1. AstroDAS: Sharing Assertions across Astronomy Catalogues through Distributed Annotation Rajendra Bose, Robert G. Mann, Diego Prina-Ricotti Digital Curation Centre 4 May 2006 International Provenance and Annotation Workshop (IPAW’06)

2. Outline 1.Astronomy catalogues and existing OpenSkyQuery system 2.Custom cross-matching algorithms: AstroDAS 3.How AstroDAS compares to other annotation systems

3. SDSS (Visual) TWOMASS (Infrared)

4. SDSS (Visual) TWOMASS (Infrared)

5. AstroDAS: Astronomy Distributed Annotation System Example astronomy catalogue schema

6. SDSS :Sky node TWOMASS :Sky node USNOB :Sky node :OpenSky Query client OpenSkyQuery Portal OpenSkyQuery SELECT s.objid, t.objid, u.objid, s.ra, s.dec, s.type, t.ra, t.dec, u.ra, u.dec FROM SDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary u WHERE XMATCH(s,t,u)<3.5 AND Region(’CircleJ2000 200 -1 0.02’) AND s.type=3 AND ADQL query SDSS: Sloan Digital Sky Survey TWOMASS: the Two Micron All Sky Survey USNOB: U.S. Naval Observatory USNO-B1.0 catalogue X-Match cross-matching algorithm built into OpenSkyQuery based on spatial proximity; user specifies parameter sigma which encodes tolerance of match AstroDAS: Astronomy Distributed Annotation System Existing OpenSkyQuery system for astronomy catalogue access National Virtual Observatory. (2006). Open SkyQuery Help: The XMatch Algorithm

7. AstroDAS: Astronomy Distributed Annotation System Existing OpenSkyQuery system for astronomy catalogue access http://openskyquery.net/

8. SDSS :Sky node TWOMASS :Sky node USNOB :Sky node :OpenSky Query client OpenSkyQuery Portal OpenSkyQuery SELECT s.objid, t.objid, u.objid, s.ra, s.dec, s.type, t.ra, t.dec, u.ra, u.dec FROM SDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary u WHERE XMATCH(s,t,u)<3.5 AND Region(’CircleJ2000 200 -1 0.02’) AND s.type=3 AND ADQL query AstroDAS: Astronomy Distributed Annotation System Existing OpenSkyQuery system provides X-Match results based on proximity

9. SDSS :Sky node TWOMASS :Sky node USNOB :Sky node :OpenSky Query client OpenSkyQuery Portal OpenSkyQuery SELECT s.objid, t.objid, u.objid, s.ra, s.dec, s.type, t.ra, t.dec, u.ra, u.dec FROM SDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary u WHERE XMATCH(s,t,u)<3.5 AND Region(’CircleJ2000 200 -1 0.02’) AND s.type=3 AND ADQL query AstroDAS: Astronomy Distributed Annotation System But X-Match results based on proximity not always adequate Catalogue1 Catalogue2

10. SDSS :Sky node TWOMASS :Sky node USNOB :Sky node :OpenSky Query client OpenSkyQuery Portal OpenSkyQuery SELECT s.objid, t.objid, u.objid, s.ra, s.dec, s.type, t.ra, t.dec, u.ra, u.dec FROM SDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary u WHERE XMATCH(s,t,u)<3.5 AND Region(’CircleJ2000 200 -1 0.02’) AND s.type=3 AND ADQL query AstroDAS: Astronomy Distributed Annotation System UEdinburgh: ↔ URome: ↔ So group produces its own cross-match results

11. URome :AstroDAS Server SDSS :Sky node UEdinburgh :AstroDAS Server TWOMASS :Sky node USNOB :Sky node :OpenSky Query client :AstroDAS client AstroDAS Portal OpenSkyQuery Portal AstroDAS OpenSkyQuery AstroDAS: Astronomy Distributed Annotation System UEdinburgh: ↔ URome: ↔ SELECT s.objid, t.objid, u.objid, s.ra, s.dec, s.type, t.ra, t.dec, u.ra, u.dec FROM SDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary u WHERE XMATCH(s,t,u)<3.5 AND Region(’CircleJ2000 200 -1 0.02’) AND s.type=3 AND ADQL query Storing annotations to map database objects

12. AstroDAS: Astronomy Distributed Annotation System Storing annotations to map database objects db_object SDSS_58778470TWOMASS_35773478 annote1 authorannote_source SAME OBJECT (algorithm1) researcher1 (algorithm1) researcher1 ……………… id 1 2 3 SDSS_58778470 USNOB_13317280 UEdinburgh: ↔ URome: ↔ SAME OBJECT NOT SAME OBJECT (algorithm2) researcher2 SDSS_58778470 TWOMASS_35773478

13. URome :AstroDAS Server SDSS :Sky node UEdinburgh :AstroDAS Server TWOMASS :Sky node USNOB :Sky node :OpenSky Query client :AstroDAS client AstroDAS Portal OpenSkyQuery Portal null3577751258778583 13317184null58777039 133172803577347858778470 USNOBTWOMASSSDSS AstroDAS OpenSkyQuery mapping table created dynamically from annotations 1 2 3 4 AstroDAS: Astronomy Distributed Annotation System Querying annotations on astronomy catalogues SELECT s.objid, s.ra, s.dec, s.type, t.objid, t.ra, t.dec u.objid, u.ra, u.dec FROM SDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary u AS:UEdinburgh e, AS:URome r WHERE Region(’CircleJ2000 200 -1 0.02’) AND s.type=3 AND e.author=’algorithm1’ AND r.author=’algorithm2’ DSQL query

