SS-1: A way to connect our ingredient chemical composition database to your Open Food Facts Server

[Sulstice]

Problem

Hi, we started recording chemical compositons to food and colour additive lists used in food in our open source chemical knowledge graph.

We recorded chemical lists of a Mango:

https://github.com/Global-Chem/global-chem/blob/development/global_chem/global_chem/food/fruits/mango/constituents_of_mango.py

Salt:

https://github.com/Global-Chem/global-chem/blob/development/global_chem/global_chem/food/salt/salt.py

And Federal Food and Drug Administration Colour Lists:

https://github.com/Global-Chem/global-chem/blob/development/global_chem/global_chem/food/color_additives/fda_list_one.py

Proposed solution

We are hoping to connect our API's somehow if people are interested in learning the chemical composition of different foods and their 1-D molecular representation.

Number of products impacted

Could be a lot if everyone can query ingredients based on the chemical composition.

Time per product

A linkage between us could take about a week of development with testing.

[alexgarel]

Hi @Sulstice

Of course this is of interest to us, because it can help people with rare disease.

Do you propose it as a contribution ?

[Nickspizza001]

Hello @alexgarel I am Damilola from GlobalChem. That's great to hear! GlobalChem would like to contribute to OpenFoodFacts, What is any possible way to link both our data together?

[alexgarel]

Hi @Nickspizza001 (sorry for late reply, summer is a bit full of work !).

I don't know what @stephanegigandet, @aleene, @moon-rabbitOFF or @teolemon think, but a first way could be to add to link ingredients / additives / etc. to the id in your database in the taxonomies (see https://wiki.openfoodfacts.org/Global_taxonomies)

Also I'm not sure about the license of your database. Is MPL 2.0 the license for the data ?

[Sulstice]

Hi @alexgarel,

No worries, I totally get it. We can move slow, I care more that we do it correctly.

Yeah so here's an output of our knowledge graph which puts it nicely how it's organized:

               ┌tainted_sexual_enhancements
                  │       ┌exsens_products
             ┌sex─├exsens─└lube
             │    └contraceptives─oral_contraceptives
             │          ┌pihkal
             │          ├schedule_five
             │          ├schedule_three
             ├narcotics─├schedule_four
             │          ├schedule_two
             │          └schedule_one
             ├animals─snakes─drugs_from_snake_venom
             ├interstellar_space─asteroid_ryugu
             │              ┌amino_acids
             │              ├vitamins
             ├miscellaneous─├open_smiles
             │              └regex_patterns
             │                       ┌allergen_inactive_ingredients
             ├formulation─excipients─├monoclonal_antibodies
             │                       └biopharmaceutics_class_three─cimetidine_and_acyclovir
             ├warfare─organophosphorous_nerve_agents
             │                            ┌privileged_kinase_inhibitors
             │                            ├common_r_group_replacements
             ├proteins─kinases─┌scaffolds─├privileged_scaffolds
             │                 │          └iupac_blue_book
             │                 └braf─braf_inhibitors
             │            ┌alternative_jet_fuels
             ├environment─├emerging_perfluoroalkyls
             │            └chemicals_from_biomass
             │          ┌clay─montmorillonite_adsorption
             ├materials─└polymers─common_monomer_repeating_units
             │     ┌salt
             │     │             ┌mango_flavonoids
             │     │             ├mango_phytocompounds
             │     │             ├mango_fatty_acids
             │     ├fruits─mango─├mango_vitamins
             │     │             ├mango_phenolic_acids
             │     │             └mango_amino_acids
             ├food─│                ┌fda_list_one
             │     │                ├fda_list_three
             │     │                ├fda_list_two
             │     └color_additives─├fda_list_seven
             │                      ├fda_list_six
             │                      ├fda_list_four
             │                      └fda_list_five
             ├education─cengage─organic_and_inorganic_bronsted_acids
global_chem──│     ┌transdermal_and_dermal_delivery─surfactants
             ├skin─└sunscreen
             │                  ┌bidendate_phosphine_ligands─nickel_ligands
             ├organic_synthesis─├solvents─common_organic_solvents
             │                  └protecting_groups─amino_acid_protecting_groups
             │                                               ┌medical_gases
             │                                               ├anaesthetics
             │                                               ├cysticidal_medicines
             │                                               ├access_group_antibiotics
             │                                               ├antidotes
             │                                               ├watch_group_antibiotics
             │                                               ├reserve_group_antibiotics
             │                                               ├anticonvulsants
             │                    ┌world_health_organization─├opioid_analgesics
             │                    │                          ├anaphylaxis_medicines
             │                    │                          ├antifilarials
             │                    │                          ├preoperative_medicines
             │                    │                          ├intestinal_anthelminthics
             │                    │                          ├palliative_care
             │                    │                          ├non_steroidal_anti_inflammatory_medicines
             │                    │                          └antischistosomals_medicines
             │                    │             ┌hydrocarbons
             │                    │             ├proteins_glycoproteins_enzymes
             │                    │             ├nitrogenous_compounds
             ├medicinal_chemistry─│             ├alcohols
             │                    │             ├sugars
             │                    │             ├esters_and_lactones
             │                    │             ├pigments
             │                    │             ├acids
             │                    ├cannabinoids─├flavanoidglycosides
             │                    │             ├fatty_acids
             │                    │             ├constituents_of_cannabis_sativa
             │                    │             ├terpenes
             │                    │             ├steroids
             │                    │             ├ketones
             │                    │             ├aldehydes
             │                    │             ├non_cannabinoids_phenols
             │                    │             └phytocannabinoids
             │                    │         ┌electrophilic_warheads_for_kinases
             │                    ├warheads─└common_warheads_covalent_inhibitors
             │                    │      ┌iupac_blue_book_rings
             │                    ├rings─├rings_in_drugs
             │                    │      └phase_2_hetereocyclic_rings
             │                    └chinese─how_to_live_longer
             └peptides─lanthipeptides

nodes can be fetched by their literal name. For example.

from global_chem import GlobalChem
gc = GlobalChem()

gc.build_global_chem_network()
smiles = gc.get_node('mango')

Yes it is MPL 2.0 for the data. It's also got a U.S. copyright for the dictionary given to my personal name.

[alexgarel]

@Nickspizza001 and @Sulstice it might be a good idea to join the #taxonomies chan on our slack

[aleene]

Do you support links to wikidata? Links to OFF have been added to Wikidata. For me it seems a bit to much if we add other links. I rather keep things centralised on wikidata.

[raphael0202]

Hello! Another approach is to link your database against Wikidata, and when we're working on project that involves using your database, we can very easily link our taxonomy against your database through Wikidata.

[Sulstice]

https://www.wikidata.org/wiki/Wikidata:Dataset_Imports/Chemical_Composition_of_a_Mango

How is this?

[github-actions[bot]]

This issue has been open 90 days with no activity. Can you give it a little love by linking it to a parent issue, adding relevant labels and projets, creating a mockup if applicable, adding code pointers from https://github.com/openfoodfacts/openfoodfacts-server/blob/main/.github/labeler.yml, giving it a priority, editing the original issue to have a more comprehensive description… Thank you very much for your contribution to 🍊 Open Food Facts