User:Kat: Difference between revisions

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=Progress=
=Progress=
==Weeks before June 16==
* extended ICBO workshop draft
* Reviewed data set from Lucia
==Weeks before May 26 2021==
* Call recap
* Joint food ontology call recap
==Week before 4 May 2021==
{| class="wikitable"
|+ Item counts
|-
!  Item class!! Count
|-
| food items (produce) || 592
|-
| foods that are natural products of some taxon || 483
|-
| foods with FoodOn id || 109
|-
| ingested FCTs || 6
|}
{| class="wikitable"
|+ New Queries
|-
!  Query topic !! Link
|-
| Foods with Smiling Laos food code  || https://tinyurl.com/yjukcrck
|-
| Nutrient properties and related CHEBI ids || https://tinyurl.com/yeocz45v
|}
* Ran smiling Laos bot
* Joint Food Ontology WG meeting 4/28
** http://obofoundry.org/ontology/cdno
* 465,431 items in wikiFCD, available from: https://wikifcd.wiki.opencura.com/wiki/Special:Statistics
* All items in wikiFCD that are in the class "taxon name" have a mapping to their equiv WD item. HMDB ids found on WD items.
* 5/20
==Week before 27 April 2021==
{| class="wikitable"
|+ Item counts
|-
!  Item class!! Count
|-
| food items (produce) || 477
|-
| foods that are natural products of some taxon || 442
|-
| foods with FoodOn id || 109
|-
| ingested FCTs || 5
|}
{| class="wikitable"
|+ New Queries
|-
!  Query topic !! Link
|-
| Food items with Smiling Vietnam food code || https://tinyurl.com/yeexgbyk
|}
* Ran Smiling Vietnam bot
* In progress: manual clean up of common name from the bot run
* Prepped Smiling Laos data
* Drafted Smiling Laos bot
== Week before 20 April 2021==
* Prepared Smiling Vietnam data
* Drafted Smiling Vietnam bot
==Week before 13 April 2021==
{| class="wikitable"
|+ Item counts
|-
!  Item class!! Count
|-
| food items (produce) || 311
|-
| foods that are natural products of some taxon || 442
|-
| foods with FoodOn id || 109
|-
| ingested FCTs || 4
|}
{| class="wikitable"
|+ New Properties
|-
! Property ID !! EN Label !! Link !! datatype
|-
| P315 || SMILING Thailand food code id  ||[[Property:P315]]  || string
|}
{| class="wikitable"
|+ New Queries
|-
!  Query topic !! Link
|-
| Foods with Smiling Thailand food code  || https://tinyurl.com/yg76omv2
|-
| Foods that are natural products of a plant taxon and an image of the plant|| https://tinyurl.com/yfjx9byl
|-
| Foods with Smiling Thailand food code that are natural products of a taxon and a pic of the taxon || https://tinyurl.com/yggsb8p4
|}
* Created new document in Overleaf for workshop paper
* Prepared Smiling Thailand CSV (mapping scientific names to Qids, removing -, nd)
* ran bot for Smiling Thailand
* cleaning up common names
==Week before 6 April 2021==
* Extended Nutrients draft
* ICBO workshop (CEUR template, APC, timeline to publication, audience, quality/depth of feedback)
* Cleaning up Smiling Cambodia data
* Completed Malawi bot run
{| class="wikitable"
|+ New Queries
|-
!  Query topic !! Link
|-
| Foods with Malawi food code  || https://tinyurl.com/yz9j7has
|}
==Week before 1 April 2021==
{| class="wikitable"
|+ Item counts
|-
!  Item class!! Count
|-
| food items (produce) || 173
|-
| foods that are natural products of some taxon || 367
|-
| foods with FoodOn id || 109
|-
| ingested FCTs || 3
|}
{| class="wikitable"
|+ New Properties
|-
! Property ID !! EN Label !! Link !! datatype
|-
| P313 || Smiling Cambodia food id  ||[[Property:P313]]  || string
|-
| P314 || location sourced from  || [[Property:P314]] || item
|}
{| class="wikitable"
|+ New Items
|-
! class !! EN Label !! Link
|-
| chemical compound || zeaxanthin‎‎ || [[Item:Q567982]]
|-
| chemical compound  || phytofluene  || [[Item:Q567981]]
|-
| chemical compound  ||  phytoene  || [[Item:Q567980]]
|-
| chemical compound  ||  calcifediol‎‎  || [[Item:Q567979]]
|-
| chemical compound  || lutein  || [[Item:Q567984]]
|-
| chemical element || boron  || [[Item:Q567985]]
|-
| chemical element|| nickel  || [[Item:Q567986]]
|-
| chemical compound|| biotin  || [[Item:Q567987]]
|-
| chemical compound|| inositol  || [[Item:Q567988]]
|-
| chemical compound|| 5-methyl tetrahydrofolate  || [[Item:Q567989]]
|-
| chemical compound|| choline  || [[Item:Q567990]]
|-
| chemical compound|| phosphocholine  || [[Item:Q567991]]
|-
| chemical compound|| phosphatidylcholine  || [[Item:Q567992]]
|}
{| class="wikitable"
|+ New Queries
|-
!  Query topic !! Link
|-
| Foods with Smiling Cambodia food code  || https://tinyurl.com/yzf8twmo
|}
* 15, 16, 19, 20 April
* Added new column to Cambodia CSV for Taxon ID
* Replaced , with . in Cambodia CSV
* Drafted Smiling Cambodia bot
* Smiling Cambodia bot run complete
==Week before 23 March, 2021==
{| class="wikitable"
|+ Item counts
|-
!  Item class!! Count
|-
| food items (produce) || 83
|-
| foods that are natural products of some taxon || 316
|-
| foods with FoodOn id || 93
|-
| ingested FCTs || 2
|}
{| class="wikitable"
|+ New Properties
|-
! Property ID !! EN Label !! Link !! datatype
|-
| P309 || FoodOn ID  || [[Property:P309]]  || string
|-
| P296|| formatter URL  || [[Property:P310]] || string
|-
| P297|| yeild || [[Property:P311]] || quantity
|-
| P298 || serving size  || [[Property:P312]] || quantity
|}
{| class="wikitable"
|+ New Items
|-
! class !! EN Label !! Link
|-
| food item || Beef mince, fried  || [[Item:Q567782]]
|-
| food item || Beef stew  || [[Item:Q567783]]
|-
| food item || Beef, kidney, raw  || [[Item:Q567784]]
|-
| food item || Beef, liver, raw  || [[Item:Q567785]]
|-
| food item  ||Beef, liver, stew  || [[Item:Q567786]]
|-
| food item  || Beef, raw  || [[Item:Q567787]]
|-
| food item || Beef, tripe, raw  || [[Item:Q567788]]
|-
| too many to list ||(Check recent changes)||
|-
|chemical compound ||  alpha-cryptoxanthin || [[Item:Q567964]]
|-
|chemical compound || nitrogen || [[Item:Q567965]]
|-
|chemical compound || citric acid || [[Item:Q567967]]
|-
|chemical compound || sorbitol  || [[Item:Q567968]]
|-
|chemical compound || xylitol || [[Item:Q567970]]
|-
|chemical compound || ribose || [[Item:Q567971]]
|-
|chemical element || chlorine || [[Item:Q567972]]
|-
|chemical element || sulfur || [[Item:Q567973]]
|-
|chemical element || chromium || [[Item:Q567974]]
