Skip to content

/MassBank-data

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error in DTXSID mapping? #68

Open
schymane opened this issue May 16, 2019 · 11 comments

Comments

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
3 participants
@schymane @meier-rene @ChemConnector
@schymane
Copy link
Member

commented May 16, 2019 •
edited

Bug report from external user:

First of all, thank you for the massive effort in developing and maintaining MassBank! I was very pleased to see in the News that all the records were linked to Comptox (if registered), so I gave it a go: the first record I randomly tested was MSJ01067 (Acetamiprid; GC-EI-Q; MS; Positive; M+), I clicked the Comptox link (DTXSID60861331) and...the substance ID does not exist - Acetamiprid ID is DTXSID0034300.

I therefore tested many other records which were all ok, so I assume that I was really unlucky (or an excellent proof-reader) :-)

I don't know if it's an isolated case, but give it a check.

Follow-up:
Indeed that DTXSID doesn't appear to exist in the public Dashboard, nor do I get a match for that InChIKey. If this is a name match, it's wrong ...
https://massbank.eu/MassBank/RecordDisplay.jsp?id=MSJ01067
image

https://comptox.epa.gov/dashboard/dsstoxdb/results?search=DTXSID60861331
image

https://comptox.epa.gov/dashboard/dsstoxdb/results?search=WCXDHFDTOYPNIE-UHFFFAOYSA-N
image

This is the correct match:
https://comptox.epa.gov/dashboard/dsstoxdb/results?search=DTXSID0034300
and is also found by name:
https://comptox.epa.gov/dashboard/dsstoxdb/results?search=Acetamiprid

Any ideas what went wrong here @meier-rene @ChemConnector ?
PubChem link looks fine
https://pubchem.ncbi.nlm.nih.gov/compound/213021
@meier-rene

This comment has been minimized.

Sign in to view
Copy link
Collaborator

commented May 16, 2019

That's my issue. I take care of it.
@ChemConnector

This comment has been minimized.

Sign in to view
Copy link

commented May 16, 2019

I hope @meier-rene can resolve the issue as it is not obvious at all to me how this would happen. We do have that DTXSID60861331 in our internal production but it is not yet public and certainly is not Acetamiprid. Rene, please let me know whether you can fix it . Thanks
@schymane

This comment has been minimized.

Sign in to view
Copy link
Member Author

commented May 16, 2019

I hope @meier-rene can find the cause but it's worrying that this exists but is not yet in production - it is going to get very confusing if we can access DTXSIDs that are not yet in production via the web services ... we will end up with broken links everywhere and no way to control it?
@ChemConnector

This comment has been minimized.

Sign in to view
Copy link

commented May 16, 2019

@meier-rene meier-rene referenced this issue May 16, 2019

Open

Add DTXSIDs to all MassBank records with InChIKey match #66

@meier-rene

This comment has been minimized.

Sign in to view
Copy link
Collaborator

commented May 16, 2019

Because the InChI key resolver at https://actorws.epa.gov is my only source for DTXSID I have to wait until this service is fixed.
@ChemConnector

This comment has been minimized.

Sign in to view
Copy link

commented May 16, 2019

@meier-rene

This comment has been minimized.

Sign in to view
Copy link
Collaborator

commented May 17, 2019

The service is back, thank you @ChemConnector. Unfortunately there waits some more work for you. The erroneous record https://massbank.eu/MassBank/RecordDisplay.jsp?id=MSJ01067 contains the InChI key WCXDHFDTOYPNIE-UHFFFAOYSA-N. If I put this in the resolver https://actorws.epa.gov/actorws/chemIdentifier/v01/resolve?identifier=WCXDHFDTOYPNIE-UHFFFAOYSA-N I get DTXSID60861331. This does not resolve to an valid substance https://comptox.epa.gov/dashboard/dsstoxdb/results?search=DTXSID60861331. Please have a look into this.
@schymane

This comment has been minimized.

Sign in to view
Copy link
Member Author

commented May 17, 2019

Interesting ... tautomer issue maybe contributing - plus differing stereochem in the InChIKeys?
image

@schymane schymane referenced this issue May 17, 2019

Open

Add DTXSIDs into RMassBank identifiers #215

@ChemConnector

This comment has been minimized.

Sign in to view
Copy link

commented May 17, 2019

I am still researching but I think I know what it is and need to check out with the developer. One comment though is that Acetamiprid is explicit stereo (E-form) for the chemicals. See https://comptox.epa.gov/dashboard/dsstoxdb/results?search=DTXSID0034300 . I have confirmed this will multiple resources so you may wish to update your structure and associated InChIKey to WCXDHFDTOYPNIE-RIYZIHGNSA-N. This resolves correctly. https://actorws.epa.gov/actorws/chemIdentifier/v01/resolve?identifier=WCXDHFDTOYPNIE-RIYZIHGNSA-N

This is NOT the cause of the error you are seeing for sure. If my hypothesis is correct it's the fact that one of the synonyms for this chemical https://comptox.epa.gov/dashboard/dsstoxdb/results?search=FAIL%20peptide in the synonym table is "FAIL" and I believe that the service is passing a FAIL message and then resolving to this chemical....it matches the IndigoInChIKey here https://actorws.epa.gov/actorws/chemIdentifier/v01/resolve?identifier=WCXDHFDTOYPNIE-UHFFFAOYSA-N. I am off to go prove it...
@schymane

This comment has been minimized.

Sign in to view
Copy link
Member Author

commented May 17, 2019

@meier-rene can you take care of updating the record, or should I add it to my list along with the CASMI and UFZ ones to resolve (hope to do this next week). Just let me know, thanks!

meier-rene pushed a commit that referenced this issue May 17, 2019

René Meier
Fix chemical information and database identifier according to #68
Loading status checks…
ce95e20
@meier-rene

This comment has been minimized.

Sign in to view
Copy link
Collaborator

commented May 17, 2019

I changed the chemical information for all records of Acetamiprid.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.