Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

place for protocols.io IDs #577

Open
bendichter opened this issue Jun 22, 2024 · 1 comment
Open

place for protocols.io IDs #577

bendichter opened this issue Jun 22, 2024 · 1 comment
Assignees
Labels
category: enhancement improvements of code or code behavior
Milestone

Comments

@bendichter
Copy link
Contributor

This came from a convo I had with Matt Lewis at the BRAIN meeting. He was asking for a place to put protocols.io IDs. Currently, the DANDI Archive has a metadata slot that expects these IDs. We have a field called protocol:

- name: protocol
dtype: text
doc: Experimental protocol, if applicable. e.g., include IACUC protocol number.
quantity: '?'

As far as I know this is rarely used, but we could change the description a bit to encourage users to provide their protocols.io IDs here.

@rly
Copy link
Contributor

rly commented Jun 22, 2024

Good idea. Scanning the first 199 dandisets with NWB data (with h5tojson), I found five with a value for "protocol":

{'dandi_json/000045/sub-00778394-c956-408d-8a6c-ca3b05a611d5/sub-00778394-c956-408d-8a6c-ca3b05a611d5_ses-07497983-2229-4cb2-8a45-50cee3fe9089_behavior+image.nwb.json': '_iblrig_tasks_trainingChoiceWorld5.2.7',
 'dandi_json/000149/sub-92130c1b-4fdb-4acc-86e0-1853d429c41a/sub-92130c1b-4fdb-4acc-86e0-1853d429c41a_ses-c7bd79c9-c47e-4ea5-aea3-74dda991b48e_behavior+ecephys+image.nwb.json': '_iblrig_tasks_ephysChoiceWorld6.4.2',
 'dandi_json/000221/sub-HI215/sub-HI215_ses-HI215-071019_ecephys+ogen.nwb.json': 'IACUC',
 'dandi_json/000409/sub-PL015/sub-PL015_ses-1d4a7bd6-296a-48b9-b20e-bd0ac80750a5_behavior+ecephys+image.nwb.json': '_iblrig_tasks_ephysChoiceWorld6.6.1',
 'dandi_json/000572/sub-BAYLORNL23/sub-BAYLORNL23_ses-20190225_ecephys+ogen.nwb.json': 'IACUC'}

None are externally interpretable.

The DANDI metadata field says:

A list of persistent URLs describing the protocols (e.g., protocols.io, or other DOIs).

We could change the NWBFile protocol doc to say:

A comma-separated list of persistent URLs describing the protocols, such as protocols.io or other DOIs. 
For example: "https://dx.doi.org/10.17504/protocols.io.e6nvwjo87lmk/v2".

Users could additionally use HERD to link this field and value to the URI https://dx.doi.org/10.17504/protocols.io.e6nvwjo87lmk/v2.

(We could also make this a 1-D array of protocol DOIs. Providing more than 1 DOI hasn't come up yet, so maybe it's best to just punt on this until it is needed since it is a more complicated change.)

@rly rly added the category: enhancement improvements of code or code behavior label Jun 22, 2024
@rly rly self-assigned this Jun 22, 2024
@rly rly added this to the 2.8.0 milestone Jun 22, 2024
@rly rly modified the milestones: 2.8.0, Future Sep 19, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
category: enhancement improvements of code or code behavior
Projects
None yet
Development

No branches or pull requests

2 participants