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(→Week before 9 March, 2021: phytosterols) |
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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== | ==Week before 9 March, 2021== | ||
{| class="wikitable" | {| class="wikitable" | ||
Line 17: | Line 319: | ||
! Property ID !! EN Label !! Link !! datatype | ! Property ID !! EN Label !! Link !! datatype | ||
|- | |- | ||
| | | || || || | ||
|} | |} | ||
Line 59: | Line 361: | ||
| class of chemical compounds || phytosterols || [[Item:Q567760]] | | class of chemical compounds || phytosterols || [[Item:Q567760]] | ||
|- | |- | ||
| chemical compound || || [[Item: | | chemical compound ||stigmasterol || [[Item:Q567761]] | ||
|- | |- | ||
| chemical compound || | | chemical compound || campesterol || [[Item:Q567762]] | ||
|- | |- | ||
|chemical compound || || [[Item: | |chemical compound || brassicasterol || [[Item:Q567763]] | ||
|- | |- | ||
| chemical compound || | | chemical compound || beta-sitosterol18:2 CLAs || [[Item:Q567764]] | ||
|- | |- | ||
|chemical compound || | |chemical compound || campestanol || [[Item:Q567765]] | ||
|- | |- | ||
| chemical compound || || [[Item: | | chemical compound ||pentadecanoic acid || [[Item:Q567766]] | ||
|- | |- | ||
| chemical compound || || [[Item: | | chemical compound ||margaric acid || [[Item:Q567767]] | ||
|- | |- | ||
| chemical compound || || [[Item: | | chemical compound ||lignoceric acid || [[Item:Q567768]] | ||
|- | |- | ||
|chemical compound || || [[Item: | |chemical compound || elaidic acid || [[Item:Q567771]] | ||
|- | |- | ||
| chemical compound || || [[Item: | | chemical compound ||tridecanoic acid || [[Item:Q567772]] | ||
|- | |- | ||
| chemical compound || || [[Item: | | chemical compound ||undecylic acid || [[Item:Q567773]] | ||
|- | |- | ||
| chemical compound || | | chemical compound || epigallocatechin-3-gallate || [[Item:Q567774]] | ||
|- | |- | ||
|chemical compound || || [[Item: | |chemical compound ||inulin || [[Item:Q567775]] | ||
|- | |- | ||
| chemical compound || | | chemical compound || alpha-linolenic acid || [[Item:Q567776]] | ||
|- | |- | ||
| chemical compound || || [[Item: | | chemical compound ||dihomo-γ-linolenic acid || [[Item:Q567777]] | ||
|} | |} | ||
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! Query topic !! Link | ! 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 | * wikiFCD is the largest wikibase on wbStack | ||
* self-heal curation report | * 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? | ||
* 14:1 t | * 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== | ==Week before 2 March, 2021== |