FAANG interaction

[only1chunts]

Is there opportunity to work with the FAANG project? https://www.faang.org/groups?ticket=&name=metadata&email= Their sample metadata checklist appears to largely overlap our anyway, so it might be an opportunity to get more exposure and alignment between more standards. I notice @cmungall is listed on the list of participants for the Metadata and Data Sharing page.

[lschriml]

Hello Chris, Agreed. Do you want to reach out to them ? Please cc me too. Their contact email is: faang@iastate.edu Steering Committee chairs ? Elisabeth Giuffra and Christopher Tuggle

Cheers, Lynn

Sent from my iPhone

On Sep 30, 2019, at 1:48 PM, Chris Hunter notifications@github.com wrote:

Is there opportunity to work with the FAANG project? https://www.faang.org/groups?ticket=&name=metadata&email= Their sample metadata checklist appears to largely overlap our anyway, so it might be an opportunity to get more exposure and alignment between more standards. I notice @cmungall is listed on the list of participants for the Metadata and Data Sharing page.

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[lschriml]

Hello @only1chunts have you met with the FAANG group ?

Cheers, Lynn

[only1chunts]

I did, I summarized the meeting in an email (5-Nov-2019) that I now paste here:

I've just had a chat with the FAANG people at EBI. They have an open source solution to the JSON standards that is very similar to what we're aiming for. I'll try to summarize what they have, which is very similar to what we want.

FAANG = Functional Annotation of ANimal Genomes, their aims are on their website https://www.faang.org/

They use many (almost all) of the same terms that SRA (and us) use. This is the Github repo of the metadata standards (rules): https://github.com/FAANG/dcc-metadata e.g. the samples rules: https://github.com/FAANG/dcc-metadata/blob/master/rulesets/faang_samples.metadata_rules.json

The rules are also shown on their portal, which is auto generated/updated from the above github pages: e.g. https://data.faang.org/ruleset/samples#standard
they also allow users to download excel templates directly from that page

They have a validator tool currently in perl but are very close to releasing a python version. https://github.com/FAANG/dcc-validate-metadata https://github.com/FAANG/dcc-validate-metadata/tree/new_python_validator

They also have a data portal (https://data.faang.org/home) which collects all the public BioSamples from the BioSamples repository at EBI that are labeled with a specific metadata field (Project=FAANG). The code to generate the portal is also available in github: https://github.com/FAANG/dcc-portal-backend
https://github.com/FAANG/dcc-portal-frontend

They dont have the funding or bandwidth to do any of the development for us, but are very happy to chat and advise as required if we should decide to fork their repo and just adapt it to our needs. The only requirement would be to acknowledge their work.

[lschriml]

Thank you Chris !! I appreciate your posting the email here, help us remember the outcome.

Do you think they would want to work together on the CZI grant. ?

I missed the last GSC CIG call, was this option discussed ?

Looks like a great way to move forward.

Cheers, Lynn

On Thu, Dec 12, 2019 at 1:57 AM Chris Hunter notifications@github.com wrote:

I did, I summarized the meeting in an email (5-Nov-2019) that I now paste here:

I've just had a chat with the FAANG people at EBI. They have an open source solution to the JSON standards that is very similar to what we're aiming for. I'll try to summarize what they have, which is very similar to what we want.

FAANG = Functional Annotation of ANimal Genomes, their aims are on their website https://www.faang.org/

They use many (almost all) of the same terms that SRA (and us) use. This is the Github repo of the metadata standards (rules): https://github.com/FAANG/dcc-metadata e.g. the samples rules:

https://github.com/FAANG/dcc-metadata/blob/master/rulesets/faang_samples.metadata_rules.json

The rules are also shown on their portal, which is auto generated/updated from the above github pages: e.g. https://data.faang.org/ruleset/samples#standard they also allow users to download excel templates directly from that page

They have a validator tool currently in perl but are very close to releasing a python version. https://github.com/FAANG/dcc-validate-metadata https://github.com/FAANG/dcc-validate-metadata/tree/new_python_validator

They also have a data portal (https://data.faang.org/home) which collects all the public BioSamples from the BioSamples repository at EBI that are labeled with a specific metadata field (Project=FAANG). The code to generate the portal is also available in github: https://github.com/FAANG/dcc-portal-backend https://github.com/FAANG/dcc-portal-frontend

They dont have the funding or bandwidth to do any of the development for us, but are very happy to chat and advise as required if we should decide to fork their repo and just adapt it to our needs. The only requirement would be to acknowledge their work.

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[ramonawalls]

Follow up complete. Closing issue.