Fixes #1901 Oenocyte definition #1954
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Fixes #1901 Oenocyte definition. Discussion of edits in the ticket.
| @@ -7412,7 +7412,8 @@ SubClassOf(obo:CL_0000486 obo:CL_0002520) | |||
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| # Class: obo:CL_0000487 (oenocyte) | |||
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| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:bf") Annotation(oboInOwl:hasDbXref "PMID:11171397") obo:IAO_0000115 obo:CL_0000487 "A large secretory cell found in clusters underlying the epidermis of the abdominal segments of larval abdominal segments.") | |||
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:bf") Annotation(oboInOwl:hasDbXref "PMID:11171397") Annotation(oboInOwl:hasDbXref "PMID:24397521") Annotation(oboInOwl:hasDbXref "PMID:34208190") Annotation(oboInOwl:hasDbXref "https://www.merriam-webster.com/dictionary/oenocyte") obo:IAO_0000115 obo:CL_0000487 "A secretory cell of ectodermal origin in connection with the fat bodies and tracheae. This cell may have important functions in fatty acid and hydrocarbon metabolism.") | |||
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Regarding this comment:
"... I agree with keeping the taxon restriction to arthropods instead of tightening it to only insects."
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I recommend reflecting this in the text definition. It may be inferred by the reference to "fat bodies" (if they are only found in Arthropoda), but I recommend making the restriction explicit.
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Unsure if only
SubClass Of 'in taxon' some Arthropodaconstitutes a taxon restriction. I don't think a protocol for declaring taxon restrictions has been finalised, but I have seen annotations using "present in taxon" and SubClass of axioms using the 'only in taxon' object property. -
Unclear what "in connection with" means in the sentence... in what way is the cell type connected to these structures?
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Will defer to @gouttegd on content, but the definition may benefit from adding more specific differentia. Cell is noted as secretory, but unclear what it secretes.
PMID:34208190 provides description of morphology and other descriptors to consider.
Also suggest to make note that anatomical location varies across species. Unsure if the two anatomical structures in the present definition were arbitrarily selected.
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Thank you for your comments, @bvarner-ebi.
I recommend reflecting this in the text definition. It may be inferred by the reference to "fat bodies" (if they are only found in Arthropoda), but I recommend making the restriction explicit.
Agree, I have added it.
Unsure if only SubClass Of 'in taxon' some Arthropoda constitutes a taxon restriction. I don't think a protocol for declaring taxon restrictions has been finalised, but I have seen annotations using "present in taxon" and SubClass of axioms using the 'only in taxon' object property.
'only in taxon' is more appropriate.
Unclear what "in connection with" means in the sentence... in what way is the cell type connected to these structures?
Probably associated would be more correct. The meaning is that there is cross-talk between them.
Also suggest to make note that anatomical location varies across species. Unsure if the two anatomical structures in the present definition were arbitrarily selected.
Yes, it is good to note the variability on localisation as well. The fat body and the trachea are structures that extends along the larva, so they are not describing an anatomical location in this case.
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Yes, it is good to note the variability on localisation as well.
Don't see this reflected in updated definition.
" ... that is associated with... "
Consider less vague language for a definition.
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Don't see this reflected in updated definition.
It's in the comment: An oenocyte is highly variable in shape, anatomical location and size across species.
| @@ -7412,7 +7412,8 @@ SubClassOf(obo:CL_0000486 obo:CL_0002520) | |||
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| # Class: obo:CL_0000487 (oenocyte) | |||
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| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:bf") Annotation(oboInOwl:hasDbXref "PMID:11171397") obo:IAO_0000115 obo:CL_0000487 "A large secretory cell found in clusters underlying the epidermis of the abdominal segments of larval abdominal segments.") | |||
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:bf") Annotation(oboInOwl:hasDbXref "PMID:11171397") Annotation(oboInOwl:hasDbXref "PMID:24397521") Annotation(oboInOwl:hasDbXref "PMID:34208190") Annotation(oboInOwl:hasDbXref "https://www.merriam-webster.com/dictionary/oenocyte") obo:IAO_0000115 obo:CL_0000487 "A secretory cell of ectodermal origin in connection with the fat bodies and tracheae. This cell may have important functions in fatty acid and hydrocarbon metabolism.") | |||
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24397521") Annotation(oboInOwl:hasDbXref "PMID:34208190") rdfs:comment obo:CL_0000487 "An oenocyte is highly variable in shape and size across species. This cell typically forms clusters. In adults, oenocytes tend to be smaller but more numerous, while in larvae they are larger and form smaller clusters. While oenocytes have been found in arachnids and crustaceans, they have been most abundantly described in insects.") | |||
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After cursory review, did not see mention of variation of shape across species.
