some more questions about arteries/trunks

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Alan Ruttenberg

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Jul 24, 2010, 8:09:34 PM7/24/10
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(1) If I understood things, an artery in the FMA sense is a tree, and
includes all the branches (transitively). A trunk, on the other hand
is a regional part of tree that I thought is a part that doesn't
include branches - i.e. has a tube shape.

However there are items like Thyrocervical trunk which has branch
relations to arteries. Since branch implies part, that would
contradict that an arterial trunk is disjoint from an artery, since a
trunk with branches would be a (sub)tree.

--

(2) There are a number of terms, particularly in the arteries, that
are called something like "Variant xxxx". In addition there is a class
Variant Artery, which isn't the parent of all these terms. An example
is Variant superficial cervical artery. What does variant mean in
these cases? A full list is at the end of the message.

--

(3) While browsing I came across and absent parts, so I searched for
any more. Here is the list. I presume these should be deprecated?

Absent thoracic duct
Absent left common carotid artery
Absent ostium of left coronary artery
Absent ostium of right coronary artery
Absent cisterna chyli
Absent left coronary artery
Absent right coronary artery

--

(4) In an earlier message (e.g. http://tinyurl.com/2fs7zue) I
discussed adding axioms that "left" things have parts that are only
"left things" and similarly for right.

There are apparently legitimate cases in the vascular tree that don't
follow this rule. An example is Basilar artery, which is a branch of
both the left and right vertebral arteries, and which in turn branches
out into e.g. both the Left and Right posterior cerebral artery.

Would it be possible to identify the set of such legitimate cases so
that I can modify the left/right axioms to allow them?

I note that there is not an attributed part relationship that marks
the basilar artery as a shared part. Should there be?

-Alan


List of terms with "Variant" in their name, that are subclasses of
Region of vascular tree

Branch of variant right bronchial artery
Left variant dorsal scapular artery
Left variant superficial cervical artery
Left vertebral artery (variant)
Middle lobe branch of variant right bronchial artery
Middle lobe branch of variant right first bronchial artery
Middle lobe branch of variant right second bronchial artery
Right anterior basal branch of variant right bronchial artery
Right anterior branch of variant right bronchial artery
Right apical branch of variant right bronchial artery
Right lateral basal branch of variant right bronchial artery
Right lateral branch of variant right bronchial artery
Right lower lobe branch of variant right bronchial artery
Right lower lobe branch of variant right first bronchial artery
Right lower lobe branch of variant right second bronchial artery
Right medial basal branch of variant right bronchial artery
Right medial branch of variant right bronchial artery
Right posterior basal branch of variant right bronchial artery
Right posterior branch of variant right bronchial artery
Right superior branch of variant right bronchial artery
Right upper lobe branch of variant right bronchial artery
Right upper lobe branch of variant right first bronchial artery
Right upper lobe branch of variant right second bronchial artery
Right variant dorsal scapular artery
Right variant superficial cervical artery
Segmental branch of variant right bronchial artery
Thyroidea ima artery (variant)
Trunk of circumflex humeral artery (variant)
Trunk of variant atrial branch of left coronary artery
Trunk of variant coronary artery
Variant artery
Variant atrial branch of left coronary artery
Variant branch of right coronary arterial tree
Variant bronchial artery
Variant coronary artery
Variant dorsal scapular artery
Variant pulmonary artery
Variant right bronchial artery
Variant right first bronchial artery
Variant right second bronchial artery
Variant right third bronchial artery
Variant segmental branch of left pulmonary artery
Variant segmental branch of pulmonary artery
Variant segmental branch of right pulmonary artery
Variant segmental vein
Variant subsegmental branch of left pulmonary artery
Variant subsegmental branch of pulmonary artery
Variant subsegmental branch of right pulmonary artery
Variant superficial cervical artery
Variant supraduodenal artery
Variant systemic artery
Variant third left pulmonary vein

Christine Golbreich

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Jul 25, 2010, 5:34:57 AM7/25/10
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Tout ceci ressemble curieusement aux idees de notre article

cdt

--

--

--

-Alan

--
Christine


Please do not print this e-mail unless you really need to. Wasting
paper costs trees and releases carbon into the atmosphere.

