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Sign upUpload and link raw mass spectral data #79
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Its already on the roadmap, but technical procedure is still undefined. We have this as WP in our next de.NBI funding period. We can use this issue for discussion. You suggest any repository. This needs to be defined. I doubt that github is the right place because of the size of the data, because data might not be text based and will most likely not changed once it has been deposed. |
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I have been using Zenodo a lot recently and am very happy so far - diverse datasets and very few issues (>56 datasets and only one failure on one file associated with one that I could solve in the end). |
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We are also discussing internal possibilities here ... we would have the capabilities but they are not up and running even internally yet for us as a group, our BioCore are running this for others. |
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I was just thinking about our UFZ repository for our records. However, they still not have DOI and thus the landing page and URL may change at any time.... |
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However, we may firstly indroduce a new tag for the linking or should be use the comment tag? |
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If this is something we want to try to implement systematically, I would prefer a new tag rather than overloading the COMMENT field with too many diverse comments. |
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meowcat
commented
Jun 25, 2019
I would kind of like to use MassIVE or alternatively MetaboLights or MetabolomicsWorkbench so we don't fragment (pun intended) mass spec data over even more repositories. But if Zenodo is getting mass-spectrified already then I guess the argument is not so strong. |
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Yes to considering MetaboLights and the MetabolomicsWorkbench but I have also heard a lot of feedback that it takes a while to get data into those two ... |
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Does Metabolights store raw data (meaning ventors' format, not mzML)? Actually, we have to store both vendor and open format.... I will talk to Reza Salek to discuss opportunities. |
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justinjjvanderhooft
commented
Jun 25, 2019
Yes, it does store raw data formats. Keeva from MetaboLights is also
present at the Metabolomics2019 conference.
…On Tue, 25 Jun 2019, 10:33 Tobias Schulze, ***@***.***> wrote:
Does Metabolights store raw data (meaning ventors' format, not mzML)?
Actually, we have to store both vendor and open format.... I will talk to
Reza Salek to discuss opportunities.
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Thanks for the advice, I already contacted Keeva. |
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If referencing one or more individual spectra in some repository, the PSI spectrum identifier |
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Sebastian's request was to be able to obtain the input spectrum/spectra used in a record prior to processing. |
tsufz commentedJun 24, 2019
#MetSoc2019, Towards FAIR Spectral Libraries workshop. There is a request to make raw mass spectral files associated with MassBank records available for the public via any repository. Should be vendor's format, not mzML.