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Changes to Syntax for Metabolomics USIs #250

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meier-rene opened this issue Jun 30, 2020 · 1 comment
Open

Changes to Syntax for Metabolomics USIs #250

meier-rene opened this issue Jun 30, 2020 · 1 comment
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@meier-rene
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@meier-rene meier-rene commented Jun 30, 2020

We got this information:
Letting you all know, Wout and I had a few conversations with the
Proteomics USI team about identifiers that would conform in style to
proteomics spectral libraries. There are basically 3 changes that
we'd need to do that would simply require in most cases an
few characters on your side. These are basically made to support
versioning of spectra if that were the case (though likely we
wouldn't have it on the GNPS side but would be consistent with
Proteomics libraries).

These are the changes that would happen for libraries

  1. The first block becomes mzdraft for ones that have not
    specifically been verified by the PSI USI folks
  2. The third block would denote some version, but could be left blank
  3. The fourth block denotes the type of value for the
    identifier (fifth block)

mzspec:MASSBANK:SM858102 -> mzdraft:MASSBANK::accession:SM858102
mzspec:MOTIFDB:motif:171163 -> mzdraft:MOTIFDB::accession:171163

For our own analysis tasks

  1. The first block becomes mzdraft for ones that have not
    specifically been verified by the PSI USI folks
  2. Second block determines the resource
  3. The third block is a dataset accession
  4. The fourth block denotes the type of value for the
    identifier (fifth block)

mzspec:MS2LDATASK-38:document:43062 -> mzdraft:MS2LDA:TASK-
190:accession:43062
mzspec:GNPSTASK-
c95481f0c53d42e78a61bf899e9f9adb:spectra/specs_ms.mgf:scan:1943 ->
mzdraft:GNPS:TASK-c95481f0c53d42e78a61bf899e9f9adb-
spectra/specs_ms.mgf:scan:1943

Wout and I have already updated the metabolomics USI website to
handle these new styles, but have not merged/deployed.

What we need from you:

  1. Simon -> Update links for MS2LDA/MOTIFDB to the new USI style
  2. Rene/Tobias -> Update Massbank links to the new USI style
  3. Ming -> Update linkouts on GNPS Libraries/Tasks to the new USI
    style

Once we have all these in place along, we will switch everything over
on the resolution side to make sure we have minimal downtime.

I was hoping we'd aim for 2 weeks from now to make the change. Let me
know if that works for you all!

@meier-rene meier-rene self-assigned this Jun 30, 2020
@schymane
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@schymane schymane commented Jun 30, 2020

... this is all fair enough and understandable (and hopefully achievable?), semantically I am not a fan of mzdraft and would be keen to know what we could do to earn the mzspec upgrade from PSI ASAP ... does anyone know how to do this?

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