raphe nuclei development

[gocentral]

GO:0021724 ! inferior raphe nucleus development [part_of: "rhombencephalic reticular formation development"] [subclass: "neural nucleus development"] [DEF: "The process whose specific outcome is the progression of the inferior raphe nucleus over time, from its formation to the mature structure."] GO:0021725 ! superior raphe nucleus development [part_of: "rhombencephalic reticular formation development"] [subclass: "neural nucleus development"] [DEF: "The process whose specific outcome is the progression of the superior raphe nucleus over time, from its formation to the mature structure."]

the terms are not defined, there are no authoritative references for the terms. There are no annotations to the term.

inferior and superior are not listed here: http://en.wikipedia.org/wiki/Raphe\_nuclei (although the median RN is also called the "superior central nucleus)

The only AO to have these is ZFA/TAO:

ZFA:0000366 ! inferior raphe nucleus [SYNONYM: "posterior raphe nucleus" (exact)] [xref: TAO:0000366] [xref: ZFIN:ZDB-ANAT-011113-290] ZFA:0000440 ! superior raphe nucleus [SYNONYM: "anterior raphe nucleus" (exact)] [xref: TAO:0000440] [xref: ZFIN:ZDB-ANAT-011113-365]

are these teleost specific structures? If so, consider adding a taxon constraint.

Reported by: cmungall

Original Ticket: geneontology/ontology-requests/8297

[gocentral]

Chris,

Perhaps we can find an expert at the CL-INCF meeting in two weeks to give us an answer to this question. I suspect we ought to be careful about limiting these terms to teleost structures before consulting with an actual neuroscientist.

Thanks,

Alex

Original comment by: addiehl

[gocentral]

Thanks Alex- I'll wait to hear back from the meeting then.

thanks, Becky

Original comment by: rebeccafoulger

[gocentral]

Hi Alex,

Please see below, we were wondering if anything came back from that meeting about Chris' request?

Thanks, Jane, Becky, Paola

Original comment by: paolaroncaglia

[gocentral]

• assigned_to: nobody --> paolaroncaglia
• labels: --> neurobiology

Original comment by: paolaroncaglia

[gocentral]

Hi Chris and Alex,

Please see the discussion below. Did you have a chance to consult with a neuroscientist to find out if inferior and superior raphe nuclei are teleost-specific structures or not? Otherwise, I might email Doug Howe at ZFIN to ask for advice.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

A PubMed search doesn't allow to sort out strictly for "inferior/superior raphe nucleus". I've found a 1982 paper about "inferior raphe nuclear complex" in cats (PMID: 7171992), but not much else.

Wikipedia lists 7 raphe nuclei, including "inferior central nucleus" and "superior central nucleus". Based on the figures and the references in the Wikipedia page, it's clear that the page refers to mammals. However, following its links to "inferior central nucleus" and "superior central nucleus", and the links to NIF from therein, it appears that these terms may be synonyms for: Sublingual nucleus (inferior central nucleus, nucleus of Roller) and median raphe nucleus (also referred to as superior central nucleus).

Apparently, in the last 20-30 years, different names have been used for different species, and this adds to the confusion. But I haven't found direct references to the precise term "inferior/superior raphe nucleus" in mammals anywhere. I've also asked one of the Neurobiology professors at my previous affiliation, and he didn't have an answer to that either. Since ZFIN provides precise definitions for these terms, I'd opt for adding a taxon constraint for teleosts. Raphe nuclei are clearly present in other organisms, but it's not clear if the nomenclature listed in Wikipedia refers to non-mammals as well. I feel that we might need an up-to-date and more exhaustive reference before we're able to create terms for this area of the ontology.

I'm going to email Doug Howe at ZFIN and ask him to have a look at this, and if he too feels that "inferior/superior raphe nuclei" belong to teleosts only, I'll add a taxon rule and close this item for now.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

HI All, I've had a cruise around for info, and I agree the anatomy in this area is a mess across species. My hunch is that the zebrafish "raphe nucleus" is equivalent to the "paramedic raphe nucleus" in other species. The zebrafish "superior raphe nucleus" is the same as "superior central nucleus" in other species. The zebrafish "inferior raphe nucleus" is the same as "inferior central nucleus" in other species. But thats just slightly more than a gut feeling based on what I've read. Based on what these structures do physiologically, I seriously doubt they are teleost specific structures. I think the nomenclature is just super messy and inconsistent across species. Will probably require some significant reading to sort out what cell types are in the structures to figure out which ones are homologous to which before names might have a hope of being standardized. For the moment I suggest NOT placing a taxon constraint other than limiting it to vertebrates perhaps.

Original comment by: doughowe

[gocentral]

Ha...thanks to autocomplete..my 'paramedian' was converted to 'paramedic'..sorry!

Original comment by: doughowe

[gocentral]

I think the names inferior and superior raphe are used in to describe nuclei that have different names in mammals because of the different brain morphology. Mammalian brains curve in on themselves more then zebrafish. I wasn't able to determine which mamalian nuclei were homologous when I defined the terms. PMID 19003874 has some information about the types of neurons in the zebrafish raphe nuclei and compares them to the raphe of other organisms. I agree with Doug that these nuclei are probably not zebrafish specific just.

Original comment by: cerivs

[gocentral]

Thanks to all for your comments - The terms are currently restricted to Eukaryotes. As per Doug's suggestion, I will restrict them further to Vertebrates, but not to Teleosts.

The terms currently have no synonyms. I'll add the following as broad synonyms: GO:0021724 ! inferior raphe nucleus development: "inferior central nucleus development", "posterior raphe nucleus development"; GO:0021725 ! superior raphe nucleus development: "superior central nucleus development", "anterior raphe nucleus development". (The "posterior" and "anterior" wordings are exact synonyms to the anatomical structures in ZFIN, but I'd rather have them as broad synonyms in GO, based on the confused nomenclature across species.)

I'll also add PMID: 19003874 as a Dbxref to both terms.

Unless you have additional comments, I'll proceed as above and then close the item. You may re-open it if/when additional references can be provided to clarify the nomenclature.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

All done: Added taxon constraint (to Vertebrates), xrefs and synonyms to GO:0021724 inferior raphe nucleus development and GO:0021725 superior raphe nucleus development Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed-accepted

Original comment by: paolaroncaglia