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					               Leveraging ontologies to transform insect
                     taxonomy and phylogenetics




                                          Andy Deans
                                  North Carolina State University




John Hallmén
                             Acknowledgments
funding:
    • NSF Advances in Biological Informatics
    • Morphbank (NSF DBI-0446224)
    • HymAToL (NSF EF-0337220)
    • PEET: Monographic research on parasitic Hymenoptera (NSF DEB-0328922)

intellect and enthusiasm:
    • István Mikó, Katja Seltmann, Matt Yoder (NSCU)
    • Fredrik Ronquist (NRM)
    • Jim Balhoff, Hilmar Lapp, Todd Vision, Wasila Dahdul (NESCent)
    • Paula Mabee (USD)
    • Anne Maglia (MUS & T)
    • All the contributors! (especially the International Society of Hymenopterists)

                                                  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/
Part I Anatomy in Hymenoptera systematics

Part II Hymenoptera Anatomy Ontology

Part III How to build this resource

Part IV How to use this resource


                The End

               Questions?
                         Hymenoptera
                          >115,000 spp.
                             sawflies
                               ants
                                            sanmartin
                               bees
                           social wasps
                          parasitic wasps
orionmystery

                                                        Gary McDonald




               chi-liu         Art
       >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




202 terms




                                    ad hoc
                                  glossaries
Terminological Nightmare
Homonyms

 paramere
                 Synonyms

unguis
tarsal claw
pretarsal claw
          Other Terminological Problems
                          alitrunk
  uninformative terms                     gaster
  (=to be discouraged?)

           and

  taxon-specific terms




“lost” terms

thigmomere
thigmus
thigmochore
The ever increasing confusion in the
application of anatomical terminology in
entomology, is rapidly producing an
absolutely intolerable state of affairs...


Such chaotic ... needless confusion
would not ... be tolerated in any other
branch of research
                                             Grimaldi & Engel 2005


       - Guy C. Crampton (1915)
Serious Implications for Systematics

   25 taxonomic revisions from 5 lineages:
          5 “Symphyta”
          5 Ichneumonoidea
          5 Evaniomorpha + misc.
          5 Aculeata
          5 Chalcidoidea
Serious Implications for Systematics


 296 total anatomical terms (mean=43):
        • 28 common across all
        • 155 lineage-specific
        • 3-5 overlapped within a lineage
        • 86 author-specific
Serious Implications for Systematics

       1.   non-homologous characters
       2.   duplicated characters
       3.   miscommunication
       4.   wasted effort
            Serious Implications for Genomics

                   1. mutant phenotype description
                   2. gene expression annotation



“stumpy” = abdomen shortened
“hunchback” = thoracic segments compressed
“glass” = eye facets poorly differentiated and number reduced
“short wings” = small mesothoracic wings; metathoracic wings project out from body
Part I   Anatomy in Hymenoptera systematics

Part II Hymenoptera Anatomy Ontology

Part III How to build this resource

Part IV How to use this resource


                The End

               Questions?
                       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 =

a) textual definition            anatomical structures
b) annotation



  Formal representation of concepts within a domain
    and the relationships between those concepts.


                                            Hymenoptera
                                            anatomy
          is_a
          part_of

                    (in Computer Science)
harpe

 The sclerite on the external male
 genitalia that is connected basally to
 the gonostipes via cojunctiva and the
 proximal and distal gonostipes-harpe
 muscles.

  Formal representation of concepts within a domain
    and the relationships between those concepts.




        harpe            is_a         sclerite
        harpe           part_of       external male genitalia
        paramere       synonym        harpe
        palette        synonym        harpe
                gonosquama      synonym        harpe
                     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



leg is a segmented appendage
that is involved in locomotion
 Hymenoptera anatomy...

                              mesoscutum                fore wing
                                                        costal vein   fore wing
                                           tegula                     pterostigma
                           head

       eye (or
                                                                                              tergite
       compound eye)



flagellomere




                 clypeus                                                                    sternite


               fore leg
               tibia                                                                               hind leg tibia
                                                    mesopleuron
        fore leg
        basitarsus                                                         hind leg femur

     tarsal claw

John Hallmén
               Other relevant ontologies

Gene Ontology


                 eye pigment biosynthetic process

"The chemical reactions and pathways resulting in the formation of eye
pigments, any general or particular coloring matter in living organisms,
found or utilized in the eye." (GOC:ai)


eye pigment anabolism      synonym eye pigment biosynthetic process
eye pigment biosynthesis synonym eye pigment biosynthetic process
eye pigment formation      synonym eye pigment biosynthetic process
eye pigment synthesis      synonym eye pigment biosynthetic process
eye pigment biosynthetic process is_a eye pigment metabolic process
eye pigment biosynthetic process is_a pigment biosynthetic process
              Other relevant ontologies

