Editing Talk:Mika/Temp/WikiFCD

=Related Work=
This paper from ISWC 2019 describes a knowledge graph that includes nutrient data.
[http://www.cs.rpi.edu/~zaki/PaperDir/ISWC19.pdf]
Data:
[https://foodkg.github.io/foodkg.html]

=Wikiprojects to notify=
* [https://www.wikidata.org/wiki/Wikidata:WikiProject_Food Wikiproject Food]
:: What's the best to notify them? [[User:Mika|Mika]] ([[User talk:Mika|talk]]) 12:33, 20 January 2020 (EST)
::: I think there is a ping project template that we can use. [https://www.wikidata.org/wiki/Template:Ping_project Ping Project]. [[User:Hweyl|Hweyl]] ([[User talk:Hweyl|talk]]) 19:51, 21 January 2020 (CET)
:::: Great! Is the plan to  say that we'll build this in a way that'd be easy to be incorporated into WikiData if they choose to do so in the future? [[User:Mika|Mika]] ([[User talk:Mika|talk]]) 22:17, 21 January 2020 (CET)
::::: Draft text: Greetings members of WikiProject Food! We'd like to let you know about a complementary set of work we are planing related to food composition data. We are planing to create a Wikibase just for food composition data. To support this work we are proposing a Grant. We invite your review of the description of the project so we can learn of any feedback you may be willing to share with us.

= People to review =

== Gene Wiki ==
*[http://sulab.org/research/crowdbio/gene-wiki/]

== About WD ==

* draft response

* Thank you for the feedback! We have been thinking about this for a while as we'd initially planned to do this in Wikidata. Knowing how variable the types and depths of information are in FCDs, it is possible that we will include data that may never be appropriate for Wikidata. We decided that it'd make sense to build a Wikibase where we can hold all the details. 

Example datasets may look like this FAO data on [http://www.fao.org/fileadmin/templates/food_composition/documents/PhyFoodComp_1.0.xlsx detailed information on phytate] or [https://cdn1.sph.harvard.edu/wp-content/uploads/sites/30/2012/10/tanzania-food-composition-tables.pdf more standard data] which includes aggregate phytate data. And this is just one nutrient; there are many more nutrient data as well as meta data. We believe that it is important have these discussions in WD. We also feel that the discussion on WD and this Wikibase database could develop simultaneously.

Our approach includes the creation of ShEx schemas [https://www.wikidata.org/wiki/Wikidata:WikiProject_Schemas Wikidata:WikiProject Schemas] we will publish these schemas in Wikidata's E [https://www.wikidata.org/wiki/Help:Namespaces namespace] for entity schemas. This way the data models that we are discussing could also be shared and discussed on Wikidata. Our approach is to prepare data in a Wikibase and then help coordinate getting the data into Wikidata once the Wikidata community has built consensus on how much nutrient data will be appropriate for Wikidata.

== Response to other project ==
::: Happy to clarify these points! 

::: First, we want to emphasize that our focus in this project is the '''re-organization''' and '''standardization''' of the '''existing databases''' and we will do our best to classify and store every bit of information from each database. We will not limit the amount of data to be included in our Wikibase instance, with the hope that different communities, such as Wikidata, can pick and choose what to include in their own databases. Our Wikibase instance can serve as a place to sort data from all the databases that are available on the Internet, including ones you mentioned,  into one place, so that users can pull, combine, and analyze necessary data more easily. We believe that this project will be able to offer something these FCDs currently do not/cannot do, by harnessing the power of peer production. 

::: I use many of these FCDs as a nutritional epidemiologist for research, and also as a migrant individual who records dietary information related to foods from my native country as well as other countries. The current situation of having multiple incomplete databases in various formats is much less than ideal for meeting the needs of diverse communities and individuals. For instance:

:::: * I keep my daily dietary records in English. The software I'm using primarily uses the data from USDA.
:::: * I sometimes eat foods more commonly consumed in Japan like [[:ja:クビレズタ|海ぶどう]].
:::: * I look for this item in the USDA databases, using several keywords including its scientific name, but I can't find the information. Perhaps this data exists in another database but I'd need to check each database one by one.
:::: * I use another algae item as a substitute in my record but the nutrient data are available in the [https://fooddb.mext.go.jp/result/result_top.pl?USER_ID=15560 Japanese database].

