James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-28 10:54:20

@James Fellows Yates has joined the channel

Miriam Bravo (bravolomiriam@gmail.com)
2022-01-28 10:54:36

@Miriam Bravo has joined the channel

Ophélie Lebrasseur (ophelie.lebrasseur@liverpool.ac.uk)
2022-01-28 10:54:36

@Ophélie Lebrasseur has joined the channel

aidanva (aida.andrades@gmail.com)
2022-01-28 10:54:37

@aidanva has joined the channel

Arthur Kocher (arthur.kocher@gmail.com)
2022-01-28 10:54:37

@Arthur Kocher has joined the channel

Kelly Blevins (blevinske1@gmail.com)
2022-01-28 10:54:37

@Kelly Blevins has joined the channel

Meriam Guellil (meriam.guellil.ac@gmail.com)
2022-01-28 10:54:37

@Meriam Guellil has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-28 10:54:47

Hey guys, you can all coordinate here for your meeting 👍

👍 Meriam Guellil
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-28 10:55:45

And feel free to invite whoever else

Kelly Blevins (blevinske1@gmail.com)
2022-01-28 11:04:59

Hi, everyone! I set up a WhenIsGood so that we can start planning our first meeting: https://whenisgood.net/z4j3spr

whenisgood.net
👍:skin_tone_6: Miriam Bravo
Kelly Blevins (blevinske1@gmail.com)
2022-01-28 11:05:38

*Thread Reply:* You can change your time zone at the top of the grid

Kelly Blevins (blevinske1@gmail.com)
2022-01-28 11:06:21

*Thread Reply:* I blocked out times that won’t work for me, but I may be able to be more flexible on those days if we can’t find anything else that works for everyone.

Meriam Guellil (meriam.guellil.ac@gmail.com)
2022-01-28 13:01:45

*Thread Reply:* Done!

Miriam Bravo (bravolomiriam@gmail.com)
2022-01-28 15:35:01

*Thread Reply:* done too! 🙂

Arthur Kocher (arthur.kocher@gmail.com)
2022-01-31 11:36:07

*Thread Reply:* Done. Thanks Kellly!

aidanva (aida.andrades@gmail.com)
2022-02-01 09:49:27

*Thread Reply:* Done!

Kelly Blevins (blevinske1@gmail.com)
2022-02-01 11:51:45

*Thread Reply:* how is there not a single hour we are all available 😂

😬 Meriam Guellil
😂 Miriam Bravo
aidanva (aida.andrades@gmail.com)
2022-02-01 11:53:00

*Thread Reply:* 🤪

Kelly Blevins (blevinske1@gmail.com)
2022-02-01 11:53:29

*Thread Reply:* the best days are Thursdays Feb 17 and 24th at 1PM London time. Would you be willing to meet at 7AM (CDMX time) either of those days, @Miriam Bravo? If not, I could be free on Friday Feb 18th.

Miriam Bravo (bravolomiriam@gmail.com)
2022-02-01 15:19:00

*Thread Reply:* It's fine for me 🙂

Arthur Kocher (arthur.kocher@gmail.com)
2022-02-02 10:13:29

*Thread Reply:* Can we do feb 17 then? Something popped up on the 24th for me

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-02-01 07:50:30

and don't forget to decide on a chair - I will then coorindate with them 🙂 Are there any volunteers for that? This is primarily just to organise the meetings, and gather all teh feedback into one consistent place we can disseminate to the other groups

Kelly Blevins (blevinske1@gmail.com)
2022-02-01 11:47:38

*Thread Reply:* I don’t mind being chair

:mask_parrot: James Fellows Yates, Meriam Guellil
🎉 Ophélie Lebrasseur
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-02-01 11:53:26

OK Kelly volunteers - thanks!

Kelly Blevins (blevinske1@gmail.com)
2022-02-02 11:11:10

Thanks to everyone who filled out the When is Good! We will meet on ➡️Thursday, Feb 17th at 13:00 London time.⬅️ We should be prepared to talk about the core MIxS (minas-alpha.xlsx) fields that are relevant to aDNA overall and which, if any, are specific to pathogen/microbial aDNA. Additionally, we should review the env packages (third tab in minas-alpha.xlsx). It is unclear to me if we should be thinking about designing a pathogen/microbial env package from scratch or if we would be pulling from existing env packages. Maybe @James Fellows Yates could clarify.

👍:skin_tone_6: Miriam Bravo
👍 Ophélie Lebrasseur
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-02-02 14:09:11

Tasks are go through core MiXs to define just ar especific for pathonge/microibial aDNA (not for aDNA overall)

And identify env packages that are relevant and go through these.

