unsatisfiable classes when merged into vertebrate.owl #36
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Thanks! Some of the unsatisfiablities may only be solved much later in the year! Feel free to drop me an email so I can tell you about the general trajectory of uPheno and ZP -> we are working hard on pushing for a fresh, conflict free Unified Phenotype ontology by the end of the month, and I would love to get your input/requirements if you have any! :) vertebrate.owl will hopefully be deprecated before the summer. |
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This is great to know. Very much looking forward to having an error-free
vertebrate.owl replacement. Since my work is primarily fish oriented, ZP
and improved mapping of ZP terms to zebrafish genes are of great
importance. I will continue to provide feedback as issues come up down the
road. Thanks so much for your effort!
…On Mon, Jan 6, 2020 at 7:23 AM Nico Matentzoglu ***@***.***> wrote:
Thanks! Some of the unsatisfiablities may only be solved much later in the
year! Feel free to drop me an email so I can tell you about the general
trajectory of uPheno and ZP -> we are working hard on pushing for a fresh,
conflict free Unified Phenotype ontology by the end of the month, and I
would love to get your input/requirements if you have any! :)
vertebrate.owl will hopefully be deprecated before the summer.
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Can you describe a bit what you are using vertebrate.owl for that you cant get from simply using ZP? Which table to you use for the gene:phenotype annotations? |
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Vertebrate.owl serves as the foundation of semantic analysis of chemical
toxicities. While my target species are fish, I have broad interest on
other vertebrates, particularly human and mouse, and a range of biological
domains as well. My last use (a year ago) of zf gene:phenotype
associations came from
https://github.com/obophenotype/zebrafish-phenotype-ontology-build. It
seems to have been deprecated since.
…On Thu, Jan 9, 2020 at 11:07 AM Nico Matentzoglu ***@***.***> wrote:
Can you describe a bit what you are using vertebrate.owl for that you cant
get from simply using ZP? Which table to you use for the gene:phenotype
annotations?
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So basically you are looking for a phenotype ontology that integrates all vertebrate phenotypes (and their anatomy, gene functions etc)? How exactly do you use vertrebrate.owl if you dont mind me asking? In a software tool? Or just to retrieve stuff using Protege? EDIT: This is not official yet, but you can probably check
For the data you need now. Note, and this is very important, that these tables are under development and only work for abnormal phenotypes. There are some wrong associations in there between abnormal ZP classes and NORMAL phenotypes. |
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Yes. I use a java application I put together based on the OWAPI,
reasoners, and the Semantic Measure Library (
https://www.semantic-measures-library.org/sml/). Thanks!
…On Mon, Jan 13, 2020 at 7:31 AM Nico Matentzoglu ***@***.***> wrote:
So basically you are looking for a phenotype ontology that integrates all
vertebrate phenotypes (and their anatomy, gene functions etc)? How exactly
do you use vertrebrate.owl if you dont mind me asking? In a software tool?
Or just to retrieve stuff using Protege?
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Can you describe your project in a bit more detail? Is your code on GitHub? What do you need from vertebrate.owl that you cant get from zp.owl all by itself? |
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My apologies for this delayed response. Our general interest is in the
realm of mapping chemical-induced toxicity responses, particularly those of
non-molecular nature, to their biology: genes, pathways, and diseases.
This is why ontology-based semantic analysis is such an useful tool. While
our focus is on fish and zp is great, having vertebrates included gives us
a much wider coverage of biology and greater utilization of phenomics data
available. The Java application is currently not available on Github. It
is based on OWLAPI, Semantic Measure Library (
https://www.semantic-measures-library.org/sml/), and various reasoners, all
publicly available.
…On Thu, Feb 6, 2020 at 8:25 AM Nico Matentzoglu ***@***.***> wrote:
Can you describe your project in a bit more detail? Is your code on
GitHub? What do you need from vertebrate.owl that you cant get from zp.owl
all by itself?
