Requesting CPATH related OBA traits

[matentzn]

ID	Label
NBO:0000351	body coordination
NBO:0000342	limb coordination
NBO:0000346	upper limb coordination
NBO:0000345	lower limb coordination
NBO:0000339	motor coordination
NBO:0000347	gross motor coordination
NBO:0000348	fine motor coordination
NBO:0000341	eye-hand coordination
OBA:XXXXXX1	whole organism stability
OBA:XXXXXX2	facial muscle performance
OBA:XXXXXX3	peripheral nervous system function
OBA:XXXXXX4	knee joint functionality
OBA:XXXXXX5	ankle joint functionality
OBA:XXXXXX6	tendon of biceps brachii functionality
OBA:XXXXXX7	brachioradialis functionality

@Daniel-Olson

Can you provide:

1. Uberon terms (with labels and Ids) for all of these?
2. PATO qualities (with labels and ids) for all of these?

I will deal with politics around NBO.

[Daniel-Olson]

@matentzn I couldn't find comparable terms in Uberon for fine-motor/eye-hand and two of the motor terms from NBO are already being used by Uberon.

<style> </style>

ID	Label	Uberon_ID	Uberon_Label	PATO_ID	PATO_Label
NBO:0000351	body coordination	UBERON:0000468	multicellular organism	PATO:0000188	coordination
NBO:0000342	limb coordination	UBERON:0002101	limb	PATO:0000188	coordination
NBO:0000346	upper limb coordination	UBERON:0002102	forelimb	PATO:0000188	coordination
NBO:0000345	lower limb coordination	UBERON:0002103	hindlimb	PATO:0000188	coordination
NBO:0000339	motor coordination	NBO:0000339	motor coordination	PATO:0000188	coordination
NBO:0000347	gross motor coordination	NBO:0000347	gross motor coordination	PATO:0000188	coordination
NBO:0000348	fine motor coordination	x	x	PATO:0000188	coordination
NBO:0000341	eye-hand coordination	x	x	PATO:0000188	coordination
OBA:XXXXXX1	whole organism stability	UBERON:0000468	multicellular organism	PATO:0015026	stability
OBA:XXXXXX2	facial muscle performance	UBERON:0001577	facial muscle	PATO:0001509	functionality
OBA:XXXXXX3	peripheral nervous system function	UBERON:0000010	peripheral nervous system	PATO:0001509	functionality
OBA:XXXXXX4	knee joint functionality	UBERON:0001485	knee joint	PATO:0001509	functionality
OBA:XXXXXX5	ankle joint functionality	UBERON:0001488	ankle joint	PATO:0001509	functionality
OBA:XXXXXX6	tendon of biceps brachii functionality	UBERON:0008188	tendon of biceps brachii	PATO:0001509	functionality
OBA:XXXXXX7	brachioradialis functionality	UBERON:0011011	brachioradialis	PATO:0001509	functionality

[matentzn]

Excellent @Daniel-Olson

couldn't find comparable terms in Uberon for fine-motor/eye-hand and two of the motor terms from NBO are already being used by Uberon.

1. If the term does not specify a specific anatomical system, we can link it to "UBERON:anatomical entity"
2. eye-hand coordination is an interesting case. @rays22 do you have an idea how to best represent these?

gross motor coordination

All the values in this column should be Uberon - what anatomical system is meant when we say "motor coordination"? Skeletal system? Muscular system? Any anatomical part? Any muscle? Any limb?

When you are done with the above, can you (maybe with Emily's help) make a PR adding these new terms in the appropriate columns here: https://github.com/obophenotype/bio-attribute-ontology/blob/master/src/patterns/data/default/entity_attribute.tsv

Note that it is important that the diff of that file really only encompasses your added rows (not all rows, because for example, you change the line endings or something).

[Daniel-Olson]

@matentzn the motor/eye-hand coordination terms were originally subclasses of upper/lower limb coordination but as the mapping template evolved they were deprecated. So we can map them broadly to the terms below for potential future use or it might make the most sense to just leave them out for now and worry about them if they ever resurface?

