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UMBC an Honors University in Maryland Examples of Integrating Ecological Information on the Semantic Web Joel Sachs and Cynthia Simms Parr contact:

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Presentation on theme: "UMBC an Honors University in Maryland Examples of Integrating Ecological Information on the Semantic Web Joel Sachs and Cynthia Simms Parr contact:"— Presentation transcript:

1 UMBC an Honors University in Maryland Examples of Integrating Ecological Information on the Semantic Web Joel Sachs and Cynthia Simms Parr contact: Joint work with: Andriy Parafiynyk, Li Ding, Rong Pan, Lushan Han, and Tim Finin

2 UMBC an Honors University in Maryland Overview of Talk Introduction and background –What are we going to integrate? –And why? ELVIS –The Food Web Constructor and the Evidence Provider ETHAN –An ontology for evolutionary trees and natural history Tripleshop and Swoogle Questions

3 UMBC an Honors University in Maryland An NSF ITR collaborative project with University of Maryland, Baltimore County University of Maryland, College Park U. Of California, Davis Rocky Mountain Biological Laboratory NASA Goddard Space Flight Center NBII An NSF ITR collaborative project with University of Maryland, Baltimore County University of Maryland, College Park U. Of California, Davis Rocky Mountain Biological Laboratory NASA Goddard Space Flight Center NBII

4 UMBC an Honors University in Maryland An invasive species scenario Nile Tilapia fish have been found in a California lake. Can this invasive species thrive in this environment? If so, what will be the likely consequences for the ecology? So…we need to understand the effects of introducing this fish into the food web of a typical California lake

5 UMBC an Honors University in Maryland Bacteria Microprotozoa Amphithoe longimana Caprella penantis Cymadusa compta Lembos rectangularis Batea catharinensis Ostracoda Melanitta Tadorna tadorna ELVIS: Ecosystem Localization, Visualization, and Information System Oreochromis niloticus Nile tilapia ? ?... Species list constructor Food web constructor

6 UMBC an Honors University in Maryland The problem We have data on what species are known to be in the location and can further restrict and fill in with other ecological models But we dont know which of these the Nile Tilapia eats of who might eat it. We can reason from taxonomic data (similar species) and known natural history data (size, mass, habitat, etc.) to fill in the gaps.

7 UMBC an Honors University in Maryland Food Web G S node link Evolutionary tree step G taxon S A

8 UMBC an Honors University in Maryland Food Web Constructor Predict food web links using database and taxonomic reasoning. In a new estuary, Nile Tilapia could compete with ostracods (green) to eat algae. Predators (red) and prey (blue) of ostracods may be affected

9 UMBC an Honors University in Maryland Food Web Constructor generates possible links

10 UMBC an Honors University in Maryland Evidence provider gives details

11 UMBC an Honors University in Maryland Food web database 4600 distinct taxa Food web data: Cohen 1989, Dunne et al. 2006, Vazquez 2006, Jonsson et al Evolutionary tree: Parr et al plants from ITIS + hierarchy of non-taxonomic nodes

12 UMBC an Honors University in Maryland Testing the algorithm Take each web out of the database Attempt to predict its links Compare prediction with actual data Accuracy percentage of all predictions that are correct 89% Precision percentage of predicted links that are correct 55% Recall percentage of actual links that are predicted 47%

13 UMBC an Honors University in Maryland Evolutionary distance threshold 2 steps up and 4 steps down steps up steps down precision steps up recall

14 UMBC an Honors University in Maryland Evolutionary direction penalty not very sensitive ancestor descendent siblings

15 UMBC an Honors University in Maryland Negative evidence discount is sensitive

16 UMBC an Honors University in Maryland Some phyla are easier to predict than others

17 UMBC an Honors University in Maryland Trait space distance weighting Euclidean distance in natural history N-space Parameterize functions from the literature that might predict links using characteristics of taxa. For example, size or stoichiometry. LinkStatus AB = ƒ(α, size A, size B ), ƒ(β, stoich A, stoich B ) … …need more data How can we do better predicting links?

18 UMBC an Honors University in Maryland Status Goal is ELVIS (Ecosystem Location Visualization and Information System) as an integrated set of web services for constructing food webs for a given location. Background ontologies –SpireEcoConcepts: concepts and properties to represent food webs, and ELVIS related tasks, inputs and outputs –ETHAN (Evolutionary Trees and Natural History) Concepts and properties for natural history information on species derived from data in the Animal diversity web and other taxonomic sources Under development –Connect to visualization software –Connect to triple shop to discover more data

19 UMBC an Honors University in Maryland ETHAN Evolutionary Trees and Natural History ontology Animal Diversity Web geographic range habitats physical description reproduction lifespan behavior and trophic info conservation status Esox lucius hasMaxMass 1.4 kg Esox lucius isSubclassOf Esox Esox eats Actinopterygii Triples

20 UMBC an Honors University in Maryland Triple Shop Actinopterygii.owl webs_publisher.php? published_study=11 Esox_lucius.owl

21 UMBC an Honors University in Maryland Triple Shop What are body masses of fish that eat fish? Enter a SPARQL query SELECT DISTINCT ?predator ?prey ?preymaxmass ?predatormaxmass WHERE { ?link rdf:type spec:ConfirmedFoodWebLink. ?link spec:predator ?predator. ?link spec:prey ?prey. ?predator rdfs:subClassOf ethan:Actinopterygii. ?prey rdfs:subClassOf ethan:Actinopterygii. OPTIONAL { ?predator kw:mass_kg_high ?predatormaxmass }. OPTIONAL { ?prey kw:mass_kg_high ?preymaxmass } }... leaving out the FROM clause

22 UMBC an Honors University in Maryland Which fish eat other fish? Show their max body masses.

23 UMBC an Honors University in Maryland Enter query w/o FROM clause! log in specify dataset

24 UMBC an Honors University in Maryland

25 UMBC

26 UMBC 302 RDF documents were found that might have useful data.

27 UMBC an Honors University in Maryland Well select them all and add them to the current dataset.

28 UMBC an Honors University in Maryland Well run the query against this dataset to see if the results are as expected.

29 UMBC an Honors University in Maryland The results can be produced in any of several formats

30 UMBC an Honors University in Maryland Results

31 UMBC an Honors University in Maryland Looks like a useful dataset. Lets save it and also materialize it the TS triple store.

32 UMBC an Honors University in Maryland

33 UMBC We can also annotate, save and share queries.

34 UMBC an Honors University in Maryland Work in Progress There are a host of performance issues We plan on supporting some special datasets, e.g., –FOAF and SPIRE data collected from Swoogle –Definitions of RDF and OWL classes and properties from all ontologies that Swoogle has discovered Expanding constraints to select candidate SWDs to include arbitrary metadata and embedded queries –FROM documents trusted by a member of the SPIRE project Qurantine needed to handle conflicts.

35 UMBC an Honors University in Maryland An RDF Dictionary We hope to develop an RDF dictionary. Given an RDF term, returns a graph of its definiton –Term definition from official ontology –Term+URL definition from SWD at URL –Term+* union definition –Optional argument recursively adds definitions of terms in definition excluding RDFS and OWL terms –Optional arguments identifies more namespaces to exclude

36 UMBC an Honors University in Maryland Review All Elvis functionality is encapsulated as web services, and all input and output is OWL based. –So Elvis integrates easily with other semantic web applications, like the TripleShop. ELVIS as a platform for experimenting with different approached to food web prediction. TripleShop as an integrating platform TripleShop allows researchers to semi-automatically construct datasets in response to ad-hoc queries. Contact to


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