matentzn
commented
2 years ago First draft of this:
Scroll down to
"Matches involving "Volume"
But I think its a good idea for both of you @rays22 and @dosumis to study the notebook for flaws.
Open dosumis opened 2 years ago
matentzn
commented
2 years ago First draft of this:
Scroll down to
"Matches involving "Volume"
But I think its a good idea for both of you @rays22 and @dosumis to study the notebook for flaws.
dosumis
commented
2 years ago Notebook moved?
matentzn
commented
2 years ago dosumis
commented
2 years ago From meeting (08/06/22): For brain only, we treat all terms as meaning increase in volume of whole structure or of some brain region that is part of it.
cmungall
commented
2 years ago What’s the rationale for this?
Why not have more precise terms and part of links between the volume terms?
It seem really unintuitive to say I have an increased brain volume if my actual brain volume is decreased and there is some small part with an increased volume
Can we at least rename to eg X region volume?
On Wed, Jun 8, 2022 at 5:15 AM David Osumi-Sutherland < @.***> wrote:
From meeting (08/06/22): For brain only, we treat all terms as meaning increase in volume of whole structure or of some brain region that is part of it.
— Reply to this email directly, view it on GitHub https://github.com/obophenotype/bio-attribute-ontology/issues/97#issuecomment-1149837697, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOJXOMUYVWQZYIW5XSLVOCFG3ANCNFSM5WPYE7TA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
The list below are all EFO (measurement) terms with volume in the name. Most of them refer to an AS in Uberon.
From this list:
BUT:
Suggested initial fix:
use pattern with characteristic_of_part_of
volume and characteristic_of_part_of - this classifies volume and characteristic_of some x due to property hieriarchy, but can also classify volume of any part of brain no matter how small, e.g. dendritic spine. # We use this solution for now but make ticket suggesting future better fix:
['volumetric brain MRI', 'caudal middle frontal gyrus volume measurement', 'superior temporal gyrus volume measurement', 'cuneus cortex volume measurement', 'choroid plexus volume measurement', 'dentate gyrus volume measurement', 'thalamus volume', 'inferior temporal gyrus volume measurement', 'parahippocampal gyrus volume measurement', 'hippocampal amigdala transition area volume', 'entorhinal cortical volume', 'infant white matter volume measurement', 'postcentral gyrus volume measurement', 'rostral anterior cingulate cortex volume measurement', 'subiculum volume', 'infant cerebrospinal fluid volume measurement', 'banks of the superior temporal sulcus volume measurement', 'hippocampal CA4 volume', 'precuneus cortex volume measurement', 'nucleus accumbens volume', 'Left ventricular mass to end-diastolic volume ratio', 'white matter volume measurement', 'third ventricle volume measurement', 'lateral orbital frontal cortex volume measurement', 'posterior cingulate cortex volume measurement', 'pars opercularis volume measurement', 'transverse temporal cortex volume measurement', 'mean reticulocyte volume', 'corpus callosum anterior volume measurement', 'superior frontal gyrus grey matter volume measurement', 'hippocampal volume', 'brain volume measurement', 'caudate nucleus volume', 'cerebellar cortex volume measurement', 'kidney volume', 'hippocampal tail volume', 'fusiform gyrus volume measurement', 'corpus collosum mid-posterior volume measurement', 'lingual gyrus volume measurement', 'hippocampal fissure volume', 'brain cortex volume measurement', 'corpus callosum posterior volume measurement', 'corpus callosum mid-anterior volume measurement', 'insular cortex volume measurement', 'amygdala volume', 'medial orbital frontal cortex volume measurement', 'pallidum volume', 'cerebellar volume measurement', 'superior parietal cortex volume measurement', 'spleen volume', 'lateral ventricle volume measurement', 'hippocampal CA3 volume', 'thyroid volume', 'pancreas volume', 'middle temporal gyrus volume measurement', 'granule cell layer dentate gyrus volume', 'superior frontal gyrus volume measurement', 'temporal horn of lateral ventricle volume measurement', 'left atrial volume measurement', 'forced expiratory volume', 'lung volume', 'occipital lobe volume measurement', 'hippocampal CA1 volume', 'grey matter volume measurement', 'caudal anterior cingulate cortex volume measurement', 'isthmus cingulate cortex volume measurement', 'lateral occipital cortex volume measurement', 'infant grey matter volume measurement', 'brain stem volume measurement', 'rostral middle frontal gyrus volume measurement', 'intracranial volume measurement', 'pars orbitalis volume measurement', 'ventral diencephalon volume measurement', 'volumetric bone mineral density', 'fourth ventricle volume measurement', 'parietal lobe volume measurement', 'hippocampus molecular layer volume', 'liver volume', 'corpus callosum central volume measurement', 'temporal lobe volume measurement', 'left inferior lateral ventricle volume measurement', 'putamen volume', 'frontal pole volume measurement', 'infant intracranial volume measurement', 'temporal pole volume measurement', 'mean platelet volume', 'whole-brain volume', 'mean corpuscular volume', 'presubiculum volume', 'pericalcarine cortex volume measurement', 'precentral gyrus volume measurement', 'supramarginal gyrus volume measurement', 'inferior parietal cortex volume measurement', 'paracentral lobule volume measurement', 'urine volume measurement', 'pars triangularis volume measurement']