Create slim for public release

cmungall commented 11 years ago

Need to check with @hkawaji - what are the criteria for being in the slim?

hkawaji commented 11 years ago

The slim version should include only the samples in the phase1 freeze as leaves ( https://fantom5-collaboration.gsc.riken.jp/files/data/shared/FREEZE_PHASE1.1/ )
It would be better to take out (original) internal nodes connected to only the deleted leaves

Does this sound clear?

cmungall commented 11 years ago

pre-release available for verification

Navigate to: https://github.com/cmungall/fantom5-ontology/blob/master/src/ontology/ff-phase1.obo

click on 'raw'

(alternatively, git clone the repo)

This consists of

only 1351 samples tagged phase1
only descendant sample grouping classes (FF:0nnnnnn) of those 1351, and uberon/cl/do/etc terms that are in this graph closure

hkawaji commented 11 years ago

Cool. We are going to have a look. I'll get back to you soon.

hkawaji commented 11 years ago

Hi, Chris,

I got a repot below from my colleague, Kasukawa-san. He found the terms below are not included in the OBO file:

PATO:0002099 (which is a parent node of FF:0000245 and FF:0000246) UBERON:0001272 (which is a parent node of UBERON:0000981) UBERON:0009778 (which is a parent node of UBERON:0002048)

Do you think these have to be added?

best, Kawaji H

cmungall commented 11 years ago

I just made a new release of the subset

PATO:0002099 is included
UBERON:0001272 ! innominate bone is not - but UBERON:0000981 ! femur is included. The relationship between these is one of articulation, to make the subset I only include parthood, developmental and subclass relationships

hkawaji commented 11 years ago

Hi,

Kasukawa-san found FF terms that are not linked to any Phase 1 samples seem to be re-appeared.

For example, FF:0000640 "Fibroblast - Aortic Adventitial, cytoplasmic fraction" The samples linked to this term including "FF:14310-155C8" are Phase 2 samples.

cmungall commented 11 years ago

You're right, sorry about this, thanks for checking.

I was using the OWLAPI code to extract the graph closure, this appears too liberal. I will use my own code which I have vetted to do this and regenerate.

On Jul 11, 2013, at 6:27 PM, hkawaji wrote:

Hi,

Kasukawa-san found FF terms that are not linked to any Phase 1 samples seem to be re-appeared.

For example, FF:0000640 "Fibroblast - Aortic Adventitial, cytoplasmic fraction" The samples linked to this term including "FF:14310-155C8" are Phase 2 samples.

— Reply to this email directly or view it on GitHub.

hkawaji commented 11 years ago

It looks fine. I will start to make it public soon.

cmungall commented 11 years ago

Fantastic! Is it OK if I send a copy to the ENCODE DCC folks?

On Wed, Jul 24, 2013 at 6:04 PM, hkawaji notifications@github.com wrote:

It looks fine. I will start to make it public soon.

— Reply to this email directly or view it on GitHubhttps://github.com/cmungall/fantom5-ontology/issues/6#issuecomment-21527357 .

hkawaji commented 11 years ago

Year, I am now thinking to prepare this directory:

http://fantom.gsc.riken.jp/5/suppl/pre_release/ (not available yet.)

Here is the current idea of the content:

https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/110419-FF-ontology/pre_release/

Could you please let me know your opinion (in particular, readme file). We can move this forward if you are OK.

best, kawaji H

cmungall commented 11 years ago

OK - I made a minor change in the ontology header. Ready to go!

INCATools / fantom5-ontology

Create slim for public release #6