Introducing the HAO's analyzer, feedback, and API

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

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

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

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.

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

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

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.