Semantic Ecoblogging and other news from SPIRE

1
Semantic Eco-blogging(and other news from SPIRE)

• Joel Sachs
• jsachs_at_cs.umbc.edu
• Cyndy Sims Parr
• csparr_at_umd.edu

2
Overview of Presentation

• Background on the SPIRE project.
• System concept global human sensor net
• Spotter and semantic eco-blogging
• Splickr
• A brief description of an experiment to correlate
  water quality data with invasive species
  occurrence data.

3
SPIRE(Semantic Prototypes in Research
Ecoinformatics)

• 5-year, NSF funded, inter-disciplinary effort
  involving UMBC University of Maryland UC Davis
  Rocky Mountain Biological Lab NASA Goddard Space
  Flight Centre.
• NBII in the middle.
• General focus on biodiversity and biocomplexity.
• Specific focus on invasive species.

4
Buzzword Glossary

• Ontology (Philosophy) The attempt to answer the
  question What exists?
• Ontology (Computer Science) A model of a domain
  (typically specifying classes, individuals, and
  possible relationships amongst classes and
  individuals) so explicit even a computer can
  understand it.
• Semantic Web The use of XML to represent
  ontologies, and to make assertions about the
  world based on those ontologies.
• Heavy emphasis on linking amongst datasets.
• Goal a web of data that can be treated as one
  big distributed database.

5
So far

• ELVIS
• A suite of tools motivated by the belief that
  food web structure plays a role in determining
  the success or failure of potential species
  invasions.
• Species List Constructor.
• Give a location, get a species list.
• Food Web Constructor.
• Give a species list, get a food web.
• Evidence Provider.
• Drill down on a predicted trophic link, and see
  evidence for and against the existence of that
  link.
• This illustrates our general attitude move away
  from answer providers to evidence providers.

6
So far Ontologies

• SpireEcoConcepts
• Medium size. Used for expressing trophic links
  and related information, including bibliographic
  info on studies.
• ETHAN
• Evolutionary trees and natural history.
• Huge.
• Observation ontology
• For semantic eco-blogging.
• Tiny.
• Invasives ontology
• Lightweight and extensible in the most trivial of
  manners.

7
So far Integration

• Swoogle
• Google for the semantic web.
• Crawls and indexes RDF documents.
• Computes metadata, including ontoRank.
• Tripleshop
• A SPARQL query engine.
• Leave out the FROM clause.
• Data comes from Swoogle
• Semi-automatic dataset constructor
• Our main platform for integration

8
Semantic Eco-blogging.

• Eco-blogs are popping up all over the place.
• Bloggers are both amateur nature-lovers, and
  working biologists.
• On April 24 in Washington DC, I saw a leopard
  slug. Heres a picture.
• These observations are, potentially, an important
  part of the ecological record.
• What was the earliest sighting of a robin
  hatching?
• What was the Northernmost sighting of the Asian
  Longhorn Beetle?
• Etc.
• System concept global human sensor net.
• SPOTTER
• A firefox plugin for creating OWL from field
  observations.
• Spotter map lets you see all spots
• Being tested at http//ebiquity.umbc.edu/fieldmark
  ing/ and other blogs near you.

9
(No Transcript)
10
(No Transcript)
11
(No Transcript)
12
Live Demo of Spotter and Fieldmarking

• (The following 4 slides are for those
  following along at home.)

13
(No Transcript)
14
(No Transcript)
15
(No Transcript)
16
(No Transcript)
17
A Brief Tour of Some Relevant Ontologies

• http//spire.umbc.edu/ontologies/InvasivesOntology
  .owl
• http//spire.umbc.edu/ontologies/lists/
• http//spire.umbc.edu/ontologies/lists/USFWSInjuri
  ousAnimals.owl
• http//spire.umbc.edu/ontologies/lists/Cal-IPC.owl
  

18
The Blogger Bioblitz

• Bioblitz a 24 hour inventory of all living
  things in a given area.
• Dual aims of establishing degree of biodiversity
  and popularizing science.
• The recent Blogger bioblitz.
• 17 bloggers from
• Sitka, Alaska Greece Toronto Santa Cruz DC
  etc.
• 1200 observations.
• Tripleshop was able, by combining the
  observations with background data, to respond to
  a number of ad-hoc queries.
• E.g. Show all observations of species defined as
  of concern.

19
Splickr

• Flickr has been handling geotagged pictures since
  late last year.
• Over 20 million.
• Splickr is a Flickr/Yahoo maps mashup that makes
  it easy to find pictures of particular species in
  a given area.
• All data gets represented in OWL.

20
(No Transcript)
21
(No Transcript)
22
(No Transcript)
23
(No Transcript)
24
A few Next steps

• More bioblitzes
• Drop-down invasives lists in Splickr
• Mining other sources
• E.g. birdwatcher listservs
• Making semantic eco-blogging easier
• Cyndy worked with children this summer as we were
  developing Spotter 1.0.
• More data in Swoogle/Tripleshop!

25
Presentation is Over

• The next slides are on a totally different
  subject.

26
Water Quality and Aquatic Invasives

• What is the relationship between water quality
  and susceptibility to invasion?
• A very tricky question
• Correlations need to take into account pathways
  of invasion.
• In some cases, pollutants depress native
  populations, creating a niche for invaders.
• In others, pollutants are a barrier to invasion.
• But can we answer some ad-hoc queries
• E.g. As the health of Dutch estuaries has
  improved, has invasives occurrence risen or
  fallen?
• More importantly can we provide the data
  required for serious analysis?

27
6 Month Experiment

• Create a toolkit for overlaying water quality
  data with invasive and other biodiversity data.
• Strong capability for ad-hoc querying AND for
  ad-hoc addition of datasets.
• Tripleshop as integrating platform
• Now forming science committee!
• Will advise on subject area and queries of
  interest.
• Will test usability.