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

Tracking #: 2967-4181

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. The import was aligned 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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Reviewed

Decision/Status: 
Minor Revision

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Review #1
Anonymous submitted on 19/Jan/2022
Suggestion:
Minor Revision
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.

This paper presents advances as to how the WikiFCD knowledge base of Food Composition and Nutrient Values, is reusing terms from FoodOn— the Food Ontology. This is a worthwhile effort, that will ultimately contribute to much better interoperability and hopefully, easier access to data regarding the nutritional value of various food items, including international products and food stuffs. Their primary goal is to serve data to "food tracking applications” that individuals can use to monitor their dietary consumption patterns for nutrition, calories, etc.

While the article reports on some useful progress, I felt that some of the main features were not well-described in the text, nor the accompanying Figures. I also had issues following the logic in several places, and experienced challenges replicating some of the functionalities that were asserted in the paper. It may be that the various resources, like Wikidata, USDA FDC, or FoodON that are being “linked” with WikiFCD are themselves so dynamic that identifiers and associated contents have changed since the paper was authored. However, if that is the case, it would recommend some updating of the article.

Following are some more specific observations:

The title is somewhat misleading in its emphasis on “Reuse of FoodOn”, as there is much more description of linkages between WikiFCD and Wikidata. In fact, I could not detect any extant linkages between WikiFCD and FoodOn that could not be as readily achieved through the already established re-use of Wikidata by WikiFCD. This could use clarification, as Wikidata already provides rich multi-lingual information, as well as mappings to diverse taxonomic identifiers, including NCBI Taxon ID, and others.

FoodOn is hardly even mentioned until the end of pg. 3. Nor could I find any representation of FoodOn mappings in Figures 1-3. In Figure 4 there is a mapping that shows a relationship of WikiFCD with FoodON through a shared NCBI Taxon ID. However, in neither WikiFCD nor FoodON, are there any direct Biological Taxon identifier mappings to Food PRODUCTs per se. As an example neither “Tomato Paste (Q141709)” in WikiFCD, nor “Tomato Paste (FOODON:03301455) are explicitly linked to “Solanum lycopersicum( NCBI:4081)”. The expected axioms for making this connection of Food Product to the taxonomic entity from which it is derived— are accessible only by following a fairly long property chain in FoodOn. This is the case for most food products in FoodOn. Some additional detail about the value of using NCBI Taxon ID’s to make these links would be useful. It would seem more beneficial, e.g. to link FoodOn identifiers for the food products themselves to their analogues in WikiFCD.

The paper also mentions the benefit of re-using “food groupings” defined in FoodOn, but I could not identify any of these linkages in the WikiFCD resource. For example, “tomato paste” is a subclass several layers deep in FoodOn— being a “plant fruit food product” with subclass “solanaceous fruit food product” etc. Re-using these categorizations would make exploration of WikiFCD easier, but I could not test this in the WikiFCD interfaces suggested in the paper. Note that I tried to examine such linkages/re-uses using several exemplars, including Ice Cream (a FoodOn “Dairy product”?) and Potato Chips (FoodOn “Solanaceous root food product”?)— but could not find re-use of the FoodOn groupings.

In addition, unlike in Wikidata, linkages in WikiFCD were not readily dereferenceable. For example, when you search WikiFCD for “tomato paste” you get several dozens of results, many of which are simply labelled “Tomato Paste” without any more useful identifying information (e.g. Brand Labelling) to refine one's search. A direct HTTP URI to the item in the USDA FDC would be extremely helpful!!!

The author’s mention an example using the term: "Brussels Sprouts” and mention how this yields information on 218 products. Again, these are all described along with their (non- immediately dereferenceable USDA FDC ID's). One might however miss a search by misspelling "Brussels sprouts" as “Brussel sprouts” (N=9) or “Brussel sprout” (N=2). Small improvements to the search facilities in WikiFCD might ameliorate missed entries due to such small variations in the spelling of names.

In Section 6 allusion is made to a property “natural product of taxon” but I could not find where this was implemented in WikiFCD.

Small grammatical issues:
Abstract 18 “Wit”= “With"

p2.48: suggest renaming all properties indicating food content of various nutrients as "nutrient xx content” rather than just “nutrient xx": “Copper content” instead of “Copper"

Review #2
Anonymous submitted on 20/Jun/2022
Suggestion:
Minor Revision
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.

I think this paper is a great example of applications of ontologies, FoodOn in this particular instance. However, I think some of the properties used in this knowledge base create ambiguity. The authors go through a long explanation as to why they use "copper" as a property (along with other nutrient components). However, I think this is a good way of naming and/or querying for the proposed use of this knowledge base. I propose the authors represent the components' names and how the food items contain particular nutrients in a more systematic way that is more compatible with other research going on in this area.

Otherwise this is a well written paper for a useful Wiki Interface.

On the wiki page itself, users can find example queries which is useful.

Review #3
Anonymous submitted on 05/Jul/2022
Suggestion:
Accept
Review Comment:

I really enjoy reading this paper. It deals with a very sensitive topic. Food information. I appreciated the original approach of creating a wikiFCD and linking to the food ontology as well as other OBO foundry ontologies.