Hymenoptera Anatomy Ontology

Introducing the HAO's analyzer, feedback, and API

2011-09-15T16:16:00.000-04:00

Today we're taking the wraps off of two simple, but handy tools that we have developed to encourage wider adoption of the HAO. The first, our "analyzer" is simply a tool that takes a block of text and compares it to labels found in the HAO. This tool is aimed at addressing a commonly seen element of taxonomic revisions: the statements in a Materials and Methods section that indicate where anatomic concepts were first defined or in what context they are being used (e.g. "wing venation is described following the conventions of Smith, 1945). The analyzer allows users to explicitly reference anatomical concepts by providing resolvable URIs for them. It further highlights where potential conflicts may arise, for example, "you're using 'paramere', did you know that 'paramere' many different ways?" (try "paramere" for fun).

The HAO has pretty good lexical coverage, but you'll inevitably find some favorite term that's not included when you deploy the analyzer. When this happens you can use the second new feature, a simple feedback form that notifies the curators regarding improvements, corrections, or additions.

For those of you who are a little hacking-savvy we're also unwrapping the (very) alpha version of our API to the HAO. The API provides the underlying functionality used by the analyzer to your Web applications. Please feel free to provide feedback on the API directly on the wiki.

Finally- note that all of these new components are just core pieces of mx, i.e. they can be adopted for new ontology projects completely unrelated to the HAO, if so desired.

RCN working group meeting - Boulder, CO

2011-08-26T20:30:00.000-04:00

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!

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

2011-08-08T09:22:00.001-04:00

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.

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

2011-08-02T15:38:00.000-04:00

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

-------------------------------------------------

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.

2011-07-25T10:27:00.002-04:00

Recap from last post: For the first class, "HAO:0000889: The area that is located proximally on the scape, is limited distally by a constriction and bears proximally the basal knob" we had no responses, so we will keep "radicle" as the preferred label. Both Fernández-Triana and Jennings suggested "malar sulcus" for the second class - since it is already preferred we will keep that label as it is.

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For this week:

ID: HAO:0000319

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/4166

DEFINITION: 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.

TERM OPTIONS: facial pit, fosette scrobale, fossette frontale, pore facial

HOMONYM NOTES: none

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ID: HAO:0000326

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1196

DEFINITION: The scrobe that is located on the mesopleuron into which the mid leg fits when pressed against the mesosoma.

TERM OPTIONS: femoral depression, femoral groove, scrobal groove

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.

What's the Preferred Term - 7/18/2011

2011-07-18T11:17:00.000-04:00

Recap from last post: It has been a while since the last post (grants!!!) but last time both Jennings and Fernandez Triana both suggested "malar space" for the class "HAO:0001393: The area that is extends between the lower (anerior) eye margin and the anterolateral margin of the cranium, and its width is delimited by the width of the mandible". As for the class "HAO:0000221: The area of the integument that is weakly sclerotized, with thin exocuticle" we will keep the label "conjunctiva" since no one had any opinions.

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For this week:

ID: HAO:0000889

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/551

DEFINITION: The area that is located proximally on the scape, is limited distally by a constriction and bears proximally the basal knob.

TERM OPTIONS: antennal condyle, articulatory bulb, radicle, radicula

HOMONYM NOTES: none

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ID: HAO:0000504

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1635

DEFINITION: The sulcus that extends between the ventral margin of the compound eye and the base of the mandible.

TERM OPTIONS: frontogenal suture, genal sulcus, malar groove, malar sulcus, subocular groove, subocular sulcus

HOMONYM NOTES: "malar groove" is also used for the class "HAO:0001394: The groove that extends between the compound eye and the base of the mandible"

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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.

What's the Preferred Term - 6/28/2011

2011-06-28T10:13:00.001-04:00

Recap from last post: We had a response for both the terms from Burks who suggested "lateral ocellus" and "frontal depression" for the corresponding classes HAO:0000481 and HAO:0000911 respectively. Unless there is consensus against it, we will make the according changes.

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For this week:

ID: HAO:0000221

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1072

DEFINITION: The area of the integument that is weakly sclerotized, with thin exocuticle.

TERM OPTIONS: arthrodial membrane, conjunctiva, corium

HOMONYM NOTES: none

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ID: HAO:0001393

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1595

DEFINITION: The area that is extends between the lower (anerior) eye margin and the anterolateral margin of the cranium, and its width is delimited by the width of the mandible.

TERM OPTIONS: cheek, malar area, malar region, malar space

HOMONYM NOTES: "cheek" is also used for the class "HAO:0000200: The area that is located ventrally in between the eye and the oral foramen"; "malar space" is also used by the class "HAO:0000503: The anatomical line that is the shortest between the lower orbit and the ventrolateral margin of the cranium"

- 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 - 6/20/2011

2011-06-20T11:37:00.002-04:00

Recap from last post: We did not have any responses last week, so we will keep the current preferred labels for those two classes (HAO:0000292 & HAO:0000468), unless objections are made.

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For this week:

ID: HAO:0000911

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/857

DEFINITION: The anatomical cluster that is composed of antennal scrobes.

TERM OPTIONS: frontal depression, frontal scrobe, scrobal cavity, scrobal channel, scrobal depression

HOMONYM NOTES: none

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ID: HAO:0000481

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1780

DEFINITION: The ocellus that is paired.

