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microbiomedata / metaMS

GC-MS Based Metabolomics Workflow
BSD 2-Clause "Simplified" License
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identify additional metadata / configuration data needed for metabolomics including the use of blanks #4

Closed dehays closed 3 years ago

dehays commented 3 years ago

@corilo Move this issue to whichever issue queue you deem appropriate.

Once you have defined the necessary metadata / configuration data - there would be nmdc-schema issues to align those needs with changes to the metabolomics metadata specified in the schema

corilo commented 3 years ago

@mslarae13 could you please help with the necessary metadata definitions?

mslarae13 commented 3 years ago

@yuricorilo Yes! I definitely can! This I think would fall under preparation metadata. Could we chat about details and a path forward?

ssarrafan commented 3 years ago

@yuricorilo @mslarae13 @dehays I was going to move this to the May sprint since it's not done. Let me know if you're not planning to work on it during May otherwise I'll move it over.

ssarrafan commented 3 years ago

From: Setareh Sarrafan ssarrafan@lbl.gov Date: Mon, May 3, 2021 at 9:12 AM Subject: Re: [EXTERNAL] GitHub issues To: Hu, Bin bhu@lanl.gov Cc: Kjiersten Fagnan kmfagnan@lbl.gov

Hi Bin,

Is it ok if I move the open workflow related GitHub issues to the May sprint?  If there are any that you don't plan to work on in May let me know, or if there are ones that you made some progress and would like to close let me know, otherwise I was planning to move the following to May sprint:

Thanks, Setareh

On Fri, Apr 23, 2021 at 1:03 PM Setareh Sarrafan ssarrafan@lbl.gov wrote: Thanks for the update Bin.  If you'd like Michal to get a GitHub account let me know.  For now I'll leave the GitHub issues as they are and we'll see how it goes next week.  Best, Set

ssarrafan commented 3 years ago

@corilo should this issue be closed or moved to the June sprint?

ssarrafan commented 3 years ago

Moving to June per @yuricorilo on Slack

ssarrafan commented 3 years ago

Will be closed by @mslarae13 after a meeting tomorrow.

mslarae13 commented 3 years ago

Proteomics: Agilent tune mix and a complex proteome are used to check the run, but are not used in analyses https://github.com/microbiomedata/metaPro/issues/21

metabolomics: agilent tune mix, see follow up issuse for confirmation of prep -blanks, FAMES standard or alkane mixer, see follow up issue for confirmation or prep & what is used at PNNL https://github.com/microbiomedata/metaMS/issues/8

NOM: blanks, FAMES standard or alkane mixer, see follow up issue for confirmation -QC, SURFA internal standard. see follow up issue for confirmation of prep https://github.com/microbiomedata/enviroMS/issues/4