fixes#2400-NTR-fish-terms #2702

paulacalipho · 2022-10-31T08:00:41Z

fixes #2400 NTR-fish-terms

github-actions · 2022-10-31T09:17:45Z

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-11-03/uberon-simple.owl
Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-simple.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-11-03/uberon-simple.owl
Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

IAO_0000232 `http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/IAO_0000232`

Added

AnnotationProperty: IAO_0000232

UBERON_8480038 `http://purl.obolibrary.org/obo/UBERON_8480038`

Added

UBERON_8480038 has_obo_namespace "uberon"
UBERON_8480038 definition "Lymphomyeloid tissue that consists mainly in granulopoietic cells but that also contains erythroid and lymphoid cells in different stages of maturation."
- database_cross_reference "PMID:3765338"
UBERON_8480038 label "meningeal myeloid tissue"
UBERON_8480038 date "2022-10-31T07:50:56Z"^^dateTime
UBERON_8480038 id "UBERON:8480038"
UBERON_8480038 curator notes "May be present in Amia and Lepisosteus, Polyodon and Acipenser, but not Polypterus."
- database_cross_reference "https://doi.org/10.1111/j.1096-3642.1998.tb02524.x"
UBERON_8480038 contributor 0000-0002-0819-0473
Class: UBERON_8480038
UBERON_8480038 SubClassOf lymphomyeloid tissue

UBERON_8480040 `http://purl.obolibrary.org/obo/UBERON_8480040`

Added

UBERON_8480040 has_obo_namespace "uberon"
UBERON_8480040 contributor 0000-0002-0819-0473
UBERON_8480040 label "ovarian fluid"
UBERON_8480040 date "2022-10-31T07:56:47Z"^^dateTime
UBERON_8480040 definition "Fish ovary secretion released with eggs."
- database_cross_reference "PMID:8526977"
UBERON_8480040 id "UBERON:8480040"
Class: UBERON_8480040
UBERON_8480040 SubClassOf female reproductive gland secretion

seminal fluid `http://purl.obolibrary.org/obo/UBERON_0006530`

Added

seminal fluid has_narrow_synonym "milt"
- IAO_0000232 "A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs."
- database_cross_reference "PMID:31287811"
- database_cross_reference "PMID:35203131"

github-actions · 2022-10-31T09:17:47Z

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
Version IRI: None
Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-edit.obo

Right

Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
Version IRI: None
Loaded from: file:/work/src/ontology/uberon-edit.obo

Ontology imports

Ontology annotations

IAO_0000232 `http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/IAO_0000232`

Added

AnnotationProperty: IAO_0000232

UBERON_8480038 `http://purl.obolibrary.org/obo/UBERON_8480038`

Added

UBERON_8480038 has_obo_namespace "uberon"^^string
UBERON_8480038 label "meningeal myeloid tissue"^^string
UBERON_8480038 date "2022-10-31T07:50:56Z"^^dateTime
UBERON_8480038 id "UBERON:8480038"^^string
UBERON_8480038 definition "Lymphomyeloid tissue that consists mainly in granulopoietic cells but that also contains erythroid and lymphoid cells in different stages of maturation."^^string
- database_cross_reference "PMID:3765338"^^string
UBERON_8480038 curator notes "May be present in Amia and Lepisosteus, Polyodon and Acipenser, but not Polypterus."^^string
- database_cross_reference "https://doi.org/10.1111/j.1096-3642.1998.tb02524.x"^^[string](http://www.w3.org/2001/XMLSchema#string)
UBERON_8480038 contributor 0000-0002-0819-0473
Class: UBERON_8480038
UBERON_8480038 SubClassOf in taxon some Actinopterygii
UBERON_8480038 SubClassOf lymphomyeloid tissue

UBERON_8480040 `http://purl.obolibrary.org/obo/UBERON_8480040`

Added

UBERON_8480040 has_obo_namespace "uberon"^^string
UBERON_8480040 contributor 0000-0002-0819-0473
UBERON_8480040 label "ovarian fluid"^^string
UBERON_8480040 date "2022-10-31T07:56:47Z"^^dateTime
UBERON_8480040 definition "Fish ovary secretion released with eggs."^^string
- database_cross_reference "PMID:8526977"^^string
UBERON_8480040 id "UBERON:8480040"^^string
Class: UBERON_8480040
UBERON_8480040 SubClassOf in taxon some Actinopterygii
UBERON_8480040 SubClassOf female reproductive gland secretion

seminal fluid `http://purl.obolibrary.org/obo/UBERON_0006530`

Added

seminal fluid has_narrow_synonym "milt"^^string
- database_cross_reference "PMID:35203131"^^string
- database_cross_reference "PMID:31287811"^^string
- IAO_0000232 "A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs."^^string

shawntanzk · 2022-10-31T09:50:31Z

don't think I can help with content, I know nothing about fish >.< but this is something I noticed:

