OnDemand script analyses a web page contents
through the browser document object model (DOM), which defines the
content, structure and style of an HTML document.
● To predict the field specific ontology pool, CEDAR OnDemand script takes
associated text of input fields in a webpage as inputs and invokes the CEDAR
ontology server API through restful web services.
● To access the biomedical ontologies available on bioportal through CEDAR
ontology server API, we use AJAX (asynchronous JavaScript and XML).
AJAX communicates with CEDAR server asynchronously (in the background)
through XMLHttpRequest Object to send and retrieve the data.

20. http://data.bioontology.org
Ontology
Search
• Download
• Traverse
• Search
• Comment
Widgets
• Tree-view
• Auto-complete
• Graph-view
Annotator
Recommender
Mapping
Services
• Create
• Download
• Upload
● Term recognition
● Ontology
association
● Class
Recommendation
http://bioportal.bioontology.org
NCBO Tools and services in summary

21. ● Our algorithm syntactically matches the keywords mentioned in associated text of
the field with the ontology description and fetches the relevant ontology URI
(Universal Resource Identifier).
● To find the relevant ontology terms, our algorithm looks from the domain ontology
first. [NCBITAXON, DOID, GO, OBI, PR,CL]
● Our approach narrows down the scope of ontology class research which helps to
provide relevant semantic vocabulary runtime.
● While functioning, CEDAR OnDemand displays most relevant classes run-time
when to author scientific metadata.

22. CEDAR OnDemand In action

23. CEDAR OnDemand In action

24. Other potential usage of CEDAR OnDemand
What could be other application areas?

25. ● Auto-reading the web page contents, Its vulnerable, could be used for
browser based eavesdropping attacks. E.g passwords, Credit Card
■ Gave control to users through manual activation
● Diversity in the input field. E.g <input type=text, <div, <inputfield, <text
■ Support <input type=text, <div, HTML5
■ Limited support for twitter bootstrap
● Right ontology selection. Most of the ontologies in bioportal do not have
definitions and description.
■ String mapping algorithm is currently used to fetch the right ontology ID
● Run-time delay
■ Limited to a set of ontologies
(challenges and limitations)

26. Future Work
● Topic to ontology prediction is the area where I have plan to focus in future to
increase the precision.
● Required more metadata to display run-time e.g definitions It takes several
minutes to display with in current setup.
○ Downloading ontologies to a local server could be possible solution
● Auto-filling feature would a great addition based on the pre filled fields

27. Summary
● CEDAR OnDemand is a Chrome browser extension that help to create
standardized high-quality metadata on the web forms available on web.
● It utilizes the functionality of cutting edge ontology web services and tools
available at the NCBO and CEDAR workbench and make them available out of
their working environment
● CEDAR OnDemand is an application independent browser extension which can
work on mobile platform as well.

28. Availability
● CEDAR OnDemand is available on chrome webstore freely. Source code can be
accessed at Github http:/github.com/ahmadchan/cedarondemand

29. Acknowledgement
Kei-Hoi Cheung, Yale University, Dept. of Medical Informatics
Kleinstein Lab, Yale University, Dept. of Pathology