Comments (13)
matentzn
commented on June 9, 2024
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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RLWOHIO
commented on June 9, 2024
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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matentzn
commented on June 9, 2024
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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RLWOHIO
commented on June 9, 2024
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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matentzn
commented on June 9, 2024
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
- https://github.com/obophenotype/zebrafish-phenotype-ontology/blob/master/src/curation/zp_zfin_phenoGeneCleanData_fish.tsv
- https://github.com/obophenotype/zebrafish-phenotype-ontology/blob/master/src/curation/zp_zfin_phenotype_fish.tsv
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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RLWOHIO
commented on June 9, 2024
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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matentzn
commented on June 9, 2024
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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RLWOHIO
commented on June 9, 2024
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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matentzn
commented on June 9, 2024
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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RLWOHIO
commented on June 9, 2024
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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RLWOHIO
commented on June 9, 2024
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.
upheno_all_with_relations.owl.PLUS.mine2.owl.unsatisfiableZPs.pptx
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matentzn
commented on June 9, 2024
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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RLWOHIO
commented on June 9, 2024
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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Related Issues (20)
- ZFIN uses obsolete GO:0044424 and GO:0044420 HOT 2
- Add abnormalBiologicalProcess back to external.txt HOT 1
- Test whether an obsoleted class gets re-introduced into ZP, so the obsoletion can be revoked
- Get all phenotypes that refer to Qualitative traits and inhere in BPs
- Gather example(s) for electrophysiology terms
- Add obofoundry topic to repo metadata HOT 1
- Uses of obsolete GO and ZFA terms HOT 1
- Odd ZFA term in data (ZFA:0005943)
- ZP:0008499 and ZP:0000998 have the same label HOT 1
- ZFIN migration to pre-composed ZP curation?
- Integration with NBO HOT 3
- Handle obsolete fillers in ZP (December 2022) HOT 2
- ZP:0144208 - "cone photoreceptor outer segment ZFA:0005945 morphology, abnormal"
- ZP:0101932 - "obsolete nucleosome positioning process quality, abnormal" HOT 4
- ZP:0019257 - "obsolete mitotic chromosome decondensation premature, abnormal" HOT 6
- ZP December release
- ZP:0101990, 'retinal pigmented epithelium disrupted obsolete chemical homeostasis within retina, abnormal'
- AHHHHHHnsats. HOT 2
- Retiring the NBO Phenotype branch HOT 2
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