TERM OPTIONS: hindocellus, lateral ocellus, posterior ocellus

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 - 6/13/2011

2011-06-13T09:53:00.001-04:00

Recap from last post: Jennings suggested the preferred term "metathoracic spiracle" for the class "HAO:0000769: The spiracle that is located dorsally on the border between the mesopectus and the metapectus" so we will provide that accordingly. For the second class "HAO:0001665: The sulcus that is longitudinal and extends posteriorly of the first abdominal spiracle" we had some discussion (initiated by Burks) about the validity of the definition and labels having to do with a sulcus, something that cannot be determined easily for all groups. An agreement was made to possibly substitute "groove" for "sulcus". For now, we will go with Burks' suggestion of using "postspiracular furrow" until a better definition can be achieved.

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For this week:

ID: HAO:0000292

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/522

DEFINITION: The carina that delimits posteriorly the epicnemium.

TERM OPTIONS: acetabular carina, epicnemial carina, prepectal carina

HOMONYM NOTES: "acetabular carina" is also used for the classes "HAO:0000080: The area that is located medially on the epicnemial carina" and "HAO:0001428: The area that is located on the epicnemial carina posterior to the site of origin of the omaulus"; "prepectal carina" is also attributed to the class "HAO:0001803: The carina that divides the prepectus for the vertical lateral portion and the horizontal, ventral prepectal shelf".

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ID: HAO:0000468

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/3248

DEFINITION: The area that is located laterally on the axilla and is delimited medially by the axillar carina.

TERM OPTIONS: lateral axillar area, lateral axillar surface, lateral panel of axilla, outer panel of axilla, postalar plate, posterior alar plate

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 - 6/6/2011

2011-06-06T09:08:00.001-04:00

Recap from last post: Last time we had no responses, so we will remain using "acropleuron" for the class "HAO:0001155: The area that corresponds with the site of origin of the third mesopleuro-mesonotal and first mesopleuro-third axillary sclerite of fore wing muscle" and the term "basitarsal comb" for the class "HAO:0001180: The row of setae that extends along the ventral margin of the probasitarsus".

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For this week:

ID: HAO:0000769

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/4535

DEFINITION: The spiracle that is located dorsally on the border between the mesopectus and the metapectus.

TERM OPTIONS: metathoracic spiracle, posterior thoracic spiracle, second spiracle

HOMONYM NOTES: none

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ID: HAO:0001665

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/6427

DEFINITION: The sulcus that is longitudinal and extends posteriorly of the first abdominal spiracle.

TERM OPTIONS: paraspiracular sulcus, postspiracular sulcus, spiracular sulcus, spiracular sulcus of propodeum

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 - 5/23/2011

2011-05-23T14:09:00.000-04:00

Recap from last week: For the first class, "HAO:0001205: The line that is longitudinal, extends ventrally on the mesopleuron and corresponds with the site of origin of the second and third mesopleuro-third axillary sclerite of fore wing and the second mesopleuro-mesonotal muscles", "sternaulus" was initially chosen, but Broad pointed out that the label is applied to another feature in ichneumonoids (and, indeed this is another class in the ontology - see HAO:0000953) so we will keep "transepisternal line" as the pereferred label. For the second class, "HAO:0000808: The pit that is located on upper face adjacent the anterior margin of the median ocellus and corresponds internally to a conical apodeme and not the tentorium" Gergely chose "preocellar pit".

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For this week:

ID: HAO:0001155

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/877

DEFINITION: The area that corresponds with the site of origin of the third mesopleuro-mesonotal and first mesopleuro-third axillary sclerite of fore wing muscle.

TERM OPTIONS: acropleuron, anapleurite, subalar area

HOMONYM NOTES: "anapleurite" has been used for "HAO:0001175: The pleurite that extends ventrally of the lateral margin of the tergum and dorsally of the coxopleurite."; "subalar area" has been used for "HAO:0000960: The area that is delimited by the mesepimeral inflection and corresponding subalar ridge and bears the mesopleural wing process."

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ID: HAO:0001180

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/5988

DEFINITION: The row of setae that extends along the ventral margin of the probasitarsus.

TERM OPTIONS: basitarsal comb, pecten, tarsal comb

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 - 5/3/2011

2011-05-03T10:35:00.001-04:00

Recap from last week: For the first class, "HAO:0000395: The sclerite that is located distally of the gonostipes" we will keep "harpe" as the preferred term (as suggested by Schulmeister), but have added "harpago" to the list of synonyms as suggested by Yoshimura. For the second class, "HAO:0000920: The line that traverses the alinotum between the postmedian notal wing processes", Burks suggested "scutoscutellar suture" be the preferred term.

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For this week:

ID: HAO:0000492

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/816

DEFINITION: The apodeme that is located laterally on the postnotum.

TERM OPTIONS: accessory sclerite of 4th axillary sclerite, lateral lobe of secondary phragma, laterophragma, lateropostnotum, mesopostnotal apodeme, muscle bearing process of mesopostphragma, postalar bridge, postalare

HOMONYM NOTES: none

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ID: HAO:0000625

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/623

DEFINITION: The area that is located posteromedially on the metanotum, is delimited laterally by the metanotal trough and corresponds to the reservoir of the dorsal vessel.

TERM OPTIONS: dorsellum, metanotal plate, metascutellum, postscutellum

HOMONYM NOTES: "postscutellum" is also attributed to "HAO:0001809: The area that is located medially on the dorsellum and bears the metanotal flange."

