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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 - [email protected]. Matthew Yoder – [email protected]. Andrew Deans – [email protected]. István Mikó – [email protected]. Katja seltmann – [email protected]. Andrew Ernest
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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
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Hymenoptera
>115,000 spp.
sawflies
ants
bees
social wasps
parasitic wasps
Art
orionmystery
sanmartin
Gary McDonald
chi-liu
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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...
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>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.
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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.
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We have NO single anatomical reference
ad hoc glossaries
202 terms
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Terminological Problems - Homonyms
a.k.a. the paramere problem
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unguistarsal clawpretarsal claw
Terminological Problems - Synonyms
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“lost” terms
uninformative terms (=to be discouraged?Concept of preferred
terms?)and
taxon-specific terms
alitrunk
gaster
Terminological Problems - Other
thigmomerethigmusthigmochore
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1. non-homologous characters
2. duplicated characters
3. miscommunication
4. wasted effort
Serious Implications for Systematics
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1. mutant phenotype description
2. gene expression annotation
3 Nasonia spp.
Apis mellifera
Serious Implications for Genomics
3 Formicidae spp.
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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).
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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
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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
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How to do this...
http://oboedit.org/ (2.0)http://www.geneontology.org/GO.format.obo-1_2.shtml (1.2)
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Why do this? (ontology solving real
issues)
Solution (ontology creation)
?
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[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
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Accessioning data - manually
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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
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Reaccessioning data - tagging
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Accessioning data - batch upload
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Accessioning data - batch upload
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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
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Accessioning data - text mining and extraction
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visualization
defined?tags?figured?# children?is parent?
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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...
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1. Text Mark-up
• quality control
• provide definitions
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proofing tool http://hymglossary.tamu.edu/
homonym!
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http://evanioidea.info
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Web-accessible taxon descriptions
• high-lighting for definitions
• and feedback
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• exploit the logic for efficient queries
• diagnostic tools
2. Search Algorithm(future)
Community consensus. Never has to happen. No preferred term.
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OR
“pretarsus”
[] include related
terms
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Search for -“claw”
“auxilia”
“empodium”
“empodia”
“planta”
“plantae”
“pretarsus”
“pretarsi”
“orbicula”
“orbiculae”
“arolium”
“pulvillum”
“pulvilla”
“unguifer”
“manubrium”
“ungues”
“unguis”
“arcus”
“dorsal plate”
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>115,000 species descriptions
Which taxa have tarsal claw pectinate?
Which taxa have fore wing M+CU
absent?
Which taxa have mesoscutellum
orange?
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• 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
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• exploit the logic to score morphology
4. Auto-scoring characters(future)
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Flagellomere 1:
(0) without multiporous plate sensilla
(1) with multiporous plate sensilla
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5. SUPERUBER ARTHROPOD ONTOLOGY
Flies
Hyms
Other arthropods
wing = wing = wing ?
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Summary
1. anatomical terminology is currently messy2. we intend to straighten it out, and...3. we will provide two resources for the research community:
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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 ([email protected]), Matthew Yoder ([email protected])Andrew Deans ([email protected]), István Mikó ([email protected])Katja seltmann – [email protected]
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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
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XML- EXtensible Markup Language.
http://www.w3schools.com/XML/default.asp
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XML- EXtensible Markup Language.
http://www.w3schools.com/XML/default.asp
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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/
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is_a, part_of
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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
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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