spectral-workbench
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Support open standards for exporting spectra
Because open data and portability are good things(TM), we probably want to support open standards for this sort of data. The custom exports that currently exist certainly work, but might not be as portable or as easy to work with as open standards.
We might want to export some small amount of metadata regarding ownership and licensing for each spectra which I don't think is part of any standard.
uhm, not sure if our analysis are compatible with mass spec, but this is an interesting reference of open data formats for use with mass spectrometers. https://en.wikipedia.org/wiki/Mass_spectrometry_data_format#Open_formats
Hi, Bryan, just to be clear, how is this issue distinguished from the export formats available in the left side of each page: http://spectralworkbench.org/analyze/spectrum/43491
It was a request by someone to the web@ list. I'll have to look at that later. It isn't showing up on the mobile version, which makes sense. On Feb 10, 2015 5:46 PM, "Jeffrey Warren" [email protected] wrote:
Hi, Bryan, just to be clear, how is this issue distinguished from the export formats available in the left side of each page: http://spectralworkbench.org/analyze/spectrum/43491
— Reply to this email directly or view it on GitHub https://github.com/publiclab/spectral-workbench/issues/24#issuecomment-73800809 .
Ah I see the export functions now. I'm not sure what the person wanted who emailed web@, but I think it might be worth keeping this ticket open to investigate open standard formats for data of this kind.
The current export formats are custom and arbitrary based on how we store the data, right?
If the open standards aren't important, we can close this ticket.
I think the only standards are for csvs, and we do have an open ticket for that. On Feb 10, 2015 11:13 PM, "Bryan Bonvallet" [email protected] wrote:
Ah I see the export functions now. I'm not sure what the person wanted who emailed web@, but I think it might be worth keeping this ticket open to investigate open standard formats for data of this kind.
The current export formats are custom and arbitrary based on how we store the data, right?
If the open standards aren't important, we can close this ticket.
— Reply to this email directly or view it on GitHub https://github.com/publiclab/spectral-workbench/issues/24#issuecomment-73831738 .
Did you see the wikipedia link, posted in an earlier comment on this ticket, with a list of open standards of mass spec data?
JCAMP-DX is an ASCII based standard, ANSI-MS is based on netCDF (whatever that is), etc.
oh cool, i do remember that; was looking in email view only.
On Wed, Feb 11, 2015 at 11:40 AM, Bryan Bonvallet [email protected] wrote:
Did you see the wikipedia link, posted in an earlier comment on this ticket, with a list of open standards of mass spec data?
JCAMP-DX is an ASCII based standard, ANSI-MS is based on netCDF (whatever that is), etc.
— Reply to this email directly or view it on GitHub https://github.com/publiclab/spectral-workbench/issues/24#issuecomment-73914373 .
I can rename the ticket to be more appropriate for exporting standard mass spec formats. Under the current title of exporting spectra, this ticket is already resolved.
Cool, and let's disambiguate from the CSV requests in the other issue. Thanks!
On Wed, Feb 11, 2015 at 12:27 PM, Bryan Bonvallet [email protected] wrote:
I can rename the ticket to be more appropriate for exporting standard mass spec formats. Under the current title of exporting spectra, this ticket is already resolved.
— Reply to this email directly or view it on GitHub https://github.com/publiclab/spectral-workbench/issues/24#issuecomment-73923882 .
