1. BioRDF Overview and Update By Kei Cheung, Ph. D
BioRDF Overview and Update By Kei Cheung, Ph.D. Yale Center for Medical Informatics
C-SHALS 2009, Boston, Massachusetts, February 25, 2009

2. BioRDF Objectives Participants Enhance the HCLS KB
Increase the value and use of HCLS KB by identifying scientific use case
Work on human-friendly user interface
Document and publish findings to help accelerate/promote adoption of the Semantic Web
Participants
Universities, pharmaceutical companies, start-up companies, government institutes, W3C, etc

3. BioRDF Activities/Tasks
Invited Talks
UMLS, NCBO, NIF, Biogateway, WikiNeuron, Gene Wiki, 3D Web Visualization, BioSIOC/aTag, VoID
HCLS KB
Two instances of HCLS KB have been created
DERI (Virtuoso)
Neurocommons
Free University in Berlin (Allegro Graph)
SenseLab and TCMGeneDIT
Neuroscience use case
add receptors to the picture
aTags
Matthias Samwald, Kei Cheung
Query Federation
Kei Cheung, Rob Frost, Kingsley Idehen, Scott Marshall, Adrian Paschke , Eric Prud’hommeaux, Matthias Samwald, Jun Zhao

4. Brain: Neuron and Synapse
Courtesy of NIDA

5. aTags

6. aTags Very simple, generic way of expressing biomedical statements
A short snippet of text + a list of ontology terms used for describing the text
Using established vocabulary (SIOC, OBO ontologies)
Encoded in RDFa (easy to embed in existing HTML-based systems)

7. aTags Transmitter T seems to activate receptor R
Receptor R is expressed in brain region B
Region B has strong axonal projections
into brain region B2

8. aTags aTags will be created by
conversion of existing biomedical datasets
manual curation of data (highlight text snippet in browser & click on del.icio.us – like bookmarklet)
Design philosophy: simplicity and practicality
Use existing resources
Play along with existing systems (HTML content management, RDFa-enabled search engines)

9. Query Federation

10. A Journey to Query Federation: from SPARQL Endpoint to Linked Data
Application demo
Receptor explorer
Mismatch between Wikipedia and DBpedia
Comparison of Triplestores
Linked Data description and deployment
voiD
FeDeRate
URI

11. Receptor Explorer VectorC Semantic Service Bus Receptor App
Genes involved in receptor
Publications about gene
Clinical trials referencing publications
RDF
Bio2RDF
linkedct.org
Clinicaltrials.gov
PubMed
Entrez Gene
HCLS KB
DERI
DBpedia
map
Receptors
SenseLab
VectorC Semantic Service Bus
ESB/SOA
Clinicaltrials.gov
PubMed
Wikipedia
web sites
Copyright 2008 VectorC, LLC 11

15. A Semantic Mismatch between Wikipedia and DBpedia

16. Triplestore Comparison
Features
Virtuoso
Allegro Graph
Class Hierarchy Inference
Yes
Linked Data Deployment
Built-in support
3rd party software (e.g., Pubby)
Query Federation
Linked Data Spaces (SPARQL against resource URI’s)
Built-in support (Sesame and Oracle only). For other triplestores, a 3rd party middleware approach is required.

17. Federated Query (FeDeRate)
Mediation
Local query 1
Local query 2
Local query n
DBPedia
(RDF)
IUPHAR
(SQL)

18. Federation Scenario
PREFIX db: <
PREFIX re: <
PREFIX dp: <
SELECT ?abstract ?code ?ligand ?hum_seq_id ?chr ?refseq
FROM NAMED db:IUPHAR.prop
FROM NAMED db:DBPedia.rdf
WHERE {
# Get info from the (SQL) IUPHAR receptor tables.
GRAPH db:IUPHAR.prop {
?r re:Code ?code .
?r re:Ligand ?ligand .
?r re:Human_nucleotide ?hum_seq_id }
# Get info from (RDF) DBPedia.
GRAPH db:DBPedia.rdf {
?p dp:chromosome ?chr .
?p dp:refseq ?refseq .
?p dp:symbol ?symbol .
?p db:abstract ?abstract } }

19. Example Join between IUAPHAR & DBPedia (GABAB receptor)
IUPHAR
DBPedia

20. voiD: vocabulary of interlinked Datasets
Motivation
Effective Dataset Selection
Efficient Discovery of Datasets, by search engines or data publishers
SPARQL query optimisation and query federation
Two high-level concepts
Dataset: a dataset is published and maintained by a single provider and accessible on the Web through de-referenceable URIs or a SPARQL endpoint
Linkset: a subset of a void:Dataset; store triples to express the interlinking relationship between dataset
voiD Vocabulary,
voiD User's Guide,

21. Biological Dataset in voiD Format
:senselabontology a void:Dataset ;
dcterms:title "SenseLab Neuron Ontology" ;
dcterms:description "Neuroscience ontology derived from the SenseLab NeuronDB database.";
dcterms:license <> ; # TODO
foaf:homepage < ;
void:exampleResource < ;
void:exampleResource < ;
void:exampleResource < ;
dcterms:creator :senselab ; ## this organization can be further defined
dcterms:source < ;
dcterms:subject < ;
dcterms:subject < ;
dcterms:subject < ;
dcterms:subject < ;
dcterms:source <doi: /bib/bbm018> ;
void:feature :owl ; ## this technical feature can be further defined
void:sparqlEndpoint < ;
void:vocabulary < .

22. voiD Deployment
Deploy a voiD file (in either Turtle, RDF/XML or RDFa format) onto the Web server
Make it accessible to search engines, such as Sindice (
Publish a Semantic Sitemap file (sitemap.xml) on the server
“ allows Data publishers to state where documents containing RDF data are located, and to advertise alternative means to access it ” [1]
Use the datasetURI property in the sitemap.xml to point to the voiD description of a dataset, e.g.,
[1]

23. URI Issues Proliferation of synonymous URI’s
Potential problems
Performance
Maintenance
Possible solutions
Involvement of nomenclature committee (e.g., IUPHAR) and domain authority (e.g., Neuroscience Information Framework or NIF)
Persistent/permanent URI scheme (e.g., PURL)
E.g.,
Dereferenceable URI’s
A dereferenceable URI is a resource identification mechanism that uses the HTTP protocol to obtain a representation of the resource it identifies
For Linked Data, the representation takes the form of an information resource that describes the resource that the URI identifies.

24. Future Directions
Submit a paper describing the query federation work to a journal or conference
Continue and extend current tasks: Query Federation and aTag
Add new tasks
e.g., semantic wiki, workflow, user interface, …
Expand the HCLS KB (both instances)
e.g., new datasets such as UMLS
Collaborate with other task forces
e.g., LODD (natural alternative use case, Faviki) and SWAN/SIOC

25. The End