|-
|chemical compound || fluoride || [[Item:Q567975]]
|-
|chemical element ||  iodine || [[Item:Q567976]]
|-
|chemical element || molybdenum || [[Item:Q567977]]
|-
|chemical compound || vitamin D ||[[Item:Q567978]]
|}
{| class="wikitable"
|+ New Queries
|-
!  Query topic !! Link
|-
|Food items with FoodOn id  || https://tinyurl.com/yf7njljc
|-
| Federated query for food items with FoodOn id and all metabolites known to Wikidata that are found in the taxon of which the food is a natural product || https://tinyurl.com/yz5seocf
|}
* Extended Nutrients draft
* Created subject items to go with properties for linking props to Wikidata project
* Created a new column "Taxon ID" in Malawi FCT CSV to store the Qids from our Wikibase for each taxon named
* Malawi bot run report
* Tried to search fatty acids in Chebi
* Tried to search fatty acids in LipidMaps
* FoodOn overview
** https://foodon.org/
** paper:https://www.nature.com/articles/s41538-018-0032-6
** contact
** meeting
** higher level groupings
** SPARQL endpoint via OBO
** reuse of all data FoodOn links to: environmental terms from ENVO, agriculture terms from AGRO, plant and animal anatomy terms from UBERON, and PO, organisms from NCBITaxon, relations from RO, and soon nutritional components from CDNO
** mappings to resources that reuse FoodOn: ENVO, CDNO, ONE, ONS, FIDEO, FOBI, ECTO, and DOID
** working group
* Mapped foods to FoodOn ids
* FoodBasket
* MyFitnessPal
* MyPlate
==Week before 9 March, 2021==
{| class="wikitable"
|+ Item counts
|-
!  Item class!! Count
|-
| food items (produce) || 57
|-
| foods that are natural products of some taxon || 252
|}
{| class="wikitable"
|+ New Properties
|-
! Property ID !! EN Label !! Link !! datatype
|-
|  ||  ||  ||
|}
{| class="wikitable"
|+ New Items
|-
! class !! EN Label !! Link
|-
| chemical compound ||myristic acid  || [[Item:Q567744]]
|-
| chemical compound ||palmitic acid  || [[Item:Q567745]]
|-
| chemical compound ||stearic acid  || [[Item:Q567746]]
|-
| chemical compound || arachidic acid || [[Item:Q567747]]
|-
| chemical compound  || vaccenic acid  || [[Item:Q567748]]
|-
| chemical compound  ||linolelaidic acid  || [[Item:Q567749]]
|-
| chemical compound || arachidonic acid  || [[Item:Q567750]]
|-
| chemical compound || docosahexaenoic acid || [[Item:Q567751]]
|-
| chemical compound || behenic acid || [[Item:Q567752]]
|-
| chemical compound || palmitoleic acid  || [[Item:Q567753]]
|-
| chemical compound || stearidonic acid || [[Item:Q567754]]
|-
|chemical compound || paullinic acid || [[Item:Q567755]]
|-
| chemical compound || eicosapentaenoic acid  || [[Item:Q567756]]
|-
| chemical compound || erucic acid || [[Item:Q567757]]
|-
| chemical compound || docosapentaenoic acid || [[Item:Q567758]]
|-
|class || class of chemical compounds with similar source or occurrence  || [[Item:Q567759]]
|-
| class of chemical compounds || phytosterols  || [[Item:Q567760]]
|-
| chemical compound ||stigmasterol  || [[Item:Q567761]]
|-
| chemical compound || campesterol || [[Item:Q567762]]
|-
|chemical compound || brassicasterol  || [[Item:Q567763]]
|-
| chemical compound || beta-sitosterol18:2 CLAs  || [[Item:Q567764]]
|-
|chemical compound || campestanol || [[Item:Q567765]]
|-
| chemical compound ||pentadecanoic acid  || [[Item:Q567766]]
|-
| chemical compound ||margaric acid  || [[Item:Q567767]]
|-
| chemical compound ||lignoceric acid || [[Item:Q567768]]
|-
|chemical compound || elaidic acid  || [[Item:Q567771]]
|-
| chemical compound ||tridecanoic acid  || [[Item:Q567772]]
|-
| chemical compound ||undecylic acid  || [[Item:Q567773]]
|-
| chemical compound || epigallocatechin-3-gallate  || [[Item:Q567774]]
|-
|chemical compound ||inulin  || [[Item:Q567775]]
|-
| chemical compound || alpha-linolenic acid  || [[Item:Q567776]]
|-
| chemical compound ||dihomo-γ-linolenic acid  || [[Item:Q567777]]
|}
{| class="wikitable"
|+ New Queries
|-
!  Query topic !! Link
|-
|Metabolites found in foods that are natural products of Prunella vulgaris ||https://tinyurl.com/y8638btj
|-
| Which wikiFCD foods are known to contain the 2D structure of beta-sitosterol|| https://tinyurl.com/y7g4jd8h
|-
| Metabolites found in foods that are natural products of Vaccinium deliciosum and what they physically interact with || https://tinyurl.com/y7qplyjh
|}
* wikiFCD is the largest wikibase on wbStack
* self-heal curation report (Prunella vulgaris: A Comprehensive Review of Chemical Constituents, Pharmacological Effects and Clinical Applications )
* Extended Nutrients draft
* Extended NSF proposal draft
* Read Open Natural Products Research: Curation and Dissemination of Biological Occurrences of Chemical Structures through Wikidata
* Read Let Food Be Thy Medicine- Its Role in Crohn's Disease
* Read Dietary Vitamin K is remodeled by gut microbiota and influences community composition
* Read Wikipathways:Connecting Communities
* Read Consumer attitudes toward genetic testing and personalised nutrition in Hungary
* Read Ten simple rules for developing public biological databases
* Read Impact of Dietary Flavanols on Microbiota, Immunity and Inflammation in Metabolic Diseases
* 14:1?
* 14:1 t
* Delta-5-avenasterol
* 16:1 t
* 22:1 t
* 18:2 i
* 18:2 t,t
* 18:2 CLAs
* 24:1 c is this nervonic acid (Q414231)?
* 20:2 n-6 c,c
* 16:1 c
* 18:1 c
* 18:2 n-6 c,c
* 22:1 c
* 18:3 n-6 c,c,c
* 17:1
* 20:3
* 15:1
* 22:2
* 20:3 n-3 is this all-cis-icosa-11,14,17-trienoic acid (Q27124062)?
==Week before 2 March, 2021==
{| class="wikitable"
|+ Item counts
|-
!  Item class!! Count
|-
| food items (produce) || 57
|-
| foods that are natural products of some taxon || 252
|}
{| class="wikitable"
|+ New Properties
|-
! Property ID !! EN Label !! Link !! datatype
|-
| P308 || Total Carbohydrate for UDB  || [[Property:P308]]  || quantity
|}
{| class="wikitable"
|+ New Items
|-
! class !! EN Label !! Link
|-
| chemical compound || phenylalanine  || [[Item:Q567712]]
|-
| chemical compound || tyrosine  || [[Item:Q567713]]
|-
| chemical compound || alanine  || [[Item:Q567714]]
|-
| chemical compound || glutamic acid  || [[Item:Q567715]]
|-
| chemical compound  || glycine  || [[Item:Q567716]]
|-
| chemical compound  || proline  || [[Item:Q567717]]
