Format addition request

[kdharris101]

Hi everyone,

I would like to make quite a large number of suggested additions to the nwb data model.

Short story: we have developed a relational database system for keeping track of data in our lab. We have been using it for several months now and are happy with it. We based the schema on NWB 1.0 but there were many additions needed in order to capture all the data we need to store. While doing this we also had in mind the forthcoming IBL project, and I believe that these additions to the data model will cover most of what is needed there also.

The full data model is at:

http://alyx.readthedocs.io/en/latest/models.html

It's formatted as a Django specification.

All the best, Kenneth.

[oruebel]

Thanks for the pointer to this work. At first glance it looks like there are a large number of additions to the metadata, i.e., items that would belong probably in /general in the NWB schema. Currently /general is a bit hard to extend but once we have implemented #19 this should become much simpler so that one could start compiling and proposing specific extensions for this.

I haven't had the chance yet to review your data model in detail, i.e., I don't fully understand yet what changes or additions you and your team have made in other parts of the schema (e.g., in TimeSeries or Interface types).

I think we eventually want to break these enhancements up into smaller proposal for extensions so that we can go through and work on more manageable chunks rather than all at once. However, for now, I think let's have a look at these changes and setup a plan for what we want to do. I'll send a note to the EB as well so that they can have a look as well.

[kdharris101]

Thanks for the quick reply! Yes, the main changes are to general metadata (to do with husbandry, genotyping, lineage etc). But there are also a few others to do with things like linking to files on disk allowing for backups and multiple copies, aligning timeseries to multiple timebases, etc.

We also have a convention for naming files on diskhttps://github.com/cortex-lab/alf2neuroscope/blob/master/README.md#what-is-alf which could be worth thinking about as a potential NWB backend.

One other thing is that we are now committed to using a relational database for organizing metadata. It isn’t currently clear to me exactly how the current NWB spec would translate to relational form. The sooner this can be clarified the better: for the international brain lab project we need to commit to a data spec the very near future, and if we don’t get it compatible with NWB now it could soon be too late.

I’d be happy to give a more detailed explanation of all this by skype.

From: Oliver Ruebel [mailto:[email protected]] Sent: 13 September 2017 13:03 To: NeurodataWithoutBorders/nwb-schema [email protected] Cc: Harris, Kenneth [email protected]; Author [email protected] Subject: Re: [NeurodataWithoutBorders/nwb-schema] Format addition request (#57)

Thanks for the pointer to this work. At first glance it looks like there are a large number of additions to the metadata, i.e., items that would belong probably in /general in the NWB schema. Currently /general is a bit hard to extend but once we have implemented #19https://github.com/NeurodataWithoutBorders/nwb-schema/issues/19 this should become much simpler so that one could start compiling and proposing specific extensions for this.

I haven't had the chance yet to review your data model in detail, i.e., I don't fully understand yet what changes or additions you and your team have made in other parts of the schema (e.g., in TimeSeries or Interface types).

I think we eventually want to break these enhancements up into smaller proposal for extensions so that we can go through and work on more manageable chunks rather than all at once. However, for now, I think let's have a look at these changes and setup a plan for what we want to do. I'll send a note to the EB as well so that they can have a look as well.

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