Create a glossary page?

[DanNBullock]

It might be useful to create a glossary page for terminology that is used throughout the platform. That way, within apps, there can be hyperlinks back to this glossary whenever terms are used so that (novice) users can better understand what the terms refer to. The glossary entries can also include a few links to relevant publications.

[soichih]

What kind of terminologies are you referring to? Do they already exist within our doc?

I am not opposed to the idea of a glossary page, but what I've been doing is to link it to specific chapter / paragraphs within various pages in the doc. This way, user can find out information surrounding the concept within the page, and at the same time improve the content of the doc for users who are just reading through the doc.

[DanNBullock]

I quickly scanned the docs page, but I didn't see anywhere that would strike me as housing definitions for the sorts of things I'm thinking. Terms that are used across apps but not really defined might be relevant, things like:

Whole brain fiber group
Tractogram
Connectome
Mask
Streamline
Parcellation
Segmentation
ROI
Retnitopy
etc...

"what I've been doing is to link it to specific chapter / paragraphs within various pages in the doc"
Is this similar to that or is it distinct from it?

[soichih]

OK. If you can draft a page (google doc will do) I will set up a page under /doc. By the way, looking at the list of terms, I think you could write a tutorial on how to do ROI based fiber tracking (maybe also showing which brainlife app they can use to do each steps?) We might be needing this for Franco's class next semester anyways, so it might be good to discuss this. Soichi

…

On Mon, Dec 9, 2019 at 7:39 PM Daniel Bullock ***@***.***> wrote: I quickly scanned the docs page, but I didn't see anywhere that would strike me as housing definitions for the sorts of things I'm thinking. Terms that are used across apps but not really defined might be relevant, things like: Whole brain fiber group Tractogram Connectome Mask Streamline Parcellation Segmentation ROI Retnitopy etc... "what I've been doing is to link it to specific chapter / paragraphs within various pages in the doc" Is this similar to that or is it distinct from it? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#12?email_source=notifications&email_token=AAHBR6FFM7UK7CKRD26ZZYDQX3QKZA5CNFSM4JYRRMVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGLGV2Y#issuecomment-563505899>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHBR6FM63WDFQSUSQ5GW7TQX3QKZANCNFSM4JYRRMVA> .

[DanNBullock]

Tracking isn't particularly my forte. But maybe. If you're more interested in segmentation though, that's the entire goal of the python notebook I'm making. On Mon, Dec 9, 2019, 8:02 PM Soichi Hayashi <[email protected]> wrote:

…

This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. OK. If you can draft a page (google doc will do) I will set up a page under /doc. By the way, looking at the list of terms, I think you could write a tutorial on how to do ROI based fiber tracking (maybe also showing which brainlife app they can use to do each steps?) We might be needing this for Franco's class next semester anyways, so it might be good to discuss this. Soichi On Mon, Dec 9, 2019 at 7:39 PM Daniel Bullock ***@***.***> wrote: > I quickly scanned the docs page, but I didn't see anywhere that would > strike me as housing definitions for the sorts of things I'm thinking. > Terms that are used across apps but not really defined might be relevant, > things like: > > Whole brain fiber group > Tractogram > Connectome > Mask > Streamline > Parcellation > Segmentation > ROI > Retnitopy > etc... > > "what I've been doing is to link it to specific chapter / paragraphs > within various pages in the doc" > Is this similar to that or is it distinct from it? > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > < #12?email_source=notifications&email_token=AAHBR6FFM7UK7CKRD26ZZYDQX3QKZA5CNFSM4JYRRMVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGLGV2Y#issuecomment-563505899 >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AAHBR6FM63WDFQSUSQ5GW7TQX3QKZANCNFSM4JYRRMVA > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#12?email_source=notifications&email_token=ADFXNPI344ECSJMS52JPNYLQX3TCDA5CNFSM4JYRRMVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGLIDKA#issuecomment-563511720>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADFXNPJXZIUP5LATSOHDJBLQX3TCDANCNFSM4JYRRMVA> .

[soichih]

@DanNBullock Are you still interested in drafting the glossary page? I think we could ask folks (experts on certain terminologies?) from other labs to collaborate with us also - to have a bit more visibility.

[soichih]

Ah idea came up while talking with @bhatiadheeraj

Once we have the list of glossary, we could look for keywords that are registered in various README / description that we display in various places, add popup/tooltip for those words so that user can hover over and understand what those words mean.

[DanNBullock]

I think something like this is inevetible and essential. Part of the trick may be incentivising contributions. And yes, I think we should throw this out to the broader community, even beyond the brainlife community. I'll be back from my internship in the next week or so and think about a framework for this.

…

On Thu, Aug 6, 2020, 7:42 PM Soichi Hayashi ***@***.***> wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. Ah idea came up while talking with @bhatiadheeraj <https://github.com/bhatiadheeraj> Once we have the list of glossary, we could look for keywords that are registered in various README / description that we display in various places, add popup/tooltip for those words so that user can hover over and understand what those words mean. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#12 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADFXNPPENXLOMOMAFXOCIT3R7M5WBANCNFSM4JYRRMVA> .

[DanNBullock]

Will we be creating a separate project for this or will it be within the overarching brainlife/master repo?

[francopestilli]

How about we make a branch "glossary." Then we can merge back to 'master' after receiving enough suggestions/comments?

[soichih]

We could do that, or we can just keep it as a stealth page (not listed in the index) until we are ready to make it available publicly.

If we want this to be computer readable (so that brainlife.io can automatically embed links to the glossary), we should probably store this in something like yaml. Something similar to this > https://github.com/tsalo/bids-specification/blob/master/src/schema/entities.yaml Our doc page can convert the yaml into markdown/html on the fly to show the list of vocabulary.

[soichih]

Also.. I think it makes sense to create a new repo (brainlife/glossary?) as we want this to be used outside our doc and probably outside brainlife.io itself as well?