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obophenotype / zebrafish-phenotype-ontology

A vocabulary for describing Zebrafish Phenotypes
https://obophenotype.github.io/zebrafish-phenotype-ontology/
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a large number of ZP classes unsatisfiable #15

Closed RLWOHIO closed 4 years ago

RLWOHIO commented 5 years ago

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RLWOHIO commented 5 years ago

Hi, Thanks much for keeping ZP updated!

Just tested the latest zp.owl as part of the vertebrate.owl. A total of 309 ZP classes are still not satisfiable, mostly because of the underlying unsatisfiable 70 ZFA classes. For instance, ZP_0000035 is not satisfiable because of ZFA_0000042. ZP.unsatisfiable.txt

matentzn commented 5 years ago

Hey @RLWOHIO !

Which version of ZP are you looking at? There should not be any unsatisfiable classes right now!

Perhaps download this one: http://purl.obolibrary.org/obo/zp.owl

and check again?

Which reasoner are you using? Which exact file did you open?

RLWOHIO commented 5 years ago

Hi Nico,

The most current version, http://purl.obolibrary.org/obo/zp/releases/2019-01-16/zp.owl

The zp.owl was imported as part of the vertebrate.owl into Protege and reasoned by using Elk. Also included were some of my own EQ-derived classes, which were all satisfiable. Most, if not all, of the unsatisfiable ZP classes are caused by the underlying unsatisfiable ZFA classes used in their class expressions.

Thanks, Ronglin

By the way, when using the older versions of zp.owl, the number of unsatisfiable ZP classes became far worse:

2015-11-30 release: 1108

2017-07-05 release: 1836

2019-01-16 release: 309 ZP + 70 ZFA

On Thu, Feb 21, 2019 at 11:29 AM Nico Matentzoglu notifications@github.com wrote:

Hey @RLWOHIO https://github.com/RLWOHIO !

Which version of ZP are you looking at? There should not be any unsatisfiable classes right now!

Perhaps download this one: http://purl.obolibrary.org/obo/zp.owl

and check again?

Which reasoner are you using? Which exact file did you open?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/obophenotype/zebrafish-phenotype-ontology/issues/15#issuecomment-466066836, or mute the thread https://github.com/notifications/unsubscribe-auth/AOJjxe0W-QKdnKuluHgBa-5hGIevy4kKks5vPslggaJpZM4bHiNu .

-- Rong-Lin Wang

RLWOHIO commented 5 years ago

Presentation1.pptx Here is an example of ZP_0000035 being unsatisfiable: [image: image.png]

On Thu, Feb 21, 2019 at 11:29 AM Nico Matentzoglu notifications@github.com wrote:

Hey @RLWOHIO https://github.com/RLWOHIO !

Which version of ZP are you looking at? There should not be any unsatisfiable classes right now!

Perhaps download this one: http://purl.obolibrary.org/obo/zp.owl

and check again?

Which reasoner are you using? Which exact file did you open?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/obophenotype/zebrafish-phenotype-ontology/issues/15#issuecomment-466066836, or mute the thread https://github.com/notifications/unsubscribe-auth/AOJjxe0W-QKdnKuluHgBa-5hGIevy4kKks5vPslggaJpZM4bHiNu .

-- Rong-Lin Wang

matentzn commented 5 years ago

Can you share the exact ontology you are using that has the unsatisfiable classes?

RLWOHIO commented 5 years ago

Please first download the vertebrate.owl from this link: http://purl.obolibrary.org/obo/upheno/vertebrate.owl

and modify the line therein from

into

so it points to your latest zp.owl. After that, let Protege open the vertebrate.owl and start ELK reasoner. The unsatisfiable ZP classes will show up.

Thanks much!

On Thu, Feb 21, 2019 at 5:14 PM Nico Matentzoglu notifications@github.com wrote:

Can you share the exact ontology you are using that has the unsatisfiable classes?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/obophenotype/zebrafish-phenotype-ontology/issues/15#issuecomment-466188551, or mute the thread https://github.com/notifications/unsubscribe-auth/AOJjxY-qbmZYTeejWyqhTsqD-_OJ27-Sks5vPxovgaJpZM4bHiNu .

-- Rong-Lin Wang

matentzn commented 5 years ago

Yeah, this might be a bit hard to debug due to the size. The situation is this: Because we are working on all ontologies now, there are some which import incompatible versions of ontologies, most importantly UBERON. I suspect that a few of these classes you found will be due to that.

I just tried to import all of ZFA into ZP, and there are no problems; So I cant deal with those unsatisfiability issues here at this point. What do you need vertebrate.owl for if I may ask? In a few months, all of these upheno sub ontologies will be retired, and something better and stable will take their place..

RLWOHIO commented 5 years ago

I agree that the issues now appear to stem from how ZFA/ZP are related to other relevant ontologies. I use vertebate.owl in conjunction with my own EQ-derived phenotypic classes to conduct semantic analysis of phenotypes across species.

Could you elaborate a little more about updating upheno sub ontologies in terms of the scope, time frame, and the people involved in the work? I imagine uberon, hp, and mp will all be included? What gitHub site should I follow in order to track the progress of this effort and stay informed?

On Fri, Feb 22, 2019 at 6:02 AM Nico Matentzoglu notifications@github.com wrote:

Yeah, this might be a bit hard to debug due to the size. The situation is this: Because we are working on all ontologies now, there are some which import incompatible versions of ontologies, most importantly UBERON. I suspect that a few of these classes you found will be due to that.

I just tried to import all of ZFA into ZP, and there are no problems; So I cant deal with those unsatisfiability issues here at this point. What do you need vertebrate.owl for if I may ask? In a few months, all of these upheno sub ontologies will be retired, and something better and stable will take their place..

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/obophenotype/zebrafish-phenotype-ontology/issues/15#issuecomment-466359851, or mute the thread https://github.com/notifications/unsubscribe-auth/AOJjxagB7sJ8nXg_Y80DYE9_ka1tTnLHks5vP85SgaJpZM4bHiNu .

-- Rong-Lin Wang

matentzn commented 5 years ago

Ah cool! Sounds interesting. Can you drop me an email about this?

the upheno repository is a good place for such issues in general. We aim to present a prototype at biocuration this year (April 7-10), so around then you should see something of a start. These people are actively involved: https://github.com/obophenotype/upheno/wiki/Phenotype-Ontologies-Reconciliation-Effort

(plus a few more technical people like Chris Mungall)

UBERON, MP, HP, CL, NBO, GO, CHEBI and many more are taken into account.

matentzn commented 4 years ago

I will close this for now, please re-open if still an issue.