::: This is just one example of the kinds of problems people may run into because of the incomplete connectivity among the existing databases. A global FCD can open up ways to explore many, many more new questions and solutions not just in food and nutrition but in many other topics that Wikimedians may be interested in. We believe that having this placeholder for all FCD information is a good way to contribute to different Wikimedia projects.

::: I believe OFF and our Wikibase instance take distinct approaches. According to their website:

:::: "Open Food Facts is a database of food products with ingredients, allergens, nutrition facts and all the tidbits of information we can find on product labels."

::: OFF builds up the database by individually contributing nutrient data from food product labels. Our project's approach is different. We will be using existing databases and compile them into a standardized and structured database. As I mentioned before, OFF and our Wikibase instance are complimentary. On of the strengths of OFF is the ability to have product nutrient data that are not yet in larger public databases like USDA databases. Combining OFF and our Wikibase instance, we can have a more comprehensive FCD than any single database. 

::: Great point about the plan beyond data importation. Like any Wikimedia project, peer production has the potential to actually keeping information more up-to-date than any working groups with limited numbers of participants. Any methods we employ to import, check updates, and maintain this database will be documented, so that future participants can easily learn how to do each of these activities and start contributing to the project. We will engage in outreach activities to involve diverse participants and we hope that documentation/tutorials and community engagement will increase the chance of frequent updates of the data. 

::: In short, there is an enormous amount of food composition data on the Internet already. There have been several attempts to combine some of these databases but none has succeeded in creating a comprehensive and easy-to-use global database. Open and collaborative peer production has its advantage over smaller working groups in compiling these databases into one place and maintain the data. We believe that this is a powerful solution to the decades-old problem in nutrition and will benefit a wide range of audiences, from Wikidata users to FCD developers. 

::: We hope this clarifies your questions. Thanks for engaging in this topic!

== Response to alex ==
::: Thank you so much for the comments and suggestions! I love the idea of digital community engagement through content drive/contest. We will work with the community engagement intern to plan and incorporate this idea. We will edit the proposal to add this point. 

::: We hope that our wikibase will be useful to OFF and we'll be able to demonstrate seamless data exchanges between the two. I completely agree that this is an important knowledge base for several SDGs and we look forward to working with diverse communities to improve it. 

::: Thanks again for the feedback!

=Wikibase for prototyping wikiFCD=

=Testing Wikibase=
* Main page [https://wikifcd.wiki.opencura.com/wiki/Main_Page]
* List of properties [https://wikifcd.wiki.opencura.com/wiki/Special:ListProperties]
=Inventory of FCTs=
* We may want to consider using our wikibase to inventory the FCTs of interest.
* example item for FCT [https://wikifcd.wiki.opencura.com/wiki/Item:Q13]
:: YES!!! [[User:Mika|Mika]] ([[User talk:Mika|talk]]) 22:18, 12 March 2020 (CET)
* Here is a [https://tinyurl.com/y7rlxbn4 Query for all food composition tables listed the wikifcd wikibase]. I also created some additional properties as we discussed in our last meeting. Properties 55-58 mentioned on [https://wikifcd.wiki.opencura.com/w/index.php?title=Special:ListProperties/&limit=500&offset=0 this page] can also be used now. [[User:Hweyl|Hweyl]] ([[User talk:Hweyl|talk]]) 00:45, 21 April 2020 (CEST)
:: Great! Thank you. As I work through the list on FAO/INFOODS, I'm discovering more and more about the complexity of these databases. Regional databases are tricky as they combine existing databases from different countries and sometimes add new information. The easiest thing to do may be to stick with single-country databases that are not based off another database...will keep you posted. [[User:Mika|Mika]] ([[User talk:Mika|talk]]) 03:12, 21 April 2020 (CEST)

=Useful links=
*[https://www.nutrientdirectory.org/indd/index.cfm? International Nutrition Databases] at Harvard; not clear if it's still maintained but it has information on some databases (overlapping information with FAO/INFOODS).
* [https://www.cropcomposition.org/query/sources.html Crop Composition Database] by ISLI/Agriculture and Food Systems Institute.
* [https://foodsystems.org/ meta data on nutrition databases] by ISLI/Agriculture and Food Systems Institute.
* [http://www.langual.org/Default.asp Framework for food description].