Units of Measurement



                            millimeter

    "A length unit which is equal to one thousandth of a meter
    or 10^[-3] m." (http://physics.nist.gov/cuu/Units/)

    millimeter is_a         length unit
    mm         synonym      millimeter
              Other relevant ontologies

Phenotypic Quality (PATO)



                              yellow

    "A color hue with medium wavelength of that portion of the
    visible spectrum lying between orange and green, evoked
    in the human observer by radiant energy with wavelengths
    of approximately 570 to 590 nanometers."
    (http://dictionary.reference.com/)

    yellow is_a     color
          Other relevant ontologies

Spatial



                       dorsal to

          dorsal to   inverse_of ventral to
          superior to synonym dorsal to
            Other relevant ontologies

Taxonomic


                          Apis

            Apis   is_a   Apini

            Apis andreniformis    is_a   Apis
            Apis florea           is_a   Apis
            Apis dorsata          is_a   Apis
            Apis cerana           is_a   Apis
            Apis koschevnikovi    is_a   Apis
            Apis mellifera        is_a   Apis
            Apis nigrocincta      is_a   Apis
                 Why do this?

1. standardize our vocabulary for future publications




2. extract information from publications/databases
partonomy!
Part I   Anatomy in Hymenoptera systematics

Part II Hymenoptera Anatomy Ontology

Part III How to build this resource

Part IV How to use this resource


                The End

               Questions?
getting started...
                                                            backend



                                                      data dump




mx                                                                                 .obo


                                                [Term]
                                                id: 587

              CS colleagues:                    name: scrobal groove
                                                def: "A horizontal groove on the mesopleuron that may be
              - unsupervised machine learning   continuous with the episternal groove anteriorly and ends at the
                                                pleural grove posteriorly”
              - semantic image searching        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

OBO Foundry
Accessioning data - manually
    Accessioning data - text mining and extraction




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
Reaccessioning data - tagging
               Where we are now...

   2,214 terms
   2,234 relationships
   13 contributors (of 40 added to the project)


homonyms:
   e.g., anellus, speculum, pedicel, gaster, face, stigma,
   disc, metapleural triangle, uncus, paramere...etc.

chaotic character systems:
   e.g., propodeal ridges, pronotal ridges, glands,
   occipital carinae, cuticular patches, male and female
   genitalia, thoracic musculature
Part I   Anatomy in Hymenoptera systematics

Part II Hymenoptera Anatomy Ontology

Part III How to build this resource

Part IV How to use this resource


                The End

               Questions?
      1. Text Mark-up


• quality control
• provide definitions
proofing tool   http://hymglossary.tamu.edu/




                                               homonym!
http://evanioidea.info
Web-accessible taxon descriptions
   • high-lighting for definitions
          • and feedback
      1. Text Mark-up


• quality control
• provide definitions
• in concert with other ontologies
                (future)
distance from the carina posterior to the mesoscutellum to
the process dorsal to the propodeal foramen = 0.11 mm



                           PATO
                          spatial
                           HAO
                   units of measurement
       2. Search Algorithm
                (future)

• exploit the logic for efficient queries
• diagnostic tools
Search for -
 “claw”
 “auxilia”
 “empodium”
 “empodia”
 “planta”
 “plantae”
 “pretarsus”
 “pretarsi”
 “orbicula”
 “orbiculae”
 “arolium”
 “pulvillum”
 “pulvilla”
 “unguifer”
 “manubrium”
 “ungues”
 “unguis”
 “arcus”
 “dorsal plate”
     OR


“pretarsus”
       []
include related
     terms
Flagellomere 1:

(0) without multiporous
plate sensilla

(1) with multiporous
plate sensilla
>115,000 species descriptions




 Which taxa have
 mesoscutellum
    orange?

 Which taxa have
   tarsal claw
   pectinate?

 Which taxa have
 fore wing M+CU
     absent?
 3. Gene annotations
                       (future)

• describe mutant phenotypes
• gene expression information




                              .obo
    [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
  4. Auto-scoring characters
                (future)

• exploit the logic to score morphology




  5. Species description tools
                (future)

            • clickable
            • autocomplete
                 Summary
1. anatomical terminology is currently messy
2. we intend to straighten it out, and...
3. provide two resources for the research community:
Part I   Anatomy in Hymenoptera systematics

Part II Hymenoptera Anatomy Ontology

Part III How to build this resource

Part IV How to use this resource


                The End

               Questions?

				
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