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A vocabulary for describing Zebrafish Phenotypes

Home Page: https://obophenotype.github.io/zebrafish-phenotype-ontology/

Dockerfile 0.03% Makefile 38.23% Shell 8.40% Batchfile 0.07% Python 48.99% Ruby 1.98% Scala 2.31%

ontology obofoundry anatomy-ontology anatomy developmental-stages zebrafish

zebrafish-phenotype-ontology's Introduction

zebrafish-phenotype-ontology

This ontology... YOUR DESCRIPTION HERE

Versions

Stable release versions

The latest version of the ontology can always be found at:

http://purl.obolibrary.org/obo/zp.owl

(note this will not show up until the request has been approved by obofoundry.org)

Editors' version

Editors of this ontology should use the edit version, src/ontology/zp-edit.owl

Contact

Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.

Acknowledgements

This ontology repository was created using the ontology starter kit Initial construction from ZFIN data has been performed using https://github.com/obophenotype/zebrafish-phenotype-ontology-build.

zebrafish-phenotype-ontology's People

Contributors

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drseb standardgalactic sal101282

zebrafish-phenotype-ontology's Issues

73 unsatisfiable ZP classes

By far the majority will not be root unsatisfiable; I need to run some experiments and see which ones are broken ones (probably only a handful using part of instead of occurs in), and submit them to ZFIN to be fixed.

Get all phenotypes that refer to Qualitative traits and inhere in BPs

... that are not process qualities.

Improve ZP diff reports

How did the annotations change?
Which new ZP terms do these relate to?
Which ZP terms are merged/obsoleted?
Yvonne: 
- the annotations should really not change
- Exceptions: GO terms change (obsoleted)
- Relationship issues don't really exist anymore

ZP December release

Blockers

Odd ZFA term in data (ZFA:0005943)

ZFIN references ZFA:0005943, but I cannot find it in ZFA at all.. @ybradford can you track this term down?

Not on OLS, nor on Ontobee, e.g. https://www.ebi.ac.uk/ols/search?q=ZFA%3A0005943&groupField=iri&exact=on&start=0

ZDB-FISH-150901-15216	TU	ZDB-STAGE-010723-10	Pharyngula:Prim-5	ZDB-STAGE-010723-10	Pharyngula:Prim-5	GO:0006508	proteolysis	BFO:0000066	occurs_in	ZFA:0005943	perivitelline fluid	PATO:0002304	increased process quality	abnormal							ZDB-PUB-200207-23	ZDB-EXP-210520-3	GO:0006508-BFO:0000066-ZFA:0005943-PATO:0002304-abnormal-0-0-0	
ZDB-FISH-150901-15216	TU	ZDB-STAGE-010723-13	Pharyngula:Prim-25	ZDB-STAGE-010723-13	Pharyngula:Prim-25	GO:0006508	proteolysis	BFO:0000066	occurs_in	ZFA:0005943	perivitelline fluid	PATO:0002304	increased process quality	abnormal							ZDB-PUB-200207-23	ZDB-EXP-210520-3	GO:0006508-BFO:0000066-ZFA:0005943-PATO:0002304-abnormal-0-0-0

Two different annotation properties for 'source_information' are used

@matentzn commented on Wed Sep 12 2018

http://zfin.org/definition/source_information

http://zfin/definition/source_information

Should be the former to be valid URL type IRI.

NTR abnormal tail morphology

For new term requests, please provide the following information:

Preferred term label

abnormal tail morphology

Synonyms

Textual definition

combination of UBERON tail and PATO malformed

Suggested parent term

not sure

Attribution

If you would like a nanoattribution, please indicate your ORCID id

If a ZFIN term uses an obsolete class, this should be flagged

Output should be a table with
ZP, ZFIN EQ ID, OBSOLETE CLASS
ZP:001,0-0-0-PATO:001-0-0-0,GO:0001

ZP:0008499 and ZP:0000998 have the same label

ZP:0008499
ZP:0000998

These two phenotypes have the same label, but are defined differently. @ybradford in our next face 2 face, we can look at this one.

Add obofoundry topic to repo metadata

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

ZP Phenotype Class definition incomplete

is:

'has part' some quality

should be:

'has part' some (quality and inheres in some owl:Thing and 'has modifier' some abnormal)

Uses of obsolete GO and ZFA terms

ZP_0100153: GO_0008003 epidermis absent, abnormal
ZP_0100155: GO_0031513 neuromast hair cell absent, abnormal
ZP_0100156: GO_0005605 notochord absent, abnormal
ZP_0100206: GO_0031512 Kupffer's vesicle increased length, abnormal
ZP_0100208: GO_0072372 somite increased length, abnormal
ZP_0139819: ZFA_0005943 increased process quality proteolysis, abnormal

ZFIN sometimes uses GO:0005623 (cell) rather than ZFA. Intended?