- 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 - 4/25/2011

2011-04-25T12:06:00.001-04:00

Recap from last week: For the first definition, "HAO:0001358: The pit that corresponds with the mesopleural apodeme", Fernández-Triana and Jennings both agreed that "mesopleural pit" is the most clear and accurate term for that class. For the other class, "HAO:0000735: The carina that is located laterally on the propodeum" there was much discussion regarding the identity of the class (in relation to other carinae on the propodeum of Ichneumonoidea and Chalcidoidea), but otherwise the term "plica" was chosen as the preferred one.

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For this week:

ID: HAO:0000395

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/3937

DEFINITION: The sclerite that is located distally of the gonostipes.

TERM OPTIONS: distal segment of gonopod, dististyle, gonoharpe, gonosquama, gonostylus, harpe, harpes, harpide, palette, paramere, squama, telomere

HOMONYM NOTES: "paramere" (http://glossary.hymao.org/projects/32/public/label/show/4259), and "squama" (http://glossary.hymao.org/projects/32/public/label/show/1418) have been used for other classes.

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ID: HAO:0000920

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1378

DEFINITION: The line that traverse the alinotum between the postmedian notal wing processes.

TERM OPTIONS: para-axillary suture, scutellar suture, scuto-scutellar suture, scutoscutellar suture

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 - 4/19/2011

2011-04-19T10:11:00.003-04:00

Recap from last week: For the first term, Burks argued that "purely linguistic grounds suggest that auxilium is
best. Auxilia is the plural, and I don't see why the extra word "sclerite" would be needed", so we will use the term "auxilium" to describe the sclerite. For the second term, both Jennings and Burks agreed that "anterior ocellus" is too relative with regards to head direction, etc. The term "median ocellus" was deemed the most accurate, thus we will use it as the preferred label.

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For this week:

ID: HAO:0001358

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/8253

DEFINITION: The pit that corresponds with the mesopleural apodeme.

TERM OPTIONS: episternal scrobe, mesopleural pit, scrobe

HOMONYM NOTES: "scrobe" is a label that is also applied to "HAO:0000912: The area that is impressed and is for the reception or concealment of another sclerite"

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ID: HAO:0000735

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1700

DEFINITION: The carina that is located laterally on the propodeum.

TERM OPTIONS: plica, plical carina

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 - 4/11/2011

2011-04-11T15:59:00.001-04:00

Recap from last week: For the class "HAO:0000945: The anatomical space that serves as the storage of sperm" (applied to the structure for female sperm storage), we have chosen "spermatheca" as the preferred term as per at least one response. For the second class, "HAO:0000164: The process that is linear and wider apically than distally" we had an interesting discussion about the actual validity of the class definition and also whether there should be more classes applied to different structures (e.g. a true "bar", a true "trabecula" and the entire H-shaped structure in Mymaridae "trabecula?"). We will need to further clarify these classes, but until then we will hold off on assigning preferred terms.

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For this week:

ID: HAO:0000154

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/3905

DEFINITION: The sclerite that is located between the unguitractor and the bases of claws.

TERM OPTIONS: auxilia, auxiliar sclerite, auxilium

HOMONYM NOTES: none

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ID: HAO:0000526

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1779

DEFINITION: The ocellus that is located medially on the cranium.

TERM OPTIONS: anterior ocellus, medial ocellus, median ocellus

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 - 4/4/2011

2011-04-04T13:11:00.001-04:00

Recap from last week: For the class "HAO:0000109: The frontal line that is a carina", Jennings suggested that the homonym "frontal carina" be with the class "HAO:0000810: The carina that is located on the face and parallels the inner orbit"; thus we have made "central keel" the preferred term for the former class. No decisions were made about "HAO:0000916: The depression that is medially located on the scutoscutellar suture" thus the current term, "scutellar fovea", remains as the preferred one.

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For this week:

ID: HAO:0000164

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1089

DEFINITION: The process that is linear and wider apically than distally.

TERM OPTIONS: bar, trabecula

HOMONYM NOTES: none

-------------------------------------------------

ID: HAO:0000945

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1474

DEFINITION: The anatomical space that serves as the storage of sperm.

TERM OPTIONS: receptaculum seminis, spermatheca

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 - 3/28/2011

2011-03-28T10:50:00.001-04:00

Recap from last week: For the first class, "The seta that is located on the anterior margin of the hind wing and interlocks with the recurved posterior edge of the fore wing in Hymenoptera during flight, making them functionally one winged", Schulmeister and Jennings both chose "hamulus (hamuli)" a choice that surely surprised no one in the community. As for the second class, "The malar line that is a carina", no one gave their opinion so we will keep "malar carina" as the preferred term.

-------------------------------------------------
For this week:

ID: HAO:0000109

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/535

DEFINITION: The frontal line that is a carina.

TERM OPTIONS: central keel, frontal carina

HOMONYM NOTES: "frontal carina" is also used for the classes "HAO:0000810: The carina that is located on the face and parallels the inner orbit" and "HAO:0001533: The carina that extends along the lateral margin of the intertorular area (median margin of the antennal foramen) towards the vertex".

-------------------------------------------------

ID: HAO:0000916

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1183

DEFINITION: The depression that is medially located on the scutoscutellar suture.