=response to the committee=

Thank you so much for reviewing our proposal! We saw three major themes in the comments and we would like to respond to these concerns (Point 1-3 below). We also added a response to comments that did not fit into one of these categories as well (Point 4). 

Before we address each point, we would like to note that based on the feedback, we have communicated further with '''Open Food Facts''' (OFF). We felt that it would be wonderful to have inputs from and collaborate with the OFF community. Upon discussion with his OFF team, Stéphane Gigandet (founder of OFF) has graciously agreed to advise us on the project. Stéphane has added his name to the list of advisors on this proposal. OFF has worked on incorporating some fruit and vegetable data from USDA and CIQUAL and experienced first-hand some of the issues (e.g. diverse formats) our team discusses in this proposal. A new Wikibase instance like WikiFCD can substantially reduce these burden for various communities such as Wikidata, so that they can focus on their main project aims instead. We plan to work with OFF and test and demonstrate how other Wikibase instances can incorporate data from WikiFCDs. 

1. Relationships with existing initiatives

We understand your concern on our relationships with existing initiatives, especially Open Food Facts. As mentioned above, an OFF founder/member has joined us and is listed on our advisor list. We hope that this shows that our project is complementary to the existing efforts. 

Based on the in-depth discussion both with various WM members and nutrition researchers and also amongst ourselves over the past year, we decided that it would be most useful to diverse communities if we build a comprehensive Wikibase instance for all existing FCDs from around the world. Our recent conversion with Stéphane Gigandet from OFF strengthened our belief that this Wikibase instance will be able to meet the needs of diverse communities and mitigate the burden associated with unstructured databases and non-unified data formats. We want to emphasize the point on diverse needs among different communities. While some communities may be only interested in the most common nutrient information (e.g. total fat, trans fat, calories, sugar), other communities may want more specific information (e.g. Phytic acid (by HPLC/HPAE) : Zinc ratio) or other information related to the food item (e.g. scientific names, varieties of fruits, geo-locations). 

WikiFCD can make significant contributions to various WM communities with interests in nutritional data. The Wikibase we are creating will be an expert-curated data set that is mapped to Wikidata. The Wikidata community as well as any other wikibase community will be able to reuse entity schemas or entity data (or both!) from our system. Data will flow back into Wikidata if desired. We strongly believe that WikiFCD will make a positive impact on WM and other communities by accommodating their varying needs and bringing more equitable access to an easily usable database. This Wikibase instance is a new and innovative approach that addresses problems that need to be, and yet have not been, solved. 

2. Community engagement   

We have reached out several communities, both within Wikimedia projects and outside. One of our main interests is to introduce and engage newcomers to WM projects. Through seminars and discussions, we have garnered strong interests among the nutritionists at Harvard School of Public Health and Johns Hopkins University, who are keen to contribute to both WikiFCD and Wikimedia projects related to food and nutrition as they have decades of hands-on experiences working with various FCDs globally and recognize the potential to contribute to and use the vast amount of information curated in various Wikimedia projects, which goes beyond nutrient data. For instance, translation work of FCDs would be an important part of reducing knowledge gaps. 

We are engaging stakeholders from academic communities who may not be aware of Wikidata or Wikibase. This type of outreach nourishes partnerships which could lead to expansion and diversification of Wikimedia contributors. Our approach is to provide domain experts experiences with Wikimedia systems and tooling  that they find valuable. This strategy for engaging domain experts is consistent with the findings and recommendations of the [https://tools.wmflabs.org/scholia/topic/Q5531528 GeneWiki program of work]. This newcomer engagement will be a large part of what the intern will work on. 

3. Impact of the project

We believe that the current project will have both immediate and long-term impact. This project will demonstrate how to add data from different databases and quickly build a comprehensive database. The ultimate goal of this project is simple and clear as it will include *all* FCDs. This project will have a direct impact on addressing knowledge gaps and also introducing and engaging newcomers to peer production and Wikimedia projects. WikiFCD can serve as one example of how to build a Wikibase instance that can contribute to Wikidata and other Wikibase instances.  

4. Other
*    The scope can be achieved within 12 months or less and the budget is realistic and efficient. But it isn't clear from the budget what the Community outreach/communication intern would be doing for 8 hours per week for 8 months
:: The intern will be working with the project manager to create online learning tools and seminars to teach newcomers about peer production, WM projects, and ways to contribute to Wiki-based projects using our Wikibase instance as an example. We aim to have a student who is interested in working with online communities who can support us one day a week for two semesters (so as not to create burden on their workload and interfere with their academic work).


