vasculature

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GO currently has a term 'vasculature development' (GO:0001944) which is a child of 'organ development'...but GO has no term "vascular system development' as a child of 'system development'.

A few questions follow from this:

1. Should a new term exist for 'vascular system development', and if so...how is it different from 'vasculature development'?

2. If both terms were to exist..should they be related...and how?

3. In fish, the vascular system develops from a structure named the 'vascular cord', formed by aggregation of angioblast cells along the embryonic midline. If a mutation disrupts formation of this 'vascular cord', would that gene be annotated to a new term 'vascular cord development' (with what parentage?), or would it be annotated to 'vascular system development'..or maybe 'vasculature development'?

David:

since the system development term is new, I think that we just haven't moved vasculature development to the right place yet. Can you think of components of the vascular system that are not considered vasculature?

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/3326":https://sourceforge.net/p/geneontology/ontology-requests/3326

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Doug writes--

I guess this sort of leads into another question then. If 'vasculature development' had a synonym 'vascular system development', would the term 'vascular development' then be an is_a child of both 'organ development' and 'system development'? Doesn't that mean that the vascular system is simultaneously an organ and a system? Leveraging Midori's "I'm not an expert" clause...I would hazard a guess that something cannot be both an organ and a system at the same time...?

-Doug

David writes back----

O.K. So I am no expert either, but I turn to the anatomical dictionary. [i]cardiovascular system [MA:0000010] ---[p]blood ---[p]blood vessel ---[p]cardiovascular system endothelium ---[p]heart ---[p]lymphatic vessel ---[p]outflow tract

Therefore we should have cardiovascular system development in the GO. new GO structure:

system development ; GO:0048731 ---[i] cardiovascular system development ; GO:new ------[p] heart development ; GO:0007507 ------[p] vasculature development ; GO:0001944 ---------[i] blood vessel development ; GO:0001568 ---------[i] lymph vessel development ; GO:0001945

I don't think we can add blood development because it is not really appropriate for GO. We can add the endothelia and outflow tract as parts of each anatomical component as needed.I also think we should change the term string of lymph vessel development to be lymphatic vessel development. According to the anatomical dictionary, a heart is an organ, but vasculature is not. Currently, the vasculature has no is_a parent in the anatomical dictionary. I have asked our AD curator about this and she is thinking about it.

Original comment by: ukemi

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That works for me.

'cardiovascular system development' would be is_a 'system development'

Would you retain 'vasculature development' is_a 'organ development'?

-Doug

Original comment by: doughowe

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I would be inclined not to becasue it is not consistent with the anatomy. Let's wait and see what Terry decides to do in the anatomical dictionary.

David

Original comment by: ukemi

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Hmm...Based on Alex's comment that the lymphatic and cardiovascular systems are both vascular systems...what about this?

system development ; GO:0048731 ---[i]vascular system development; GO:0001944 ------[i]cardiovascular system development ; GO:new ---------[p] heart development ; GO:0007507 ---------[p] blood vessel development ; GO:0001568 ---------[p] vascular cord development ; GO:New ------[i]lymphatic system development ; GO:0001945 ---------[p] lymph vessel development ; GO:New

I've renamed 'lymph vessel development' (GO:0001945) to the 'system develpment' format, and added a new child specifically for development of the lymph vessels themselves.

I've also renamed 'vasculature development' (GO:0001944) to the 'system developoment' format, and added 'cardiovascular system dev.' and 'lymphatic system dev.' as children.

Then I also added the source of all this angst..'vascular cord development'...as a child of 'cardiovascular system dev.'

What about that?

Original comment by: doughowe

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Doug,

I like your term hierarchy. Would lymph node development ; GO:0048535 then be a part_of lymphatic system development?

-- Alex

Original comment by: addiehl

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This won't work because lymphatic vessels are a part of the cardiovascular system.I think we should let the anatomy experts work this out. I just spoke with Terry. She plans to make a term called vascular system (synonymous with our term vasculature) to be a part of the cardiovascular system. Vascular system will be an is_a system. Vascular system will have two is_a children, blood vessel and lymph vessel.These anatomical terms describe the entirety of blood vessels and lymph vessels. We will then have:

system development ; GO:0048731 ---[i]cardiovascular system development ; GO:new ------[p] heart development ; GO:0007507 ------[p] vascular cord development ; GO:New ------[p] vascular system development ; GO:0001944 ---------[i]blood vessel development ; GO:0001568 ---------[i]lymph vessel development ; GO:0001945 ---[i]vascular system development ; GO:0001944

I can't find cardiovascular cord in your anatomy, so I'm not sure where it should be placed.

Original comment by: ukemi

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Should circulatory system development be a synonym for vasculature development as well?

Many definitions of organ are based on functionality, that the organ has a specific function required for the organism. Systems are groups of organs, so if there were no children then vasculature could be considered an organ.

However, lymph development and blood vessel development are the children, so by this definition, vasculature development would be system development whereas lymph development and blood vessel development could be children of organ development.

This is confounded by the fact that 1) in the future one could imagine that vein and artery development would be children of blood vessel development, and 2) many people use "system" very losely, like the the venous system, etc.

