Friday, August 26, 2011

RCN working group meeting - Boulder, CO

Last June the Phenotype RCN organized a set of concurrent working group meetings—focused on arthropod anatomy, vertebrate anatomy, plant phenotypes, and the informatics associated with phenotype data and ontologies—that were very graciously hosted by by Google's office in Boulder, CO. The meeting agenda and subsequent notes are already posted on the Phenotype RCN website, though I noticed today that the arthropod anatomy working group summary never got posted!

The longer version is available as a Google doc. Here's the short version: We are working towards developing two higher-level anatomy ontologies, one for classes in common across Arthropoda and another for Insecta. We've identified a series of potential classes, proposed candidate definitions for notoriously difficult ones (what's a 'segment'?!), identified some tools we can use to facilitate communication (an email list, Dropbox, Google docs, Git), development (mx, Protégé) and visualization (C-Map, Vue), and identified several highly motivated people to collaborate with.

I'll also use this opportunity to thank our host at Google's Boulder office, John Day-Richter, for hosting what ended up being an inspirational, productive meeting! Our next group meeting is at the National Evolutionary Synthesis Center in Durham, NC. Watch for more details!

Monday, August 8, 2011

What's the Preferred Term - 8/8/2011

Recap from last post: For the first class, "HAO:0000647: The line that extends submedially along the mesoscutum and corresponds to the median border of the site of origin of the first mesopleuro-mesonotal muscle" we had no responses so we will keep "notaulus" as the preferred term. For the second class, "HAO:0001044: The area that is located dorsally of the ventral margin of toruli and ventrally of the anterior ocellus medial to the inner margins of the eye and malar line", Burks and Jennings suggested "frons".

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For this week:

CLASS: HAO:0001022: The foramen that is located on the head in which the radicle positioned.

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/611

TERM OPTIONS: alveolus, antennal foramen, antennal insertion, antennal socket, torulus

HOMONYM NOTES: "antennal socket" and "torulus" are both also used for the class "HAO:0000103: The rim that surrounds the antennal foramen."

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CLASS: HAO:0000362: The anatomical cluster that is composed of flagellomeres located between the pedicel and clava or the distalmost anellus and clava.

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/485

TERM OPTIONS: funicle, funiculus, funiculus of antenna

HOMONYM NOTES: none

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- WHAT TERMS (from the above options) would you use to refer to these concepts?
- ARE THERE terms that we are missing for these concepts?

Please remember to send replies to the emailing list (hao@lists.hymenopterists.org) and not just the original sender.

If you would like to reply to the questions above or have comments, questions, suggestions, etc., please sign up for the HAO email list and post your views there. We will not be moderating WTPT discussions here on the blog.

Tuesday, August 2, 2011

What's the Preferred Term - 8/2/2011

Recap from last post: For the first class "HAO:0000319: The pit that is located on the upper face dorsal to the intertorular carina and corresponds internally to a conical apodeme and not the tentorium" we had no responses and will thus maintain "pore facial" as the preferred term. For the second class "HAO:0000326: The scrobe that is located on the mesopleuron into which the mid leg fits when pressed against the mesosoma", Krogmann suggested a new label, "mesofemoral depression" as the preferred one. Thus we have added the label and it is now the preferred one.

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For this week:

ID: HAO:0000647

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/601

DEFINITION: The line that extends submedially along the mesoscutum and corresponds to the median border of the site of origin of the first mesopleuro-mesonotal muscle.

TERM OPTIONS: notaular line, notaulix, notaulus

HOMONYM NOTES: none

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ID: HAO:0001044

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/655

DEFINITION: The area that is located dorsally of the ventral margin of toruli and ventrally of the anterior ocellus medial to the inner margins of the eye and malar line.

TERM OPTIONS: frons, frontal area, supra-antennal area, upper face

HOMONYM NOTES: "frons" is also used for the class "HAO: 0001523: The area that is situated between the epistomal line and the anterior ocellus and limited laterally by the inner margin of compound eye"

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- WHAT TERMS (from the above options) would you use to refer to these concepts?
- ARE THERE terms that we are missing for these concepts?

Please remember to send replies to the emailing list (hao@lists.hymenopterists.org) and not just the original sender.

If you would like to reply to the questions above or have comments, questions, suggestions, etc., please sign up for the HAO email list and post your views there. We will not be moderating WTPT discussions here on the blog.