TERM OPTIONS: anterior scutellar pit, scutellar fovea

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 - 3/21/2011

2011-03-21T09:43:00.001-04:00

Recap from last week: We had no responses this past week so we will keep our current preferred terms: 1) for the class "HAO:0000891: The process that is located proximally on the first valvula" we have "ventral ramus of the first valvula" as the term of choice; 2) for "HAO:0000780: The sulcus that corresponds with the postgenal ridge" we have "postgenal sulcus" as the preferred term.

-------------------------------------------------
For this week:

ID: HAO:0000394

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/486

DEFINITION: The seta that is located on the anterior margin of the hind wing and interlocks with the recurved posterior edge of the fore wing in Hymenoptera during flight, making them functionally one winged.

TERM OPTIONS: frenal hook, hamulus

HOMONYM NOTES: none

-------------------------------------------------

ID: HAO:0001590

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/6320

DEFINITION: The malar line that is a carina.

TERM OPTIONS: malar carina, malar keel, malar ridge

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.

2011-03-14T15:36:00.000-04:00

Recap from last week: Last week we had no responses, so we will keep using the current preferred terms - for 1) "HAO:0000918: The ridge that extends along the anterior margin of the mesoscutellum and corresponds to the scutoscutellar suture." we have "scutoscutellar ridge" as the preferred term; for 2) "HAO:0000742: The projection that is located anterolaterally on the mesoscutellar-axillar complex." we have "postalar process" as the preferred term.

-------------------------------------------------
For this week:

ID: HAO:0000891

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1259

DEFINITION: The process that is located proximally on the first valvula.

TERM OPTIONS: ramal rod, ventral ramus of the first valvula

HOMONYM NOTES: none

-------------------------------------------------

ID: HAO:0000780

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/862

DEFINITION: The sulcus that corresponds with the postgenal ridge.

TERM OPTIONS: gular sulcus, postgenal sulcus

HOMONYM NOTES: "postgenal sulcus" has been applied to the class "HAO:0001811: The sulcus that extends between the malar sulcus and the occipital foramen."

- 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 - 3/7/2011

2011-03-07T13:50:00.002-05:00

Recap from last week: We got one response for each of the classes from last week. First, Jennings suggested we use "basiconic capitate peg sensillum" for the class "HAO:0001098: Mushroom-shaped sensory structure on the flagellum, particularly the clava; sometimes called the sensilla ampullacea." Second, Schulmeister suggested a couple of labels for the class "HAO:0000427: The compound organ that functions as producer and transporter of sperm, spermatophore and semen, composed of the testes, vas deferens, accessory glands and ductus ejaculatorius. Ecto- and mesodermal in origin" including "internal male genitalia" or "internal male reproductive organs". We will use Jennings' selection for the first class, and have continued using "internal male genitalia" for the second class in accordance with Schulmeister's suggestions and our current selection.

-------------------------------------------------
For this week:

ID: HAO:0000918

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/3293

DEFINITION: The ridge that extends along the anterior margin of the mesoscutellum and corresponds to the scutoscutellar suture.

TERM OPTIONS: scutoscutellar ridge, V-shaped notal ridge

HOMONYM NOTES: none

-------------------------------------------------

ID: HAO:0000742

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1180

DEFINITION: The projection that is located anterolaterally on the mesoscutellar-axillar complex.

TERM OPTIONS: metategula, postalar process, scutellar crest

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 - 2/28/2011

2011-02-28T16:47:00.002-05:00

Apologies for missing last week's WTPT post.

Recap from 2 weeks ago: We did not get any responses for either term, so we will keep the current preferred terms: "HAO:0000942: The sclerite that is unpaired and located just dorsally of the basal part of the aedeagus in some Aculeata" we chose the term "spatha"; "HAO:0001027: The line that traverses the mesoscutum between the antemedian and postmedian wing processes." we chose the term "transcutal line".

-------------------------------------------------
For this week:

ID: HAO:0001098

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/5995

DEFINITION: Mushroom-shaped sensory structure on the flagellum, particularly the clava; sometimes called the sensilla ampullacea.

TERM OPTIONS: basiconic capitate peg sensillum, capitate peg sensillum, sensilla ampullacea

HOMONYM NOTES: none

-------------------------------------------------

ID: HAO:0000427

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/4239

DEFINITION: The compound organ that functions as producer and transporter of sperm, spermatophore and semen, composed of the testes, vas deferens, accessory glands and ductus ejaculatorius. Ecto- and mesodermal in origin.

TERM OPTIONS: inner male genitalia, internal male genitalia

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?

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 - 2/15/2011

2011-02-15T11:38:00.002-05:00

Recap from last week: Last week we had one response for the first preferred term and none for the second. Schulmeister stated "I use external male genitalia and copulatory apparatus and copulatory organ. If Latin, then armatura genitalis", later suggesting "armatura genitalis". We would like to maintain using English terms (as decided in a previous WTPT), so we will use "external male genitalia" for the preferred term for "HAO:0000312: The anatomical cluster that is composed of the cupula, gonostyle, volsella and the aedeagus". For the second term, representing "HAO:0000271: The ridge that is marginal or submarginal, extends along the dorsal margin of the propleuron and serves as the site of origin of the lateral propleuro-postoccipital muscle" we have chosen "dorsal propleural ridge".

-------------------------------------------------
For this week:

ID: HAO:0000942

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1417

DEFINITION: The sclerite that is unpaired and located just dorsally of the basal part of the aedeagus in some Aculeata.

TERM OPTIONS: median lobe, spatha, uncus

HOMONYM NOTES: "uncus" is currently the preferred term for "HAO:0001041 - The abscissa that extends anteriorly from the stigmal vein."