|-
| chemical compound || cholesterol  || [[Item:Q567718]]
|-
| chemical compound || delta-tocopherol || [[Item:Q567719]]
|-
| chemical compound || gamma-tocotrienol || [[Item:Q567720]]
|-
| chemical compound ||  delta-tocotrienol || [[Item:Q567721]]
|-
| chemical compound || alpha-tocopherol || [[Item:Q567722]]
|-
|chemical compound || beta-tocopherol  || [[Item:Q567723]]
|-
| chemical compound || gamma-Tocopherol  || [[Item:Q567724]]
|-
| chemical compound || alpha-Tocotrienol || [[Item:Q567725]]
|-
| chemical compound || beta-tocotrienol || [[Item:Q567726]]
|-
|chemical compound ||  isoleucine || [[Item:Q567727]]
|-
| chemical compound || leucine  || [[Item:Q567728]]
|-
| chemical compound ||  lysine || [[Item:Q567729]]
|-
| chemical compound ||cystine  || [[Item:Q567730]]
|-
|chemical compound || valine  || [[Item:Q567731]]
|-
| chemical compound || arginine  || [[Item:Q567732]]
|-
|chemical compound ||  histidine || [[Item:Q567733]]
|-
| chemical compound || aspartic acid  || [[Item:Q567734]]
|-
| chemical compound || serine || [[Item:Q567735]]
|-
| chemical compound || theobromine || [[Item:Q567736]]
|-
|chemical compound || ergocalciferol  || [[Item:Q567737]]
|-
| chemical compound || cholecalciferol  || [[Item:Q567738]]
|-
| chemical compound || butyric acid  || [[Item:Q567739]]
|-
| chemical compound || caproic acid  || [[Item:Q567740]]
|-
|chemical compound || caprylic acid  || [[Item:Q567741]]
|-
| chemical compound || capric acid  || [[Item:Q567742]]
|-
| chemical compound || lauric acid || [[Item:Q567743]]
|}
{| class="wikitable"
|+ New Queries
|-
!  Query topic !! Link
|-
| Nutrient properties and their subject items || https://tinyurl.com/ycow73nf
|-
| Federated query producing bubble chart viz of food items ranked by number of metabolites known to Wikidata || https://tinyurl.com/ycufjhj4
|}
* Created section in Nutrients Introducing WikiFCD paper draft describing steps for incorporating FCTs into wikibase @ line 212
* Complete work to break out common name and taxon from Malawi FCT into their own columns for bot usage
* Extended Project B in description section of NSF grant proposal draft
* Read "The Role of Gut Bacterial Metabolites in Brain Development, Aging and Disease"
* Curated FDC items with 'raw' in the label with their presumed taxa info so the metabolite query would return more results
* Continued creating subject items for our property graph in order to map our nutrients to Wikdiata
==Week before 23 Feb, 2021==
{| class="wikitable"
|+ Item counts
|-
!  Item class!! Count
|-
| food items (produce) || 57
|-
| foods that are natural products of some taxon || 84
|}
{| class="wikitable"
|+ New Properties
|-
! Property ID !! EN Label !! Link !! datatype
|-
| P305 || Phytic acid  || [[Property:P305]]  || quantity
|-
| P306 || Malawian Food Composition Table 2019 food id  || [[Property:P306]] || string
|}
{| class="wikitable"
|+ New Items
|-
! class !! EN Label !! Link
|-
|  || chemical compound  || [[Item:Q567677]]
|-
| chemical compound || vitamin B12  || [[Item:Q567676]]
|-
|  ||vitamin  || [[Item:Q567678]]
|-
|chemical element  || zinc  || [[Item:Q567679]]
|-
| chemical element  || copper  || [[Item:Q567680]]
|-
| chemical element  || manganese  || [[Item:Q567681]]
|-
| chemical element || selenium  || [[Item:Q567682]]
|-
| chemical compound || vitamin C || [[Item:Q567683]]
|-
| chemical compound || Thiamine || [[Item:Q567684]]
|-
| chemical compound ||riboflavin || [[Item:Q567685]]
|-
| chemical compound || niacin || [[Item:Q567686]]
|-
| chemical compound || pantothenic acid|| [[Item:Q567687]]
|-
| chemical compound || vitamin B6  || [[Item:Q567688]]
|-
| chemical compound || sucrose || [[Item:Q567689]]
|-
| || Malwaian food id || [[Item:Q567690]]
|-
| chemical compound || glucose || [[Item:Q567691]]
|-
| chemical compound || fructose || [[Item:Q567692]]
|-
| chemical compound || lactose || [[Item:Q567693]]
|-
| chemical compound || maltose || [[Item:Q567694]]
|-
| chemical compound || galactose || [[Item:Q567695]]
|-
| chemical compound || folic acid || [[Item:Q567696]]
|-
|chemical compound || choline || [[Item:Q567697]]
|-
| chemical compound || Betaine || [[Item:Q567698]]
|-
| chemical compound || vitamin A || [[Item:Q567699]]
|-
| chemical compound || beta-carotene || [[Item:Q567700]]
|-
| chemical compound || alpha-carotene || [[Item:Q567701]]
|-
| chemical compound ||Beta-cryptoxanthin || [[Item:Q567702]]
|-
| chemical compound || lycopene || [[Item:Q567703]]
|-
| chemical compound || lutein || [[Item:Q567704]]
|-
| chemical compound || zeaxanthin || [[Item:Q567705]]
|-
| chemical compound || phylloquinone|| [[Item:Q567706]]
|-
| chemical compound || menaquinone 4 || [[Item:Q567707]]
|-
| chemical compound || retinol ||[[Item:Q567708]]
|-
| chemical compound || vitamin E || [[Item:Q567709]]
|-
| chemical compound ||threonine || [[Item:Q567710]]
|}
{| class="wikitable"
|+ New Queries
|-
!  Query topic !! Link
|-
| federated query overview of chemical compounds || https://tinyurl.com/y98t58pw
|-
| federated query for chemical compounds that are part of a biological pathway and the works that discuss this || https://tinyurl.com/ybtgwgby
|-
| federated query for taxa in wikiFCD in which metabolites are known to be found along with the Human Metabolome ids for those metabolites || https://tinyurl.com/y7yto56c
|-
| federated query for chemical compounds and processes of which they are a part || https://tinyurl.com/y6wbw7cg
|}
* Extended description section on NSF grant proposal document
* Read a Langual paper
* Read a FoodOn paper
* Read a FOBI paper
* FoodEx2 could be a source of the broader categories for foods
* No idea if anyone has mapped between FoodEx2 and FDC
* Requested FoodEx2 SPARQL endpoint be considered for federation
* FoodEx2 record for lettuce: https://data.food.gov.uk/codes/foodtype/id/A05EC
* LanguaL has a really awesome thesaurus: https://www.langual.org/langual_thesaurus.asp?termid=B4958&haschildren=False&owner=B1231&openstr=00000_J0107_B1564_B1347_B1140_B1231
* LanguaL bot to parse XML and then write new items to wikiFCD
* FoodOn builds on LanguaL
* Only 7 items from FoodOn in Wikidata so far: https://w.wiki/$2A
