1. HCLS Scientific Discourse C-SHALS 2009
Tim Clark
Massachusetts General Hospital
& Harvard Medical School
February 25, 2009

2. Scientific Discourse

3. Science is experiment + discourse
Interpretation of experimental evidence;
Placement of results within a model;
Conflicts in models and interpretation;
Resolution of conflicts.

4. Discourse includes Hypotheses, claims and evidence
Data and interpretations;
Rebuttal, agreement or comment;
Open questions.

5. Example: Gaps and Inconsistencies in Research
Amongst the 20 top candidate theories about how Alzheimer Disease works, there are at least
49 key scientific disagreements and
32 key open questions to be resolved.
Experiment, theory development and argument should eventually resolve them.

6. The HCLS Discourse Task
Develop use cases.
Neuroscience-related in this case
Integrate relevant ontologies.
SIOC, SWAN, myExperiment, Lilly Experiment
Validate in applications.
Revise and publish integrated ontologies.
In progress: SWAN+SIOC IG Note

7. SWAN+SIOC SIOC http://sioc-project.org
Activities and contributions of online communities
Integration with blogging, wiki and CMS software
Use of existing ontologies e.g. FOAF, SKOS, DC
SWAN
Hypotheses, claims, evidence, concepts, entities
Schema for SWAN Alzheimer knowledge base
Ongoing integration into SCF Drupal toolkit

10. SWAN-SIOC integration
Discourse categories: research questions, scientific assertions or claims, hypotheses, comments and discussion, and evidence.
Biomedical categories: genes, proteins, antibodies, animal models, laboratory protocols, biological processes, reagents, disease classifications, user-generated tags, and bibliographic references.
Driving Biological Project: cross-application of discoveries, methods and reagents in stem cell, Alzheimer and Parkinson disease research.
Informatics use cases: interoperability of web-based research communities with
(a) each other (b) key biomedical ontologies (c ) algorithms for bibliographic annotation and text mining (d) key resources.

11. SWAN-SIOC + Experiment
What the discourse is about, or “warrant for belief” within discourse.
Link hypothesis and interpretation to data and data analysis.
Meta-analysis, replication, re-analysis.
Provenance of evidence / analysis.

12. SWAN-SIOC + myExperiment
DRAFT integration model

13. Semantic Search Examples
Find all discussion of NF-kappaB by any synonym.
Find discussion on [“NF-KB1” ∧ “inflammatory response”]
Find experiments on other genes and proteins relevant to “neuroinflammation”.
Find conflicting assertions about PD “anti-inflammatory response” and supporting experimental data for both.
What workflows were used to analyze the experiments?
Retrieve the data for re-analysis or meta-analysis.

14. Summary
HCLS Scientific Discourse connects: hypothesis, experiment, interpretation, citation, evidence and discussion.
Extensive re-use of other ontologies.
Use case “laboratory” in neuroscience focused on neurodegenerative diseases and regenerative medicine.
Progress
SWAN-SIOC integration complete, IG Note forthcoming.
SWAN-SIOC myExperiment is in progress.

15. Credits Uldis Bojars (DERI) * John Breslin (DERI) Kei Cheung (Yale)
Paolo Ciccarese (Harvard)
* Tim Clark (Harvard)
Sudeshna Das (Harvard)
David deRoure (Southampton)
Ronan Fox (DERI)
Tudor Groza (DERI)
Christoph Lange (Jacobs University)
David Newman (Southampton)
Marco Ocana (MGH)
Alex Passant (DERI)
Eric Prud’hommeaux (W3C)
Matthias Samwald (DERI)
Holger Stenzhorn (DERI)
Susie Stephens (Eli Lilly)
Elizabeth Wu (Alzheimer Research Forum)
*task co-chairs

16. With special thanks to Paolo Ciccarese David Newman Alexandre Passant
Eric Prud’hommeaux
Susie Stephens