Example:

ZDB-FISH-150901-29105	WT	ZDB-STAGE-010723-8	Larval:Protruding-mouth	ZDB-STAGE-010723-8	Larval:Protruding-mouth					ZFA:0001315	atrioventricular canal	PATO:0002001	has fewer parts of type	abnormal	GO:0005623	cell	BFO:0000050	part_of	ZFA:0001320	endocardium	ZDB-PUB-130709-36	ZDB-EXP-140306-9	0-0-ZFA:0001315-PATO:0002001-GO:0005623-BFO:0000050-ZFA:0001320	ZP:0014564

Compared to:

ZDB-FISH-150901-24930	gdf6a<sup>m233/m233</sup>(AB)	ZDB-STAGE-010723-35	Larval:Day 4	ZDB-STAGE-010723-35	Larval:Day 4	ZFA:0009000	cell	BFO:0000050	part_of	ZFA:0000119	retinal inner nuclear layer	PATO:0001997	decreased amount	abnormal							ZDB-PUB-101115-22	ZDB-EXP-041102-1	ZFA:0009000-BFO:0000050-ZFA:0000119-PATO:0001997-0-0-0	ZP:0006134

This causes confusion for the labels: both classes GO:0005623 and ZFA:0009000 are labelled 'cell'. Intentional?

Pipeline should fail with a meaningful message if deprecated classes are used

@matentzn commented on Tue Nov 13 2018

The following classes are used across ZP, but are obsoleted/deprecated:

What should happen to the phenotypes? Note that only some of them are in the ZFIN annotations; some are in the current manual intermediate layer.

@drseb

BSPO_0000101
GO_0000046
GO_0004872
GO_0005578
GO_0005605
GO_0006200
GO_0007067
GO_0008002
GO_0008003
GO_0008105
GO_0015992
GO_0016023
GO_0016265
GO_0016271
GO_0016337
GO_0021865
GO_0021867
GO_0031512
GO_0031513
GO_0040023
GO_0042384
GO_0042516
GO_0043205
GO_0043206
GO_0071436
GO_0072372
GO_0090002
GO_0097369
GO_2001273
GO_2001274
GO_2001275
ZFA_0000283
ZFA_0005182

Terms that existed once but no longer exist should be obsoleted instead of removed

@matentzn commented on Tue Sep 25 2018

For example, 'abnormally abnormal angiogenic sprout' (ZP_0003681) in the last main build refers to the quality 'abnormal' (PATO:0000460). In the current ZFIN metadata (neither gene nor genome data), there is no single annotation that refers to both the angiogenic sprout (ZFA:0005604) and the PATO quality 'abnormal'.

@drseb is that possible?

@matentzn commented on Tue Sep 25 2018

In the case that a phenotype that previously existed now changed, we should obsolete the existing class (remove the definition) but still add it to the new ontology.

@drseb commented on Tue Sep 25 2018

Can you help debug? Which gene/genotype/morpholino has previously been associated with that?

@matentzn commented on Tue Sep 25 2018

I looked through the old versions of the old ZFIN raw data. There are many annotations with the sprout, but none that have the abnormal Qualifier in the place of the Quality. I gladly keep looking at this issue, but my expectation is that such changes can and will occur from time to time..

@drseb commented on Tue Sep 25 2018

Yes. Those issues will arise often. Hmm... we need a new strategy. Obsoletion is probably not solving the issue, because what will happen if it is used in a future release? Unobsolete again?

@matentzn commented on Tue Sep 25 2018

That is what I was thinking! Why not :P

@drseb commented on Tue Sep 25 2018

If you think it is a valid option I am okay with it. Would love to hear from others if that is okay. @balhoff ?

@matentzn commented on Tue Sep 25 2018

I mean, there are three alternatives:

they are removed, and we track the fact that they existed once in a separate file to ensure the same IRI is not used again.
they are obsoleted (EQ is removed) and unobsoleted as ZFIN raw data changes
they are carried over and from release to release, and simply never change.

