wikifcd

Kat

Joined 2 March 2020
User page Discussion

User:Kat (view source)

Revision as of 18:38, 10 October 2022

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=Progress=
=Progress=


==Week before 23 Feb, 2021==
 
==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"
{| class="wikitable"
|+ Item counts
|+ Item counts
Line 9: Line 310:
!  Item class!! Count
!  Item class!! Count
|-
|-
| food items || 57
| food items (produce) || 57
|-
|-
| foods that are natural products of some taxon || 72
| foods that are natural products of some taxon || 252
|}
|}
{| class="wikitable"
{| class="wikitable"
Line 18: Line 319:
! Property ID !! EN Label !! Link !! datatype
! Property ID !! EN Label !! Link !! datatype
|-
|-
| P295 ||  ||  || quantity
| ||  ||  ||  
|}
 
{| 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
|-
|-
| P296||   ||  || quantity
| Which wikiFCD foods are known to contain the 2D structure of beta-sitosterol|| https://tinyurl.com/y7g4jd8h
|-
|-
| P297|| || [[Property:P297]] || quantity
| 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
|-
|-
| P298 ||    || [[Property:P298]] || quantity
!  Item class!! Count
|-
|-
| P299 ||   || [[Property:P299]] || quantity
| food items (produce) || 57
|-
|-
| P300 || || [[Property:P300]] || quantity
| foods that are natural products of some taxon || 252
|}
{| class="wikitable"
|+ New Properties
|-
|-
| P301 ||  || [[Property:P301]] || quantity
! 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
|}
|}


Line 55: Line 581:
|-
|-
| chemical compound || vitamin C || [[Item:Q567683]]
| 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]]
|}
|}


Line 62: Line 642:
!  Query topic !! Link
!  Query topic !! Link
|-
|-
| federated query for chemical elements that are part of a biological pathway and the works that discuss this || https://tinyurl.com/y9t2258t
| 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 food items that are a natural product of a taxon in which a metabolite is known to be found showing food names || https://tinyurl.com/ya8e2mp3
| 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
* FoodEx2 could be a source of the broader categories for foods
* No idea if anyone has mapped between FoodEx2 and FDC
* No idea if anyone has mapped between FoodEx2 and FDC
Line 72: Line 661:
* 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 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
* 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==
==Week before 16 Feb, 20201==
Retrieved from "https://wikifcd.wikibase.cloud/wiki/Special:MobileDiff/468518...531391"