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[Linking] Linking from MassBank #62

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mwang87 opened this issue Jan 21, 2020 · 7 comments · May be fixed by MassBank/MassBank-web#218
Open

[Linking] Linking from MassBank #62

mwang87 opened this issue Jan 21, 2020 · 7 comments · May be fixed by MassBank/MassBank-web#218

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@mwang87
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@mwang87 mwang87 commented Jan 21, 2020

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@mwang87 mwang87 commented Jan 26, 2020

Hey @schymane ! I was wondering if you know if you all would be interested (and easily feasible) to link to the metabolomics-usi page (e.g. https://metabolomics-usi.ucsd.edu/spectrum/?usi=mzdata:MASSBANK:BSU00002) to help users draw vector versions of the spectra for publication. We're planning on rolling out more links within GNPS and MS2LDA (already have it from results from GNPS). We think its relatively nice and thank you so much for the feedback so far. We're already linking back to the parent resource so hopefully it'll help connect people with the data! Let us know!

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@schymane schymane commented Jan 26, 2020

@sneumann @tsufz @sdrogers let's discuss while at Dagstuhl

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@sneumann sneumann commented Jan 28, 2020

Is there any documentation ? Or is it as simple as adding a URL
<a href="https://metabolomics-usi.ucsd.edu/spectrum/?usi=mzdata:MASSBANK:$ACCESSION">Additional visualisation</a>
to the Record JSP rendering page near the spectrum ? Yours, Steffen

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@mwang87 mwang87 commented Jan 28, 2020

@sneumann Yes, apologies for the lack of documentation, i'll add a bit, but it is that easy.

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@schymane schymane commented Jan 28, 2020

Hi @mwang87 out on a tangent: would it be possible to resolve by splash?

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@sneumann sneumann commented Jan 28, 2020

ok, @meier-rene is the expert. I quickly hacked into
https://github.com/MassBank/MassBank-web/blob/master/MassBank-Project/MassBank/src/main/webapp/RecordDisplay.jsp#L555
to do

<tr>
<td><a href="https://metabolomics-usi.ucsd.edu/spectrum/?usi=mzdata:MASSBANK:<%=accession%>">Additional visualisation</a></td>
</tr>

Which will give you https://msbi.ipb-halle.de/MassBank/RecordDisplay.jsp?id=PS004505&dsn=RIKEN_ReSpect
Will now create a pull request for MassBank. Yours, Steffen

sneumann added a commit to MassBank/MassBank-web that referenced this issue Jan 28, 2020
Prototype for Link out to external Visualisation via the https://metabolomics-usi.ucsd.edu/
Closes mwang87/MetabolomicsSpectrumResolver#62
Improvements could be a nicer element (Link out icon ?) 
Currently an example is e.g. https://msbi.ipb-halle.de/MassBank/RecordDisplay.jsp?id=UA002901
Yours, Steffen
@sneumann sneumann linked a pull request that will close this issue Jan 28, 2020
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@sneumann sneumann commented Jan 28, 2020

@schymane : SPLASH is tracked in #66

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