Both 2 and 3 are valid, as a phenotypic description does not necessarily become invalid just because it is not used in any of the annotations. Above case is a bit of an exception, because I am trying to push the community to distinguish between modifiers and qualities, and abnormal is not a quality, it is a modifier, and therefore does not belong in the quality slot. I advocate 2. I dont think 1. is a good option at all, both for administrative and conceptual reasons.

@matentzn commented on Tue Sep 25 2018

@dosumis @cmungall if you have strong opinions here

@drseb commented on Tue Sep 25 2018

At the moment (I have to think about it again later) I vote for 3, as it is the simplest solution.
But this would require more information about the reason for the class' disappearance in the ZFIN data. Can we get a comment from ZFIN on typical reasons? If they simply replaced it with a more specific annotation, then the previously chosen class is still correct. If it was a clear error in the first place than option 2 would be the better choice. Let's hear what others say ;-)

@matentzn commented on Tue Sep 25 2018

I pinged them on slack. :)

@matentzn commented on Tue Sep 25 2018

I quickly took a look at the diffs:

Number of phenotypes in the current build (2015): 18,461
Number of phenotypes in new build (today): 26,197
Number of phenotypes appearing in both: 17,211
Number of phenotypes that are only in old, i.e. disappeared (file list): 1,250

As an irrelevant side note: I also noticed that 105 labels (from all those phenotypes that appear in both versions of ZP) vary quite significantly (either because labels in GO change, or in PATO, or perhaps in ZFA).

@balhoff commented on Tue Sep 25 2018

I'm okay with "un-obsoleting" when needed. However I feel like if the expression is satisfiable, it doesn't hurt anything to keep in (option 3). Some others outside of ZFIN are using ZP (for example Rong-Lin).

@drseb commented on Wed Sep 26 2018

@cmungall this is all so long ago... (we were so young back then ;-) ). Do you remember more details from our work? It is not written in the F1000 paper, but looking at the classes that have no direct gene association I assume that we automatically generated more general class expressions. E.g. abnormal length X would imply that we add abnormal X to ZP. (I think we have done this, but I am not sure)

Add abnormalBiologicalProcess back to external.txt

After #32 is closed, we need to add abnormalBiologicalProcess back to external.txt. Currently, abnormalBiologicalProcess uses PATO:quality rather than PATO:process quality to capture all the abnormal biological processes in ZFIN.

Some normal phenotypes snug into ZFIN?

'cilium multi-ciliated epithelial cell normal, abnormal'
'determination of left/right asymmetry in lateral mesoderm normal, abnormal'
'determination of pancreatic left/right asymmetry normal, abnormal'
'embryonic heart tube left/right pattern formation normal, abnormal'
'trunk normal neural crest cell development, abnormal'
'whole organism normal, abnormal'

Here are the ZFIN annotations I found:

phenotype_fish.txt:ZDB-FISH-150901-10141	WT + MO1-mir34b + MO2-myb	ZDB-STAGE-010723-13	Pharyngula:Prim-25	ZDB-STAGE-010723-13	Pharyngula:Prim-25	GO:0005929	cilium	BFO:0000050	part_of	ZFA:0005242	multi-ciliated epithelial cell	PATO:0000461	normal	normal							ZDB-PUB-130703-10	ZDB-EXP-140205-10
phenotype_fish.txt:ZDB-FISH-150901-12354	eif3ba<sup>la024215Tg/la024215Tg</sup>	ZDB-STAGE-010723-10	Pharyngula:Prim-5	ZDB-STAGE-010723-10	Pharyngula:Prim-5	GO:0014032	neural crest cell development	BFO:0000066	occurs_in	ZFA:0001115	trunk	PATO:0000461	normal	normal							ZDB-PUB-130710-52	ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-16886	katnb1<sup>mh103/mh103</sup>	ZDB-STAGE-010723-2	Gastrula:Shield	ZDB-STAGE-010723-2	Gastrula:Shield					ZFA:0001094	whole organism	PATO:0000461	normal	normal							ZDB-PUB-141219-3	ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-19627	kif6<sup>gw326/gw326</sup>	ZDB-STAGE-010723-30	Segmentation:14-19 somites	ZDB-STAGE-010723-30	Segmentation:14-19 somites		GO:0003140	determination of left/right asymmetry in lateral mesoderm	PATO:0000461	normal	normal							ZDB-PUB-141007-7	ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-19627	kif6<sup>gw326/gw326</sup>	ZDB-STAGE-010723-30	Segmentation:14-19 somites	ZDB-STAGE-010723-8	Larval:Protruding-mouth			GO:0035469	determination of pancreatic left/right asymmetry	PATO:0000461	normal	normal							ZDB-PUB-141007-7	ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-19627	kif6<sup>gw326/gw326</sup>	ZDB-STAGE-010723-32	Pharyngula:Prim-15	ZDB-STAGE-010723-32	Pharyngula:Prim-15				GO:0060971	embryonic heart tube left/right pattern formation	PATO:0000461	normal	normal							ZDB-PUB-141007-7	ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-3309	katnb1<sup>mh101/mh101</sup>; katnb1<sup>mh102/mh102</sup>	ZDB-STAGE-010723-2	Gastrula:Shield	ZDB-STAGE-010723-2	Gastrula:Shield			ZFA:0001094	whole organism	PATO:0000461	normal	normal

