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_addr...
1. Define our problem 2. Define Ontology (in part) 3. Show how ontology could be a solution with lots of added benefits Wo...
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 w...
>115,000 species descriptions Head  transverse to subquadrate in dorsal view;  hyperoccipital carina  absent;  occipital c...
7,900 morphological phylogenetics papers 1. Shape of  tentorial bridge : (0) straight (1) distinctly arched.  2.  Corpoten...
We have  NO  single anatomical reference ad hoc  glossaries 202 terms
Terminological Problems -  Homonyms a.k.a. the paramere problem
unguis tarsal claw pretarsal claw Terminological Problems -  Synonyms
“ lost” terms uninformative terms  (=to be discouraged? Concept of preferred terms?) and taxon-specific terms alitrunk gas...
 
<ul><li>non-homologous characters </li></ul><ul><li>duplicated characters </li></ul><ul><li>miscommunication </li></ul><ul...
<ul><li>mutant phenotype description </li></ul><ul><li>gene expression annotation </li></ul>3  Nasonia  spp. Apis mellifer...
 
What is an ontology? ontology ≠ ontogeny The history of structural change in a unity, which can be a cell, an organism, or...
ontology  An explicit formal specification of how to represent the objects,  concepts and other entities that are assumed ...
Formal representation of concepts within a domain and the relationships between those concepts. ontology = (in Computer Sc...
 
 
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: &quot;A horizontal groove on th...
 
Accessioning data  - manually
 
distance from the carina posterior to the mesoscutellum to the process dorsal to the propodeal foramen = 0.11 mm distance ...
Reaccessioning data  - tagging
Accessioning data  - batch upload
Accessioning data  - batch upload
Fisher BL, Smith MA. 2008.  A revision of Malagasy species of  Anochetus  Mayr and  Odontomachus  Latreille (Hymenoptera: ...
 
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 ...
 
 
1. Text Mark-up <ul><li>quality control </li></ul><ul><li>provide definitions </li></ul>
proofing tool http://hymglossary.tamu.edu/ homonym!
http://evanioidea.info
Web-accessible taxon descriptions •  high-lighting for definitions •  and feedback
<ul><li>exploit the logic for efficient queries </li></ul><ul><li>diagnostic tools </li></ul>2. Search Algorithm (future) ...
OR “ pretarsus” [  ]  include related terms
Search for - “ claw” “ auxilia” “ empodium” “ empodia” “ planta” “ plantae” “ pretarsus” “ pretarsi” “ orbicula” “ orbicul...
>115,000 species descriptions Which taxa have tarsal claw pectinate? Which taxa have fore wing M+CU absent? Which taxa hav...
<ul><li>describe mutant phenotypes </li></ul><ul><li>gene expression information </li></ul>3. Gene annotations (future) “ ...
<ul><li>exploit the logic to score morphology </li></ul>4. Auto-scoring characters (future)
Flagellomere 1: (0)  without multiporous plate sensilla (1)  with multiporous plate sensilla
 
5.  SUPERUBER ARTHROPOD ONTOLOGY Flies Hyms Other arthropods wing = wing = wing ?
Summary 1. anatomical terminology is currently messy 2. we intend to straighten it out, and... 3. we will provide two reso...
<ul><li>funding: </li></ul><ul><ul><li>NSF Advances in Biological Informatics ( DBI-0850223 ) </li></ul></ul><ul><ul><li>M...
 
Exercise 1: 1. get an ontology from obo foundry 2. get obo edit 2.0 from sourceforge and install 3. upload and verify one ...
XML- EXtensible Markup Language. http://www.w3schools.com/XML/default.asp
XML- EXtensible Markup Language. http://www.w3schools.com/XML/default.asp
https://lists.sourceforge.net/lists/listinfo/obo-discuss http://oboedit.org/ (2.0) http://www.geneontology.org/GO.format.o...
is_a, part_of
genus-differentia  = 1.  definiendum : the term being defined 2.  genus : the broader category for that term (the difinien...
harpe The sclerite that is connected basally to the gonostipes via cojunctiva and the proximal and distal gonostipes-harpe...
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Getting Started with the Hymenoptera Anatomical Ontology

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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

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  • 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
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  • Matthew Bertone - [email_address] Matthew Yoder – diapriid@gmail.com Andrew Deans – andy_deans@ncsu.edu Katja seltmann – katja_seltmann@ncsu.edu 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

