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MassBank / MassBank-web

The web server application and directly connected components for a MassBank web server
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Changes to Syntax for Metabolomics USIs #250

Closed meier-rene closed 4 years ago

meier-rene commented 4 years ago

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!

schymane commented 4 years ago

... 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?

meier-rene commented 4 years ago

Done