I thought phenotype fish only contained 'abnormal' now? We need to account for this soon, because we know have abnormally normal phenotypes which looks a bit funny. :P

Mass obsoletion

Lots of duplicates where removed, dont forget to obsolete before next release @matentzn

Unsatisfiable ZP:0100801 (Fix ZFIN)

Logical definition:

'has part' some 
('increased occurrence' and ('inheres in' some 
('protein kinase activity' and ('part of' some 'cardiac ventricle'))) 
and ('has modifier' some abnormal))

Problem: kinase activity is a process, cardiac ventrical a material entity. part_of is the wrong relation.
Solution: ZFIN record should use 'occurs_in' in column Post-composed Relationship ID instead of 'part_of'.

Refer to this table to find the broken record.

ZFIN migration to pre-composed ZP curation?

Advantages

If EQ changes, database (ZFIN) needs to changes, which creates a circular dependency between ZP and ZFIN (burden on curation seems high).
If we need a term for which no EQ can be formulated, we need a way to do that - only with precoordinatd

Problems to overcome

When we don't have a term, we need to rapidly create new terms.

Test whether an obsoleted class gets re-introduced into ZP, so the obsoletion can be revoked

GO pipeline: Check whether we can restrict to taxon

genus differentia

Integration with NBO

Hi. My understanding from ZFIN is that they won't integrate with NBO but are staying with the levels of behavioural process provided by integrating with GO. If so, I am puzzled to find a single example of an NBO term (and its parents) in the ZP ontology: ‘chewing’ (NBO:0000073). I wonder why, not least because the ZP ontology also contains its synonym 'mastication' (GO:0071626).

Gather example(s) for electrophysiology terms

These will not be logically defined (but maybe partially)

@ybradford to gather one or more examples with human readable definition that we can work on together.

Retiring the NBO Phenotype branch

The NBO is planning to retire its Phenotype branch (no date set yet). We are not aware that ZP has been using any terms from this branch, but you may want to double-check. I recommend tagging @matentzn in follow-up comments, not least if you need a technical discussion.

ZFIN pipeline seems to be only additive

When running ZFIN pipeline, I only ever see classes added, not anything removed. This is a note to self and does not require action for now.

ZP classes derived from the ZFIN-EQs no longer present should be deprecated

NTR yolk edema

For new term requests, please provide the following information:

Preferred term label

yolk edema

Synonyms

Textual definition

combination of yolk in UBERON and edetamous in PATO

Suggested parent term

not sure

Attribution

If you would like a nanoattribution, please indicate your ORCID id

Missing GO terms?

We have the following 18 missing GO terms needed to construct a total of 44 classes in ZP. Most likely these classes were, at some point in the past, used by ZFIN to describe phenotypes. We need to decide what to do with these.

@ybradford while I am preparing a new release, can you determine what happened with these and if they are still needed by ZFIN? I could just mass obsolete all phenotypes related to these classes, but it seems unfortunate to keep obsoleting so many classes per year.

(a) what happened with these (some don't resolve in GO)

a large number of ZP classes unsatisfiable

For new term requests, please provide the following information:

Preferred term label

(e.g., Asplenia)

Synonyms

(e.g., Absent spleen)

Textual definition

the definition should be understandable even for non-specialists. Include a PubMed ID to refer to any relevant article that provides additional information about the suggested term.