You don't need to think explicitly about making a new one from scratch at this moment, but if you find glaring entries that are missing, do note these down

👍:skin_tone_2: Kelly Blevins
👍:skin_tone_6: Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-02-03 08:48:17

@Nasreen Broomand ☝️

Nasreen Broomand (nbrooman@ucsc.edu)
2022-02-03 08:48:19

@Nasreen Broomand has joined the channel

Kelly Blevins (blevinske1@gmail.com)
2022-02-14 11:25:56

Hi, @channel! We are meeting this Thursday at 13:00 London time in the SPAAM gather.town

Prior to the meeting, it would be great if everyone could identify which MIxS fields they think are specific to pathogen/microbial aDNA. I made a MInAS-pathogen google sheet for us to share our thoughts. I’ve gone through the MIxS tab and indicated my proposed assignments with some justifications. Please add yours to the same cells (but be careful not to delete anyone else’s text).

Looking forward to discussing metadata with you all!

app.gather.town
👍:skin_tone_6: Miriam Bravo
Arthur Kocher (arthur.kocher@gmail.com)
2022-02-14 14:24:28

*Thread Reply:* Thanks Kelly! By “specific to microbial/pathogen aDNA”, do you mean that the requirement category (M, C, etc..) might be different from other types of aDNA data? Or that the definition of the field might be different (maybe a question for @James Fellows Yates actually)? Also, should we also go through the environmental packages already or do we do that during/after the meeting?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-02-14 14:27:04

*Thread Reply:* Yes, correct. You guys only do it for pathogens. Some fields might not be applicable in pathogens for human DNA for example.

But we will infer the common ones in later meetings

Kelly Blevins (blevinske1@gmail.com)
2022-02-14 18:28:50

*Thread Reply:* I filled it out as if I were only thinking about pathogens. Some of the fields I said were mandatory/conditionally mandatory for pathogens could also apply to aDNA in general, but, like James said, I figured we would deal with the overlap in the wider metadata standards group.

👍 James Fellows Yates
Kelly Blevins (blevinske1@gmail.com)
2022-02-14 18:30:41

*Thread Reply:* If you have time, go through the env packages. That way we can discuss everyone’s thoughts during the meeting. Since the whole group is meeting pretty soon (March 4th), we should try to talk about them at this meeting.

👍:skin_tone_6: Miriam Bravo
Kelly Blevins (blevinske1@gmail.com)
2022-02-22 15:28:19

Hi, @channel! I have condensed and organized the MINAS fields based on our meeting last week. You will find the edits in the first three tabs:

• MIxS Core-pathogens/microbes - fields from MIxS core that we decided are essential for pathogen/microbe aDNA • EnvPackages-pathogens/microbes - fields from EnvPackages that we decided were applicable for pathogen/microbe aDNA • MINAS extension-pathogens/microbes - fields that we decided were important for pathogen/microbe aDNA that are not present in MIxS Core or EnvPackages I copied James’s formatting to make things easier to collate down the road.

Overall, our biggest concerns/points of discussion for the next meeting are

  1. How do we deal with taxon/organism-specific fields when the raw data from one library may contain >1 studied microbe from the publication and will contain many unstudied microbes not reported/analyzed in the publication?
  2. Is it necessary to repeat content between base ENA/SRA upload, MIxS core, and EnvPackage fields? For example, can we just include the project name in the base ENA metadata entry, or do we have to repeat it for each package?
  3. Do we want to include metadata that is independent of the sample and the uploaded raw data? For example, do we want to include fields for screening and decontamination software and parameters? Please have a look and feel free to change anything, but please leave a comment so we can follow the changes until our next discussion. I drafted some options for burial-context. I am not married to the proposed options, but I do think it needs to be required and not optional so people are more likely to provide the information.

Link to spreadsheet: https://docs.google.com/spreadsheets/d/1m8aW6EWc19ASvqIkNpSnKPvXKW-_ZWr1qqjessvz2lc/edit?usp=sharing

👍:skin_tone_2: Meriam Guellil
👍:skin_tone_6: Miriam Bravo
👍 Nasreen Broomand
Biancamaria Bonucci (biancamaria.bonucci@ut.ee)
2022-06-14 12:16:26

@Biancamaria Bonucci has joined the channel

Reed Harder (reedharder@gmail.com)
2023-06-01 22:03:57

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Hannes (hschroeder@sund.ku.dk)
2023-10-15 08:15:00

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