UBERON_8480039 SubClassOf in taxon some Actinopterygii

UBERON_8480039 SubClassOf in taxon some Mollusca

There probably shouldn't be two in taxon -> I think this either should use a higher up the taxon tree or a present in taxon annotation instead (see taxon guide here if you need help with adding taxon restriction stuff https://github.com/OBOAcademy/obook/blob/8496fe87df5ed0640d4467163c1650b1c3d78817/docs/explanation/taxon-constraints-explainer.md ; ps sorry its not fully in obook yet, in PR stage atm)

paulacalipho · 2022-10-31T09:54:13Z

@shawntanzk Thanks for the feedback. I will wait until I find any reviewer to do this modification

cmungall · 2022-10-31T16:02:15Z

good catch @shawntanzk - but why didn't the pipeline catch this?

shawntanzk · 2022-10-31T16:10:45Z

good catch @shawntanzk - but why didn't the pipeline catch this?

Is there suppose to be a check for this, or is this something we need to look into? or is it something that certain disjointness should have pinged and we have to go figure out why the pipeline did not disjoint them?

balhoff · 2022-10-31T18:09:47Z

@shawntanzk this class should have been found unsatisfiable by the reasoner. It means taxon constraints are not set up correctly. Four things are needed:

taxon constraints in ontology
robot expansions (only for never_in_taxon)
import of taxonomy hierarchy
import of taxonomy in_taxon sibling disjointness

shawntanzk · 2022-10-31T19:24:22Z

thanks @balhoff - I will write a ticket and hopefully we can get to the bottom of if with the tech support team :)

cmungall · 2022-10-31T20:17:30Z

src/ontology/uberon-edit.obo

+[Term]
+id: UBERON:8480038
+name: meningeal myeloid tissue
+def: "Lymphomyeloid tissue that consist mainly in granulopoietic cells but that also contains erythroid and lymphoid cells in different stages of maturation." [PMID:25130144]


Thank you for providing a reference for your definition!

In uberon and other OBO ontologies, we prefer sources that are more focused around the definition itself, rather that experimental results papers that might embed the definition and give another sources.

Here we have:

The meningeal tissue is a unique hemopoietic site in sturgeon
located over the medulla oblongata between the brain and cartilaginous
skull capsule, in a saddle-like manner [26,35]. The
meningeal tissue is mainly granulopoietic, with erythroid and
lymphoid cell lines in different stages of maturation and resembles
the hemopoietic bone marrow in mammals, histologically [26].

F€ange R. Lymphoid organs in sturgeons (Acipenseridae). Vet Immunol
Immunopathol 1986;12:153e61.

Scharrer E. The histology of the meningeal myeloid tissue in the Ganoids Amia
and Lepisosteus. Anat Rec 1944;88:291e310.

I might prefer to have one of the two cited papers above as the cited reference

@cmungall OK, I will change to one of these

cmungall · 2022-10-31T20:18:55Z

src/ontology/uberon-edit.obo

+id: UBERON:8480038
+name: meningeal myeloid tissue
+def: "Lymphomyeloid tissue that consist mainly in granulopoietic cells but that also contains erythroid and lymphoid cells in different stages of maturation." [PMID:25130144]
+is_a: UBERON:0034769 ! lymphomyeloid tissue


Can you also add a part-of? Is this part of the meninges or overlaying it? I think there is only a single meninx in this clade, yes?

@cmungall The only information I found (and got access) is the one indicated in PMID:25130144 (citing PMID:3765338 and Anat Rec 1944;88:291e310), "the meningeal tissue is ... located over the medulla oblongata between the brain and cartilaginous skull capsule, in a saddle-like manner".
I would say that is part_of meninges, but I am not really sure

cmungall · 2022-10-31T20:20:39Z

src/ontology/uberon-edit.obo

+def: "Seminal fluid of fish, mollusks, and certain other water-dwelling animals which reproduce by spraying this fluid, which contains the sperm, onto the egg cells." [https://en.wikipedia.org/wiki/Milt]
+is_a: UBERON:0006536 ! male reproductive gland secretion
+relationship: dc-contributor http://orcid.org/0000-0002-0819-0473
+relationship: in_taxon NCBITaxon:6447 ! Mollusca


as mentioned separately, this should have been caught by our pipeline and the PR flagged. Nothing can be only in molluscs and fish.

I wonder if we want to split this into two concepts?

@cmungall I found mainly references about fish seminal fluid. Should I only use 'in taxon' some Actinopterygii and give it up Mollusca?

cmungall · 2022-10-31T20:24:31Z

src/ontology/uberon-edit.obo

+[Term]
+id: UBERON:8480039
+name: milt
+def: "Seminal fluid of fish, mollusks, and certain other water-dwelling animals which reproduce by spraying this fluid, which contains the sperm, onto the egg cells." [https://en.wikipedia.org/wiki/Milt]


We like to have a genus-differentia definition, where the genus is an existing term.

Here we might write as

"Seminal fluid which "

Where the genus is an is-a parent or ancestor

Here we run into a challenging issue. We have "seminal fluid" in uberon already, you opted not to use it in your is-a, likely wisely, as the existing term may be vertebrate specific (not totally clear). But we should be consistent in terminology and use the same term in your is-a that is in your definition

Wikipedia is sometimes a decent source proxy but in this case the wikipedia page is not really helpful and is more about culinary aspects.

