Map cell_shape in big trait table

[cmungall]

Split from #2

1 spirochete 1 ring 1 triangular 1 cell_shape 2 tailed 3 branced 3 spindle 3 star 4 irregular 5 flask 7 square 11 disc 12 fusiform 60 pleomorphic 289 vibrio 328 filament 400 spiral 402 coccobacillus 1563 coccus 3794 NA 4035 bacillus

I think the majority should map to PATO. We may want to consider making OBA terms for some

[hrshdhgd]

Shape itself maps to PATO:0000052. This is what I found from OLS. Note: I know you'd like a single ontology and preferably PATO (or OBA) but for the ones, I couldn't find PATO (or OBA), I've included MICRO just as a placeholder. One term was in OBA (cell shape). So we may explore the option of making OBA terms for the (blanks) and MICRO terms?

@cmungall , manual curation for these too? or OGER?

Shape	CUI
bacillus	MICRO:0000401
coccus	MICRO:0000402
coccobacillus	MICRO:0000366
spiral	PATO:0000404 (coiled?)
filament	MICRO:0000042 (cell filament?)
disc	PATO:0001874 (discoid?)
vibrio	MICRO:0000414 (vibrioid cell?)
pleomorphic	PATO:0001356
square	PATO:0000413
fusiform	PATO:0002400
flask	-
star	PATO:0002065 (star-shaped)
spindle	PATO:0001409 (spindle-shaped)
triangular	PATO:0001875
irregular	PATO:0001781 (irregular thickness); PATO:0002141 (irregular density); MICRO:0000333 (irregular cell)
ring	PATO:0002539 (ring-shaped)
branced	PATO:0000402 (brancHed?)
spirochete	-
tailed	PATO:0001880 (caudate?)
cell shape	OBA:0000052

[wdduncan]

How formal do we want to be about defining anaerobe as an organism? The definitions is straight forward (to me at least):

an organism that does not require oxygen for growth

Do we want to add a class anaerobic growth process and add axiom like this:

participates in some anaerobic growth process

Also, how far much detail do we want in defining anaerobic growth process? Minimally, I think it would be something like:

biological process
  - growth process
     - anaerobic growth process

If we wanted, we could formally define anaerobic growth process equivalent to:

growth process and not (has input some oxygen)

This would allow for more general queries that use (or don't use) certain materials as during growth.

[cmungall]

Is this done?

On Thu, Feb 18, 2021, 10:35 marcin joachimiak notifications@github.com wrote:

Closed #4 https://github.com/Knowledge-Graph-Hub/kg-microbe/issues/4.

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[hrshdhgd]

Nodes for shapes with a prefix of 'Shape:' were created. The CURIEs listed above were neither confirmed nor rejected.

[hrshdhgd]

We'll still need direction on how to address this. Is the temporary 'Shape:' prefix okay or do we hard-code the above CURIEs corresponding to the various shapes?

[cmungall]

Let's keep this open while we decide our long term strategy:

• use PATO?
• use MICRO?
• make a new microbial trait ontology

However, for now, it is OK to just do something like what we are doing

However, can you make the CURIEs like this:

microtraits.cell_shape_enum:disc

To correspond to our schema (#13 )