For Biodiversity Informatics workshop in Stockholm, Friday September 18. Describing the Hymenoptera Anatomical Ontology. Authors: Matthew Yoder, Andrew Deans, Katja Seltmann, István Mikó, Matthew Bertone
Matthew Bertone - [email_address] Matthew Yoder – firstname.lastname@example.org Andrew Deans – email@example.com Katja seltmann – firstname.lastname@example.org Andrew Ernest Elizabeth McLoud
1 of 4 megadiverse insect orders important models of ecology and behavior
hymenopterans made of parts the phenotypes of which
Common use of some surface sculptuer terms are because they are the best illustrated. We are loosing neuance
Typically obo used by community Feeling that owl is where we want to be, more robust. Its what the CS people use
Introduce the obo format file: Namespace, autogenerated, unique id (once a HAO term must always be a HAO term), curator term.
Discovery by development of ontology along with the development of tools for creating and working with ontologies.
Getting Started with the Hymenoptera Anatomical Ontology
Getting Started with the Hymenoptera Anatomical Ontology (HOW H.A.O.) HAO group (http://hymao.org/)
1 2 5 6 4 3 hymao.org hymao.blogspot.com hao_project 6. Matthew Bertone - [email_address] 1. Matthew Yoder – [email_address] 5. Andrew Deans – [email_address] 2. István Mikó – [email_address] 4. Katja seltmann – [email_address] 3. Andrew Ernest
1. Define our problem 2. Define Ontology (in part) 3. Show how ontology could be a solution with lots of added benefits Workshop: - Go into detail of the process of creating an ontology - Goal? Remove some of the mystery
Hymenoptera >115,000 spp. sawflies ants bees social wasps parasitic wasps Art orionmystery sanmartin Gary McDonald chi-liu
John Hallmén Hymenoptera anatomy... flagellomere eye (or compound eye) head mesoscutum tegula fore wing costal vein fore wing pterostigma tergite clypeus fore leg tibia fore leg basitarsus tarsal claw mesopleuron hind leg femur sternite hind leg tibia
>115,000 species descriptions Head transverse to subquadrate in dorsal view; hyperoccipital carina absent; occipital carina complete, crenulate, closely approximated to foramen magnum dorsally; lateral ocellus contiguous with inner orbit ; eye glabrous or sparsely setose; frons nearly flat, antennal scrobe not developed; inner orbits distinctly diverging ventrally.
7,900 morphological phylogenetics papers 1. Shape of tentorial bridge : (0) straight (1) distinctly arched. 2. Corpotendon (anterior process from upper tentorial bridge forming the tendon of the posterior contractor of the pharynx ): (0) absent; (1) present. 7,150 functional morphology papers The entry into the wood can be done by first retracting the abdominal segments into their normal position and then by pressure of the whole abdomen ; in most cases observed, the stylus comes into contact with the wood. (Le Lannic & Nénon 1999)
We have NO single anatomical reference ad hoc glossaries 202 terms
Terminological Problems - Homonyms a.k.a. the paramere problem
What is an ontology? ontology ≠ ontogeny The history of structural change in a unity, which can be a cell, an organism, or a society of organisms, without the loss of the organization that allows that unity to exist (Maturana and Varela, 1987).
ontology An explicit formal specification of how to represent the objects, concepts and other entities that are assumed to exist in some area of interest and the relationships that hold among them. OBO http://www.geneontology.org/GO.format.obo-1_2.shtml http://protege.stanford.edu/doc/owl/getting-started.html http://www.cs.utexas.edu/~hamid/research/obo2owl.cgi#intro - dictonary.com
Formal representation of concepts within a domain and the relationships between those concepts. ontology = (in Computer Science) anatomical structures Hymenopterology is_a part_of a) genus-differentia b) annotation
How to do this... http://oboedit.org/ (2.0) http://www.geneontology.org/GO.format.obo-1_2.shtml (1.2)
Why do this? (ontology solving real issues) Solution (ontology creation) ?