* Would be great to mass import FoodOn into wikiFCD or Wikidata or create Mix'n'Match catalog
* Wrote the Malawi FCT bot
** Wait to run bot until 51 reference items are created
** Run bot in 2 phases- one phase now, one phase after ref items are complete to add those references
==Week before 16 Feb, 20201==
{| class="wikitable"
|+ Item counts
|-
!  Item class!! Count
|-
| food items || 53
|-
| foods that are natural products of some taxon || 67
|}
{| class="wikitable"
|+ New Properties
|-
! Property ID !! EN Label !! Link !! datatype
|-
| P302 || sourcing circumstances  || [[Property:P302]]  || item
|-
| P303||  Wikibooks Cookbook Entry || [[Property:P303]]  || URL
|-
| P304 ||subject item of this property || [[Property:P304]] || item
|}
{| class="wikitable"
|+ New Items
|-
! class !! EN Label !! Link
|-
|sourcing circumstance || presumably  || [[Item:Q567658]]
|-
| sourcing circumstance|| misprint  || [[Item:Q567660]]
|-
| sourcing circumstance ||miscalculation  || [[Item:Q567661]]
|-
| sourcing circumstance || approximately  || [[Item:Q567662]]
|-
| sourcing circumstance  || contradiction  || [[Item:Q567663]]
|-
| taxon name  || Koenigia alaskana    || [[Item:Q567664]]
|-
| food item || Hop Shoots  || [[Item:Q567657]]
|-
| food item || Narrowleaf Plantain || [[Item:Q567665]]
|-
| food item || Broadleaf Plantain || [[Item:Q567666]]
|-
| chemical element ||calcium || [[Item:Q567669]]
|-
| chemical element ||iron ||[[Item:Q567671]]
|-
|chemical element || magnesium || [[Item:Q567672]]
|-
| chemical element || phosphorus || [[Item:Q567673]]
|-
| chemical element || potassium ||[[Item:Q567674]]
|-
| food item || Purslane || [[Item:Q567668]]
|}
{| class="wikitable"
|+ New Queries
|-
!  Query topic !! Link
|-
| Query for packaged food items from the sr_legacy dataset of FDC || https://tinyurl.com/yyp2oz6o
|-
| Query for all properties with descriptions and aliases and types || https://tinyurl.com/y35fddfk
|-
| Query for chemical elements with International Chemical Identifier  || https://tinyurl.com/y68n4cbk
|-
| Query for chemical elements with MeSH Tree Code(s) || https://tinyurl.com/y8uwcbmy
|-
| Query for food items that are a natural product of some taxon || https://tinyurl.com/ya4p9onl
|-
| Graph viz for food items that are a natural product of some taxon || https://tinyurl.com/y9pslqv8
|}
* drinkkit
* Redesign Main Page
* Added ideas for contribution
* Report on searching for words like "raw", "fresh", "shoots", "leaves"
* Share example [[Item:Q562624]]
* Share example [[Item:Q562500]]
* Share example [[Item:Q209064]], but several others listed https://en.wikipedia.org/wiki/Bamboo_shoot
* Share example [[Item:Q567665]] look at use of qualifier on P
* Share CulinaryDB: Bagler, G. CulinaryDB: https://cosylab.iiitd.edu.in/culinarydb/. Indraprastha Institute
of Information Technology Delhi (IIIT-Delhi) (2017).
* How will we help users select between https://tinyurl.com/y66tj86q ?
* How will we help users select between 40+ brussels sprouts entries from FDC? (Advanced search for phrase)
* Review [[Item:Q562688]] as example of why it might be confusing to combine USDA food items with other fct food items, would be difficult to ensure that people not assume that the common names and the natural product of taxon info from Edible Wild Foods is also valid for the FDC statements
* Draft of Introducing WikiFCD for Nutrients
* NSF grant: Expanded text for Projects B and C
* Great paper calling for projects like ours: https://academic.oup.com/database/article/doi/10.1093/database/baab003/6119904
** figure 1
** figure 3
** comprehensive list of ontologies and knowledge bases
** Their approach is a biomedical ontologist's approach -> we can enhance this approach with Wikidata
** Path forward for NIH funding for personalized medicine
** Potential collaborators
** Leverage the working groups mappings
* https://github.com/FoodOntology/joint-food-ontology-wg
==Week before Feb 9, 20201==
{| class="wikitable"
|+ New Properties
|-
! Property ID !! EN Label !! Link !! datatype
|-
| P295 || Dehydroascorbic acid || [[Property:P295]] || quantity
|-
| P296|| Vitamin K || [[Property:P296]] || quantity
|-
| P297|| Phenolic acids || [[Property:P297]] || quantity
|-
| P298 || Hydroxibenzoic acids  || [[Property:P298]] || quantity
|-
| P299 || Hydroxycinnamic acids  || [[Property:P299]] || quantity
|-
| P300 || Flavonols || [[Property:P300]] || quantity
|-
| P301 ||Anthocyanins  || [[Property:P301]] || quantity
|}
{| class="wikitable"
|+ New Items
|-
! class !! EN Label !! Link
|-
| taxon name || Wasabia koreana || [[Item:Q567651]]
|-
| food item || Lamb's quarters || [[Item:Q567652]]
|-
| food item || Skeleton weed || [[Item:Q567653]]
|-
| food item || Shepherd’s-purse || [[Item:Q567650]]
|-
| food item  || Chicory || [[Item:Q567654]]
|-
| food item  || Hawthorn berries || [[Item:Q567655]]
|-
| food item || Wild fennel || [[Item:Q567656]]
|}
{| class="wikitable"
|+ New Queries
|-
!  Query topic !! Link
|-
| Wikidata query for items with OFF ingredient id and the articles about these foods in all 'pedias with lang label ||
https://w.wiki/yRo
|}
==Week before Feb 2, 20201==
==Week before Feb 2, 20201==
{| class="wikitable"
{| class="wikitable"
|+ New Properties
|+ New Properties
|-
|-
! Property ID !! EN Label !! Link
! Property ID !! EN Label !! Link !! datatype
|-
|-
| P283 || editor || [[Property:P283]]
| P283 || editor || [[Property:P283]] || string
|-
|-
| P284 || Oxalic acid || [[Property:P284]]
| P284 || Oxalic acid || [[Property:P284]] || quantity
|-
|-
| P285 || Fumaric acid || [[Property:P285]]
| P285 || Fumaric acid || [[Property:P285]] || quantity
|-
|-
| P286 || Phenolics || [[Property:P286]]
| P286 || Phenolics || [[Property:P286]] || quantity
|-
|-
| P287 || Flavonoids || [[Property:P287]]
| P287 || Flavonoids || [[Property:P287]] || quantity
|-
| P289 || Carotenoids || [[Property:P289]] || quantity
|-
| P290 || Neoxanthin || [[Property:P290]] || quantity
|-
| P291 || Violaxanthin || [[Property:P291]] || quantity
|-
| P292 || Quinic acid || [[Property:P292]] || quantity
|-
| P293 || Shikimic acid || [[Property:P293]] || quantity
|-
| P294 || Nitrate || [[Property:P294]] || quantity
|}
|}


