Comments (10)
RLWOHIO
commented on June 9, 2024
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
from zebrafish-phenotype-ontology.
matentzn
commented on June 9, 2024
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?
from zebrafish-phenotype-ontology.
RLWOHIO
commented on June 9, 2024
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 ***@***.***> 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?
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RLWOHIO
commented on June 9, 2024
[Presentation1.pptx](https://github.com/obophenotype/zebrafish-phenotype-ontology/files/2891270/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 ***@***.***> 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?
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<#15 (comment)>,
or mute the thread
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Rong-Lin Wang
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matentzn
commented on June 9, 2024
Can you share the exact ontology you are using that has the unsatisfiable classes?
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RLWOHIO
commented on June 9, 2024
Please first download the vertebrate.owl from this link:
http://purl.obolibrary.org/obo/upheno/vertebrate.owl
and modify the line therein from
<owl:imports rdf:resource="&obo;upheno/zp.owl"/>
into <owl:imports rdf:resource="&obo;zp.owl"/>
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 ***@***.***> wrote:
Can you share the exact ontology you are using that has the unsatisfiable
classes?
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Rong-Lin Wang
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matentzn
commented on June 9, 2024
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..
from zebrafish-phenotype-ontology.
RLWOHIO
commented on June 9, 2024
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 ***@***.***> 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..
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Rong-Lin Wang
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matentzn
commented on June 9, 2024
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.
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matentzn
commented on June 9, 2024
I will close this for now, please re-open if still an issue.
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- Uses of obsolete GO and ZFA terms HOT 1
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- Missing GO terms? HOT 2
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