Suggested parent term

Please look in the hierarchy in a browser such as OLS

Attribution

If you would like a nanoattribution, please indicate your ORCID id

ZP:0101990, 'retinal pigmented epithelium disrupted obsolete chemical homeostasis within retina, abnormal'

Obsolete GO term in ZFIN:

ZDB-FISH-170831-28	WT + MO1-tyrp1a + MO2-tyrp1b	ZDB-STAGE-010723-9	Hatching:Long-pec	ZDB-STAGE-010723-9	Hatching:Long-pec	GO:0048876	obsolete chemical homeostasis within retina	BFO:0000066	occurs_in	ZFA:0000144	retinal pigmented epithelium	PATO:0001507	disrupted	abnormal							ZDB-PUB-160505-5	ZDB-EXP-041102-1	GO:0048876-BFO:0000066-ZFA:0000144-PATO:0001507-abnormal-0-0-0

ZFIN uses obsolete GO:0044424 and GO:0044420

http://amigo.geneontology.org/amigo/term/GO:0044420
http://amigo.geneontology.org/amigo/term/GO:0044424

These are the corresponding annotations:

ZDB-FISH-180927-4	olfm1a<sup>sa221/sa221</sup> ; olfm1b<sup>sa157/sa157</sup>(TL)	ZDB-STAGE-010723-32	Pharyngula:Prim-15	ZDB-STAGE-010723-32	Pharyngula:Prim-15	GO:0044424	obsolete intracellular part	BFO:0000050	part_of	ZFA:0000152	retina	PATO:0001997	decreased amount	abnormal							ZDB-PUB-171005-5	ZDB-EXP-180927-1	GO:0044424-BFO:0000050-ZFA:0000152-PATO:0001997-0-0-0	ZP:0110355
ZDB-FISH-150901-2115	gpc4<sup>m119/m119</sup>	ZDB-STAGE-010723-36	Larval:Day 5	ZDB-STAGE-010723-36	Larval:Day 5	GO:0044420	obsolete extracellular matrix component	BFO:0000050	part_of	ZFA:0001458	cranial cartilage	PATO:0000060	spatial pattern	normal							ZDB-PUB-110518-25	ZDB-EXP-041102-1	GO:0044420-BFO:0000050-ZFA:0001458-PATO:0000060-0-0-0	ZP:0110354
ZDB-FISH-150901-24314	ext2<sup>to273b/to273b</sup>	ZDB-STAGE-010723-36	Larval:Day 5	ZDB-STAGE-010723-36	Larval:Day 5	GO:0044420	obsolete extracellular matrix component	BFO:0000050	part_of	ZFA:0001458	cranial cartilage	PATO:0000060	spatial pattern	abnormal							ZDB-PUB-110518-25	ZDB-EXP-041102-1	GO:0044420-BFO:0000050-ZFA:0001458-PATO:0000060-0-0-0	ZP:0110354
ZDB-FISH-150901-2448	slc35b2<sup>to216z/to216z</sup>	ZDB-STAGE-010723-36	Larval:Day 5	ZDB-STAGE-010723-36	Larval:Day 5	GO:0044420	obsolete extracellular matrix component	BFO:0000050	part_of	ZFA:0001458	cranial cartilage	PATO:0000060	spatial pattern	abnormal							ZDB-PUB-110518-25	ZDB-EXP-041102-1	GO:0044420-BFO:0000050-ZFA:0001458-PATO:0000060-0-0-0	ZP:0110354
ZDB-FISH-150901-28521	b3gat3<sup>hi307Tg/hi307Tg</sup>	ZDB-STAGE-010723-36	Larval:Day 5	ZDB-STAGE-010723-36	Larval:Day 5	GO:0044420	obsolete extracellular matrix component	BFO:0000050	part_of	ZFA:0001458	cranial cartilage	PATO:0000060	spatial pattern	normal							ZDB-PUB-110518-25	ZDB-EXP-041102-1	GO:0044420-BFO:0000050-ZFA:0001458-PATO:0000060-0-0-0	ZP:0110354
ZDB-FISH-150901-29430	uxs1<sup>hi954Tg/hi954Tg</sup>	ZDB-STAGE-010723-36	Larval:Day 5	ZDB-STAGE-010723-36	Larval:Day 5	GO:0044420	obsolete extracellular matrix component	BFO:0000050	part_of	ZFA:0001458	cranial cartilage	PATO:0000060	spatial pattern	abnormal							ZDB-PUB-110518-25	ZDB-EXP-041102-1	GO:0044420-BFO:0000050-ZFA:0001458-PATO:0000060-0-0-0	ZP:0110354

Remove equivalent classes from ZP

There are currently a few duplicate classes in ZP that need to go.

ZP:0144208 - "cone photoreceptor outer segment ZFA:0005945 morphology, abnormal"

Add GO phenotypes to ZP (analogous to anatomy pipeline)

We also need to find out how this relates to GO:0001PHENOTYPE classes in dipper.