<style> </style>

ID	Label	Uberon_ID	Uberon_Label	PATO_ID	PATO_Label
NBO:0000351	body coordination	UBERON:0000468	multicellular organism	PATO:0000188	coordination
NBO:0000342	limb coordination	UBERON:0002101	limb	PATO:0000188	coordination
NBO:0000346	upper limb coordination	UBERON:0002102	forelimb	PATO:0000188	coordination
NBO:0000345	lower limb coordination	UBERON:0002103	hindlimb	PATO:0000188	coordination
NBO:0000339	motor coordination	UBERON:0025525	motor system	PATO:0000188	coordination
NBO:0000347	gross motor coordination	UBERON:0025525	motor system	PATO:0000188	coordination
NBO:0000348	fine motor coordination	UBERON:0025525	motor system	PATO:0000188	coordination
NBO:0000341	eye-hand coordination	UBERON:0001062	anatomical entity	PATO:0000188	coordination
OBA:XXXXXX1	whole organism stability	UBERON:0000468	multicellular organism	PATO:0015026	stability
OBA:XXXXXX2	facial muscle performance	UBERON:0001577	facial muscle	PATO:0001509	functionality
OBA:XXXXXX3	peripheral nervous system function	UBERON:0000010	peripheral nervous system	PATO:0001509	functionality
OBA:XXXXXX4	knee joint functionality	UBERON:0001485	knee joint	PATO:0001509	functionality
OBA:XXXXXX5	ankle joint functionality	UBERON:0001488	ankle joint	PATO:0001509	functionality
OBA:XXXXXX6	tendon of biceps brachii functionality	UBERON:0008188	tendon of biceps brachii	PATO:0001509	functionality
OBA:XXXXXX7	brachioradialis functionality	UBERON:0011011	brachioradialis	PATO:0001509	functionality

[matentzn]

I think this is reasonable (leaving them out for now). The mapping also looks good. I think you are ready to make a PR now, as described in my previous comment!

[Daniel-Olson]

Thanks @matentzn! I have a few questions:
How do I handle the IDs?

1. Do the NBO IDs remain verbatim or should they be changed to OBA IDs?
2. I looked through the other bio-attribute PRs and I see that they all have OBA IDs but I didn't see a place to reserve IDs for new terms. Do I just need to come up with IDs that don't already exist or do I just commit the PR with 'OBA:xxxxxx" IDs and allow the OBA folks to assign correct IDs?
3. Lastly the contributing.md file recommends creating detailed requests for new terms with definitions and PMIDs. Can I go straight to a PR without this step?
   Thanks!

[matentzn]

Do the NBO IDs remain verbatim or should they be changed to OBA IDs?

Change to OBA IDs.

I looked through the other bio-attribute PRs and I see that they all have OBA IDs but I didn't see a place to reserve IDs for new terms. Do I just need to come up with IDs that don't already exist or do I just commit the PR with 'OBA:xxxxxx" IDs and allow the OBA folks to assign correct IDs?

Make a PR here: https://github.com/obophenotype/bio-attribute-ontology/blob/master/src/ontology/oba-idranges.owl, copy an existing range and adopt it to assign yourself one as well. Once the PR is there, I can fix it for you, so don't worry about making mistakes!

Lastly the contributing.md file recommends creating detailed requests for new terms with definitions and PMIDs. Can I go straight to a PR without this step?

No its fine, the terms you request are pretty standard OBA, no need for a detailed issue. Thanks!

[rays22]

2. eye-hand coordination is an interesting case. @rays22 do you have an idea how to best represent these?

gross motor coordination

All the values in this column should be Uberon - what anatomical system is meant when we say "motor coordination"? Skeletal system? Muscular system? Any anatomical part? Any muscle? Any limb?

The NBO:0000339 motor coordination definition looks correct to me, because motor coordination is a process. It is this process that should bear the quality, not the anatomical entities. The anatomical entities like the hand, eye limbs are just participants in the process.
PATO:0000188 coordination is an organismal quality. Our hands or limbs just participate in the process.
The 'anatomical entity - coordination' pairs other than the 'UBERON:0000468 | multicellular organism | PATO:0000188 | coordination' pair do not look right to me.

Anatomical entities can be bearers of the other PATO qualities in the table above.

[matentzn]

@rays22 thank you for your excellent and careful review. How would you define upper limb motor coordination trait?

[rays22]

@rays22 thank you for your excellent and careful review. How would you define upper limb motor coordination trait?

@matentzn , I would define it as a process quality:

NBO:0000346 upper limb coordination PATO:0000001 quality

[matentzn]

Ok. it seems unfortunate that we cant use Uberon terms to define these, but maybe it is ok for now.

Could you redefine the coordination traits using the pattern you suggest?

[rays22]

Could you redefine the coordination traits using the pattern you suggest?

Yes, I could. I would use the quality PATO:0015002 process efficacy.

[matentzn]

Interesting! Ok! Let's do it, and see how others react when they come across this, and maybe check MP, ZP and HP if they make use of the NBO terms in their defs. It seems we should be compatible with whatever they are doing :) THANKS!