The Dataharmonizer: a Tool for Faster Data Harmonization, Validation, Aggregation, and Analysis of Pathogen Genomics Contextual Information

How to cite: Gill, I.; Griffiths, E.; Dooley, D.; Cameron, R.; Savić Kallesøe, S.; John, N.S.; Sehar, A.; Gosal, G.; Alexander, D.; Chapel, M.; Croxen, M.; Delisle, B.; Di Tullio, R.; Gaston, D.; Duggan, A.; Guthrie, J.; Horsman, M.; Joshi, E.; Kearney, L.; Knox, N.; Lau, L.; LeBlanc, J.; Li, V.; Lyons, P.; MacKenzie, K.; McArthur, A.; Panousis, E.; Palmer, J.; Prystajecky, N.; Smith, K.; Tanner, J.; Townend, C.; Tyler, A.; Van Domselaar, G.; Hsiao, W. The Dataharmonizer: a Tool for Faster Data Harmonization, Validation, Aggregation, and Analysis of Pathogen Genomics Contextual Information. Preprints 2022, 2022060335. https://doi.org/10.20944/preprints202206.0335.v1 Gill, I.; Griffiths, E.; Dooley, D.; Cameron, R.; Savić Kallesøe, S.; John, N.S.; Sehar, A.; Gosal, G.; Alexander, D.; Chapel, M.; Croxen, M.; Delisle, B.; Di Tullio, R.; Gaston, D.; Duggan, A.; Guthrie, J.; Horsman, M.; Joshi, E.; Kearney, L.; Knox, N.; Lau, L.; LeBlanc, J.; Li, V.; Lyons, P.; MacKenzie, K.; McArthur, A.; Panousis, E.; Palmer, J.; Prystajecky, N.; Smith, K.; Tanner, J.; Townend, C.; Tyler, A.; Van Domselaar, G.; Hsiao, W. The Dataharmonizer: a Tool for Faster Data Harmonization, Validation, Aggregation, and Analysis of Pathogen Genomics Contextual Information. Preprints 2022, 2022060335. https://doi.org/10.20944/preprints202206.0335.v1

Cite

Export citation file: Bib TeX | RIS

MDPI and ACS Style

Gill, I.; Griffiths, E.; Dooley, D.; Cameron, R.; Savić Kallesøe, S.; John, N.S.; Sehar, A.; Gosal, G.; Alexander, D.; Chapel, M.; Croxen, M.; Delisle, B.; Di Tullio, R.; Gaston, D.; Duggan, A.; Guthrie, J.; Horsman, M.; Joshi, E.; Kearney, L.; Knox, N.; Lau, L.; LeBlanc, J.; Li, V.; Lyons, P.; MacKenzie, K.; McArthur, A.; Panousis, E.; Palmer, J.; Prystajecky, N.; Smith, K.; Tanner, J.; Townend, C.; Tyler, A.; Van Domselaar, G.; Hsiao, W. The Dataharmonizer: a Tool for Faster Data Harmonization, Validation, Aggregation, and Analysis of Pathogen Genomics Contextual Information. Preprints 2022, 2022060335. https://doi.org/10.20944/preprints202206.0335.v1

APA Style

Gill, I., Griffiths, E., Dooley, D., Cameron, R., Savić Kallesøe, S., John, N.S., Sehar, A., Gosal, G., Alexander, D., Chapel, M., Croxen, M., Delisle, B., Di Tullio, R., Gaston, D., Duggan, A., Guthrie, J., Horsman, M., Joshi, E., Kearney, L., Knox, N., Lau, L., LeBlanc, J., Li, V., Lyons, P., MacKenzie, K., McArthur, A., Panousis, E., Palmer, J., Prystajecky, N., Smith, K., Tanner, J., Townend, C., Tyler, A., Van Domselaar, G., & Hsiao, W. (2022). The Dataharmonizer: a Tool for Faster Data Harmonization, Validation, Aggregation, and Analysis of Pathogen Genomics Contextual Information. Preprints. https://doi.org/10.20944/preprints202206.0335.v1

Chicago/Turabian Style

Gill, I., Gary Van Domselaar and William Hsiao. 2022 "The Dataharmonizer: a Tool for Faster Data Harmonization, Validation, Aggregation, and Analysis of Pathogen Genomics Contextual Information" Preprints. https://doi.org/10.20944/preprints202206.0335.v1

Abstract

Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations, as well as research. In order to make use of pathogen genomics data, it must be interpreted using contextual data (metadata). Contextual data includes sample metadata, laboratory methods, patient demographics, clinical outcomes, and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration, and its use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating, and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool’s web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission.In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.

