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View Code? Open in Web Editor NEWMetadata and website for the Open Bio Ontologies Foundry Ontology Registry
Home Page: http://obofoundry.org
License: Other
Metadata and website for the Open Bio Ontologies Foundry Ontology Registry
Home Page: http://obofoundry.org
License: Other
The website was seeded from the uberon one. Scoop all that out and replace with old content
Finally we have a field for licenses. Note ontologies without declared licenses (most) get visually highlighted on their page.
Currently we have a distinct script https://github.com/owlcollab/owltools/blob/master/OWLTools-Oort/bin/build-obo-ontologies.pl
Used in this job
http://build.berkeleybop.org/job/simple-build-obo-all/
That makes all the fallthru files on http://berkeleybop.org/ontologies/
Eventually everyone will take charge of builds but for now, the metadata hardwired in this script should be placed in the main md files
cc @proccaserra, Peter McQuilton
$ grep code.goog ontology/*md
$ grep sourceforg ontology/*md
Some may be from obsolete ontologies, but even so best to have these migrated for posterity
as per the discussion on OBO foundry operation call on August 11th, 2015.
Suggested by Erick Antezana on obo-discuss:
I think it would be useful to allow for multiple contacts for an ontology, including multiple people or mailing list(s).
Our documentation is spread in multiple places:
In addition to being spread out, much of it is confusing and stale.
I recommend consolidating as much as possible into github pages - meeting agendas and notes are best left in google docs, but for anything else, one place.
There is an argument to use the github wiki for some purposes, this has some advantages over jekyll/gh pages: easier to create new pages (but how often do we do that?), slightly easier to interlink. My vote would still be for pages
cc @ontoden
We could just output ontologies.txt from https://raw.githubusercontent.com/OBOFoundry/OBOFoundry.github.io/master/registry/ontologies.yml
But may be better if ontobee could take the native format directly. Note the new yaml offers better possibilities for ontobee users. For example, some ontologies have >1 namedGraph imported, but this is AFAICT done informally using an ad-hoc internal registry, which we can now centralize
I believe the new OLS takes in the yaml, cc @simonjupp
Many of our pages have a domain field. This is somewhat arbitrary but could be normalized.
It would be useful to have a page that lists all ontologies within a domain. Even better if this can be customized. For example, different community members could take responsibility for different domains: health, anatomy, environment, ...
See for example http://obofoundry.github.io/ontology/chebi.html
Is there a way to have wrap around or something similar that would display the full link instead of cutting with '...'
cc @zhengj2007
We would like to implement better interoperation with ncbo - ideally they would pull our metadata
Did someone volunteer for reaching out on the obo op call? @proccaserra? Bjoern?
See also #28
I set up
https://github.com/orgs/OBOFoundry/teams/community
this group doesn't have permission to directly commit or merge (I prefer this responsibility is taken on by a small circle, remember anyone is welcome to fork and PR). However, it does allow for assignment of tickets on trackers, which is useful if we need a non OBO Foundry person to handle something. It may also auto-subscribe to tickets? (which can be easily unsubscribed)
I recommend a policy whereby all main ontology contacts are encouraged to join the community team
Suggested by Erick Antezana on obo-discuss:
broken link (star): http://obofoundry.github.io/link-to-foundry-principles
Is this correct?
These ontologies don't resolve from the yaml file
http://www.berkeleybop.org/ontologies/dpo.owl
http://www.berkeleybop.org/ontologies/kisao.owl
http://www.berkeleybop.org/ontologies/lipro.owl
http://www.berkeleybop.org/ontologies/nmr.owl
http://www.berkeleybop.org/ontologies/ovao.owl
http://www.berkeleybop.org/ontologies/resid.owl
http://www.berkeleybop.org/ontologies/rnao.owl
http://www.berkeleybop.org/ontologies/xso.owl
Each person (OBO team, or possibly also ontology developers) could have an entry in the config.yml file
E.g.
team:
- name: Chris Mungall
orcid: ORCIDURL
github: cmungall
roles: [twg,...]
Or alternatively, one md per person (that can be collected same way as ontologies)
This would be easy to render as html in jekyll
The YAML would have a json-ld context allowing direct translation to RDF
We currently use depicted_by to allow people to include a logo, see http://obofoundry.github.io/ontology/obi.html
OBIB (ontology for biobanking) does not show on ontology page:
http://obofoundry.github.io/
How to add the OBIB link in?
http://obofoundry.github.io/ontology/obib.html
No product in the YAML for the following ontologies
hao
miapa
obcs
opl
sibo
tads
Is there a way to have headers following as you scroll down, or repeat them in the middle?
See for examples PRs #61 #60 #59 #58 - I modified these so that the ftp site was a (cardinality 1) 'page' property.
No reason to restrict page
to be a single valued; could be a list (but homepage
should be functional, as it is mapped to foaf:homepage)
And/or: have new properties for different page types; e.g. ftp_site
- todo - explore different vocabularies for this
How should this repo be licensed?
Should different components be licensed differently? How do we indicate this with a LICENSE file?
Some suggestions:
The authors of 2-3 are primarily members of the OBOF. For 1 could be considered joint authorship between individual ontology maintainers and OBOF.
Suggested by Erick Antezana on obo-discuss:
Note: see #2 - for now we just listed Foundry at the top.
FBcv (FlyBase controlled vocabulary) is tagged as deprecated.
http://obofoundry.github.io/ontology/fbcv.html
I would say this is not the case. Although the Drosophila Phenotype Ontology, which is included in FBcv, is released separately, the whole of FBcv is still updated regularly.
kisao is still on SF - I strongly recommend migrating to GH. See https://docs.google.com/document/d/1iyVY8kDBJIEydoWFLG9j5BoO4VmdIXES95fVhIkFXfk/edit#
(there is no tracker enabled on SF, we used to have https://sourceforge.net/tracker/?group_id=293617 registered but this no longer works)
I really like the buttons, but would it be possible to have the target displayed a mouseover?
notifications:
email:
- [email protected]
happy to do this during the teething phase, but should go to wider group. Others should add emails here https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/.travis.yml -- or should we just use obo-operations list?
The repository essentially forked at one point, @proccaserra's STATO went missing.
The old http://obofoundry.org site had a lot of pages that haven't been touched since 2007ish
These are currently in the navbar under "LEGACY"
I suggest removing forever
When using jekyll 2.5.3
Deprecation: The 'pygments' configuration option has been renamed to 'highlighter'. Please update your config file accordingly. The allowed values are 'rouge', 'pygments' or null.
Can we just use a CNAME?
Consider using angled text for the icon columns
https://css-tricks.com/rotated-table-column-headers/
Currently hardcoded to be the ancient obo format version I made. Should be made the complete ontology now it is in OWL. obo-basic can be a subproduct
Proposed recommendation:
Keep the description field concise. Don't write it like a paper abstract. Say immediately what the ontology contains.
Add more details as necessary in the markdown section
Clicking on details for FBdv shows only this sentence at the top of the page
"A structured controlled vocabulary of the development of Drosophila melanogaster."
http://obofoundry.github.io/ontology/fbdv.html
I'd like to update the details, but I'm not able to.
Suggested by Erick Antezana on obo-discuss:
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