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Sign upAdd DTXSIDs into RMassBank identifiers #215
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adelenelai
commented
May 8, 2019
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working on it |
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meier-rene
commented
May 14, 2019
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We have added this in MassBank. If you like you can skip this because its easy to post process records in MassBank. |
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@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. |
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adelenelai
commented
May 16, 2019
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Hi, EPA webservices seem to be down now, the links in @schymane 's original post don't work @ChemConnector |
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ChemConnector
commented
May 16, 2019
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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?
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The services should be up again @adelenelai can you check if they work for you now? |
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adelenelai
commented
May 27, 2019
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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 Whether an explicit declaration should be incorporated for these cases e.g. In future: if the DTXSID does come into existence over time, post-MB-record-generation-and-upload, Rene's post-processing would be handy. |
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Add getCompTox to Mbworkflow #215 #217
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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. |
schymane commentedMay 7, 2019
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