The human anatomy FMA gets around this by using "set of organ parts" where veins are a set of organ parts, and "organ system," such as the cardiovascular system (it gets even more complicated with organ system subdivisions, organ segments, etc.)

I am playing a bit of devil's advocate here....So where do we draw the line between what is an organ and what is a system? It doesn't seem as if this level of complexity would improve GO, or at least it wouldn't improve usability....

Original comment by: mellybelly

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I was considering the lymphatic system to be separate from the cardiovascular system. If they are part_of, then fine.

We are currently working to add a term for 'vascular cord' to our anatomy. I think it will end up as a child (direct or indirect) of 'cardiovascular system development'.

So the last structure David posted would probably suffice. -Doug

Original comment by: doughowe

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>>My Comments are interspersed:

Should circulatory system development be a synonym for vasculature development as well?

>> Yes, I think so.

Many definitions of organ are based on functionality, that the organ has a specific function required for the organism. Systems are groups of organs, so if there were no children then vasculature could be considered an organ.

>>This was considered by Terry, but she chose not to go this route.

However, lymph development and blood vessel development are the children, so by this definition, vasculature development would be system development whereas lymph development and blood vessel development could be children of organ development.

>>No, because blood vessel and lymphatic vessel are is_a children of vascular system. Therefore, they actually describe the blood vessel system and lymph vessel system.

This is confounded by the fact that 1) in the future one could imagine that vein and artery development would be children of blood vessel development, and 2) many people use "system" very losely, like the the venous system, etc.

>> Yes, I think this might be why Terry chose the approach she did.

The human anatomy FMA gets around this by using "set of organ parts" where veins are a set of organ parts, and "organ system," such as the cardiovascular system (it gets even more complicated with organ system subdivisions, organ segments, etc.)

>> Yes, this is a very rigorous treatment. But I think introducing all of the types such as "organ cluster", etc. into the development portion of the GO would add unecessary complexity. It would also be difficult to reject a type called "blood vessel" because while reading the scientific literature experiments often report results about things like the development of blood vessels without further specifying their kind.

I am playing a bit of devil's advocate here....So where do we draw the line between what is an organ and what is a system? It doesn't seem as if this level of complexity would improve GO, or at least it wouldn't improve usability....

>>Yes, the devil raises these points frequently, and they are good ones. There are many times when we simply need to arbitrarily create boundaries to classify things. One of my favorite and very frustrating ones is "when does a structure begin to exists?" This is important to us because it defines when development of something begins. In this discussion, from an embryologists point of view, it makes sense to me to classify anatomical types via organs and systems because the development of these things often occur in a coordinated fashion. So, timing-wise systems tend to develop together, but there are also many similarities between the development of unrelated organs. For example, at the gross level, the induction of organ primirdia often share very similar processes. I realise I am dodging the issue a bit but... I think where the cutoff is between an organ and a system is really not that important because the relationships between all the types should exist and the graph should reflect the reality despite what we decide to call things. The one interesting complication that is added is the cut-off does determine where is_a and part_of relationships are are found. This has big effects on navigating the graph via relationships. So we need to decide how we would like to see things classified. For a biologist is it more useful "truthful" to view the totality of blood vessels as an is_a system or as an is_a organ. That's where we take on the resonsibility of representing what people outside of the GO think. In this specific case of organ vs. system, it is easier for us in the GO because we let the anatomy folks decide.:)

David

Original comment by: ukemi

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I don't think this throws any wrenches into the topic at hand but plant biologists frequently refer to 'vasculature' and 'vascular tissue' (and 'vascular system' - but that's a topic for the Plant Ontology folks) to refer to the same things in plants, that is, "plant tissue that is specialized for conducting sap. It comprises phloem, which conveys chiefly dissolved sugars, and xylem, which conveys water and dissolved minerals.".

Since we do have the term:

"vascular tissue development (sensu Tracheophyta)" GO:0010087 (is_a tissue development)

this might need a synonym of 'vascular development (sensu Tracheophyta)'. I don't think that this term should be related to the vascular development terms being discussed right now, since (stating the obvious) plants don't have a cardiovascular system. (Jen, I can open another SF item for this, if you like.)

Pesky plants...

Tanya

Original comment by: tberardini

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Hi,

I am planning to implement the results of this soon, as it seems to be mostly resolved. David, do you know if Terry has finished the anatomy structure on this? It seems to me that the plant terms will fit in very nicely so that is fine.

Thanks,

Jen

Original comment by: jenclark

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• assigned_to: jenclark --> nobody

Original comment by: jenclark

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I have implemented this almost exactly as in David's comment from 2006-04-27 20:02:33 GMT, with minor adjustments (and definitions) based on UBERON. New terms are: cardiovascular system development GO:0072358 circulatory system development GO:0072359 vascular cord development GO:0072360

UBERON has oodles more parts that could be captured in GO, but since they've never been part of this request, people can open new SF items as and when they need terms for additional anatomical bits.

m

Original comment by: mah11

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• assigned_to: nobody --> gomidori
• status: open --> closed-accepted

Original comment by: mah11

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• Group: Plant Ontology --> None

Original comment by: cooperl09