14. URome :AstroDAS Server SDSS :Sky node UEdinburgh :AstroDAS Server TWOMASS :Sky node USNOB :Sky node :OpenSky Query client :AstroDAS client AstroDAS Portal OpenSkyQuery Portal null3577751258778583 13317184null58777039 133172803577347858778470 USNOBTWOMASSSDSS AstroDAS OpenSkyQuery mapping table created dynamically from annotations 1 2 3 4 AstroDAS: Astronomy Distributed Annotation System Creating a mapping table from stored annotations: inference SELECT s.objid, s.ra, s.dec, s.type, t.objid, t.ra, t.dec u.objid, u.ra, u.dec FROM SDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary u AS:UEdinburgh e, AS:URome r WHERE Region(’CircleJ2000 200 -1 0.02’) AND s.type=3 AND e.author=’algorithm1’ AND r.author=’algorithm2’ DSQL query UEdinburgh: ↔ URome: ↔

15. Outline 1.Astronomy catalogues and existing OpenSkyQuery system 2.Custom cross-matching algorithms: AstroDAS 3.How AstroDAS compares to other annotation systems

16. http://www.wormbase.org/db/das/elegans/features?segment=I http:// /das/ / ? BioDAS: Biology Distributed Annotation System (Dowell 2001) Example 1: Genome annotation and BioDAS Dowell, R., Jokerst, R., Day, A., Eddy, S., & Stein, L. (2001). The Distributed Annotation System. BMC Bioinformatics, 2(7).

17. Ensembl system which includes BioDAS functionality Example 1: Genome annotation and BioDAS http://www.ensembl.org

18. Ensembl system which includes BioDAS functionality Example 1: Genome annotation and BioDAS http://www.ensembl.org

20. Outline 1.Astronomy catalogues and existing OpenSkyQuery system 2.Custom cross-matching algorithms: AstroDAS 3.How AstroDAS compares to other annotation systems

21. AstroDAS: Sharing Assertions across Astronomy Catalogues through Distributed Annotation Rajendra Bose, Robert G. Mann, Diego Prina-Ricotti Digital Curation Centre 4 May 2006 International Provenance and Annotation Workshop (IPAW’06)

23. Annotation of the Malaria Mosquito Anopheles gambiae genome sequence Example 1: Genome annotation and BioDAS The Genome Sequence of the Malaria Mosquito Anopheles gambiae, Robert A. Holt, et al., Science 4 October 2002: Vol. 298. no. 5591, pp. 129 - 149 DOI: 10.1126/science.1076181; http://www.sciencemag.org/cgi/data/298/5591/129/DC2/1

24. Annotation of the Malaria Mosquito Anopheles gambiae genome sequence Example 1: Genome annotation and BioDAS The Genome Sequence of the Malaria Mosquito Anopheles gambiae, Robert A. Holt, et al., Science 4 October 2002: Vol. 298. no. 5591, pp. 129 - 149 DOI: 10.1126/science.1076181; http://www.sciencemag.org/cgi/data/298/5591/129/DC2/1

25. Annotation of the Malaria Mosquito Anopheles gambiae genome sequence Example 1: Genome annotation and BioDAS The Genome Sequence of the Malaria Mosquito Anopheles gambiae, Robert A. Holt, et al., Science 4 October 2002: Vol. 298. no. 5591, pp. 129 - 149 DOI: 10.1126/science.1076181; http://www.sciencemag.org/cgi/data/298/5591/129/DC2/1

26. Lauer, Kim P., Llorente, Isabel, Blair, Eric, Seto, Jason, Krasnov, Vladimir, Purkayastha, Anjan, Ditty, Susan E., Hadfield, Ted L., Buck, Charles, Tibbetts, Clark, Seto, Donald Natural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1 J Gen Virol 2004 85: 2615-2625 http://intl-vir.sgmjournals.org/cgi/citmgr?gca=vir;85/9/2615 Example of genome annotation from the biological literature Example 1: Genome annotation and BioDAS

27. Human Brain Project (HBP) image annotation (Gertz 2002, 2003) Example 2: Medical image annotation http://neuroscience.ucdavis.edu/hbp/viewer.html

28. Human Brain Project (HBP) image annotation (Gertz 2002, 2003) Example 2: Medical image annotation Gertz, M., Sattler, K.-U., Gorin, F., Hogarth, M., & Stone, J. (2002). Annotating Scientific Images: A Concept-based Approach. Proceedings of the 14th International Conference on Scientific and Statistical Database Management (SSDBM 2002), Edinburgh, Scotland. IEEE Computer Society. Gertz, M., & Sattler, K. U. (2003). Integrating scientific data through external, concept-based annotations. In Efficiency and Effectiveness of Xml Tools and Techniques and Data Integration over the Web (Vol. 2590, pp. 220-240).

29. Edinburgh Mouse Atlas Project (EMAP) (Baldock 1999) Example 2: Medical image annotation Baldock, R. A., Dubreuil, C., Hill, W., & Davidson, D. (1999). The Edinburgh Mouse Atlas: Basic Structure and Informatics. In S. I. Letovsky (Ed.), Bioinformatics: Databases and Systems (pp. 129-140). Kluwer Academic Publishers. (See http://genex.hgu.mrc.ac.uk/)

30. AstroDAS: Astronomy Distributed Annotation System Storing annotations to map database objects db_object SDSS_112233TWOMASS_445566 annote1 annote2annote_source SAME OBJECT (algorithm1) GROUP1 NOT SAME OBJECT (algorithm2) GROUP2 NOT SAME OBJECT (algorithm1) GROUP1 ……………… id 1 2 3 SDSS_112233 TWOMASS_778899 TWOMASS_445566