Wednesday, December 29, 2010

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

Wednesday, October 20, 2010

HAO/BioSynC Meeting

Group Photo

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!

Mitch's Tavern

Dinner at Mitch's Tavern

BBQ at Andy's

BBQ at Andy Deans's house


Dinner at Sitti

Thursday, October 14, 2010


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

Wednesday, July 14, 2010

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.

Tuesday, April 13, 2010

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

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.

Tuesday, February 16, 2010

The HAO is seeking a programmer!

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.


Saturday, January 30, 2010

Class, label, sensu

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.