Alan Ruttenberg

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Jul 25, 2010, 6:08:53 AM7/25/10
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Hi Christine,

In which sense? Because we are both working on DL representations or
because you dealt with some of the issues around arteries, variants,
and absents that I raise in this message?

I have read both papers, though it's possible that I've missed
something that would help with the issues I'm raising, and, if so, I
would be grateful for you bringing it to my attention.

Best,
Alan

mej...@comcast.net

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Jul 26, 2010, 11:38:42 AM7/26/10
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----- Original Message -----
From: "Alan Ruttenberg" <alanrut...@gmail.com>
To: "fma-owl-2009" <fma-ow...@googlegroups.com>
Sent: Saturday, July 24, 2010 5:09:34 PM
Subject: some more questions about arteries/trunks

(1) If I understood things, an artery in the FMA sense is a tree, and
includes all the branches (transitively). A trunk, on the other hand
is a regional part of tree that I thought is a part that doesn't
include branches - i.e. has a tube shape.

However there are items like Thyrocervical trunk which has branch
relations to arteries. Since branch implies part, that would
contradict that an arterial trunk is disjoint from an artery, since a
trunk with branches would be a (sub)tree.

OM: I agree, this is incorrect.


--

(2) There are a number of terms, particularly in the arteries, that
are called something like "Variant xxxx". In addition there is a class
Variant Artery, which isn't the parent of all these terms. An example
is Variant superficial cervical artery. What does variant mean in
these cases? A full list is at the end of the message.

This was an experiment that has not been addressed properly (and forgotten about !). It's a good time to revisit these and assign them properly in the hierarchy.


--

(3) While browsing I came across and absent parts, so I searched for
any more. Here is the list. I presume these should be deprecated?

Absent thoracic duct
Absent left common carotid artery
Absent ostium of left coronary artery
Absent ostium of right coronary artery
Absent cisterna chyli
Absent left coronary artery
Absent right coronary artery

OM: Yes, for now, until we have the appropriate method to accommodate them and other variations.


--

(4) In an earlier message (e.g. http://tinyurl.com/2fs7zue) I
discussed adding axioms that "left" things have parts that are only
"left things" and similarly for right.

There are apparently legitimate cases in the vascular tree that don't
follow this rule. An example is Basilar artery, which is a branch of
both the left and right vertebral arteries, and which in turn branches
out into e.g. both the Left and Right posterior cerebral artery.

OM: This is a tricky one. The right and left sides are connected by the basilar artery and therefore makes me wonder if there is just one arterial tree with a right side and a left side.


Would it be possible to identify the set of such legitimate cases so
that I can modify the left/right axioms to allow them?

OM:WIll get back to you on this.


I note that there is not an attributed part relationship that marks
the basilar artery as a shared part. Should there be?

OM: Good point. I need to revisit this.

Thanks!
Onard

Chris Mungall

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Jul 26, 2010, 11:56:23 AM7/26/10
to fma-ow...@googlegroups.com

On Jul 26, 2010, at 8:38 AM, mej...@comcast.net wrote:

> (3) While browsing I came across and absent parts, so I searched for
> any more. Here is the list. I presume these should be deprecated?
>
> Absent thoracic duct
> Absent left common carotid artery
> Absent ostium of left coronary artery
> Absent ostium of right coronary artery
> Absent cisterna chyli
> Absent left coronary artery
> Absent right coronary artery
>
> OM: Yes, for now, until we have the appropriate method to
> accommodate them and other variations.

Why do these need to be accommodated in the FMA at all? These should
be in a phenotype ontology.

mej...@comcast.net

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Jul 26, 2010, 1:27:27 PM7/26/10
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OM: You have to clarify this one for me. Variant structures are subtypes of FMA types, right?
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