To what extend is a new concept really required here vs just having a synonym on seminal fluid?

Having terms that group across phyla is often a sign we want two different concepts, or it's simply different nomenclature on different species for a more general concept.

cc @ddooley

@cmungall I let you decide what is more correct:

add as synonym of seminal fluid.
Is possible to indicate that is a synonym/term used in fish?

create a new concept.
Is this def. better?
"Secretion from the glands of the male genital tract containing sperm that is sprayed onto the egg cells in certain water-dwelling animals."
Difficult to find a good source of definition. What about PMID:31287811 ?

@cmungall I found that this term is also used in Petromyzon marinus (PMID:31287811), so I think the best is to add "milt" as synonym of seminal fluid

cmungall · 2022-10-31T20:27:35Z

src/ontology/uberon-edit.obo

+[Term]
+id: UBERON:8480040
+name: ovarian fluid
+def: "Fish ovary secretion released with eggs." [https://hal.archives-ouvertes.fr/hal-00899767/document]


note on definition source: We always prefer IDs like PMIDs or URLs of primary literature databases rather than secondary archives.

In this case, the relevant URL is
https://pubmed.ncbi.nlm.nih.gov/8526977/

or simply PMID:8526977

is ovarian fluid only secreted in fish?

@cmungall I do not know if ovarian fluid is only secreted in fish
@cmungall I will make the change about the reference

cmungall · 2022-10-31T20:44:09Z

src/ontology/uberon-edit.obo

+[Term]
+id: UBERON:8480039
+name: milt
+def: "Seminal fluid of fish, mollusks, and certain other water-dwelling animals which reproduce by spraying this fluid, which contains the sperm, onto the egg cells." [https://en.wikipedia.org/wiki/Milt]


Wikipedia is sometimes a decent source proxy but in this case the wikipedia page is not really helpful and is more about culinary aspects.

To what extend is a new concept really required here vs just having a synonym on seminal fluid?

Having terms that group across phyla is often a sign we want two different concepts, or it's simply different nomenclature on different species for a more general concept.

cc @ddooley

fixes#2400-NTR-fish-terms

a2a042d

paulacalipho self-assigned this Oct 31, 2022

shawntanzk mentioned this pull request Oct 31, 2022

Taxon disjointness unsat not showing up in pipeline #2707

Closed

cmungall reviewed Oct 31, 2022

View reviewed changes

cmungall approved these changes Oct 31, 2022

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fixes#2400-NTR-fish-terms

b7a7b2b

paulacalipho requested a review from cmungall November 3, 2022 08:36

cmungall approved these changes Nov 4, 2022

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paulacalipho merged commit bd56184 into master Nov 7, 2022

paulacalipho deleted the #2400-NTR-fish-terms branch November 7, 2022 06:57

fixes#2400-NTR-fish-terms #2702

fixes#2400-NTR-fish-terms #2702

Conversation

paulacalipho commented Oct 31, 2022 • edited by nicolevasilevsky Loading

github-actions bot commented Oct 31, 2022 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

IAO_0000232 http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/IAO_0000232

Added

UBERON_8480038 http://purl.obolibrary.org/obo/UBERON_8480038

Added

UBERON_8480040 http://purl.obolibrary.org/obo/UBERON_8480040

Added

seminal fluid http://purl.obolibrary.org/obo/UBERON_0006530

Added

github-actions bot commented Oct 31, 2022 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

IAO_0000232 http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/IAO_0000232

Added

UBERON_8480038 http://purl.obolibrary.org/obo/UBERON_8480038

Added

UBERON_8480040 http://purl.obolibrary.org/obo/UBERON_8480040

Added

seminal fluid http://purl.obolibrary.org/obo/UBERON_0006530

Added

shawntanzk commented Oct 31, 2022

paulacalipho commented Oct 31, 2022

cmungall commented Oct 31, 2022

shawntanzk commented Oct 31, 2022

balhoff commented Oct 31, 2022

shawntanzk commented Oct 31, 2022

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paulacalipho commented Oct 31, 2022 •

edited by nicolevasilevsky

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github-actions bot commented Oct 31, 2022 •

edited

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IAO_0000232 `http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/IAO_0000232`

UBERON_8480038 `http://purl.obolibrary.org/obo/UBERON_8480038`

UBERON_8480040 `http://purl.obolibrary.org/obo/UBERON_8480040`

seminal fluid `http://purl.obolibrary.org/obo/UBERON_0006530`

github-actions bot commented Oct 31, 2022 •

edited

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IAO_0000232 `http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/IAO_0000232`

UBERON_8480038 `http://purl.obolibrary.org/obo/UBERON_8480038`

UBERON_8480040 `http://purl.obolibrary.org/obo/UBERON_8480040`

seminal fluid `http://purl.obolibrary.org/obo/UBERON_0006530`