integration with ontobee about obofoundry.github.io

[ontoden]

Sounds good. We (Ontobee) will take a look at the yaml format and see how we can use it.
Oliver He

[cmungall]

Check out the simple python script util/processor.py to see some examples of processing the yaml - e.g. there is a command that will mirror all products on a local drive.

Note there are some interesting possibilities for ontobee - some ontologies like to have two different products on ontobee, or have the version loaded be something different from their canonical product (for example, for go we would like to have go-plus.owl loaded). Rather than hacking this with the separate ontobee repo as we have done in the past, we can simply add tags such as 'load_into_ontobee: true' - suggestions welcome

[ontoden]

I like the idea. To have tags like 'load_into_ontobee: true' would fit well with different needs.

Oliver

From: Chris Mungall [mailto:[email protected]]
Sent: Tuesday, August 18, 2015 12:20 PM
To: OBOFoundry/OBOFoundry.github.io
Cc: ontoden
Subject: Re: [OBOFoundry.github.io] integration with ontobee (#16)

Check out the simple python script util/processor.py to see some examples of processing the yaml - e.g. there is a command that will mirror all products on a local drive.

Note there are some interesting possibilities for ontobee - some ontologies like to have two different products on ontobee, or have the version loaded be something different from their canonical product (for example, for go we would like to have go-plus.owl loaded). Rather than hacking this with the separate ontobee repo as we have done in the past, we can simply add tags such as 'load_into_ontobee: true' - suggestions welcome

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/16#issuecomment-132264789.

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[cmungall]

cc @simonjupp, comments about having different "editions" of ontologies, with a selected subset of editions available in a browser. Or having a 'non-standard' edition be the default in advanced browsers. E.g. go-plus for GO, cc @dosumis

[simonjupp]

Are there many ontologies that have these "editions" then?

I'm more in favour of loading the full edition and having better support to extract views/subsets from the full edition. I think we can show things like the basic view on the fly, and we are also contemplating some other view options like "hide upper-ontology terms by default".

We will support views from slims defined in the ontology and we also have plans to support more data driven views, so generating a view from a given a list of terms or set of annotations.

I'm also happy to honour any "load_into_ols:true" tag if you go that way.

[cmungall]

On 23 Sep 2015, at 23:47, simonjupp wrote:

Are there many ontologies that have these "editions" then?

Well technically subsets count as distinct products but of course there
is no use case to load these as a separate graph. There aren't many
'superset' editions. The two main uses are GO (go.owl has any
external-pointing axioms slimmed out) and uberon
(https://github.com/obophenotype/uberon/wiki/Multi-species-composite-ontologies)

I'm more in favour of loading the full edition and having better
support to extract views/subsets from the full edition. I think we can
show things like the basic view on the fly, and we are also
contemplating some other view options like "hide upper-ontology terms
by default".

Makes sense

We will support views from slims defined in the ontology and we also
have plans to support more data driven views, so generating a view
from a given a list of terms or set of annotations.

Yep

I'm also happy to honour any "load_into_ols:true" tag if you go that
way.