Midford2015

Capturing Narrative Behavior Descriptions in the Arachnolingua Database

Peter E. [email protected]

@pmidford

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

Comparative Method in Behavior

• Martins 1996• Where have all the Trees Gone? (Price,

Clapp & Ormund 2011)• 2015 – still not a lot

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)

Narrative Data

• Ethograms• Species Descriptions• Incidental observations• Field Notes?

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?

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

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

Text from Eberhard and Huber (1998)

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.

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

Text from Eberhard and Huber (1998)

Capturing Temporal Ordering

Courtship

Approach MountDisplay

part of part of part of

Capturing Temporal Ordering

Courtship

Approach MountDisplay

part of part of part of

precedes precedes

Capturing Temporal Ordering

part ofpart of

part of

precedes precedes MountDisplay Approach

Courtship

This year

Capturing Temporal Ordering

Courtship

Approach MountDisplay

part ofpart of

part of

precedes precedes

part ofpart of

part of

precedes precedes MountDisplay Approach

Courtship

This yearLast year

Capturing Temporal Ordering

Courtship

Approach MountDisplay

part ofpart of

part of

precedes precedes

part ofpart of

part of

precedes precedes MountDisplay Approach

Courtship

This yearLast year

Capturing Temporal Ordering

Courtship

Approach MountDisplay

part ofpart of

part of

precedes precedes

part ofpart of

part of

precedes precedes MountDisplay Approach

Courtship

This yearLast year

Document/Publication

Document/Publication

Document/Publication

Narrative Narrative Narrative Narrative Narrative

Individual Individual Individual

male malefemale

femaleparent defender

intruder

new resident

Arachnolingua

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

Acknowledgements

Phenotype RCN

Anne ClarkSue MargulisCyndy ParrAnd 2014 workshop attendees

NESCentOpen Tree of Life

Jim Balhoff