reticular formation terms

[gocentral]

we have:

....po GO:0030902 ! hindbrain development .....po GO:0021550 ! medulla oblongata development ......po GO:0021723 ! rhombencephalic reticular formation development .......po GO:0021727 ! intermediate reticular formation development .......po GO:0021728 ! inferior reticular formation development .......po GO:0021729 ! superior reticular formation development

(no annotations)

The structures are undefined apart from: GO:0021723 ! rhombencephalic reticular formation development [DEF: "The process whose specific outcome is the progression of the reticular formation over time, from its formation to the mature structure. The reticular formation is a series of brain nuclei located in the medulla oblongata."]

(1) is this statement true: "The reticular formation is a series of brain nuclei located in the medulla oblongata"?

Are there not reticular nuclei in other part of the brain - pons, midbrain?

(2) The term "rhombencephalic reticular formation" is not commonly used in existing AOs.

The FMA has:

.........is_a FMA:77719 ! Reticular formation ..........is_a FMA:62406 ! Midbrain reticular formation [part_of: "Midbrain tegmentum"] ..........is_a FMA:68876 ! Pontine reticular formation [part_of: "Pontine tegmentum"] ..........is_a FMA:72241 ! Medullary reticular formation [part_of: "Medulla oblongata"] *** ..........is_a FMA:77455 ! Reticular formation of spinal cord

We would assume that the one marked *** is equivalent to the structure referenced GO:0021723, since both are in the medulla oblongata.

Consider adding as a synonym.

(3) there are no defs for intermediate, superior or inferior.

There is an intermediate ret. nucleus in FMA and in intermediate ret. formation in ZFA

There is an inferior in ZFA

Reported by: cmungall

Original Ticket: geneontology/ontology-requests/8816

[gocentral]

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

Original comment by: paolaroncaglia

[gocentral]

Hi Chris,

I think that some of the issues here stems from the naming.

....po GO:0030902 ! hindbrain development .....po GO:0021550 ! medulla oblongata development ......po GO:0021723 ! rhombencephalic reticular formation development

hindbrain = rhombencephalon medulla = medulla oblongata, is a part of the hindbrain/rhombencephalon therefore I'd rename GO:0021723 as medullary reticular formation development, with "rhombencephalic reticular formation development" as a broad synonym, and define it as: "The process whose specific outcome is the progression of the medullary reticular formation over time, from its formation to the mature structure. The medullary reticular formation is a series of brain nuclei located in the medulla oblongata." There are indeed reticular nuclei in other parts of the brain (at least in mouse and human - my source is the Allen Brain Atlas and related resources), including, as you say, pons (which is also a portion of the rhombencephalon) and midbrain, but by changing the name and def. of GO:0021723 we should avoid any ambiguity.

As for .......po GO:0021727 ! intermediate reticular formation development .......po GO:0021728 ! inferior reticular formation development .......po GO:0021729 ! superior reticular formation development

based on the anatomical tree structure from the atlas of developing human brain (http://www.brainspan.org), the intermediate reticular nucleus is a part of the medullary reticular formation, so I'd add an exact synonym "intermediate reticular nucleus development" to GO:0021727.

The atlas also lists, as parts of the medullary reticular formation, medullary reticular nucleus, dorsal part (ventral reticular nucleus) medullary reticular nucleus, ventral part (medial reticular nucleus)

I think we have two options here: a) obsolete GO:0021728 and GO:0021729 (still no annotations, and no children) b) keep them, and add the two wordings above as related synonyms, but I wouldn't know which goes where. Actually, since we've established that reticular nuclei (= reticular formations) are located in various portions of the brain, I think that the wordings "inferior reticular formation" and "superior reticular formation" are way too ambiguous. I favor the obsoletion option.

Let me know if you disagree. Otherwise, I'll make these changes after the Biocuration conference and the Easter break. Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Hi Chris,

I've implemented the changes as detailed below (Edited name and def. of GO:0021723 medullary reticular formation development. Added synonym to GO:0021727 intermediate reticular formation development.)

I'll send an obsoletion email out for GO:0021728 and GO:0021729 soon.

Cheers, Paola

Original comment by: paolaroncaglia

[gocentral]

David H. replied to the obsoletion email:

"These might have been terms that were created during the CNS development workshop, which means that the developmental neurobiologists suggested them. Might we just want to specify them as being in the medulla oblongata?"

GO:0021728 and GO:0021729 are is_a children of medullary reticular formation development, so I believe that their location in the medulla oblongata is implicit. Plus, I'm reluctant to append the names with "medullary" or similar, to keep them consistent with their siblings. I couldn't find any reference to reticular nuclei being located in the "inferior" or "superior" section of the medulla, in mouse or human brain atlases. However, Chris writes that "There is an inferior in ZFA" and indeed I can see it if I Google "inferior reticular formation ZFIN", but for some reason ZFIN is unaccessible today. Nobody else replied to the obsoletion email, however, I just found this, from a Professor at California State University: http://www.csuchico.edu/~pmccaffrey/syllabi/CMSD%20320/362unit6.html "The reticular formation is a set of interconnected nuclei that are located throughout the brain stem. Its dorsal tegmental nuclei are in the midbrain while its central tegmental nuclei are in the pons and its central and inferior nuclei are found in the medulla." So presumably GO:0021728 could stay, though I still wouldn't know how to define it any better.

I haven't found good references to a "superior reticular formation". But if the developmental neurobiologists suggested both terms, maybe we could/should leave them both in GO. So, I'm not obsoleting them, and I'm closing this item, but feel free to re-open it if you have any suggestions.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed-works-for-me

Original comment by: paolaroncaglia