Line 22: Line 851:
|+ New Items
|+ New Items
|-
|-
! QID !! EN Label !! Link
! class !! EN Label !! Link
|-
| food item || fool's watercress || [[Item:Q567642]]
|-
| food item || borage || [[Item:Q567643]]
|-
| food item || wild leek || [[Item:Q567641]]
|-
| food item || shepard's purse || [[Item:Q567650]]
|-
| unit || cup(s) || [[Item:Q567645]]
|-
| unit || Tbs || [[Item:Q567647]]
|-
| unit || tsp || [[Item:Q567648]]
|-
| dish || granola || [[Item:Q567644]]
|-
| dish || granola || [[Item:Q567649]]
|-
| packaged food item || ground flaxseed || [[Item:Q567646]]
|-
| FCT || Mediterranean Wild Edible Plants || [[Item:Q567640]]
|}
 
{| class="wikitable"
|+ New Queries
|-
|-
| Q567641 || wild leek || [[Item:Q567641]]
! Query topic !! Link
|-
|-
| Q567640 || Mediterranean Wild Edible Plants || [[Item:Q567640]]
| Query for ranked list of items containing most to least DHA (Docosahexaenoic acid) listed in this wikibase ||  
https://tinyurl.com/y56qvvr6
|}
|}

Latest revision as of 18:38, 10 October 2022

Curating data related to food composition.

