search

ZFIN / zebrafish-anatomical-ontology

Ontology describing the anatomy of Danio rerio from a single cell to adult fish. The namespace of the ontology is zebrafish_anatomical_ontology the prefix is ZFA. Updates to ZFA are released every other month. A subset of the ZFS http://purl.obolibrary.org/obo/zfs.obo is packaged with this ontology.
Other
6 stars 6 forks source link

add brain structures #108

Open cerivs opened 11 years ago

cerivs commented 11 years ago

stria medullaris bed nucleus of the stria medullaris (BNSM) from ZDB-PUB-120709-5

Original comment by: cerivs

cerivs commented 11 years ago

In case it's useful, here's the uberon def (not vetted - the assumption this is conserved across vertebrrates comes from a setence in Butler & Hodos)

[Term] id: UBERON:0006086 name: stria medullaris def: "The major afferent track to the habenula from the telencephalon (particularly in the septal side) in all vertebrates[Butler and Hodos]." [ISBN10:0471888893] synonym: "stria habenularis" EXACT [NIF_GrossAnatomy:birnlex_1066] synonym: "stria medullaris of thalamus" EXACT [NIF_GrossAnatomy:birnlex_1066, FMA:62080] synonym: "stria medullaris thalami" EXACT PLURAL [NIF_GrossAnatomy:birnlex_1066] synonym: "stria medullaris thalamica" EXACT [NIF_GrossAnatomy:birnlex_1066] synonym: "stria medullaris (wenzel - wenzel)" EXACT [NIF_GrossAnatomy:birnlex_1066] xref: FMA:62080 ! stria medullaris of thalamus xref: NIF_GrossAnatomy:birnlex_1066 ! Stria medullaris xref: BM:Die-SM ! stria medullaris of thalamus is_a: UBERON:0013199 {source="FMA"} ! stria of neuraxis relationship: part_of UBERON:0001893 ! telencephalon relationship: present_in_taxon NCBITaxon:7742 {source="ISBN10:0471888893"} ! Vertebrata relationship: overlaps UBERON:0001904 ! habenula xref: SCTID:362368004 ! Entire stria medullaris property_value: external_definition "Stria medullaris of thalamus is a slender fiber bundle on the dorsal surface of the diencephalon which terminates posteriorly in the habenular nuclei[FMA:62080]." xsd:string {source="FMA:62080"}

The only resource I know with the bed nuclei is: http://neurolex.org/wiki/Category:Bed\_nucleus\_of\_the\_stria\_medullaris neurolex is by default mammal-centric. It's a wiki so if you have interesting phylogenetic facts you could add them here.

Original comment by: cmungall

cerivs commented 11 years ago

Additional reference: ZDB-PUB-090814-14

Original comment by: nobody

cerivs commented 11 years ago

Additional reference: ZDB-PUB-090914-27 (Mueller and Wulliman 2009; An evolutionary interpretation of teleostean forebrain anatomy).

Original comment by: nobody

cerivs commented 11 years ago

ZDB-PUB-090814-14 The GAD67-positive (dorsal) entopeduncular nucleus (EN  former ENd) appears to be anatomically separate from the GAD67-negative bed nucleus of the stria medullaris (BNSM), which was formerly called the ventral part of the entopeduncular nucleus (ENv)

Right now we have ventral entopeduncular nucleus of ventral telencephalon which may need to be renamed. Topic needs more research.

Original comment by: cerivs

cerivs commented 11 years ago

Original comment by: cerivs

cerivs commented 9 years ago

Two additional nuclei (the "reticular thalamic nucleus" and the "intercalated nucleus") are described in ZDB-PUB-090814-14:

"The anterior thalamic nucleus is laterally bordered by a distinct GAD67-expressing cell population, which we interpret as the previously unidentified reticular thalamic nucleus (RTN) of teleosts. Furthermore, we identified a GAD67-positive thalamic nucleus, the intercalated nucleus (IC), which is sandwiched between the GAD67-negative dorsal (DP) and central posterior (CP) thalamic nuclei."

Original comment by: nobody