mx hymenoptera community text files. HAO curators [Term] id: 587 name: scrobal groove def: "A horizontal groove on the mesopleuron that may be continuous with the episternal groove anteriorly and ends at the pleural grove posteriorly” ref: "Goulet H, Huber JT, 1993. Hymenoptera of the World: An Identification Guide to Families. Research Branch, Agriculture Canada Publication 1894/E., Ottawa, ON. 668 pp.” relationship: part_of 157 ! mesopleuron relationship: is_a 138 ! groove data dump .obo OBO Foundry CS colleagues: - unsupervised machine learning - semantic image searching
distance from the carina posterior to the mesoscutellum to the process dorsal to the propodeal foramen = 0.11 mm distance from the carina posterior to the mesoscutellum to the process dorsal to the propodeal foramen = 0.11 mm Phenotypic Quality(PATO) spatial HAO units of measurement
Fisher BL, Smith MA. 2008. A revision of Malagasy species of Anochetus Mayr and Odontomachus Latreille (Hymenoptera: Formicidae). PLoS ONE 3(5): e1787 doi:10.1371/journal.pone.0001787 Accessioning data - text mining and extraction
Accessioning data - text mining and extraction
visualization defined? tags? figured? # children? is parent?
Total terms: 2502 Changed in last week: 1 Changed in last month: 11 Without relationships: 1112 Without definitions: 1079 Relationships: 2398 Tags on terms: 3665 Figures on terms: 53 <ul><li>homonyms: </li></ul><ul><ul><li>e.g., anellus, speculum, pedicel, gaster, face, stigma, disc, metapleural triangle, uncus, paramere...etc. </li></ul></ul><ul><li>chaotic character systems: </li></ul><ul><ul><li>e.g., propodeal ridges, pronotal ridges, glands, occipital carinae, cuticular patches, male and female genitalia, thoracic musculature </li></ul></ul>Where we are now...
1. Text Mark-up <ul><li>quality control </li></ul><ul><li>provide definitions </li></ul>
Summary 1. anatomical terminology is currently messy 2. we intend to straighten it out, and... 3. we will provide two resources for the research community:
<ul><li>funding: </li></ul><ul><ul><li>NSF Advances in Biological Informatics ( DBI-0850223 ) </li></ul></ul><ul><ul><li>Morphbank ( NSF DBI-0446224 ) </li></ul></ul><ul><ul><li>National Evolutionary Synthesis Center (NESCent) ( NSF EF-0423641 ) </li></ul></ul><ul><ul><li>PEET: Monographic research on parasitic Hymenoptera ( NSF DEB-0328922 ) </li></ul></ul><ul><li>intellect and enthusiasm: </li></ul><ul><ul><li>Fredrik Ronquist (NRM) </li></ul></ul><ul><ul><li>Jim Balhoff, Hilmar Lapp, Todd Vision, Wasila Dahdul (NESCent) </li></ul></ul><ul><ul><li>Paula Mabee (USD) </li></ul></ul><ul><ul><li>Anne Maglia (MUS & T) </li></ul></ul><ul><ul><li>All the contributors! (especially the International Society of Hymenopterists) </li></ul></ul>Hymenoptera images: http://www.flickr.com/photos/orionmystery/1777817613 http://www.flickr.com/photos/leapfrog_photo/2893205919/ http://www.flickr.com/photos/sanmartin/2320291727/ http://www.flickr.com/photos/chi-liu/400478069/ http://www.flickr.com/photos/mcduck/2307414339/ http://www.flickr.com/photos/johnhallmen/3021409417/ Acknowledgments Site: hymao.org blog: hymao.blogspot.com twitter: hao_project Matthew Bertone ( email@example.com), Matthew Yoder ( firstname.lastname@example.org) Andrew Deans ( email@example.com), István Mikó ( firstname.lastname@example.org) Katja seltmann – [email_address]
Exercise 1: 1. get an ontology from obo foundry 2. get obo edit 2.0 from sourceforge and install 3. upload and verify one ontology 4. view a tree 5. look for term in text file and in tree 6. look up that relationship in the obo specifications Exercise 2: 1. group create an ontology of the human body. Try writing genus differentiae definitions and relating part_of, synonym_of and is_obsolete, is_a 2. Grab images off of google to illustrate the ontology; get images from morphbank services 3. Refer back to obo file from the foundry and see how this is represented
genus-differentia = 1. definiendum : the term being defined 2. genus : the broader category for that term (the difiniendum’s parent) 3. differentia : how that term differs from the genus’s other children B is an A that X B : an A that X
harpe The sclerite that is connected basally to the gonostipes via cojunctiva and the proximal and distal gonostipes-harpe muscles. grabber thing obsolete_synonym, is_obsolete, synonym harpe harpe is_a sclerite harpe part_of external male genitalia paramere synonym harpe palette synonym harpe gonosquama synonym harpe B A X