Supplementary and Associated Material

https://github.com/cidgoh/DataHarmonizer/releases: DataHarmonizer GitHub repository (download app)

https://github.com/cidgoh/DataHarmonizer/wiki: DataHarmonizer Wiki

Keywords

metadata; contextual data; harmonization; genomic surveillance; data management

Subject

Computer Science and Mathematics, Information Systems

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Download PDF

Comments (0)

Not displayed online.

Importance: How significant is the paper to the field?

Outstanding/highlight paper

Significant contribution

Incremental contribution

No contribution

I am not qualified to judge

Soundness of evidence/arguments presented:

Conclusions well supported

Most conclusions supported (minor revision needed)

Incomplete evidence (major revision needed)

Hypothesis, unsupported conclusions, or proof-of-principle

I am not qualified to judge

Please leave your comment to this article below.

Mathematical equations can be typed in either LaTeX formats \\[ ... \\] or $$ ... $$, or MathML format <math> ... </math>. Try the LaTeX or MathML example.

Type equation:

Preview:

Copy equation into message below

Close menu

Please click a symbol to insert it into the message box below:

Please enter the link here:

Please enter a valid URL

Optionally, you can enter text that should appear as linked text:

Copy link into message below

Close menu

Please enter or paste the URL to the image here (please only use links to jpg/jpeg, png and gif images):

Please enter a valid URL

Copy image into message below

Close menu

Type author name or keywords to filter the list of references in this group (you can add a new citation under Bibliography):

No existing citations in Discussion Group

Wikify editor is a simple editor for wiki-style mark-up. It was written by MDPI for Sciforum in 2014. The rendering of the mark-up is based on Wiky.php with some tweaks. Rendering of mathematical equations is done with MathJax. Please send us a message for support or for reporting bugs.

Close menu

Please declare any conflicts of interest you may have with this paper, financial or otherwise.

I do not have a conflict of interest

I would like to declare a conflict of interest

Display my name on the website Send my name and email address to the authors

Captcha

Renew

I accept the following conditions:

Comments must follow the standards of professional discourse and should focus on the scientific content of the article. Insulting or offensive language, personal attacks and off-topic remarks will not be permitted. Comments must be written in English. Preprints reserves the right to remove comments without notice. Readers who post comments are obliged to declare any competing interests, financial or otherwise.

We encourage comments and feedback from a broad range of readers. See criteria for comments and our Diversity statement.

Leave a public comment
Send a private comment to the author(s)

* All users must log in before leaving a comment

what’s this?

Add a record of this review to Publons to track and showcase your reviewing expertise across the world’s journals.

Downloads 0

Comments 0

Metrics 0

Get PDF Cite Share 0

Bookmark BibSonomy Mendeley Reddit Delicious

Alerts

Notify me about updates to this article or when a peer-reviewed version is published.

Preprints.org is a free preprint server subsidized by MDPI in Basel, Switzerland.

MDPI Initiatives

SciProfiles
Sciforum
Encyclopedia
MDPI Books
Scilit
Proceedings
JAMS

Important links

How it Works
Advisory Board
FAQ
Friendly Journals
Instructions for Authors
About
Statistics

Choose the area that interest you and we will send you notifications of new preprints at your preferred frequency.

Disclaimer

We use cookies on our website to ensure you get the best experience.
Read more about our cookies here.

RSS feed for

Preprints: The Multidisciplinary Preprint Platform

Paste the URL in your RSS reader:

https://www.preprints.org/rss

If you want to subscribe our website in subject-wide, you could find the URL by choosing in the following:

https://www.preprints.org/rss

Please note that by using ScienceDirect RSS feeds, you agree to our Terms of Use and Privacy Policy.