Reuse of the FoodOn Ontology in a Knowledge Base of Food Composition Data

Submitted by Katherine Thornton on 08/04/2022 - 11:10

Tracking #: 3207-4421

Authors: 
Katherine Thornton
Kenneth Seals-Nutt
Mika Matsuzaki
Damion Dooley

Responsible editor: 
Guest Editors Global Food System 2021

Submission type: 
Full Paper
Abstract: 
We describe our work to integrate the FoodOn ontology with our knowledge base of food composition data, WikiFCD. WikiFCD is knowledge base of structured data related to food composition and food items. With a goal to reuse FoodOn identifiers for food items, we imported a subset of the FoodOn ontology into the WikiFCD knowledge base. We aligned the import via a shared use of NCBI taxon identifiers for the taxon names of the plants from which the food items are derived. Reusing FoodOn benefits WikiFCD by allowing us to leverage the food item groupings that FoodOn contains. This integration also has potential future benefits for the FoodOn community due to the fact that WikiFCD provides food composition data at the food item level, and that WikiFCD is mapped to Wikidata and contains a SPARQL endpoint that supports federated queries. Federated queries across WikiFCD and Wikidata allow us to ask questions about food items that benefit from the cross-domain information of Wikidata, greatly increasing the breadth of possible data combinations.
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Reuse of the FoodOn Ontology in a Knowledge Base of Food Composition Data
Tags: 
Reviewed

Decision/Status: 
Accept

Solicited Reviews:
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Review #1
By Anne Thessen submitted on 01/Sep/2022
Suggestion:
Minor Revision
Review Comment:

Overall, this is an interesting paper. I think making the types of connections that are described in this paper will be helpful for my work. I have a few minor suggestions.
1. I find that referring to properties by number can be confusing. This could just be me and is not an important change.
2. When I visited tinyurl.com/28uu3sm5 I got a "query malformed" error.
3. page 7 line 51 "that has" should be "that have"
4. page 8 line 12 "diaries and" should be "diaries are"
5. If you need an identifier for a taxon that is not in NCBI you would probably have more luck looking in Catalog of Life or Encyclopedia of Life. This is not an important change.

Review #2
Anonymous submitted on 05/Oct/2022
Suggestion:
Accept
Review Comment:

This manuscript was submitted as 'full paper' and should be reviewed along the usual dimensions for research contributions which include (1) originality, (2) significance of the results, and (3) quality of writing. Please also assess the data file provided by the authors under “Long-term stable URL for resources”. In particular, assess (A) whether the data file is well organized and in particular contains a README file which makes it easy for you to assess the data, (B) whether the provided resources appear to be complete for replication of experiments, and if not, why, (C) whether the chosen repository, if it is not GitHub, Figshare or Zenodo, is appropriate for long-term repository discoverability, and (4) whether the provided data artifacts are complete. Please refer to the reviewer instructions and the FAQ for further information.

Review #3
Anonymous submitted on 13/Oct/2022
Suggestion:
Accept
Review Comment:

This manuscript was submitted as 'full paper' and should be reviewed along the usual dimensions for research contributions which include (1) originality, (2) significance of the results, and (3) quality of writing. Please also assess the data file provided by the authors under “Long-term stable URL for resources”. In particular, assess (A) whether the data file is well organized and in particular contains a README file which makes it easy for you to assess the data, (B) whether the provided resources appear to be complete for replication of experiments, and if not, why, (C) whether the chosen repository, if it is not GitHub, Figshare or Zenodo, is appropriate for long-term repository discoverability, and (4) whether the provided data artifacts are complete. Please refer to the reviewer instructions and the FAQ for further information.