# Presentation: 224987

## Semantic Ecoblogging:Models and Tools for Biological Observation

**Cynthia Parr**
- _[csparr@umd.edu](mailto:csparr@umd.edu)_
**And others at the Spire project**

**Notes:**
Background on the SPIRE project.
Use Cases (1 slide, 2 minutes)
Define observation and observational data (1 slide, 2 minutes)
What constitute an observation in the model, what are the characteristcis of the observation being described
Primary orgainzation of your model (concepts, relationships , etc)
Overview of model (5 minutes, 1-2 slides)
What tools are being developed to support
What new capabilities are enabled?
What is the broader information architecture surrounding your model (e.g. other metadata standards, tools, etc)?

Associated tools, features frameworks (4 minutes, 1 slide)
Model extensibility (2 minutes, 1 slide)

** **
- Semantic Prototypes In
- Ecoinformatics

**UMBC**
**Ebiquity**

**UMD **
**MINDSWAP**

**NASA**
**GSFC**

**RMBL**
**Peace **

**UC Davis**
**ICE**

- NBII

**Semantic Web Tools**
**Infrastructure**

**Prototype Applications**
**Information Retrieval**
**Agents**

**Invasive Species Forecasting System**
**Remote Sensing Data**

**Food Webs**
**Ecological Interaction Ontologies**

**Semantic CAIN**
**Dissemination**
**Ontology Development**

**Notes:**
Final year of a 5 year 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.

Committed to generating RDF and OWL representations of data and building tools to take advantage of them.

## 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 idea of moving away from “answer providers” to “evidence providers”.

## 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.

## 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

## Semantic Ecoblogging

- Ecoblogs 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. Here’s 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.

## Use cases

**People anywhere reporting what they’ve seen so that scientists might be able to use it.**
- Surveillance
- Phenology
- Identify trends
- Improve observation skill and scientific thinking

- Semantic web approaches towards a Global Human Sensor Net

**Data sources**
- Invasive species surveys
- Flickr photos
- Citizen blogging
- Blogger BioBlitz

**Notes:**
People
Anywhere
(in nature)
Scientists AND educators
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. Here’s 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.

## Definitions

**Observation**
- Information about a taxon detected in a certain place at a certain time.

**Characteristics of observation**
- Reporter, observer, location, latlong, date, taxon, common name, number observed, source URL, image URL, comments

- . . . more to be added

## Model overview 1: Individual observations

*RDF*
*format*

*Kansas**protected species*

- Californiaweeds

- SpireEcoConcepts

- ThingsOfConcern

- E.g. blog post, Flickr photo

- Did I see something that flies?
- Did I see something that is a thing of concern?
- Did I see something that is eaten by housecats?

**Notes:**
Here I will be discussing both the representation modeling, and a bit of the implementation architecture

An observation is a very lightweight document. It consists purely of some references to source ontologies like ETHAN, indicates that this info is an observation, which has the following properties: hasTaxon, etc.

An observation references other documents whose vocabularies are being used. Right now, the only connection we make is with the ETHAN ontology.

ETHAN is our ontology for representing both evolutionary hieriarchies, and the natural history characteristics of those organisms. It is very big.
We use mainly subsumption hierarchies. So, we can say the taxon Corvus is a subclass of the taxon Corvidae, thus the genus is a subclass of its family. We can also say that Corvus is a subclass of “things that fly” or “things that are omnivores.” It also represents that the average weight of Corvus brachyrhynchos is about 500g. Because these are sophisticated assertions, they are represented in OWL rather than RDF. Both OWL and RDF are XML formats. 

Strength is that by referring to an ETHAN taxon, a machine can easily relate the taxon in the observation with the taxa in these other documents that reference the same taxon
For example, SpireEcoConcepts	
Medium size. Used for expressing trophic links and related information, including bibliographic info on studies.
Invasives ontologies, such as california weeds that lists ETHAN taxa that are on California’s list of the invasive weeds.

Each of these big boxes can be a distributed document, can be generated by different systems

Other people don’t have to use ETHAN as their authority for taxa.
Might then have a mapping document that explains in OWL or RDF what the relationship between an ETHAN taxon is and the taxon in some other ontology

## Model overview 2: Surveys and Invasives Lists

- Ecoregions

- ETHAN

**Model overview 2: ****Surveys and Invasives Lists**

- e.g. BioBlitz or other multi-observation report

- Did this survey find any taxa that are on the California weeds list for this ecoregion?

- e.g. List of invasives

**Notes:**
A survey is basically just a document that list observations. A collection of observations
We repeat the metadata about the survey (who, where, etc) in the observation, because during a survey people might move around and different people might have seen different things.
Similarly, Invasive species documents list the taxa that are on a particular list.
Lightweight and extensible in the most trivial of manners.

## Model extensibility

- Behavior
- Trust
- Ecological Interactions

## Associated tools

**Generating RDF**
- Splickr
- Spotter
- RDF123

**Using RDF and OWL**
- Swoogle
- Triple Shop
- Spotter map

## Splickr

- Flickr has been handling geotagged pictures since late last year ?
- Almost 19 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.

## Slide 14

## Slide 15

## Spotter tool

- Spotter map

## 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.

## RDF123: Map spreadsheet to ontology to output RDF

- 1200 observations.
- 47 observations of species defined as “of concern” by USFWS.

##  A few next steps

- More bioblitzes
- Drop-down invasives lists in Splickr
- Mining other sources
- E.g. birdwatcher listservs
- Making semantic eco-blogging easier
- Working with children this summer.
- More data in Swoogle/Tripleshop!
**Machine readable, machine understandable documents on the Semantic Web; easy to create, easy to visualize, easy to query**

## Water

- 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.
- Not in all cases, though.
- 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?

## UMBC	Joel Sachs, Tim Finin, Lushan Han,Andriy Parafiynyk
UC Davis	Allan Hollander, Jim Quinn
U Md	David Wang
RMBL	Neo Martinez, Jennifer Dunne

http://spire.umbc.edu/
http://ebiquity.umbc.edu

**UC Davis****	****Allan Hollander, Jim Quinn**
**U Md****	****David Wang**
**RMBL****	****Neo Martinez, Jennifer Dunne**
- _[http://spire.umbc.edu/](http://spire.umbc.edu/)_
- _[http://ebiquity.umbc.edu](http://ebiquity.umbc.edu/)_