-------------------------------------------------

ID: HAO:0001027

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/4527

DEFINITION: The line that traverses the mesoscutum between the antemedian and postmedian wing processes.

TERM OPTIONS: transscutal fissure, transscutal line, transscutal suture

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 - 2/7/2011

2011-02-07T12:54:00.004-05:00

Recap from last week: For the first class, two suggested preferred terms were selected: Broad selected "postpectal carina", while Ohl preferred "precoxal carina (of mesopleuron)". Since the "precoxal carina" part is a homonym of " HAO:0001324 - The carina that delimits dorsally the precoxal sulcus" we have chosen to use "postpectal carina" (which is prevalent in ichneumonoid and chalcidoid literature). For the second class, no responses were sent, thus we will retain our preferred label "gaine" for "The anatomical cluster composed of the second valvifer and the third valvula."

-------------------------------------------------
For this week:

ID: HAO:0000312

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/4097

DEFINITION: The anatomical cluster that is composed of the cupula, gonostyle, volsella and the aedeagus.

TERM OPTIONS: armatura genitalis, copulatoria, copulatory apparatus, external male genitalia, genital apparatus, genital appendage, genital armature, genital capsule, genital organ, genitalia, male copulatory organ, paramere, parameres, phallic apparatus, phallus

HOMONYM NOTES: The label "paramere" is attached to a number of classes including: "HAO: 0000707 - The sclerite that is paired, located in the middle of the external male genitalia, surrounds the distal part of the ductus ejaculatorius and the endophallus"; "HAO:0000389 - The anatomical cluster that is located distally of the cupula lateroventrally of the volsellae and surrounds the aedeagus"; "HAO:0000395 - The sclerite that is located distally of the gonostipes"; "HAO:0000713 - The anatomical cluster that is composed of the cupulae, gonostipites and volsellae"......The label "genitalia" has also been used for "HAO:0000374 - The anatomical system that is involved in copulation, fertilization and/or oviposition";

-------------------------------------------------

ID: HAO:0000271

HYMGLOSSARY LINK: http://glossary.hymao.org/projects/32/public/ontology_class/show_expanded/1171

DEFINITION: The ridge that is marginal or submarginal, extends along the dorsal margin of the propleuron and serves as the site of origin of the lateral propleuro-postoccipital muscle.

TERM OPTIONS: dorsal incision of the propleuron, dorsal propleural ridge, horizontal apodeme of episternum, marginal apodeme

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 - 1/31/2011

2011-01-31T12:51:00.002-05:00

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.

-------------------------------------------------
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

-------------------------------------------------

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

2011-01-24T11:48:00.003-05:00

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.

-------------------------------------------------
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

-------------------------------------------------

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

2011-01-18T15:19:00.007-05:00

**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".

-------------------------------------------------
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

-------------------------------------------------

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

2010-12-29T18:43:00.001-05:00

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

2010-10-20T12:45:00.033-04:00

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

2010-10-14T09:31:00.001-04:00

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

2010-07-14T16:04:00.011-04:00

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.

The First HAO Working Meeting - "Towards a compendium of hymenopteran musculature"

2010-04-13T15:11:00.027-04:00

Last week (April 6 - 18) the HAO was hosting our first working meeting. This workshop gathered three of the top Hymenoptera morphologists together in an effort to summarize our knowledge of hymenopteran musculature in the form of a digital compendium.

(Above) Gary Gibson and István Mikó

Our goals for the meeting were: 1) to comprehensively capture the data from Duncan, 1939; Snodgrass, 1942; Vilhelmsen, 1996; Vilhelmsen, 2000; and Vilhelmsen et al. 2010; 2) to identify, in a formalized statement, the next steps to extending this effort to be comprehensive for all hymenopteran musculature; 3) to formalize the current state of the union with respect to aligning data within the HAO to data in the Drosophila anatomy ontology; and 4) to submit a paper documenting these efforts and results.

(top) Diagramming the potential relationships muscles might be entered in the ontology based on points of attachment. (bottom) Matt Yoder and Lars Vilhelmsen.

The idea developed during the workshop to start with clear definitions of muscles based on points of attachment for the head, mesosoma, metasoma and ovipositor. Many of these are to be illustrated using the plates from the Vilhelmsen 2010 paper before the end of the two week workshop and the rest as a continuing effort . Results of the workshop (and subsequent work after) will be presented in June at the International Society of Hymenotperists meeting in Köszeg, Hungary and made available online through the HAO public glossary Website. A final publication will result consisting of list of muscles, insertion and their synonyms. We will also make a first attempt to align the HAO with the Drosophila Gross Anatomy Ontology.

Part of the working meeting was a collecting trip to G. W. Hill Demonstration Forest. The 2,450-acre forest in Durham County has been an important teaching laboratory for North Carolina State University forest since 1929.

(top) Gary Gibson is demonstrating his method of collecting sweep net samples in the field without loosing the minute and sneaky chalcid wasps. Bobb Blinn and Matt Bertone look and the catch. (bottom) is the collecting crew about to set out (before being covered in ticks!). The collecting team pictured are: Barb Sharanowski, Matt Yoder, Andrew Ernst, Bob Blinn, Gary Gibson, Trish Mullins, Matt Bertone and Lars Vilhelmsen.

The HAO is seeking a programmer!

