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dbmi-pitt / DIKB-Micropublication

Micropublication and Open Data Annotation for drug-drug interaction evidence synthesis
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use best drug identifiers #1

Open jodischneider opened 10 years ago

jodischneider commented 10 years ago

We will need to find & apply DRON and PRO identifiers

Example DRON identifiers: DRON:0001858 (escitalopram, http://wifo5-03.informatik.uni-mannheim.de/drugbank/page/drugs/DB01175 ) PRO:00006121 (cyb2d6, http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=PR_000006121 )

jodischneider commented 10 years ago

Ignore the below -- keeping here just in case I'm wrong...

(1) Drugbank does list CHEBI identifiers, for instance http://www.drugbank.ca/drugs/DB01175 has external links to CHEBI in the references section: http://www.drugbank.ca/drugs/DB01175#references

(2) Check whether CHEBI identifiers suffice DrOn's CHEBI identifiers are listed here (appears to be 1877 distinct CHEBI's): http://repos.frontology.org/dron/raw/master/dron-chebi.owl CHEBI identifiers on this list can appear in our results since they do not need to be resolved further to DRON.

(3) If not, further work is needed. For the CHEBI identifiers NOT on this list, we will need to do further work to get the correct DRON identifier.

For these terms, one possibility is to find the links between DRON and RxNorm here: http://purl.obolibrary.org/obo/dron/dron-rxnorm.owl There are 73505 occurrences in the above OWL file using DRON:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_00010006">
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aprotinin</rdfs:label>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
    <dron:DRON_00010000 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1056</dron:DRON_00010000>
</owl:Class>
jodischneider commented 10 years ago

DrOn National Drug Code info is also available but I don't think we need it: http://purl.obolibrary.org/obo/dron/dron-ndc.owl

rkboyce commented 10 years ago

Thanks for this comment and the information. We will need to have several discussions about the most appropriate drug identifiers to use to maximize the potential of other projects we are involved in including LinkedSPLs (https://github.com/bio2rdf/bio2rdf-scripts/tree/release3/linkedSPLs) and the OHDSI KnowledgeBase (https://github.com/OHDSI/KnowledgeBase)

jodischneider commented 9 years ago

We are now using CHEBI and PRO.

We are using CHEBI because we are discussing ingredients in the DIKB. By contrast, DRON only lists products (not ingredients).

Is this now resolved, or is there some further action to take on DRON vs. CHEBI? What is LinkedSPL using? What is OHDSI using?