Progress

Weeks before June 16

  • extended ICBO workshop draft
  • Reviewed data set from Lucia

Weeks before May 26 2021

  • Call recap
  • Joint food ontology call recap

Week before 4 May 2021

Item counts
Item class Count
food items (produce) 592
foods that are natural products of some taxon 483
foods with FoodOn id 109
ingested FCTs 6
New Queries
Query topic Link
Foods with Smiling Laos food code https://tinyurl.com/yjukcrck
Nutrient properties and related CHEBI ids https://tinyurl.com/yeocz45v

Week before 27 April 2021

Item counts
Item class Count
food items (produce) 477
foods that are natural products of some taxon 442
foods with FoodOn id 109
ingested FCTs 5


New Queries
Query topic Link
Food items with Smiling Vietnam food code https://tinyurl.com/yeexgbyk
  • Ran Smiling Vietnam bot
  • In progress: manual clean up of common name from the bot run
  • Prepped Smiling Laos data
  • Drafted Smiling Laos bot

Week before 20 April 2021

  • Prepared Smiling Vietnam data
  • Drafted Smiling Vietnam bot


Week before 13 April 2021

Item counts
Item class Count
food items (produce) 311
foods that are natural products of some taxon 442
foods with FoodOn id 109
ingested FCTs 4
New Properties
Property ID EN Label Link datatype
P315 SMILING Thailand food code id Property:P315 string


New Queries
Query topic Link
Foods with Smiling Thailand food code https://tinyurl.com/yg76omv2
Foods that are natural products of a plant taxon and an image of the plant https://tinyurl.com/yfjx9byl
Foods with Smiling Thailand food code that are natural products of a taxon and a pic of the taxon https://tinyurl.com/yggsb8p4
  • Created new document in Overleaf for workshop paper
  • Prepared Smiling Thailand CSV (mapping scientific names to Qids, removing -, nd)
  • ran bot for Smiling Thailand
  • cleaning up common names

Week before 6 April 2021

  • Extended Nutrients draft
  • ICBO workshop (CEUR template, APC, timeline to publication, audience, quality/depth of feedback)
  • Cleaning up Smiling Cambodia data
  • Completed Malawi bot run
New Queries
Query topic Link
Foods with Malawi food code https://tinyurl.com/yz9j7has

Week before 1 April 2021

Item counts
Item class Count
food items (produce) 173
foods that are natural products of some taxon 367
foods with FoodOn id 109
ingested FCTs 3
New Properties
Property ID EN Label Link datatype
P313 Smiling Cambodia food id Property:P313 string
P314 location sourced from Property:P314 item
New Items
class EN Label Link
chemical compound zeaxanthin‎‎ Item:Q567982
chemical compound phytofluene Item:Q567981
chemical compound phytoene Item:Q567980
chemical compound calcifediol‎‎ Item:Q567979
chemical compound lutein Item:Q567984
chemical element boron Item:Q567985
chemical element nickel Item:Q567986
chemical compound biotin Item:Q567987
chemical compound inositol Item:Q567988
chemical compound 5-methyl tetrahydrofolate Item:Q567989
chemical compound choline Item:Q567990
chemical compound phosphocholine Item:Q567991
chemical compound phosphatidylcholine Item:Q567992
New Queries
Query topic Link
Foods with Smiling Cambodia food code https://tinyurl.com/yzf8twmo
  • 15, 16, 19, 20 April
  • Added new column to Cambodia CSV for Taxon ID
  • Replaced , with . in Cambodia CSV
  • Drafted Smiling Cambodia bot
  • Smiling Cambodia bot run complete

Week before 23 March, 2021

Item counts
Item class Count
food items (produce) 83
foods that are natural products of some taxon 316
foods with FoodOn id 93
ingested FCTs 2
New Properties
Property ID EN Label Link datatype
P309 FoodOn ID Property:P309 string
P296 formatter URL Property:P310 string
P297 yeild Property:P311 quantity
P298 serving size Property:P312 quantity
New Items
class EN Label Link
food item Beef mince, fried Item:Q567782
food item Beef stew Item:Q567783
food item Beef, kidney, raw Item:Q567784
food item Beef, liver, raw Item:Q567785
food item Beef, liver, stew Item:Q567786
food item Beef, raw Item:Q567787
food item Beef, tripe, raw Item:Q567788
too many to list (Check recent changes)
chemical compound alpha-cryptoxanthin Item:Q567964
chemical compound nitrogen Item:Q567965
chemical compound citric acid Item:Q567967
chemical compound sorbitol Item:Q567968
chemical compound xylitol Item:Q567970
chemical compound ribose Item:Q567971
chemical element chlorine Item:Q567972
chemical element sulfur Item:Q567973
chemical element chromium Item:Q567974
chemical compound fluoride Item:Q567975
chemical element iodine Item:Q567976
chemical element molybdenum Item:Q567977
chemical compound vitamin D Item:Q567978
New Queries
Query topic Link
Food items with FoodOn id https://tinyurl.com/yf7njljc
Federated query for food items with FoodOn id and all metabolites known to Wikidata that are found in the taxon of which the food is a natural product https://tinyurl.com/yz5seocf
  • Extended Nutrients draft
  • Created subject items to go with properties for linking props to Wikidata project
  • Created a new column "Taxon ID" in Malawi FCT CSV to store the Qids from our Wikibase for each taxon named
  • Malawi bot run report
  • Tried to search fatty acids in Chebi
  • Tried to search fatty acids in LipidMaps
  • FoodOn overview
    • https://foodon.org/
    • paper:https://www.nature.com/articles/s41538-018-0032-6
    • contact
    • meeting
    • higher level groupings
    • SPARQL endpoint via OBO
    • reuse of all data FoodOn links to: environmental terms from ENVO, agriculture terms from AGRO, plant and animal anatomy terms from UBERON, and PO, organisms from NCBITaxon, relations from RO, and soon nutritional components from CDNO
    • mappings to resources that reuse FoodOn: ENVO, CDNO, ONE, ONS, FIDEO, FOBI, ECTO, and DOID
    • working group
  • Mapped foods to FoodOn ids
  • FoodBasket
  • MyFitnessPal
  • MyPlate

