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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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term request: common carotid artery #1141

Closed markengelstad closed 9 years ago

markengelstad commented 9 years ago

the root of the carotid arterial system no discrete class for 'common carotid artery' alone exist in uberon.

carotid artery plus branches was deprecated (and different than common carotid artery)

https://en.wikipedia.org/wiki/Common_carotid_artery

cmungall commented 9 years ago

Ignore my previous comment, I misread.

UBERON:0001530 ! common carotid artery plus branches

cmungall commented 9 years ago

Is this what you need?

UBERON:0005396 ! carotid artery segment

Apologies for the over-zealous formality in the names. New suggestions welcome

markengelstad commented 9 years ago

that's close -- in ontobee, i can see this class, which is best (UBERON_0010197) Trunk of Common Carotid Artery

But that class doesn't show up in the hp-edit.owl (github) version of UBERON

What does that mean?

cmungall commented 9 years ago

@nicolevasilevsky can you help Mark with the module generation in HP?

nicolevasilevsky commented 9 years ago

Sebastian showed me how to change my catalog file so it imported all of Uberon, @markengelstad can you ask him how to do it? Or I can help you MIREOT the term after I'm back from vacation.

cmungall commented 9 years ago

I think @drseb may be unavailable for a few weeks...

We really need to make a youtube video showing how this is done! I was just showing @pbuttigieg how to do this for ENVO. But every ontology is a little different.

drseb commented 9 years ago

@cmungall I will start working tomorrow again, but not with full force.

@cmungall @markengelstad @nicolevasilevsky I hope I can join the call on thursday. Let's discuss it then. It is not as easy with the github structure as it was with googlecode structure. (We do not have a catalog-xml per default)

RDruzinsky commented 9 years ago

Care must be taken when defining the carotid arterial system in Uberon, to avoid being anthropocentric. Although humans and many other mammals have paired common carotids, the left and right common carotids arise from different arteries. In some mammals, there is an unpaired "common" common carotid that arises from the aorta that branches into symmetrical left and right common carotids, but this is just one of the many patterns seen in mammals. To me, what is very interesting is that many of the variations seen in humans are the same patterns seen in the other mammalian clades.

Robert E. Druzinsky, Ph.D. Clinical Associate Professor Dept. of Oral Biology College of Dentistry University of Illinois at Chicago 801 S. Paulina Chicago, IL 60612 druzinsk@uic.edu

Office: 312-996-0406 Lab: 312-996-0629 Website: www.peerj.com/RobertDruzinsky

On Thu, Oct 22, 2015 at 3:37 PM, Mark Engelstad notifications@github.com wrote:

Closed #1141 https://github.com/obophenotype/uberon/issues/1141.

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/1141#event-443107672.

uberon commented 9 years ago

Yes, I think this area needs some work. The current representation is based on Kardong. However, any mistakes are probably mine, and the overview in Kardong may miss out key variations.

What I would like to do is to assemble the correct branching graph for a number of key species and to obtain the correct uberon generalization from these

On 26 Oct 2015, at 6:17, Robert Druzinsky wrote:

Care must be taken when defining the carotid arterial system in Uberon, to avoid being anthropocentric. Although humans and many other mammals have paired common carotids, the left and right common carotids arise from different arteries. In some mammals, there is an unpaired "common" common carotid that arises from the aorta that branches into symmetrical left and right common carotids, but this is just one of the many patterns seen in mammals. To me, what is very interesting is that many of the variations seen in humans are the same patterns seen in the other mammalian clades.

Robert E. Druzinsky, Ph.D. Clinical Associate Professor Dept. of Oral Biology College of Dentistry University of Illinois at Chicago 801 S. Paulina Chicago, IL 60612 druzinsk@uic.edu

Office: 312-996-0406 Lab: 312-996-0629 Website: www.peerj.com/RobertDruzinsky

On Thu, Oct 22, 2015 at 3:37 PM, Mark Engelstad notifications@github.com wrote:

Closed #1141 https://github.com/obophenotype/uberon/issues/1141.

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/1141#event-443107672.

Reply to this email directly or view it on GitHub: https://github.com/obophenotype/uberon/issues/1141#issuecomment-151130133