obo-arthropod-anatomy — Discussion of arthropod anatomy development

[Obo-arthropod-anatomy] If there is anyone still on this mail list, consider joining us on slack

[Chris M. <cjm...@lb...>]

Hi all

I am not sure whatever happened to the arthropod ontology effort. We never
got it added to OBO, but there are a number of more isolated insect anatomy
ontologies.

If you are interested there is active discussion of anatomy ontologies on
the #uberon channel in the OBO slack and you are welcome to join us here:

https://join.slack.com/t/obo-communitygroup/shared_invite/zt-yrraovr8-mOX24e_7WfgbpayiJdJ0~Q

[Obo-arthropod-anatomy] Fwd: [OBOFoundry/OBOFoundry.github.io] Request for COLL prefix and PURL (#610)

[Chris M. <cjm...@lb...>]

Hi, anyone have any time to provide guidance to Luis?

Specifically members of obo-arthropod community, how should this be 
coordinated with ARTHRO and Uberon?

Forwarded message:

> From: luis-gonzalez-m <not...@gi...>
> To: OBOFoundry/OBOFoundry.github.io 
> <OBO...@no...>
> Cc: Subscribed <sub...@no...>
> Subject: [OBOFoundry/OBOFoundry.github.io] Request for COLL prefix and 
> PURL (#610)
> Date: Thu, 03 May 2018 20:52:27 -0700
>
> I want to request a community feedback for the following ontology:
>
> Title: Collembola Anatomy Ontology
>
> Requested Prefix: COLL
>
> PURL user ID: Antonio_007
>
> Link:  https://github.com/luis-gonzalez-m/Collembola
>
> Tracking: https://sourceforge.net/p/collembola
>
> Description:
> The porpuse of ontology is applying it to the anatomical and 
> morphological description in the taxonomy of Collembola and generating 
> a template for the species description in this taxon
>
> contact email: lag...@un...
>
>
>
> -- 
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly or view it on GitHub:
> https://github.com/OBOFoundry/OBOFoundry.github.io/issues/610

Re: [Obo-arthropod-anatomy] [Obo-discuss] prefix request OArCS (oarcs) - Ontology of Arthropod Circulatory Systems

[Chris M. <cjm...@lb...>]

Thanks Matt

ID Space seems fime. Go ahead and make the pull request, we will just 
delay merging until after the 2 week comment period.

btw, it's probably a good idea to stop calling the Arthropod Anatomy 
Ontology "AAO", since this was the name of the Amphibian Anatomy 
Ontology. Even though this is deprecated and merged into Uberon, we 
can't reuse the same ID space. Why not generalize and include velvet 
worms and tardigrades, giving you a PAAO! (Pan-Arthropod Anatomy 
Ontology).

On 11 Dec 2015, at 13:18, Matt Yoder wrote:

> Hi all,
>
> I'd like to request the 'oarcs' namespace for the Ontology of
> Arthropod Circulatory Systems.  The ontology is being detailed in a
> paper to be submitted (very) shortly.  We are working out the
> technical details for deployment, it is presently deposited here:
> https://github.com/aszool/oarcs. See the link for some scope related
> details as well, including the responsible parties.
>
> This is a domain-specific ontology (circulatory systems) that will
> ultimately fit either into the AAO as an include or directly into
> UBERON.
>
> Chris M. and Foundary folks- I almost have a oarcs.yml configuration
> ready for you. I will make a pull request as soon as I hear that the
> namespace is acceptable.
>
> Thanks all,
> Matt Yoder
>
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[Obo-arthropod-anatomy] Anatomical term of the week: gears

[Chris M. <cjm...@lb...>]

http://phenomena.nationalgeographic.com/2013/09/12/this-insect-has-gears-in-its-legs/

Re: [Obo-arthropod-anatomy] [Obo-anatomy] TrON

[Matt Y. <dia...@gm...>]

--- sorry, didn't hit reply-all ---

I don't remember (but I may have missed it) TrON contacting the
broader arthropod community at all.    Best to ask István and David
O-S where things stand with respect to Arthropod related ontologies- I
know István just got back from Germany, and that some new projects
were spun up.

Related and important- I do know that there is a post-doc position
open to being working on a Neuropteran ontology (another
holometabolous insect order).  That effort will be talking to the
Arth/HAO folks a lot (lead by Shaun Winteron systematics group).  If
folks know good insect morphologists with a systematics bent looking
for a post-doc they should contact Shaun.

Matt Y.


On Fri, Aug 9, 2013 at 6:06 PM, Chris Mungall <cjm...@lb...> wrote:

> I think the tribolium folks may have claimed the coolest AO name:
>
> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0070695
>
> How is the TrON effort being integrated with the Arthropod anatomy
> ontology? And how is the Coleoptera ontology (COLEO?) coming along?
>
>
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>
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[Obo-arthropod-anatomy] TrON

[Chris M. <cjm...@lb...>]

I think the tribolium folks may have claimed the coolest AO name:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0070695

How is the TrON effort being integrated with the Arthropod anatomy
ontology? And how is the Coleoptera ontology (COLEO?) coming along?