Week before 9 March, 2021

Item counts
Item class Count
food items (produce) 57
foods that are natural products of some taxon 252
New Properties
Property ID EN Label Link datatype
New Items
class EN Label Link
chemical compound myristic acid Item:Q567744
chemical compound palmitic acid Item:Q567745
chemical compound stearic acid Item:Q567746
chemical compound arachidic acid Item:Q567747
chemical compound vaccenic acid Item:Q567748
chemical compound linolelaidic acid Item:Q567749
chemical compound arachidonic acid Item:Q567750
chemical compound docosahexaenoic acid Item:Q567751
chemical compound behenic acid Item:Q567752
chemical compound palmitoleic acid Item:Q567753
chemical compound stearidonic acid Item:Q567754
chemical compound paullinic acid Item:Q567755
chemical compound eicosapentaenoic acid Item:Q567756
chemical compound erucic acid Item:Q567757
chemical compound docosapentaenoic acid Item:Q567758
class class of chemical compounds with similar source or occurrence Item:Q567759
class of chemical compounds phytosterols Item:Q567760
chemical compound stigmasterol Item:Q567761
chemical compound campesterol Item:Q567762
chemical compound brassicasterol Item:Q567763
chemical compound beta-sitosterol18:2 CLAs Item:Q567764
chemical compound campestanol Item:Q567765
chemical compound pentadecanoic acid Item:Q567766
chemical compound margaric acid Item:Q567767
chemical compound lignoceric acid Item:Q567768
chemical compound elaidic acid Item:Q567771
chemical compound tridecanoic acid Item:Q567772
chemical compound undecylic acid Item:Q567773
chemical compound epigallocatechin-3-gallate Item:Q567774
chemical compound inulin Item:Q567775
chemical compound alpha-linolenic acid Item:Q567776
chemical compound dihomo-γ-linolenic acid Item:Q567777
New Queries
Query topic Link
Metabolites found in foods that are natural products of Prunella vulgaris https://tinyurl.com/y8638btj
Which wikiFCD foods are known to contain the 2D structure of beta-sitosterol https://tinyurl.com/y7g4jd8h
Metabolites found in foods that are natural products of Vaccinium deliciosum and what they physically interact with https://tinyurl.com/y7qplyjh
  • wikiFCD is the largest wikibase on wbStack
  • self-heal curation report (Prunella vulgaris: A Comprehensive Review of Chemical Constituents, Pharmacological Effects and Clinical Applications )
  • Extended Nutrients draft
  • Extended NSF proposal draft
  • Read Open Natural Products Research: Curation and Dissemination of Biological Occurrences of Chemical Structures through Wikidata
  • Read Let Food Be Thy Medicine- Its Role in Crohn's Disease
  • Read Dietary Vitamin K is remodeled by gut microbiota and influences community composition
  • Read Wikipathways:Connecting Communities
  • Read Consumer attitudes toward genetic testing and personalised nutrition in Hungary
  • Read Ten simple rules for developing public biological databases
  • Read Impact of Dietary Flavanols on Microbiota, Immunity and Inflammation in Metabolic Diseases
  • 14:1?
  • 14:1 t
  • Delta-5-avenasterol
  • 16:1 t
  • 22:1 t
  • 18:2 i
  • 18:2 t,t
  • 18:2 CLAs
  • 24:1 c is this nervonic acid (Q414231)?
  • 20:2 n-6 c,c
  • 16:1 c
  • 18:1 c
  • 18:2 n-6 c,c
  • 22:1 c
  • 18:3 n-6 c,c,c
  • 17:1
  • 20:3
  • 15:1
  • 22:2
  • 20:3 n-3 is this all-cis-icosa-11,14,17-trienoic acid (Q27124062)?

Week before 2 March, 2021

Item counts
Item class Count
food items (produce) 57
foods that are natural products of some taxon 252
New Properties
Property ID EN Label Link datatype
P308 Total Carbohydrate for UDB Property:P308 quantity
New Items
class EN Label Link
chemical compound phenylalanine Item:Q567712
chemical compound tyrosine Item:Q567713
chemical compound alanine Item:Q567714
chemical compound glutamic acid Item:Q567715
chemical compound glycine Item:Q567716
chemical compound proline Item:Q567717
chemical compound cholesterol Item:Q567718
chemical compound delta-tocopherol Item:Q567719
chemical compound gamma-tocotrienol Item:Q567720
chemical compound delta-tocotrienol Item:Q567721
chemical compound alpha-tocopherol Item:Q567722
chemical compound beta-tocopherol Item:Q567723
chemical compound gamma-Tocopherol Item:Q567724
chemical compound alpha-Tocotrienol Item:Q567725
chemical compound beta-tocotrienol Item:Q567726
chemical compound isoleucine Item:Q567727
chemical compound leucine Item:Q567728
chemical compound lysine Item:Q567729
chemical compound cystine Item:Q567730
chemical compound valine Item:Q567731
chemical compound arginine Item:Q567732
chemical compound histidine Item:Q567733
chemical compound aspartic acid Item:Q567734
chemical compound serine Item:Q567735
chemical compound theobromine Item:Q567736
chemical compound ergocalciferol Item:Q567737
chemical compound cholecalciferol Item:Q567738
chemical compound butyric acid Item:Q567739
chemical compound caproic acid Item:Q567740
chemical compound caprylic acid Item:Q567741
chemical compound capric acid Item:Q567742
chemical compound lauric acid Item:Q567743
New Queries
Query topic Link
Nutrient properties and their subject items https://tinyurl.com/ycow73nf
Federated query producing bubble chart viz of food items ranked by number of metabolites known to Wikidata https://tinyurl.com/ycufjhj4
  • Created section in Nutrients Introducing WikiFCD paper draft describing steps for incorporating FCTs into wikibase @ line 212
  • Complete work to break out common name and taxon from Malawi FCT into their own columns for bot usage
  • Extended Project B in description section of NSF grant proposal draft
  • Read "The Role of Gut Bacterial Metabolites in Brain Development, Aging and Disease"
  • Curated FDC items with 'raw' in the label with their presumed taxa info so the metabolite query would return more results
  • Continued creating subject items for our property graph in order to map our nutrients to Wikdiata

