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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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