Re: [Obo-arthropod-anatomy] Meeting this Friday

[Andy D. <ad...@gm...>]

Thanks, David. The doc shows up for me as 'read only'. Possible to make it
editable?
Andy

On Tue, Aug 14, 2012 at 8:24 AM, dosumis <do...@gm...> wrote:

> Hi all,
>
> Just a quick email to remind you all that we have an arthropod anatomy
> ontology meeting scheduled for this Friday at 5pm BST (GMT+1).  I've been
> working on a simplified, OBO release of the arthropod AO.  I'd like to
> discuss the possibility of extending this using the more generic classes
> from HAO (and perhaps from the Drosophila AO) to make a general template
> for building insect anatomy ontologies.
>
> Google docs agenda is here:
>
>
> https://docs.google.com/document/d/1fUTSLxeoxGJQtNwWTIlO74tfXuU2chbKm5MnK0k8Uss/edit#
>
> Not much in it yet.  Please feel free to add whatever you want.
>
> Cheers,
>
> David
>
>
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>


-- 
Andrew R. Deans
Department of Entomology
Pennsylvania State University
501 ASI Building
University Park, PA 16802 USA

Phone: +1 814 863 2863
FAX: +1 814 865 3048
skype: ardeans

[Obo-arthropod-anatomy] Meeting this Friday

[dosumis <do...@gm...>]

Hi all,

Just a quick email to remind you all that we have an arthropod anatomy ontology meeting scheduled for this Friday at 5pm BST (GMT+1).  I've been working on a simplified, OBO release of the arthropod AO.  I'd like to discuss the possibility of extending this using the more generic classes from HAO (and perhaps from the Drosophila AO) to make a general template for building insect anatomy ontologies. 

Google docs agenda is here:

https://docs.google.com/document/d/1fUTSLxeoxGJQtNwWTIlO74tfXuU2chbKm5MnK0k8Uss/edit#

Not much in it yet.  Please feel free to add whatever you want.

Cheers, 

David

[Obo-arthropod-anatomy] pretarsus - leg segment or tarsomere; part of tarsus or distal to tarsus?

[David Osumi-S. <dj...@ge...>]

http://code.google.com/p/arthropod-anatomy-ontology/issues/detail?id=4
== Classification and partonomy parent of pretarsus ==

Snodgrass has the pretarsus as a highly derived leg segment, distal to the tarsus.  The main reference for Drosophila melanogaster on this (Ferris, 1950 in Demerec, 1950) follows Snodgrass.  However, HAO treats the pretarsus as part of the tarsus, classified as an 'anatomical cluster*' rather than a tarsomere as other sections of the tarsus are.
...
More details on ticket.  Please respond there.
Cheers,
David

David Osumi-Sutherland, PhD
Curator/ Ontologist
FlyBase / Virtual Fly Brain
Department of Genetics,
University of Cambridge,
Downing Street,
Cambridge, CB2 3EH, UK
Tel: +44 (0)1223 333 963
Fax: +44 (0)1223 766 732

[Obo-arthropod-anatomy] interesting wing homolog

[Chris M. <cjm...@lb...>]

interesting case for the arthropod anatomy ontology:

http://www.nature.com/nature/journal/v473/n7345/full/nature09977.html

[Obo-arthropod-anatomy] Announce: Major updates to the HAO

[Matt <dia...@gm...>]

Dear all,

The HAO team is happy to announce a major update to the Hymenoptera
Anatomy Ontology is now available at the OBO Foundry.  Some highlights
include:

* A near doubling of the number of terms
* Nearly complete coverage for hymenopteran musculature
* Introduction of the relation, 'attached_to', used in conjunction
with musculature
* Many new synonyms and their corresponding references
* Complete genus-differentia definitions for all core terms (i.e.
terms without correspondence in other ontologies)
* Significant input from community members that attended a HAO
workshop (see wiki), and via email correspondence

This release is paralleled with major updates to the underlying
web-based architecture used to build the HAO, much of which is
documented in a paper in the final stages of review: Yoder, M.J., I.
Miko, K.C. Seltmann, M.A. Bertone and A.R. Deans. 2010. A Gross
Anatomy Ontology for Hymenoptera. PLoS ONE.

Find out more about the HAO at http://hymao.org, in particular note
the recently activated listserv, and new functionality on our public
web front-end.

A special thanks to everyone who has provided feedback during the
update period. We look forward to getting feedback on the ontology,
and hope you find it useful!

Regards,
The HAO Team