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openMetadataInitiative / openMINDS_instances

Well defined metadata instances for selected schemas of the openMINDS metadata models.
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New 'UBERONParcellation' suggestions #104

Open archgogo opened 2 years ago

archgogo commented 2 years ago

We forward these term suggestions that EBRAINS received from data providers: <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

name | suggestedTerminology | interlex ID | Notes | definition -- | -- | -- | -- | -- basal ganglia | UBERONParcellation | http://uri.interlex.org/base/ilx_0101102 |   | Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum. stratum moleculare | UBERONParcellation |   |   |   stratum cellulare | UBERONParcellation |   |   |   early visual area V3A | UBERONParcellation |   | definition on KG is odd | Visual area V3 is a term used to refer to the region of cortex located immediately in front of V2. V3 communicated directly with the respective dorsal and ventral subsystems of V2. early visual area V4v | UBERONParcellation |   | definition on KG is odd | Visual area V4 is a midtier cortical area in the ventral visual pathway. It is crucial for visual object recognition and has been a focus of many studies on visual attention. dorsal early visual area V3 | UBERONParcellation |   | definition on KG is odd | Dorsal processing stream of V3 invovled in processing motion ventral early visual area V3 | UBERONParcellation |   | definition on KG is odd | Ventral processing stream of V3 invovled in color sensitivity dorsal secondary visual area V2 | UBERONParcellation |   | definition on KG is odd | Dorsal stream of secondary visual area V2 ventral secondary visual area V2 | UBERONParcellation |   | definition on KG is odd | Ventral stream of secondary visual area V2 dorsal primary visual area V1 | UBERONParcellation |   | definition on KG is odd | Dorsal stream of secondary visual area V1 ventral primary visual area V1 | UBERONParcellation |   | definition on KG is odd | Ventral stream of secondary visual area V1 parietal area V6A | UBERONParcellation |   | definition on KG is odd | Area V6A is a visuomotor area of the dorsomedial visual stream which is involved typically in the control of arm reaching movements in both monkeys and humans cortical layers | UBERONParcellation (all the six layers are already added) | http://uri.interlex.org/base/ilx_0770104 | Interlex page is empty | The layers or laminae of cortex homotopic regions | UBERONParcellation? |   |   | same regions in the two brain hemispheres

UlrikeS91 commented 2 years ago

My feedback to the list:

term add as UBERONParcellation? UBERON ID reason
basal ganglia yes http://purl.obolibrary.org/obo/UBERON_0002420
stratum moleculare differently http://purl.obolibrary.org/obo/UBERON_0007640 "hippocampus stratum lacunosum moleculare" exists, I think this is the same
stratum cellulare no? can't find it in UBERON and not sure what else it would be called, @lzehl or @tgbugs maybe?
early visual area V3A no? can't find it in UBERON
early visual area V4v no? can't find it in UBERON
dorsal early visual area V3 no? can't find it in UBERON
ventral early visual area V3 no? can't find it in UBERON
dorsal secondary visual area V2 no can't find it in UBERON, "secondary visual cortex" exists
ventral secondary visual area V2 no can't find it in UBERON
dorsal primary visual area V1 no can't find it in UBERON, only layer-specific terms exists not topographical
ventral primary visual area V1 no can't find it in UBERON, only layer-specific terms exists not topographical
parietal area V6A no? can't find it in UBERON, "posterior parietal cortex" exists
cortical layers differently http://purl.obolibrary.org/obo/UBERON_0002301 "layer of neocortex" is the correct UBERON term; if all were meant, then all separate layers need to be added (e.g. "cortical layer I, http://purl.obolibrary.org/obo/UBERON_0005390)
homotopic regions no not an UBERON term; not sure how we would handle this, @lzehl any thoughts?

All the ones that we can't add as UBERONParcellations can be added as "CustomAnatomicalEntities" instead.

lzehl commented 6 months ago

@tgbugs @UlrikeS91 let's discuss this list