Drafting a plan for pre-coordinating amerliorated an excacerbated phenotypes

Apart from phenotypic abnormalities, ZFIN curates ameliorated and excacerbated phenotypes. These phenotypes are special in two senses

they follow a simple pattern: biological attribute (tail length, glucose levels, eye morphology) in combination with a qualifier (ameliorated, exacerbated). They are simpler therefore than phenotypic abnormalities as they don't contain directions like "increased" and "decreased". (@ybradford could they be something like "blood glucose levels" with two entities involved, eg glucose part of blood?
they don't automatically interact with "phenotypic abnormalities" hierarchically.

Now the problem is that (1) adding those into ZP will lead to two large branches with 3000 - 9000 terms being added (term proliferation), and (2) there is no integration between the two, or, indeed with anything in uPheno.

My sense is the ship to prevent term proliferation has sailed. We should just add these phenotypes the same way as the we have the others.

However, I do think we should move uPheno to the "changed" qualifier throughout so that we can group ameliorated, exacerbated and abnormal in a more general "phenotype" hierarchy.

ZFIN raw data has not anticipated use of 'BSPO:0000120' (121) (in left/right side of)

@matentzn commented on Mon Sep 10 2018

In 'Phenotype of Zebrafish Genes' dataset (https://zfin.org/downloads/phenoGeneCleanData_fish.txt), ZFIN annotates a few genes using BSPO:0000120 (in left side of) and the respective 'in right side of'. Both BSPO identifiers refer to object properties, not classes; ZPGen assumes the column contains classes. Question to @ybradford : These are only a handful of records; is it possible that the intention was to use BSPO:0000000 (left side) or BSPO:0000007 (right side) instead?

/data $ wget https://zfin.org/downloads/phenoGeneCleanData_fish.txt
/data $ grep BSPO:0000120 phenoGeneCleanData_fish.txt 
169650585	ephb4b	ZDB-GENE-990415-65	BSPO:0000120	in_left_side_of	BFO:0000050	part_of	ZFA:0000121	lateral plate mesoderm	PATO:0000462	absent	abnormal							ZDB-FISH-161209-1	TU + MO2-ephb4b	ZDB-STAGE-010723-16	ZDB-STAGE-010723-16	ZDB-GENOX-161209-3	ZDB-PUB-160612-7	ZDB-FIG-160818-15
169657538	klf8	ZDB-GENE-070424-152	BSPO:0000120	in_left_side_of	BFO:0000050	part_of	ZFA:0000101	diencephalon	PATO:0000462	absent	abnormal	ZDB-FISH-180605-11	AB + MO1-klf8	ZDB-STAGE-010723-16	ZDB-STAGE-010723-16	ZDB-GENOX-180605-12	ZDB-PUB-170720-15	ZDB-FIG-180118-30
169657540	klf8	ZDB-GENE-070424-152	BSPO:0000120	in_left_side_of	BFO:0000050	part_of	ZFA:0000101	diencephalon	PATO:0000462	absent	abnormal	ZDB-FISH-180605-12	AB + MO2-klf8	ZDB-STAGE-010723-16	ZDB-STAGE-010723-16	ZDB-GENOX-180605-13	ZDB-PUB-170720-15	ZDB-FIG-180118-30
169648499	meis3	ZDB-GENE-010406-2	BSPO:0000120	in_left_side_of	BFO:0000050	part_of	ZFA:0001323	mid intestine	PATO:0000462	absent	abnormal	ZDB-FISH-160212-5	AB + MO1-meis3	ZDB-STAGE-010723-9	ZDB-STAGE-010723-9	ZDB-GENOX-160212-9	ZDB-PUB-150912-13	ZDB-FIG-160212-9
169648501	meis3	ZDB-GENE-010406-2	BSPO:0000120	in_left_side_of	BFO:0000050	part_of	ZFA:0001076	intestinal bulb	PATO:0000628	mislocalised	abnormal							ZDB-FISH-160212-5	AB + MO1-meis3	ZDB-STAGE-010723-9	ZDB-STAGE-010723-9	ZDB-GENOX-160212-9	ZDB-PUB-150912-13	ZDB-FIG-160212-9
/data $ grep BSPO:0000121 phenoGeneCleanData_fish.txt 
169650586	ephb4b	ZDB-GENE-990415-65	BSPO:0000121	in_right_side_of	BFO:0000050	part_of	ZFA:0000121	lateral plate mesoderm	PATO:0000628	mislocalised	abnormal							ZDB-FISH-161209-1	TU + MO2-ephb4b	ZDB-STAGE-010723-16	ZDB-STAGE-010723-16	ZDB-GENOX-161209-3	ZDB-PUB-160612-7	ZDB-FIG-160818-15
169648503	meis3	ZDB-GENE-010406-2	BSPO:0000121	in_right_side_of	BFO:0000050	part_of	ZFA:0001323	mid intestine	PATO:0000462	absent	abnormal							ZDB-FISH-160212-5	AB + MO1-meis3	ZDB-STAGE-010723-9	ZDB-STAGE-010723-9	ZDB-GENOX-160212-9	ZDB-PUB-150912-13	ZDB-FIG-160212-9
169648502	meis3	ZDB-GENE-010406-2	BSPO:0000121	in_right_side_of	BFO:0000050	part_of	ZFA:0001076	intestinal bulb	PATO:0000628	mislocalisedabnormal							ZDB-FISH-160212-5	AB + MO1-meis3	ZDB-STAGE-010723-9	ZDB-STAGE-010723-9	ZDB-GENOX-160212-9	ZDB-PUB-150912-13	ZDB-FIG-160212-9
/data $