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We are developing a new version of the Unified Phenotype Ontology - this will eventually replace vertebrate.owl and the rest of upheno1; I would be interested in your feedback and see whether it covers your use cases. Its not published yet, but a test version is available here. Please let me know what you think and what is missing from in there (or too much) to cover your case. |
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This is great. I would love to try it out when I get a chance. Thanks a
lot for the offer.
…On Wed, Mar 4, 2020 at 4:51 AM Nico Matentzoglu ***@***.***> wrote:
We are developing a new version of the Unified Phenotype Ontology - this
will eventually replace vertebrate.owl and the rest of upheno1; I would be
interested in your feedback and see whether it covers your use cases. Its
not published yet, but a test version is available here
<https://ci.monarchinitiative.org/view/pipelines/job/upheno2/81/artifact/src/curation/upheno-release/all/upheno_all_with_relations.owl>.
Please let me know what you think and what is missing from in there (or too
much) to cover your case.
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I have done some testing. On its own, upheno_all_with_relations.owl (03/04/2020), is fine. Once merged with my annotations and relevant imports by OntoFox, there was a total 35 unsatisfiable classes, all from ZP. This is a huge improvement over vertebrate.owl dated Dec 2019 which had a total of 455 unsatisfiable classes including 340 ZPs. Please see the attached for details. Hope this helps. |
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Ah very cool. So it seems that all the phenotypes that are unsatisfiable are so because of ZFA, which in turn interacts badly with UBERON. Can you delete the axiom:
And check whether that is the problem? If so, I will talk to RO and UBERON and we will decide on how to fix it. |
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Yes, you are right. By eliminating ZFA_0001284 and ZFA_0005491 from the
merged ontology, all the other previously unsatisfiable ZP classes became
satisfiable.
…On Thu, Mar 12, 2020 at 1:20 PM Nico Matentzoglu ***@***.***> wrote:
Ah very cool. So it seems that all the phenotypes that are unsatisfiable
are so because of ZFA, which in turn interacts badly with UBERON. Can you
delete the axiom:
[image: image]
<https://user-images.githubusercontent.com/7070631/76547486-260c7500-6485-11ea-84e6-e6c731991670.png>
And check whether that is the problem? If so, I will talk to RO and UBERON
and we will decide on how to fix it.
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The latest release (2019-11-12) is a big improvement over the previous version. When standing alone, all classes are satisfiable. After being incorporated into vertebrate.owl though, some of them became unsatisfied, as listed below:
ZFA_0000435
ZP_0000412
ZP_0002062
ZP_0002510
ZP_0002511
ZP_0002557
ZP_0003019
ZP_0003144
ZP_0003145
ZP_0003428
ZP_0004008
ZP_0004283
ZP_0004284
ZP_0004299
ZP_0005361
ZP_0005362
ZP_0005531
ZP_0005928
ZP_0006699
ZP_0006700
ZP_0006899
ZP_0006921
ZP_0006922
ZP_0008170
ZP_0008184
ZP_0008185
ZP_0008312
ZP_0008768
ZP_0009148
ZP_0010431
ZP_0010686
ZP_0010687
ZP_0010688
ZP_0011448
ZP_0011473
ZP_0011681
ZP_0011709
ZP_0011716
ZP_0011745
ZP_0011889
ZP_0012376
ZP_0012463
ZP_0012500
ZP_0013387
ZP_0014696
ZP_0014741
ZP_0014762
ZP_0014898
ZP_0015602
ZP_0016403
ZP_0016404
ZP_0016405
ZP_0016733
ZP_0016944
ZP_0016945
ZP_0016946
ZP_0017766
ZP_0018215
ZP_0018216
ZP_0018220
ZP_0018289
ZP_0018331
ZP_0019846
ZP_0019851
ZP_0019852
ZP_0019853
ZP_0019854
ZP_0020515
ZP_0020776
ZP_0020778
ZP_0021475
ZP_0021924
ZP_0022946
ZP_0100778
ZP_0100779
ZP_0100967
ZP_0102325
ZP_0102981
ZP_0102982
ZP_0103341
ZP_0103347
ZP_0103558
ZP_0103989
ZP_0106021
ZP_0107100
ZP_0107101
ZP_0108328
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