2010-02-16T15:33:00.001-05:00

Human resources has just finalized the paperwork and we are happy to announce a new position is available within the HAO team. We're looking for a full time programmer to support the development of the Hymenoptera Anatomy Ontology, and its integration into the broader world of biodiversity informatics. The fine details are available in the links below, but in general we're looking for someone with solid experience developing web-based APIs for data exchange. This is a perfect opportunity for a recent graduate who wants to program full time while maintaining their involvement with an academic setting.

We're very excited about this position, we already have a great working group together, including world class morphologists and top notch students, and with this new addition we should have the opportunity to explore some really interesting projects.

If you have questions about the position don't hesitate to contact us through links on the lab page listed below.

Links:

The Deans Lab
Application and job requirements, search for position 101506.

Class, label, sensu

2010-01-30T09:58:00.000-05:00

In the past couple weeks we've been actively debating what the concepts like synonyms and homonyms mean in the context of the HAO. In particular how do they relate to our concepts of classes (the "real" things at the core of our ontology), and the labels we use to references those classes? We had been using tags to indicated synonyms, but our tag data-model wasn't as elegant as we needed it to be, as exemplified by the fact that too many hacks were being added to the code base to perform various calculations on our data. After much discussion and debate as to the meaning of our various tags in general we realized that we could use a new, simple model which nicely encapsulates what we wanted to capture with respect to synonyms and homonyms, classes and labels: we've called it a "Sensu".

The sensu model is simply a pointer to a label, a class, and a reference (a table with three columns). It states that so-and-so (a reference) used a label (basiparamere) for a class (The sclerite that is connected proximally with the cupula, distally with the harpe, ventrolaterally with the parossiculus). The Sensu model provides the basic functionality of linking labels to classes. In addition, from this simple table we can derive nearly everything we wanted to in the past with respect to synonymy and homonymy (and the "acts" of these). For example, if two sensus share the same class, but different labels, then those labels are synonyms, and if two classes share the same label, then that label is homonymous. If one person (reference) used two labels in conjunction with the same class, then that person performed the "act" of synonymy, if they used two classes with the same label, then they indicated homonymy.

There are some really nice consequences of this approach: for instance we don't have to specifically identify a "preferred" label or a senior synonym - if we wanted we can calculate these based on some arbitrary metric (e.g. first usage, most used, most voted for, etc.). As long as people can reference the class (some xml or similar markup), they can use whatever label (including other languages) they want for that class. We can also algorithmically detect all cases of synonymy and homonymy without specifically looking for them, i.e. if someone discovers that so-and-so used a label for a class, they need not specifically be intending to synonymize that label, but we can still calculate that a synonym is implied.

In moving this model we've also realized what appears to be a shortcoming to the OBO format, in which a singular class-label construct is the core unit (synonyms can be captured, but each class must have a unique label). The more we work on this project, the more we doubt that we can (or should) enforce labels to have just one meaning (for instance, the classic example process is both a time-based and morphological concept), and we further doubt that this is necessary for us to do some really cool things with the ontology.

profiling and extracting from the JHR

2009-11-29T00:49:00.000-05:00

In preparation for an ESA talk this year we are developing tools to more rapidly search through OCRed text for terms (classes) we might not yet have in the HAO. As a test case we retrieved all the OCRed text for the Journal of Hymenoptera Research courtesy of the BHL. Because the BHL does not yet have the functionality to return OCRed text by article (you get the whole issue of a volume at once) we manually divided the articles (we have 344) then added them to our database (in mx). In the future we hope that the BHL or someone else will provide an API to return the OCRed text for an article alone, and we can skip the step of manually handling this text.

To get a quick visual of the existing of HAO terms in a given article we added a Google chart (see above).

The OCRed text is now easily fed to our "proofer" (see part of the form below) which throws up a form of all the unique words (including some neighboring pair combinations) not in the HAO. Common words can be excluded beforehand versus a managed list. This week the real work begins as we run through these data in search of missing terms. We will profile the before and after of this effort to better understand how useful this type of approach is.

As always, the full source for all this work is available on the edge branch of mx on Sourceforge.

region, area, headache

2009-11-24T14:27:00.000-05:00

A constant and ongoing debate during our Tuesday HAO group discussion is the nature of regions and areas. In the classic approach areas have well defined boundaries, whereas regions have some boundary or compartmentalization that is not well defined. For example a region might be defined in part by a change of color wherein the precise point at which the color changes is not well defined. An example of an area might be the interocellar area, which is bound by three lines that join the centers of the ocelli. One is very precise, the other is not.

In the context of an ontology you can think of the two as matter and anti-matter. An ontology necessarily defines classes in a very specific way. Region, as we have discussed it, is a thing that has at least some non-defined boundary (areas have well defined material boundaries). Therefor regions are undefined, and may not belong in the ontology.

Our temporary solution is to assume that if something is a region in the "no boundaries/can't define a boundary" sense it doesn't belong in the ontology. We've moved everything previously under region to area, and have begun to rework some classical terms in such a way that they can be explicitly defined. For example look at the new definition for gena, a term which has never (to our knowledge) been adequately defined.

Note that areas can be defined by immaterial anatomical entities (e.g. lines connecting ocelli or planes tangential to some reference line).

Note that this is largely a pragmatic resolution that lets us get on with other things. If you have any feedback or experience in this regard we'd love to hear it.

more visualization

2009-11-19T22:46:00.002-05:00

Turns out it very easy to use ruby-graphviz. With a handful of code we can get nice dot graphs that we can render in programs like Tulip.

