make class diagram (Story 1)

MartijnAB / from-toxicological-data-to-toxicological-information

A internship project with the intent to connect existing and/or provided toxicological data, with other toxicological data in order to better understand it.

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make class diagram (Story 1) #16

Open MartijnAB opened 5 years ago

MartijnAB commented 5 years ago

https://www.draw.io/?state=%7B%22folderId%22:%221Ze239pToF8gveemPwk8IJIiZcTlzIEdV%22,%22action%22:%22create%22,%22userId%22:%22116010632024541818707%22%7D#G1jQDO5UITo0HQJ2edodrQAOZ9InftWNkm

https://drive.google.com/drive/u/0/folders/1Ze239pToF8gveemPwk8IJIiZcTlzIEdV

[x] WikiPathways
[ ] LAZAR

mkutmon commented 5 years ago

that link doesn't work for me. can you add the png file here as a comment please?

MartijnAB commented 5 years ago

done

mkutmon commented 5 years ago

Couple of small comments:

execute_sparql_query is a general execution function for all WikiPathways SPARQL query, right?
Is it needed to restrict the "make_chemical_compound" function to CAS numbers? What if a metabolite in a pathway doesn't have a CAS number? Is it then not possible to create a ChemicalCompound?
Is get_lazar really a function in the ChemicalCompound class? Shouldn't that be a spearate class like WikiPathways?
Just to double check - the aggregation goes from ChemicalCompound to Pathway, right? So a Pathway has a ChemicalCompounds.

MartijnAB commented 5 years ago

wat te doen als het enige indicatie nummer van een chemiestof uit meerder mogelijkheden bestaat? ik kan ze natuurlijk altijd in een lijstje stoppen. maar dat zal dat voor elk soort indicatie nummer moeten, wat mij een verkeert onderbuik gevoel geeft.

mkutmon commented 5 years ago

Yes, this is a very tricky issue with chemicals. We can discuss it in the sprint meeting since Denise has a lot of experience with this.

mkutmon commented 5 years ago

Decision:

let's start with only getting the Wikidata id from the Metabolites from the WP SPARQL endpoint
use Wikidata id and query wikidata SPARQL to get Inchi / SMILES (what is needed for LAZAR) --> create Wikidata class