Add DTXSIDs into RMassBank identifiers

[schymane]

The EPA have preliminary webservices now available to retrieve DTXSIDs by InChIKey, we should add this into RMassBank to retrieve these for new records (and note that this may change again in the future)

https://github.com/MassBank/RMassBank/blob/master/R/webAccess.R

https://actorws.epa.gov/actorws/chemIdentifier/v01/resolve?identifier=IKHGUXGNUITLKF-UHFFFAOYSA-N
https://actorws.epa.gov/actorws/chemIdentifier/v01/resolve.json?identifier=IKHGUXGNUITLKF-UHFFFAOYSA-N
https://actorws.epa.gov/actorws/chemIdentifier/v01/resolve.xml?identifier=IKHGUXGNUITLKF-UHFFFAOYSA-N

@adelenelai would you be interested in looking into this?

We are looking at doing this initially database side to get DTXSIDs into records already created:
MassBank/MassBank-data#66
and
MassBank/MassBank-web#80

[adelenelai]

working on it

[meier-rene]

We have added this in MassBank. If you like you can skip this because its easy to post process records in MassBank.

[tsufz]

@meier-rene I don't agree to process everything with MassBank only. MassBank records should be applicable on a private repository with parsing tools without MassBank in game. DTXSID is an important identifier and thus it should be processed with RMassBank.

[adelenelai]

Hi, EPA webservices seem to be down now, the links in @schymane 's original post don't work @ChemConnector
Are there new URLs which work?

[ChemConnector]

The services are down because they ran an update overnight and one of the certificates expired and broke things. They are working on it in production (NOT our team) and hopefully things will come up soon. Apologies for the inconvenience. Tony Williams Phone: +1 (919) 201-1516 Email: tony27587@gmail.com Skype: tony27587 My Blog: www.chemconnector.com Twitter: http://twitter.com/ChemConnector

…

On Thu, May 16, 2019 at 8:27 AM adelenelai ***@***.***> wrote: Hi, EPA webservices seem to be down now, the links in @schymane <https://github.com/schymane> 's original post don't work @ChemConnector <https://github.com/ChemConnector> Are there new URLs which work? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#215?email_source=notifications&email_token=AAEYGD6YOIOYHJGEFKWLZB3PVVHKZA5CNFSM4HLF5NC2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVRUU7Q#issuecomment-493046398>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAEYGD2VTDPX6A3QIMWVYXDPVVHKZANCNFSM4HLF5NCQ> .

[schymane]

The services should be up again @adelenelai can you check if they work for you now?
See also MassBank/MassBank-data#68 for updates

[adelenelai]

Note (mostly to self, also for documentation):

It is possible for a DTXSID to not exist for a particular compound, because not all stereochemistries of a compound exist in the CompTox Dashboard.

Assuming webservices and Dashboard are in sync, (see MassBank/MassBank-data#68) any attempts to manually curate infolists in Step 2 of mbWorkflow for DTXSID will not be successful either - the DTXSID just does not exist!

Therefore, if final MB record does not contain the field CH$LINK: COMPTOX, it should not be perceived as bug but rather reflects inherent non-existence of that particular DTXSID. (This behaviour was modelled after that of other pre-existing identifiers e.g. CHEBI.)

Whether an explicit declaration should be incorporated for these cases e.g. CH$LINK: COMPTOX **none found** is another issue...

In future: if the DTXSID does come into existence over time, post-MB-record-generation-and-upload, Rene's post-processing would be handy.

[schymane]

Yes, it is common that identifiers are missing, so modelling this on the way that ChEBI identifiers are handled is the right way to go ... I don't think we need an explicit declaration because the fact that it is missing is implicitly clear in the absence of a corresponding entry in the infolist. Some of the identifiers like KEGG, ChEBI and LipidMaps have very few matches and explicit statements would get annoying over time... and yes, Rene's workflow will catch those that do appear later.
The validation should account for potential identifier deprecation over time ... but this is another (trickier) topic ... @meier-rene