What's the Preferred Term - 1/31/2011

Recap from last week: #1 - "Mesosoma" was chosen as the preferred term for the class "HAO:0000576: The tagma that is composed of the prothorax, mesothorax and the metapectal-propodeal complex" by two people (Keller & Ohl). We agree and have made the pertinent changes. #2 - For the class "HAO:0000662: The shortest anatomical line that connects the compound eye and the lateral ocellus" we had no suggestions for a preferred term. Thus, we will choose the preferred term.

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For this week:

ID: HAO:0000794

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/544

DEFINITION: The carina that delimits anterlaterally the mesocoxal depression.

TERM OPTIONS: postpectal carina, postpectal flange, precoxal carina of mesopleuron, ventral mesopleural carina

HOMONYM NOTES: none

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ID: HAO:0001100

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/4762

DEFINITION: The anatomical cluster composed of the second valvifer and the third valvula.

TERM OPTIONS: gaine, legescheide, oblonge platte, sägescheide, sawsheath, scheide

HOMONYM NOTES: none

- 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.

What's the Preferred Term - 1/24/2011

Recap from last week: #1 - For the class "HAO:0000990: The projection that is median, membraneous and is located distally on the ventral margin of the tarsomere", there was a consensus to use just "plantula" (instead of "tarsal plantula"). We have made the changes to mx and the glossary. #2 - Although the label "strigil" is attached to several classes (homonym), none have it as the preferred term. Since there were suggestions to use "strigil" for "HAO:0000102: The anatomical cluster that is composed of the probasitarsus and calcar" we have made the change. However, since it is a common homonym, the term should be looked at more closely in the future.

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For this week:

ID: HAO:0000662

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/3848

DEFINITION: The shortest anatomical line that connects the compound eye and the lateral ocellus.

TERM OPTIONS: ocellar ocular line, ocellocular line, ocular ocellar length, ocular ocellar line

HOMONYM NOTES: none

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ID: HAO:0000576

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/473

DEFINITION: The tagma that is composed of the prothorax, mesothorax and the metapectal-propodeal complex.

TERM OPTIONS: alitrunk, mesosoma, trunk

HOMONYM NOTES: "trunk" is also used for HAO:0000182 "The anatomical cluster that is composed of the whole organism but which excludes the antennae, legs and wings." (current preference = "body")

- 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.

What's the Preferred Term - 1/19/2011

**Starting this week we will be posting 2 WTPT questions at a time. This should hasten our completion of the exercise and expand the subject matter each week to broaden interest.**

Recap from last week: For the concept "The area that is median and located between the notauli" two people (Jennings & Tucker) chimed-in and said they preferred either "medial lobe of mesoscutum", "median mesonotal lobe", or "median mesoscutal lobe". These terms are very similar, but we chose "medial lobe of mesoscutum" since it is published and specific to the mesoscutum (not just mesonotum). However, "lobe" has a particular meaning in the ontology and, for future reference, this should probably be termed an "area".

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For this week:

ID: HAO:0000990

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1040

DEFINITION: The projection that is median, single and located distally on the ventral margin of the tarsomere.

TERM OPTIONS: euplantula, plantar lobe, Sohlenbläschen, tarsal plantula, tarsal pulvillum

HOMONYM NOTES: none

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ID: HAO:0000102

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1765

DEFINITION: The anatomical cluster that is composed of the probasitarsus and calcar.

TERM OPTIONS: antenna cleaner, antennal cleaning organ, strigil, strigilis

HOMONYM NOTES: **strigilis** is also used as a term for HAO:0001222 "The anatomical cluster that is composed by transverse rows of setae on the median (posterior, inner) surface of the metabasitarsus."; **strigil** is also used as a term for HAO:0001106 "The basitarsus that is located on the protarsus."

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

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.

HAO published in PLoS ONE

Our official, peer-reviewed introduction to the HAO was published today in PLoS ONE:
Yoder MJ, Mikó I, Seltmann KC, Bertone MA, Deans AR (2010) A Gross Anatomy Ontology for Hymenoptera. PLoS ONE 5(12): e15991. doi:10.1371/journal.pone.0015991

HAO/BioSynC Meeting

Most of the participants of the meeting. For a list/labeled group photo please visit the HOA wiki.

Two weeks ago (October 13th-17th) we held our much anticipated HAO/BioSynC meeting, “Integrating ontologies with biodiversity research: an example from Hymenoptera and the EOL”, here in Raleigh, NC and we are very pleased with the outcome. The meeting consisted of a number of national and international researchers, brought in to 1) add and discuss content specific to Hymenoptera anatomy and 2) develop ways in which we can integrate our ontology into a number of web services, including the EOL (which funded the meeting). Information about the participants and some specifics of the meeting (that will be evolving with some post-meeting details) can be found here. Overall we had some great discussions (arguments?) about a number of issues during both the morphology section (Days 1-3) and the technical section (Days 4 & 5).

During the morphology section we focused on both building the ontology and teaching users how to navigate and contribute. We talked about issues such as whether/how to choose preferred terms, how to define wing veins and head areas (e.g. the limits of the gena), and did a lot of work in taxon-focused groups to audit the present HAO content. Though we encountered some difficulties, e.g. trying to detach ourselves from thinking about homology, we made clear progress and at least sowed the seeds for upcoming HAO domain/content meetings.

Morphology section

The technical section consisted of a smaller group of bioinformaticians and ontologists. We heard from David Osumi-Sutherland about the Drosophila gross anatomy ontology and from Gary Merrill on some philosophies behind building a good ontology. We also talked about integrating the HAO with the EOL and other online services (Morphster, Plazi, etc.) while brain-storming future directions and enrichment of the ontology.

Technical section

All of the days concluded with great dinners and drinks, which inspired even more conversation – either extending the day’s arguments or going into more light-hearted, dinner subjects. All-in-all the meeting went great and we really appreciate and thank all of the participants for their enthusiasm and expertise throughout the meeting!

Dinner at Mitch's Tavern

BBQ at Andy Deans's house

Dinner at Sitti

pulse

Matt Y. added a nice feature to the HAO's public interface - the pulse. It's an RSS feed that gives you the latest edits to the HAO. Check it out (to the right, as well)!

HAO pulse RSS

Visualizing our new data

We'll be submitting the HAO announcement paper this week, and have been tuning up the visualization code. First we have a part_of tree for the thorax illustrating the oldest "sensu" used for the a class/concept. Darker colors are older, the names of the internal concepts and the year of the reference are plotted on the tree &bsp; The zoomed detail of the second tree illustrates the number of muscles attached to the class/concept, hotter represent more attachments.  The count used is at the tip of the internal branch. The process needs some tweaking but for a first attempt on both we think it's pretty cool.