BAO Modeling: Learning 'blood plasma' annotated in Uberon

[linikujp]

Issue by GoogleCodeExporter Saturday May 09, 2015 at 11:32 GMT Originally opened as https://github.com/linikujp/bioassayontology/issues/7

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Reported by Stephan Schurer (with email exchange Anna Gaulton.)

Summary:

-blood qualifies as tissue, or more correctly connecting tissue
-plasma, should be under cell-free (mostly water with protein and some other 
non-cellular substances).
-also import the UBERON terms and you can annotate the specific terms when 
needed. these would go under biology component > anatomical entity

there are also some assays performed in serum, so worth adding this too

double check if there are any other types of fluids needed; most of the others 
are probably ‘organism-based’ assays though (e.g., cerebrospinal fluid) so 
wouldn’t need a format term

BAO contains 'blood plasma' from Uberon and we can also add bloodHowever, I 
understand this is not what you need as for BAO assay format (model system) we 
want a more generic categorySuggest to be consistent with UBERONs 
classification.

Uberon classifies tissue:
anatomical entity > material anatomical entity > anatomical structure > 
multicellular anatomical structure > tissueand blood (and plasma):

anatomical entity > material anatomical entity > portion of organism substance 
> haemolymphatic fluid > blood 

anatomical entity > material anatomical entity > portion of organism substance 
> haemolymphatic fluid > blood plasma(and there are of course other 
definitions, i.e. blood plasma part of some blood)

This classification suggests that assay format for blood and plasma should be 
different from cell-based, cell-free, tissue-based.

May have to come up with a new format; more research needed.

Agree that the bio-distribution assay is organism-based; sounds like 
pharmacology.

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Qiong checked the terms associated with "blood" and "plasma" in our current BAO 
2.0:

topBAOClass->'anatomical entity'->'blood plasma'
topBAOClass->'assay bioassay component'->bioassay->'membrane potential 
assay'->'plasma membrane potential assay'
topBAOClass->'assay biology component'->'anatomical entity'->'blood plasma'
topBAOClass->'assay biology component'->cellular_component->'plasma membrane'
topBAOClass->cellular_component->'plasma membrane'

Original issue reported on code.google.com by chengqiong7@gmail.com on 2 Feb 2015 at 7:15

[linikujp]

Comment by GoogleCodeExporter Saturday May 09, 2015 at 11:32 GMT

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Original comment by chengqiong7@gmail.com on 2 Feb 2015 at 7:36

[sschurer]

Nooooo! This must stay open unless somebody implemented it!!

On Fri, Jan 6, 2017 at 2:14 PM, Caty Chung notifications@github.com wrote:

Closed #7 https://github.com/BioAssayOntology/BAO/issues/7.

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