@matentzn commented on Thu Sep 20 2018

In my latest run, I found a few more of those:

http://purl.obolibrary.org/obo/BSPO_0000120 (in left side of)
http://purl.obolibrary.org/obo/BSPO_0000098 (dorsal to)
http://purl.obolibrary.org/obo/BSPO_0000099 (posterior to)
http://purl.obolibrary.org/obo/BSPO_0000121 (in right side of)
http://purl.obolibrary.org/obo/BSPO_0000096 (anterior to)

Can someone at ZFIN check whether, given, https://zfin.org/downloads/phenoGeneCleanData_fish.txt, Column D, the following replacements can be made to the annotations:

BSPO:0000120 (in left side of) -> BSPO:0000000 (left side)
BSPO:0000098 (dorsal to) -> BSPO: 0000063 (dorsal side)
BSPO:0000099 (posterior to) -> BSPO:0000056 (posterior side)
BSPO:0000121 (in right side of) -> BSPO:0000007 (right side)
BSPO:0000096 (anterior to) -> BSPO:0000055 (anterior side)

Problem with redundancy of 'part of' axioms in ZFA with ZFIN

ZFIN annotations are not free of redundancy. For example, we occasionally have annotations to somite, and on other cases somite and part of trunk. Unfortunately, somite is ALWAYS part of trunk (ZFA). The problem is, since we rely on the annotations to be logically distinct, we generate both classes: inheres in somite, and inheres in somite part of trunk, which are logically equivalent and therefore redundant and confusing. For ZP, as a workaround, we remove part of axioms from ZFA prior to generating the ontology. But that wont really help us, when ZP is combined with other ontologies.

Do you think it makes sense to fix these annotations at ZFIN @ybradford annotations;

ZP:0103989 bearer currently broken

The definition currently is (coming from ZFIN EQs):

'has part' some 
(absent and ('inheres in' some 
('intersegmental vessel' and ('part of' some 'thoracic duct'))) and ('has modifier' some abnormal))

The problem is this:
lymphatic vessel is disjoint with blood vessel.

However, the bearer above (('intersegmental vessel' and ('part of' some 'thoracic duct'))) is both a blood vessel (an intersegmental vessel is a blood vessel according to ZFA) AND a lymphatic vessel:

A lymphatic vessel is equivalentTo: a vessel that is part of some lymph vasculature.
the intersegemental vessel is obviously a vessel.
... and it is also part of the lymph vasculature, because
3.1. thoracic duct is a lymphatic vessel and 3.2. thoracic ductis part of thelymph vasculature`.

I dont know anatomy well enough to fix this, but @ybradford maybe you can see how to fix.