Semantics consideration: "This cell typically forms clusters."
Consider "This cell type is typically organized in clusters."
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Did not find resource to back up statement on variability in shape across species.
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Did not find resource to back up statement on variability in shape across species.
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The more I think about it, the less I am comfortable with the idea of packing so many details in the definitions and comments of CL terms. There’s a high risk of ending up saying things that are simply not true across the taxonomic branch where the term is supposed to be valid. There’s a reason why the definitions I write for CL are often much less precise than the ones I would normally write for FBbt.
For example, there are oenocytes that are neither circular or ovoidal (https://doi.org/10.1146%2Fannurev-ento-011613-162056, Figure 1). And one can argue about the “typicality” of the organisation in clusters, when Chapman suggests that there may be as many species in which they do form clusters as species in which they don’t (“In Lepidoptera and Orthoptera they form clusters in the body cavity, while in Homoptera, Hymenoptera and some Diptera they are dispersed and embedded in the fat body”).
Under the open world assumption, we should stick to only state what we know for sure is true and applicable to all the concerned species (which sometimes may be… “not much”). For the rest, better not to say anything rather than saying something wrong.
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(And yes, I know, the Chapman book is behind a paywall. Unfortunate, for sure, but I am not willing to skip on using reference books just because of that.)
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Thank you for your comment. I agree to make it more vague to avoid making the term class or species specific, when in this case it should describe the whole phylum. I still want to make a comment about the high variability of this cell.
(And yes, I know, the Chapman book is behind a paywall. Unfortunate, for sure, but I am not willing to skip on using reference books just because of that.)
I agree that if an article/chapter is relevant, it should be used even if it is behind a paywall. The problem is that our organisation is not subscribed to as many publishing groups as some universities, and we cannot access them unless it is quoted or there is a screenshot in the ticket/PR (not sure if that suppose copyright infringements).
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I still want to make a comment about the high variability of this cell.
Do you have access to the Makki, Cinnamon, and Gould (2014) paper? Between Figure 1 (which illustrates the morphological diversity) and the explicit statement that “the size, number, and anatomical locations of oenocytes all vary widely between insect species”, I would say it is enough to back up the high variability claim.
The problem is that our organisation is not subscribed to as many publishing groups as some universities, and we cannot access them
I understand, and I know I am in a privileged position here – I have never had access to so many journals than in the past two years, courtesy of my university. And since sometimes full-time access is done “transparently”, I may not even always realise that the link I provide is not accessible for everyone else. :(
unless it is quoted or there is a screenshot in the ticket/PR (not sure if that suppose copyright infringements).
I would assume that quoting a paragraph fits under “fair use”, though obviously the usual disclaimer “I Am Not A Lawyer” applies.
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Do you have access to the Makki, Cinnamon, and Gould (2014) paper? Between Figure 1 (which illustrates the morphological diversity) and the explicit statement that “the size, number, and anatomical locations of oenocytes all vary widely between insect species”, I would say it is enough to back up the high variability claim.
Sorry, I didn't express it very clear. I meant that I prefer to have a comment about the high variability than removing it altogether. After all, having this high variability is a characteristic.
I understand, and I know I am in a privileged position here – I have never had access to so many journals than in the past two years, courtesy of my university. And since sometimes full-time access is done “transparently”, I may not even always realise that the link I provide is not accessible for everyone else. :(
It is not a problem, and I guess "the good" side of us having limited access is that we can provide more accessible literature. But again, I believe a relevant reference should be used even if it is behind a paywall.
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Hi @ANiknejad, this PR is ready to be merged. Do you agree with the content? |
Fixes #1901 Oenocyte definition. Discussion of edits in the ticket.