Slides for Animal Behavior Society 2015 meeting on capturing narrative descriptions of behavior in database or semantic web formats.

1. Capturing Narrative Behavior
Descriptions in the Arachnolingua
Database
Peter E. Midford
peter.midford@gmail.com
@pmidford

2. What this is not about
• Not about mating systems
– Some courtship data used as example
• Not really about math modeling
– But is about data modeling
• Sort of about Ontologies
– But I’ll keep it to a minimum

3. Comparative Method in Behavior
• Martins 1996
• Where have all the Trees Gone? (Price,
Clapp & Ormund 2011)
• 2015 – still not a lot

4. Model or Data? (both)
Models
• Lots of descriptive models, not
necessarily applicable for
behavior change on a tree
• Limited comparative methods
(discrete, continuous variables)
• Maybe less than we thought
(Maddison&FitzJohn 2015)
Data
• Much less than genomics is
churning out
• Maybe more than morphology
• Morphology (and to a limited
extent genomics) have fossils
• We need to make the most of
the limited data we have (cf.
Caetano&Aisenberg 2014)

5. Narrative Data
• Ethograms
• Species Descriptions
• Incidental observations
• Field Notes?

6. Why Spiders?
• Active, terrestrial animals
• Lots of natural history
• Good test of behavior vocabularies
• Some of this applies to other arachnids
(scorpions, opiliones)
• Potential use in applied behavior?

7. Types and Individuals
Types
• Higher taxa*
• Behavior categories
• Have subtypes
• Examples:
– Class Arachnida
– Courtship behavior
– Palps that are part of some
Tetragnatha spider
– Courtship behavior
performed by some male
Habronattus spiders
Individuals
• Organisms
• Events
• Have parts
• Examples
– Courtship initiated at 06:34
on videotape PEM27
– The female spider in the
previous courtship
– The left leg I of that female

8. Ontologies
• Ontologies are vocabularies that describe types
– Types are either primitive (undefined) or
– Defined in terms of relationships between
individuals of that type and those of another
type
– Example: palps that are part of some
Tetragnatha

9. Text from Eberhard and Huber (1998)

12. Testing the vocabulary
• Arachnolingua originally set up to test a
vocabulary of behavior terms (the NBO).
• Pilot study results suggest NBO did better than
expected, but probably because NBO terms
were paired with terms from a spider anatomy
vocabulary.

13. Recent Workshops
• Phenotype Ontologies RCN 2013
– Addressed representation of behavior and mental states across
multiple vocabularies
– Identified need for a vocabulary specifically for behavioral
ecology/ethology
• ABS 2014
– Group of 4 conveners and 13 invited attendees reviewed the existing
NBO for suitability and reorganization to create a subset for behavioral
ecology
• Future Workshop (planned for this fall)
– Subset of last year’s attendees will meet with knowledge
representation experts and gatekeepers to review and start
implementation of the new vocabulary
• Ask Sue Margulis or myself for more details

14. Text from Eberhard and Huber (1998)

15. Capturing Temporal Ordering
Courtship
Approach MountDisplay
part of part of part of

16. Capturing Temporal Ordering
Courtship
Approach MountDisplay
part of part of part of
precedes precedes

17. Capturing Temporal Ordering
part of
part of
part of
precedes precedes
MountDisplay Approach
Courtship
This year

18. Capturing Temporal Ordering
Courtship
Approach MountDisplay
part of
part of
part of
precedes precedes
part of
part of
part of
precedes precedes
MountDisplay Approach
Courtship
This yearLast year

19. Capturing Temporal Ordering
Courtship
Approach MountDisplay
part of
part of
part of
precedes precedes
part of
part of
part of
precedes precedes
MountDisplay Approach
Courtship
This yearLast year

20. Capturing Temporal Ordering
Courtship
Approach MountDisplay
part of
part of
part of
precedes precedes
part of
part of
part of
precedes precedes
MountDisplay Approach
Courtship
This yearLast year

21. Document/
Publication
Document/
Publication
Document/
Publication
Narrative Narrative Narrative Narrative Narrative
Individual Individual Individual
male
male
female
female
parent defender
intruder
new resident

22. Arachnolingua

23. Open Data (figshare) ✔
Open Source Code (github) ✔
Replicable Packaging (e.g. docker) ✕
Sustainability ?
Is It Open?
Github: https://github.com/pmidford/arachadmin
https://github.com/pmidford/owlbuilder
https://github.com/pmidford/SpiderBehavior
Figshare: http://figshare.com/articles/Arachadmin_database_export/865719
This talk: http://www.slideshare.net/pmidford/midford2015

24. Acknowledgements
Phenotype RCN
Anne Clark
Sue Margulis
Cyndy Parr
And 2014 workshop attendees
NESCent
Open Tree of Life
Jim Balhoff