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Formal representation of concepts within a domain and the relationships between those concepts. ontology ≠ ontogeny Ontolo...
male genitalia  phallus  parameres  copulatoria  genital capsule  genital armature phallic apparatus  genital apparatus ar...
www.hymao.org this real thing is a class male genitalia  phallus  parameres  copulatoria  genital capsule  genital armatur...
male genitalia   phallus  parameres  copulatoria  genital capsule  genital armature phallic apparatus  genital apparatus a...
[Term] id: HAO:0000312 name: external male genitalia def: "The compound organ that is involved in coupling with the f...
Nasonia spp. >50 mutants implications: vehicle to integrate research
process mx  http://purl.oclc.org/NET/mx-database MX
process mx software (development) community feedback (Hymenoptera, ontology & computer science) exposure
2,682 labels 1,382 classes    865 references   3058 times referenced   1201 from just a few papers  
Term extraction from BHL 353 JHR
<ul><li>number of new labels added to database: 347   </li></ul><ul><li>number of papers: 23 </li></ul><ul><li>-----------...
results highest number > 50 vein (465) wing (282) cell (219) wing vein (114)
results carina (187) tergum (183) tergites (128) propodeum (83) sternum (65) highest number > 50
results smooth (94) small (87) short (85) highest number > 50
results glossa (72) highest number > 50
results cell (219) area (116) base (84) apex (76) body (71) highest number > 50
Future <ul><li>add the rest of the 353  </li></ul><ul><li>articles </li></ul><ul><li>define new classes </li></ul><ul><li>...
<ul><li>funding:  </li></ul><ul><ul><li>Advances in Biological Informatics ( NSF DBI-0850223 ) </li></ul></ul><ul><ul><li>...
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Extraction and reflection: early evolution of the Hymenoptera Anatomy Ontology

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10 min presentation from the 2009 Entomological Society of America Meeting describing the extraction of classes and labels from OCRed journal articles found on the Biodiversity Heritage Library and the building of the Hymenoptera Anatomy Ontology (http://hymao.org)

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Extraction and reflection: early evolution of the Hymenoptera Anatomy Ontology

  1. 3. Formal representation of concepts within a domain and the relationships between those concepts. ontology ≠ ontogeny Ontology domain = hymenoptera concept = class (an real anatomical thing) label = words used to represent anatomical things          ****a class can contain many labels***
  2. 4. male genitalia phallus parameres  copulatoria  genital capsule  genital armature phallic apparatus  genital apparatus armatura genitalis genital appendage copulatory apparatus external genital organ male copulatory organ www.hymao.org a class can have many labels
  3. 5. www.hymao.org this real thing is a class male genitalia phallus parameres  copulatoria  genital capsule  genital armature phallic apparatus  genital apparatus armatura genitalis genital appendage copulatory apparatus external genital organ male copulatory organ a class can have many labels
  4. 6. male genitalia  phallus parameres  copulatoria  genital capsule  genital armature phallic apparatus  genital apparatus armatura genitalis genital appendage copulatory apparatus external genital organ male copulatory organ www.hymao.org a class can have many labels this real thing is a class these are all labels
  5. 7. [Term] id: HAO:0000312 name: external male genitalia def: &quot;The compound organ that is involved in coupling with the female genitalia and with the intromission of spermatozoa and seminal fluid.&quot; [HAO:im] synonym: &quot;armatura genitalis&quot; [] synonym: &quot;copulatoria&quot; [] synonym: &quot;copulatory apparatus&quot; [] synonym: &quot;genital apparatus&quot; [] synonym: &quot;genital appendage&quot; [] synonym: &quot;genital armature&quot; [] synonym: &quot;genital capsule&quot; [] synonym: &quot;genital organ&quot; [] synonym: &quot;male copulatory organ&quot; [] synonym: &quot;parameres&quot; [] synonym: &quot;phallic apparatus&quot; [] synonym: &quot;phallus&quot; [] relationship: part_of HAO:0000505 ! male genitalia is_a: HAO:0000024 ! compound organ [Term] id: HAO:0000313 name: external paramera def: &quot;The anatomical cluster that is composed of the gonostipites and volsellae.&quot; [HAO:im] relationship: part_of HAO:0000312 ! external male genitalia is_a: HAO:0000041 ! anatomical cluster  Open Biomedical Ontologies (OBO)
  6. 8. Nasonia spp. >50 mutants implications: vehicle to integrate research
  7. 9. process mx http://purl.oclc.org/NET/mx-database MX
  8. 10. process mx software (development) community feedback (Hymenoptera, ontology & computer science) exposure
  9. 11. 2,682 labels 1,382 classes   865 references   3058 times referenced   1201 from just a few papers  
  10. 12. Term extraction from BHL 353 JHR
  11. 13. <ul><li>number of new labels added to database: 347   </li></ul><ul><li>number of papers: 23 </li></ul><ul><li>-------------------------------------------------------------- </li></ul><ul><li>137 PATO labels </li></ul><ul><li>&quot;PATO is an ontology of phenotypic qualities , intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation&quot; </li></ul><ul><li>(i.e. NOT ending up in the HAO ) </li></ul><ul><li>  </li></ul><ul><li>before: 464 </li></ul><ul><li>now: 601 </li></ul><ul><li>only 55 of these presently in PATO ----------------------------------------------------------- </li></ul><ul><li>210 new labels for the HAO </li></ul><ul><li>(Do not know how many will result in new classes) </li></ul><ul><li>---------------------------- </li></ul><ul><li>In the 23 papers….. </li></ul><ul><li>1145 distinct labels </li></ul><ul><li>8802 occurrences of those terms </li></ul><ul><li>4469 < 50 times </li></ul><ul><li>4333 > 50 times </li></ul><ul><li>  </li></ul>results
  12. 14. results highest number > 50 vein (465) wing (282) cell (219) wing vein (114)
  13. 15. results carina (187) tergum (183) tergites (128) propodeum (83) sternum (65) highest number > 50
  14. 16. results smooth (94) small (87) short (85) highest number > 50
  15. 17. results glossa (72) highest number > 50
  16. 18. results cell (219) area (116) base (84) apex (76) body (71) highest number > 50
  17. 19. Future <ul><li>add the rest of the 353 </li></ul><ul><li>articles </li></ul><ul><li>define new classes </li></ul><ul><li>define PATO terms </li></ul><ul><li>  </li></ul><ul><li>reevaluate workflow (create better proofing tools) </li></ul><ul><li>work with Biodiversity Heritage Library (link to label descriptions?) </li></ul><ul><li>capture complex information in MX and assemble information using ontology (HAO, PATO, etc..) </li></ul>
  18. 20. <ul><li>funding: </li></ul><ul><ul><li>Advances in Biological Informatics ( NSF DBI-0850223 ) </li></ul></ul><ul><ul><li>NESCent ( NSF EF-0423641 )  </li></ul></ul><ul><ul><li>Morphbank ( NSF DBI-0446224 ) </li></ul></ul><ul><ul><li>HymAToL ( NSF EF-0337220 ) </li></ul></ul><ul><ul><li>PEET: Monographic research on parasitic Hymenoptera ( NSF DEB-0328922 ) </li></ul></ul><ul><ul><li>  </li></ul></ul><ul><li>  </li></ul><ul><li>  </li></ul><ul><li>  </li></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>Rod Page, Biodiveristy Heritage Library, Rick Prelinger </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>International Society of Hymenopterists </li></ul></ul><ul><ul><li>All the contributors </li></ul></ul>Acknowledgments

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