Getting Started with the HymenopteraAnatomical Ontology(HOW H.A.O.)(HOW H.A.O.)

HAO group (http://hymao.org/)

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hymao.orghymao.blogspot.comhao_project6. Matthew Bertone - matthew.bertone@gmail.com1. Matthew Yoder – diapriid@gmail.com5. Andrew Deans – andy_deans@ncsu.edu2. István Mikó – istvan.miko@gmail.com4. Katja seltmann – katja_seltmann@ncsu.edu3. Andrew Ernest

1. Define our problem

2. Define Ontology (in part)

3. Show how ontology could be a solution with lotsof 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

flagellomere

eye (orcompound eye)

head

mesoscutum

tegula

fore wingcostal vein fore wing

pterostigma

tergite

clypeus

fore legtibia

fore legbasitarsus

tarsal claw

mesopleuron

hind leg femur

sternite

hind leg tibia

Hymenoptera anatomy...

>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

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)

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.

We have NO single anatomical reference

ad hoc glossaries

202 terms

Terminological Problems - Homonyms

a.k.a. the paramere problem

unguistarsal clawpretarsal claw

Terminological Problems - Synonyms

“lost” terms

uninformative terms (=to be discouraged?Concept of preferred

terms?)and

taxon-specific terms

alitrunk

gaster

Terminological Problems - Other

thigmomerethigmusthigmochore

1. non-homologous characters

2. duplicated characters

3. miscommunication

4. wasted effort

Serious Implications for Systematics

1. mutant phenotype description

2. gene expression annotation

3 Nasonia spp.

Apis mellifera

Serious Implications for Genomics

3 Formicidae spp.

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.

OBOhttp://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 =

anatomical structures

Hymenopterology

is_apart_of

(in Computer Science)

a) genus-differentiab) 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)

?

[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

mx

CS colleagues:- unsupervised machine learning- semantic image searching

hymenoptera community

text files. HAO curators

Accessioning data - manually

distance from the carina posterior to the mesoscutellum to the process dorsal to the propodeal foramen = 0.11 mmdistance 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

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: 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

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

Where we are now...

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

• exploit the logic for efficient queries

• diagnostic tools

2. Search Algorithm(future)

Community consensus. Never has to happen. No preferred term.

OR

“pretarsus”

[] include related

terms

Search for -“claw”

“auxilia”

“empodium”

“empodia”

“planta”

“plantae”

“pretarsus”

“pretarsi”

“orbicula”

“orbiculae”

“arolium”

“pulvillum”

“pulvilla”

“unguifer”

“manubrium”

“ungues”

“unguis”

“arcus”

“dorsal plate”

>115,000 species descriptions

Which taxa have tarsal claw pectinate?

Which taxa have fore wing M+CU

absent?

Which taxa have mesoscutellum

orange?

• describe mutant phenotypes

• gene expression information

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

• exploit the logic to score morphology

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 messy2. we intend to straighten it out, and...3. we will provide two resources for the research community:

funding:

• NSF Advances in Biological Informatics (DBI-0850223)• Morphbank (NSF DBI-0446224)• National Evolutionary Synthesis Center (NESCent) (NSF EF-0423641)• PEET: Monographic research on parasitic Hymenoptera (NSF DEB-0328922)

intellect and enthusiasm:

• 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/

Acknowledgments

Site: hymao.org blog: hymao.blogspot.com twitter: hao_projectMatthew Bertone (matthew.bertone@gmail.com), Matthew Yoder (diapriid@gmail.com)Andrew Deans (andy_deans@ncsu.edu), István Mikó (istvan.miko@gmail.com)Katja seltmann – katja_seltmann@ncsu.edu

Exercise 1:1. get an ontology from obo foundry2. get obo edit 2.0 from sourceforge and install3. upload and verify one ontology4. view a tree5. look for term in text file and in tree6. 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_a2. Grab images off of google to illustrate the ontology; get images from morphbank services3. Refer back to obo file from the foundry and see how this is represented

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.obo-1_2.shtml (1.2)

http://www.obofoundry.org/

is_a, part_of

genus-differentia =

1. definiendum: the term being defined2. 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

B

A X

harpe is_a scleriteharpe part_of external male genitaliaparamere synonym harpepalette synonym harpegonosquama synonym harpe