Week before 23 Feb, 2021

Item counts
Item class Count
food items (produce) 57
foods that are natural products of some taxon 84
New Properties
Property ID EN Label Link datatype
P305 Phytic acid Property:P305 quantity
P306 Malawian Food Composition Table 2019 food id Property:P306 string
New Items
class EN Label Link
chemical compound Item:Q567677
chemical compound vitamin B12 Item:Q567676
vitamin Item:Q567678
chemical element zinc Item:Q567679
chemical element copper Item:Q567680
chemical element manganese Item:Q567681
chemical element selenium Item:Q567682
chemical compound vitamin C Item:Q567683
chemical compound Thiamine Item:Q567684
chemical compound riboflavin Item:Q567685
chemical compound niacin Item:Q567686
chemical compound pantothenic acid Item:Q567687
chemical compound vitamin B6 Item:Q567688
chemical compound sucrose Item:Q567689
Malwaian food id Item:Q567690
chemical compound glucose Item:Q567691
chemical compound fructose Item:Q567692
chemical compound lactose Item:Q567693
chemical compound maltose Item:Q567694
chemical compound galactose Item:Q567695
chemical compound folic acid Item:Q567696
chemical compound choline Item:Q567697
chemical compound Betaine Item:Q567698
chemical compound vitamin A Item:Q567699
chemical compound beta-carotene Item:Q567700
chemical compound alpha-carotene Item:Q567701
chemical compound Beta-cryptoxanthin Item:Q567702
chemical compound lycopene Item:Q567703
chemical compound lutein Item:Q567704
chemical compound zeaxanthin Item:Q567705
chemical compound phylloquinone Item:Q567706
chemical compound menaquinone 4 Item:Q567707
chemical compound retinol Item:Q567708
chemical compound vitamin E Item:Q567709
chemical compound threonine Item:Q567710
New Queries
Query topic Link
federated query overview of chemical compounds https://tinyurl.com/y98t58pw
federated query for chemical compounds that are part of a biological pathway and the works that discuss this https://tinyurl.com/ybtgwgby
federated query for taxa in wikiFCD in which metabolites are known to be found along with the Human Metabolome ids for those metabolites https://tinyurl.com/y7yto56c
federated query for chemical compounds and processes of which they are a part https://tinyurl.com/y6wbw7cg

Week before 16 Feb, 20201

Item counts
Item class Count
food items 53
foods that are natural products of some taxon 67
New Properties
Property ID EN Label Link datatype
P302 sourcing circumstances Property:P302 item
P303 Wikibooks Cookbook Entry Property:P303 URL
P304 subject item of this property Property:P304 item
New Items
class EN Label Link
sourcing circumstance presumably Item:Q567658
sourcing circumstance misprint Item:Q567660
sourcing circumstance miscalculation Item:Q567661
sourcing circumstance approximately Item:Q567662
sourcing circumstance contradiction Item:Q567663
taxon name Koenigia alaskana Item:Q567664
food item Hop Shoots Item:Q567657
food item Narrowleaf Plantain Item:Q567665
food item Broadleaf Plantain Item:Q567666
chemical element calcium Item:Q567669
chemical element iron Item:Q567671
chemical element magnesium Item:Q567672
chemical element phosphorus Item:Q567673
chemical element potassium Item:Q567674
food item Purslane Item:Q567668
New Queries
Query topic Link
Query for packaged food items from the sr_legacy dataset of FDC https://tinyurl.com/yyp2oz6o
Query for all properties with descriptions and aliases and types https://tinyurl.com/y35fddfk
Query for chemical elements with International Chemical Identifier https://tinyurl.com/y68n4cbk
Query for chemical elements with MeSH Tree Code(s) https://tinyurl.com/y8uwcbmy
Query for food items that are a natural product of some taxon https://tinyurl.com/ya4p9onl
Graph viz for food items that are a natural product of some taxon https://tinyurl.com/y9pslqv8

of Information Technology Delhi (IIIT-Delhi) (2017).

  • How will we help users select between https://tinyurl.com/y66tj86q ?
  • How will we help users select between 40+ brussels sprouts entries from FDC? (Advanced search for phrase)
  • Review Item:Q562688 as example of why it might be confusing to combine USDA food items with other fct food items, would be difficult to ensure that people not assume that the common names and the natural product of taxon info from Edible Wild Foods is also valid for the FDC statements
  • Draft of Introducing WikiFCD for Nutrients
  • NSF grant: Expanded text for Projects B and C
  • Great paper calling for projects like ours: https://academic.oup.com/database/article/doi/10.1093/database/baab003/6119904
    • figure 1
    • figure 3
    • comprehensive list of ontologies and knowledge bases
    • Their approach is a biomedical ontologist's approach -> we can enhance this approach with Wikidata
    • Path forward for NIH funding for personalized medicine
    • Potential collaborators
    • Leverage the working groups mappings
  • https://github.com/FoodOntology/joint-food-ontology-wg

Week before Feb 9, 20201

New Properties
Property ID EN Label Link datatype
P295 Dehydroascorbic acid Property:P295 quantity
P296 Vitamin K Property:P296 quantity
P297 Phenolic acids Property:P297 quantity
P298 Hydroxibenzoic acids Property:P298 quantity
P299 Hydroxycinnamic acids Property:P299 quantity
P300 Flavonols Property:P300 quantity
P301 Anthocyanins Property:P301 quantity
New Items
class EN Label Link
taxon name Wasabia koreana Item:Q567651
food item Lamb's quarters Item:Q567652
food item Skeleton weed Item:Q567653
food item Shepherd’s-purse Item:Q567650
food item Chicory Item:Q567654
food item Hawthorn berries Item:Q567655
food item Wild fennel Item:Q567656
New Queries
Query topic Link
Wikidata query for items with OFF ingredient id and the articles about these foods in all 'pedias with lang label

https://w.wiki/yRo

Week before Feb 2, 20201

New Properties
Property ID EN Label Link datatype
P283 editor Property:P283 string
P284 Oxalic acid Property:P284 quantity
P285 Fumaric acid Property:P285 quantity
P286 Phenolics Property:P286 quantity
P287 Flavonoids Property:P287 quantity
P289 Carotenoids Property:P289 quantity
P290 Neoxanthin Property:P290 quantity
P291 Violaxanthin Property:P291 quantity
P292 Quinic acid Property:P292 quantity
P293 Shikimic acid Property:P293 quantity
P294 Nitrate Property:P294 quantity
New Items
class EN Label Link
food item fool's watercress Item:Q567642
food item borage Item:Q567643
food item wild leek Item:Q567641
food item shepard's purse Item:Q567650
unit cup(s) Item:Q567645
unit Tbs Item:Q567647
unit tsp Item:Q567648
dish granola Item:Q567644
dish granola Item:Q567649
packaged food item ground flaxseed Item:Q567646
FCT Mediterranean Wild Edible Plants Item:Q567640
New Queries
Query topic Link
Query for ranked list of items containing most to least DHA (Docosahexaenoic acid) listed in this wikibase

https://tinyurl.com/y56qvvr6

Retrieved from "https://wikifcd.wikibase.cloud/w/index.php?title=User:Kat&oldid=531391"