That's (not) highly illogical Jim

2009-11-06T11:36:00.015-05:00

Our next update to the HAO has been posted to the OBO foundry. While our existing versions passed the OBO edit verifications we were still generating logical redundancies. For example if we know that A is_a B and B part_of C then we can deduce A part_of C. In around 70 cases we were additionally adding this A part_of C statement, these are all now removed. Whether or not these are actually "harmful" is still somewhat unclear, for instance the other arthropod ontologies all have logical redundancies (Spider: 6 , Tick: 2 Mosquito: 1, and Drosophila: 464), and some non-arthropod ontologies have even higher numbers (ZFIN has 2543).

The code to generate the Newick trees seen in the previous post is now live as well. We've made a simple form (see below) that allows users to customize and output trees. Several different node and "clade" highlighting options are available and we plan to expand these as well.

Below is the result of the tree generated above. It shows a categorical summary (increasing number with color darkness) of the number of immediate part_of children.

More visualization experimenting

2009-10-23T09:41:00.005-04:00

We're working on some figures for the HAO announce paper that should be submitted any day now (tm). This is an early attempt at visualizing the complexity within the HAO. It is the is_a graph spit out from mx in Newick format with randomly chosen colors assigned from a ColorBrewer palette. Rendered in Figtree.

visualizing the HAO

2009-09-23T13:26:00.004-04:00

A sneak preview of a HAO and protovis mashup. This is the "is_a" tree.

obsolete

2009-09-18T17:16:00.004-04:00

A short update on the status of the HAO - Our progress since has largely been technical, with some major improvements to how we manage getting new versions of the HAO out of mx. These changes allow us to more confidently generate new versions, with less fear of there being logical problems with the output. In addition, a new version of the HAO has been committed and should appear shortly, thanks to those of you who caught problems with it and notified us of them.

Another important update includes handling "obsolete" tags, which are required when we make a term that has an HAO id a synonym of another term. We're already confronted with questions like like these - How do you determine which term is the right one? Why is this term obsolete? - from our colleagues.

Synonyms and obsolete status, from our perspective at least, are not quite as big a deal as our users might feel, largely because they are meant to indicate a particular status to parsers reading the ontology (i.e., machines) rather than acting as decisions or recommendations to our users. The HAO has to be a logically consistent entity that is largely focused on defining and capturing anatomical classes. The particular labels we give to these classes are not necessarily as important as how we define the class. I.e., if a bunch of hymenopterists can agree on what that their colleague means by "that little point bit over there," then well over half the battle is won. By obsoleting or synonymizing a term in the HAO we are saying that two or more classes in the ontology are really the same thing, i.e. "that little pointy bit over there". It just happens that we need at least one label for a given class, this is often called the "preferred term" in ontology-speak, but we have to be careful to not worry about this semantic. We're not saying "You, hymenoptera taxonomist, don't use that word!" We're saying if you use that word, we're going to redirect you to more information about the "little pointy bit" others are talking about.

Several other cosmetic, and work flow related changes have been made to mx. We've made it easier to navigate back and forth across synonym tags. We've also formalized the Tag object in anticipation of creating links to external resources, including on data to the BHL and HOL digital literature databases.

Australia, taxonomy, and integration

2009-08-29T17:07:00.015-04:00

I recently traveled to Canberra, Australia thanks to an invite from John La Salle at CSIRO. John is one of the driving forces behind the Atlas of Living Australia, a initiative recently funded on the scale of EOL. While there I attended a couple of short workshops on phenomics and biosecurity and presented talks on the HAO. One recurring topic was how ontologies could be used to speed taxonomy. There are obvious applications, for instance our text markup proofing tool, but clearly a lot more is possible.

La Salle, for example, is pushing the idea of automated character recognition (PDF). Imagine an anatomy ontology, such as the HAO, that has associated with it a large number of annotations on images - e.g., that light micrograph of an ant head has polygons and/or point markers superimposed over it that indicate which structures are the compound eyes, ocelli, face, antennae, etc. These core data could act as the basis for algorithmic recognition on images of other ants. While this functionality is largely science fiction at the moment, it's possible that the technology will be folded into the taxonomic workflow within my lifetime. We will spend a lot of time in the next three years thinking about this and other ways the HAO can be used to address the taxonomic impediment.

Integrating the HAO with taxonomy maybe be somewhat abstract, but by the virtue of being an OBO format file available to the others the HAO is already being integrated into the ontological world (semantic web?). Richard Cole wrote to us to point out that the HAO is now visible via the Ontology Lookup Service. This service provides a nice graph to visualize and navigate the ontology. If you have other useful or cool applications that use OBO ontologies let us know and we'll point them.

Come work with us!

2009-08-20T15:35:00.006-04:00

Undergraduate Position Available Immediately for Fall Semester

The Hymenoptera Anatomy Ontology (HAO) project is looking for a student interested in learning biodiversity informatics, library science, entomology, imaging and scientific illustrating techniques, modern museum studies and Web design.