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Extra notes
1. Relationships with existing initiatives
* I am encouraged to see this project proposal suggesting looking into another aspect of knowledge gaps. I am concerned there are already existing initiatives and wondering why the proposers have chosen to not to align with those.
* It does fit with Wikimedia's strategic priorities. However, it looks like a competitor to "Open Food Facts", another free software and open data but the concept of both projects is different.
* I do not find this project to be critical to the current state of knowledge. There are existing resources they could join to do this work.
* It does fit with Wikimedia's strategic priorities and the budget is reasonable but not enough community engagement. There is a need for a wider or major community discussion to ascertain whether this could be hosted on Wikidata or not. However, it looks like a competitor to "Open Food Facts", another free software and open data but the concept of both projects is different (from the proposal & answers to questions on the proposal talk page). 
* A lot of concerns about the creation of another instance. The answers in the discussion page don't convince me.

2. Community engagement   
* A new instance of Wikibase? Without a community?
* It does fit with Wikimedia's strategic priorities and the budget is reasonable but not enough community engagement. There is a need for a wider or major community discussion to ascertain whether this could be hosted on Wikidata or not. However, it looks like a competitor to "Open Food 
* Interesting concept but some concerns about the methodology.
* They really need to become more involved since they were not able to get any endorsements.
* The proposal has very little community engagement with current Wikipedia communities.

*    This seems iterative, but minimally so.

=Grant proposal edits=

Through this pilot project, we will write schemas to describe our data model based on five large food composition datasets that are already available online and develop good documentation for both project development and use. '''The focus on equity and global nature of the project requires diverse participants''', which is very much in line with the missions of projects supported by the Wikimedia Foundation. Through this pilot project, we hope to show how peer production can contribute to the improvement in data/knowledge disparities in global nutrition. We believe that WikiData is an awesome way to build connections between a range of free culture related nutrition projects like [https://fosdem.org/2020/schedule/event/open_food_facts/ Open Food Facts] that might do the same.
 
We will test several automated and manual methods to populate the wikibase with nutrient data from 5 food composition databases from around the world (see the Project Plan section section for details). We will write schemas to describe our data model. We will map our properties to Wikidata properties.

'''2. Why is this a good idea?'''

* First, this Wikibase instance will '''significantly improve the usability of FCD from different sources for diverse users''' - from WikiProjects and Wikipedia editors and viewers to academic researchers to public health workers. [https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Food_and_drink WikiProject food and Drink] on English Wikipedia and [https://www.wikidata.org/wiki/Q8485990#sitelinks-wikipedia its equivalents in other languages] are universally popular WikiProjects among editors and likewise, many articles on food and drink are within the top 10% of any Wikipedia's articles by pageviews. This new project can contribute to a topic that is of high interest to many people.

: Building a structured dataset is also a key step in identifying most appropriate data to borrow in resource-poor settings where up-to-date, detailed, and regionally appropriate FCD are not readily available. This new database will also open up ways to explore new research questions to explore more nuanced nutrition data (e.g. changes in nutrient content of the same product, depending on the climate conditions of the year), which can potentially make substantial advances in nutrition and health research.

* Secondly, by creating an instance of Wikibase for this project, we will be able to design our own data models, with input from Wikidata, to '''incorporate data from heterogeneous data sources'''. If subsets of the data are appropriate for Wikidata, we will be able to provide machine-actionable ShEx schemas that will help us prepare data for other systems. In this way the data will be readily-available for incorporation into Wikidata if desired.

; '''UPDATE''': In our recent communication with the Open Food Facts community, they discussed that OFF is in fact interested in using data from USDA (USA) and CIQUAL (France). However, it is burdensome having to deal with diverse and dynamic formats - they mentioned three separate format changes in USDA since they started looking at this. Having another project like WikiFCD can help each community focus on their main project goals instead of each having to deal with these issues we raised in this proposal. This conversation with OFF reinforces our belief that WikiFCD will be helpful to diverse peer production communities.

* Finally, we will '''complete this project with diverse communities from around the world''' as these FCD can be translated into/from many languages. The design of Wikibase will allow us to more easily support additional languages in the data itself, as well as in user interfaces.