Which Gene did you mean (again?) Barend Mons HGVS 12 May 2010

1. Which Gene did you mean (again?)Barend MonsHGVS 12 May 2010

2. 2005

3. Measure ANYTHING in the –omics age…. BIGNORANCE driven research

4. The problem (also with community annotation) in a nutshell Sructured data entry Nobody likes Structured data Everybody wants Free text/cut and paste Everybody likes

5. The Result….

6. Ambiguity Redundancy

7. Redundancy ? • No reviewer would accept the exact same paper twice, let alone 1000 times ! • Still the same assertion is published over and over again in traditional publishing….

8. CL

9. Nano-publications…A way out ??

10. S P O Assertion

11. Preferred Term UUID ARTA table Authority http://www.uniprot.org/uniprot/Q25190 Preferred URI Access to all nano-publications With this this concept as SUBJECT predicate Object

12. Three concepts can form an Assertion….. Concepts (UUID) 1 2 3 S P O Triples (S-P-O) S P O Assertion A1 Annotation A1 Nano-publication Cardinal Assertion NP1 (A1) NP2 (A1) CA1 NP1 A1 √e NP3 (A1) NP4 (A1)

13. Each Cardinal Assertion is supported by 1-n nano-publications • Provenance is linked but separated from Cardinal Assertions • Evidence Factor (computed by Open Algorithm) associated S S Also Referred To As ..ARTA S Nano-publications with Provenance NP1 (A1) Cardinal Assertions with Evidence score NP2 (A1) NP3 (A1) CA1 √e NP4 (A1) CA2 √e CA3 NP1 (A2) NP2 (A2) NP3 (A3)

14. Each Cardinal Assertion maps to three UUID’s • ARTA table enables mapping across URI’s • Three UUID’s (subject-predicate-object) form new UUID for CA • Computer Reasoning uses Cardinal Assertions + evidence weight S p Also Referred To As ..ARTA o Inferencing Association CA1 CA2 CA3

15. Each Cardinal Assertion maps to three UUID’s • Therefore each new assertion can be checked for uniqueness • Novel combinations of 3 UUID’s are new Cardinal Assertions • Cardinal Assertions are sent for Community Review • Daily reasoning with new ‘credible’ Cardinal Assertions Tweets, blogs Wiki’s Publications Curations Associations CA4* CA4* Inferencing Association CA1 CA2 CA3

16. Conceptwiki: People are concepts too…. • People make nano-publications • People have concept of interest • People have Smart Phones All nano-publications With this this concept as SUBJECT or generated by this Person

17. Triple detection Redundancy check • Quertle (28-12-09) on Pubmed: • CLCN2-generalized epilepsy (C=19, R=5), causes:R=0 ! Human annotation of triple> no evidence….nano-publication • PNPLA3-Alcoholic liver disease (0) > new triple reported>reviewed>nano-publication • NRAS-noonan syndrome (C=5, R=1) causes: R=0 > new triple reported>reviewed>nano-publication • DLK1-type 1 Diabetes (C=3, R=0), causes:R=0 > new triple reported>reviewed>nano-publication • IFN2-focal segmental glomerulosclerosis (C=0, R=0) > new triple reported>reviewed>nano-publication • PARK2-Glioblastoma (C=4, R=0) > new triple reported>reviewed>nano-publication

18. Wikipedia Scholar/Commontology (projects starting as I speak) The statement: phosphorylation of p21 promotes cell survival is first run through a tagger (for instance Peregrine) and sows up to the author/editor as: Phosphorylation of p21 promotes cell survival (red means ambiguous) The user, upon clicking on p21 which is a highly ambiguous term, the ‘which gene did you mean approach’ is fired and will ask the user (in a pop up) to choose from many meanings among which the highest ranking are: In case the Homo sapiens protein is chosen, the concept UUID is inserted in the ‘SMW+’ syntax phosphorylation(UUID-Prpv) of p21(UUID-S) promotes (UUID-P)cell survival." (UUID-O) S P O Assertion A1