Hours are flexible, but will be between 8am-5pm.
Salary: $8.50 per hour (10-15 hours a week)

Responsibilities may include:
* extraction of data from historical/scientific texts (primary responsibility)
* testing and design of Web-based tools for outreach (i.e., educating non-scientists
about insects, insect anatomy, and biodiversity informatics)
* development of visual/semantic Web interfaces for novel rapidly growing dataset
* learning light microscopy imaging techniques
* learning and illustrating Hymenoptera anatomy
(i.e., what the body parts of ants, bees, wasps, and sawflies are called)

More information about the HAO project is available: http://hymao.org

Contact: Katja Seltmann: katja_seltmann (at) ncsu (dot) edu; Room 3212 Gardner Hall; 5-2833

.obo encoding issues

2009-08-12T09:56:00.007-04:00

We successfully submitted the HAO to the OBO Foundry last week(!), and we hope to ascend to candidacy after some testing / evaluation / reading / questioning / etc. by the OBO community. If you access our submitted version through SourceForge here you will probably notice some diacritical messiness, mainly this --> �

That's what happens to each letter embellished with diacritics. Each instance of Mikó and Pénzes becomes Mik� and P�nzes. This is an issue because our data are UTF-8 encoded in the database.

Why not convert all those references and names to xref IDs? We will, as soon as we know our IDs will be stable. UTF-8 support will remain an important component of our ontology, though, as we go forward. Ultimately we will be attempting to account for ALL commonly used terms in Hymenoptera species descriptions, and many of those are in (accented) French, German, and Spanish: carène intertorulaire, prépectus, écailles, Ringstück, etc.

The "encoding: UTF-8" tag is supposed to be available in OBO 1.3 spec. I know we aren't the only ones longing for UTF-8 support in OBO Edit and other tools, so developers out there - take this as a little nudge.

iterating through the low hanging fruit

2009-08-07T14:45:00.023-04:00

Perhaps a little behind schedule with the blog post, but we've been busy!

After several weeks of concentrated editing the first "version" of the HAO is in the hands of the folks at the OBO Foundry, to be included as a candidate (~~it should appear in the next several days~~it's here). It was interesting to learn during this process (not process sensu HAO:0000822, but process sensu evo-devo) that no ontology is actually included in the foundry, they are all candidates.

The HAO is indeed a candidate in many senses of the word, this first effort is largely to get the editing team comfortable with the steps it takes to release versions of the HAO, and the basic skeleton logic into the hands of those who can start to provide us feedback. That said, we feel pretty good about this initial effort, even though we have perhaps been gathering the low hanging fruit. We have a full fledged ontology output from a web-based application (albeit with a hack here or two), and around 90% of the terms contain definitions in human-written genus differentia formats. We've also generated HAO ids for over 1000 terms, which is an important first step towards allowing others to reference fixed points in the ontology in meaningful ways. Perhaps most importantly, we have a product that people can begin to provide critical feedback on, like "where's the nervous system" (our first comment from a non-project member, it's not in there...yet). We're depending on this feedback, both from experts on ontologies in the broader sense, and from morphologists with much more experience than us.

Along with work on the HAO itself has come some feature development for handling the ontology. We're using tags to comment and annotate the HAO. Tags in mx contain a keyword, and an optional pointer to a reference, and option comment or "value". To make tags more useful on a day to day basis we hacked up a tag browser (see above) which lets us quickly return sets and then navigate to the results.

We also generated a quick tree viewer to browse through the ontology. Watch for a public version of the viewer to appear on the glossary in the following months. The tree gives us context, allows us to quickly edit the definitions, and we can drag terms to add relationships.

Towards HAO 0.1

2009-07-20T10:16:00.010-04:00

One central premise we're following is to release early, release often. Given this we're planning to release a very early draft of the ontology within the next week or two. We hope that releasing an early draft will drive feedback early on in the projects lifespan. The first releases will undoubtedly contain errors and glaring omissions, but it will also let people start to use the real meat of our project, the ontology itself. The first draft will only include two relationship types (is_a, part_of). As the project continues we'll consider and adopt others (has_part?), there is much talk of integrating spacial relationships (in_contact_with, adjacent_to), but these will have to be carefully reviewed.

To accommodate the editing, review, and tweaking of the ontology we're also starting to ramp up the patches to mx, the underlying editor that we're using to build the ontology. These changes are posted immediately to our SVN repository on Sourceforge (yes, we're considering a move to git). In the future, we plan to split the ontology code out of mx and turn it into a gem (plugin) that any Rails project can easily use.

Curation of the ontology is currently focused on updating all the present definitions to a genus-differentia style, and cross referencing terms to other ontologies. One stumbling point we're hitting is what to do with accented characters, since the OBO specs don't presently permit them.

The HAO team assembles...

2009-07-08T13:48:00.006-04:00

The Hymenoptera Anatomy Ontology team continues to grow, with the recent arrivals of Katja Seltmann (2nd from left) from Morphbank and Matt Yoder (far right) from the Platygastroidea PBI. Katja and Matt join István Mikó (far left) from the NCSU Insect Museum, who's been helping me (Andy Deans; 3rd from left) sort out confusing character complexes for the last six months. We now have the critical mass needed to ramp up development of the HAO and associated tools.

In that regard we've set up several outlets for discussion and news reporting, should you be interested:

the HAO Project is on on twitter
you've already found our blog
we post(ed) discussion items (and our proposal) on the HAO wiki
the ontology can be perused on the Hymenoptera glossary website

The HAO currently has 2,408 classes (i.e., anatomical terms) and 2,537 relationships. Our first order of business is to clean up a few terms (e.g., converting a few straggling definitions to genus-differentia) and then deposit the ontology at the OBO Foundry. We'll be growing again in August, with the arrival of a new grad student, and then again in October. Until then watch for frequent updates!