    1. 1. Getting Started with the Hymenoptera Anatomical Ontology (HOW H.A.O.) HAO group (http://hymao.org/)
    2. 2. 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
    3. 3. 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
    4. 4. Hymenoptera >115,000 spp. sawflies ants bees social wasps parasitic wasps Art orionmystery sanmartin Gary McDonald chi-liu
    5. 5. 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
    6. 6. >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. 7. 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)
    8. 8. We have NO single anatomical reference ad hoc glossaries 202 terms
    9. 9. Terminological Problems - Homonyms a.k.a. the paramere problem
    10. 10. unguis tarsal claw pretarsal claw Terminological Problems - Synonyms
    11. 11. “ lost” terms uninformative terms (=to be discouraged? Concept of preferred terms?) and taxon-specific terms alitrunk gaster Terminological Problems - Other thigmomere thigmus thigmochore
    12. 13. <ul><li>non-homologous characters </li></ul><ul><li>duplicated characters </li></ul><ul><li>miscommunication </li></ul><ul><li>wasted effort </li></ul>Serious Implications for Systematics
    13. 14. <ul><li>mutant phenotype description </li></ul><ul><li>gene expression annotation </li></ul>3 Nasonia spp. Apis mellifera Serious Implications for Genomics 3 Formicidae spp.
    14. 16. 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).
    15. 17. 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
    16. 18. 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
    17. 21. How to do this... http://oboedit.org/ (2.0) http://www.geneontology.org/GO.format.obo-1_2.shtml (1.2)
    18. 22. Why do this? (ontology solving real issues) Solution (ontology creation) ?
    19. 23. mx hymenoptera community text files. HAO curators [Term] id: 587 name: scrobal groove def: &quot;A horizontal groove on the mesopleuron that may be continuous with the episternal groove anteriorly and ends at the pleural grove posteriorly” ref: &quot;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
    20. 25. Accessioning data - manually
    21. 27. 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
    22. 28. Reaccessioning data - tagging
    23. 29. Accessioning data - batch upload
    24. 30. Accessioning data - batch upload
    25. 31. 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
    26. 33. Accessioning data - text mining and extraction
    27. 34. visualization defined? tags? figured? # children? is parent?
    28. 36. 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...
    29. 39. 1. Text Mark-up <ul><li>quality control </li></ul><ul><li>provide definitions </li></ul>
    30. 40. proofing tool http://hymglossary.tamu.edu/ homonym!
    31. 41. http://evanioidea.info
    32. 42. Web-accessible taxon descriptions • high-lighting for definitions • and feedback
    33. 43. <ul><li>exploit the logic for efficient queries </li></ul><ul><li>diagnostic tools </li></ul>2. Search Algorithm (future) Community consensus. Never has to happen. No preferred term.
    34. 44. OR “ pretarsus” [  ] include related terms
    35. 45. Search for - “ claw” “ auxilia” “ empodium” “ empodia” “ planta” “ plantae” “ pretarsus” “ pretarsi” “ orbicula” “ orbiculae” “ arolium” “ pulvillum” “ pulvilla” “ unguifer” “ manubrium” “ ungues” “ unguis” “ arcus” “ dorsal plate”
    36. 46. >115,000 species descriptions Which taxa have tarsal claw pectinate? Which taxa have fore wing M+CU absent? Which taxa have mesoscutellum orange?
    37. 47. <ul><li>describe mutant phenotypes </li></ul><ul><li>gene expression information </li></ul>3. Gene annotations (future) “ 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
    38. 48. <ul><li>exploit the logic to score morphology </li></ul>4. Auto-scoring characters (future)
    39. 49. Flagellomere 1: (0) without multiporous plate sensilla (1) with multiporous plate sensilla
    40. 51. 5. SUPERUBER ARTHROPOD ONTOLOGY Flies Hyms Other arthropods wing = wing = wing ?
    41. 52. 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:
    42. 53. <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 ( matthew.bertone@gmail.com), Matthew Yoder ( diapriid@gmail.com) Andrew Deans ( andy_deans@ncsu.edu), István Mikó ( istvan.miko@gmail.com) Katja seltmann – [email_address]
    43. 55. 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
    44. 56. XML- EXtensible Markup Language. http://www.w3schools.com/XML/default.asp
    45. 57. XML- EXtensible Markup Language. http://www.w3schools.com/XML/default.asp
    46. 58. https://lists.sourceforge.net/lists/listinfo/obo-discuss http://oboedit.org/ (2.0) http://www.geneontology.org/GO.format.obo-1_2.shtml (1.2) http://www.obofoundry.org/
    47. 59. is_a, part_of
    48. 60. 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
    49. 61. 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
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