Handle obsolete fillers in ZP (December 2022)

Covered by ZFIN/zebrafish-anatomical-ontology#167

Obsoleted by ZFIN

ZP:0002196 - "obsolete cell aging increased magnitude, abnormal"
ZP:0002277 - "obsolete cell aging decreased magnitude, abnormal"
ZP:0009026 - "obsolete animal organ senescence premature, abnormal"
ZP:0009491 - "GO:0006975 increased occurrence, abnormal"
ZP:0015427 - "obsolete cell aging magnitude, abnormal"
ZP:0020895 - "obsolete age-dependent general metabolic decline physiological state, abnormal"
ZP:0021774 - "obsolete protein ADP-ribosylation decreased occurrence, abnormal"
ZP:0130891 - "obsolete histone H2A-S139 phosphorylation increased occurrence, abnormal"
ZP:0142384 - "GO:0014024 delayed, abnormal"

Not covered by ZFIN/zebrafish-anatomical-ontology#167, not obsoleted

ZP:0019257 - "obsolete mitotic chromosome decondensation premature, abnormal"

@ybradford ZFIN is using the following obsolete GO term:

ZDB-FISH-151223-12	esco2<sup>hi2865Tg/hi2865Tg</sup>	ZDB-STAGE-010723-10	Pharyngula:Prim-5	ZDB-STAGE-010723-10	Pharyngula:Prim-5					GO:0007083	obsolete mitotic chromosome decondensation	PATO:0000694	premature	abnormal							ZDB-PUB-150606-7	ZDB-EXP-041102-1	0-0-GO:0007083-PATO:0000694-abnormal-0-0-0

Unsatisfiable 'activity in anatomy' Classes (Fix ZFIN)

It appears that all the following classes follow the same problem: a kind of activity occurs in an anatomy, but ZFIN uses 'part_of' instead of 'occurs_in' to model this. So I guess our unsatisfiable problem is smaller than I thought.

Phenotypes with activities that occur in an anatomical structure:

Laminase binding

http://purl.obolibrary.org/obo/ZP_0008731

Example:

'has part' some 
('increased occurrence' and ('inheres in' some 
('protein kinase activity' and ('part of' some 'cardiac ventricle'))) 
and ('has modifier' some abnormal))

Problem: 'protein kinase activity' is a process, cardiac ventrical a material entity. part_of is the wrong relation.
Solution: ZFIN record should use 'occurs_in' in column Post-composed Relationship ID instead of 'part_of'.

Refer to this table to find the broken record.

If the record is not found in the above table, it means that the culprit lies in one of the intermediate classes we have already added; just post here which ones and I will fix them.

ZP:0101932 - "obsolete nucleosome positioning process quality, abnormal"

@ybradford

ZFIN is using the following obsolete GO term in annotation:

ZDB-FISH-170818-7	TU + MO2-bptf + MO3-bptf	ZDB-STAGE-010723-18	Gastrula:75%-epiboly	ZDB-STAGE-010723-18	Gastrula:75%-epiboly					GO:0016584	obsolete nucleosome positioning	PATO:0001236	process quality	abnormal							ZDB-PUB-150605-3	ZDB-EXP-070511-5	0-0-GO:0016584-PATO:0001236-abnormal-0-0-0

Unsat ZP_0100030: (peritoneum and ('occurs in' some 'macrophage chemotaxis'))

ZP_0100030 is defined as.

'has part' some 
('increased occurrence' and ('inheres in' some 
(peritoneum and ('occurs in' some 'macrophage chemotaxis'))) and ('has modifier' some abnormal))

Is it possible that the intention was to record 'macrophage chemotaxis' and ('occurs in' some peritoneum)?

If you agree, review whether this is a general mix up in the ontology (i.e. ALL ZP classes are simply reversed in terms of the 'occurs in' relation), or this is a problem with the ZFIN EQ annotations.

If you find it is a problem with the ZFIN EQs, just fix it in ZFIN, and let me know when the fix is applied and the fish_phenotypes.txt data in the ZFIN downloads sections is updated!

I think fixing that class alone solves about 200 unsatisfiable classes.

Add anatomy pipeline to ZP

Analogously to XPO, we would like to have ZFA intermediate classes to make browsing the ZP hierarchy easier. (abnormal morphology, abnormal anatomy)

unsatisfiable classes when merged into vertebrate.owl

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

Design pipeline for recording when a ZP term is replaced by new ZP term

Currently will need to make use of existing annotations to establish the link. Other ideas?

Unsatisfiable ZP:0103876 (Fix ZFIN)

Logical definition:

'has part' some 
('process quality' and ('inheres in' some 
('glutathione transferase activity' and ('part of' some 'whole organism')))

Problem: 'glutathione transferase activity' is a process, 'whole organism' a material entity. part_of is the wrong relation.
Solution: ZFIN record should use 'occurs_in' in column Post-composed Relationship ID instead of 'part_of'. Note that this entry comes from a 'normal' phenotype entry; it should nevertheless be correct.

Refer to this table to find the broken record.