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Curating data related to food composition.
Progress
Week before 23 March, 2021
Item class | Count |
---|---|
food items (produce) | 83 |
foods that are natural products of some taxon | 316 |
foods with FoodOn id | 93 |
ingested FCTs | 2 |
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 | 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 |
chemical compound |
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 class | Count |
---|---|
food items (produce) | 57 |
foods that are natural products of some taxon | 252 |
Property ID | EN Label | Link | datatype |
---|---|---|---|
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 |
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 class | Count |
---|---|
food items (produce) | 57 |
foods that are natural products of some taxon | 252 |
Property ID | EN Label | Link | datatype |
---|---|---|---|
P308 | Total Carbohydrate for UDB | Property:P308 | quantity |
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 |
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 class | Count |
---|---|
food items (produce) | 57 |
foods that are natural products of some taxon | 84 |
Property ID | EN Label | Link | datatype |
---|---|---|---|
P305 | Phytic acid | Property:P305 | quantity |
P306 | Malawian Food Composition Table 2019 food id | Property:P306 | string |
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 |
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
Item class | Count |
---|---|
food items | 53 |
foods that are natural products of some taxon | 67 |
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 | 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 |
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
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 | 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 |
Query topic | Link |
---|---|
Wikidata query for items with OFF ingredient id and the articles about these foods in all 'pedias with lang label |
Week before Feb 2, 20201
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 |
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 |
Query topic | Link |
---|---|
Query for ranked list of items containing most to least DHA (Docosahexaenoic acid) listed in this wikibase |