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AstroDAS : Sharing Assertions across Astronomy Catalogues through Distributed Annotation

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). Outline.

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AstroDAS : Sharing Assertions across Astronomy Catalogues through Distributed Annotation

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  1. AstroDAS: Sharing Assertionsacross Astronomy Cataloguesthrough 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 • Astronomy catalogues and existing OpenSkyQuery system • Custom cross-matching algorithms: AstroDAS • How AstroDAS compares to other annotation systems

  3. TWOMASS (Infrared) SDSS (Visual)

  4. TWOMASS (Infrared) SDSS (Visual)

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

  6. AstroDAS: Astronomy Distributed Annotation System Existing OpenSkyQuery system for astronomy catalogue access X-Match cross-matching algorithm built into OpenSkyQuerybased on spatial proximity; user specifies parameter sigmawhich encodes tolerance of match SDSS:Sky node TWOMASS:Sky node USNOB:Sky node :OpenSky Query client OpenSkyQuery Portal ADQL query 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 OpenSkyQuery SDSS: Sloan Digital Sky Survey TWOMASS: the Two Micron All Sky Survey USNOB: U.S. Naval Observatory USNO-B1.0 catalogue National Virtual Observatory. (2006). Open SkyQuery Help: The XMatch Algorithm <http://openskyquery.net/Sky/SkySite/help/algo.asp>

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

  8. AstroDAS: Astronomy Distributed Annotation System Existing OpenSkyQuery system provides X-Match results based on proximity SDSS:Sky node TWOMASS:Sky node USNOB:Sky node :OpenSky Query client OpenSkyQuery Portal ADQL query 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 OpenSkyQuery

  9. AstroDAS: Astronomy Distributed Annotation System But X-Match results based on proximity not always adequate Catalogue1 Catalogue2 SDSS:Sky node TWOMASS:Sky node USNOB:Sky node :OpenSky Query client OpenSkyQuery Portal ADQL query 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 OpenSkyQuery

  10. AstroDAS: Astronomy Distributed Annotation System So group produces its own cross-match results SDSS:Sky node TWOMASS:Sky node USNOB:Sky node :OpenSky Query client OpenSkyQuery Portal ADQL query 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 OpenSkyQuery UEdinburgh: <SDSS, 58778470> ↔ <TWOMASS, 35773478> <SDSS, 58778470> ↔ <USNOB, 13317280> <SDSS, 58777039> ↔ <USNOB, 13317184> URome: <SDSS, 58778583> ↔ <TWOMASS, 35777512>

  11. AstroDAS: Astronomy Distributed Annotation System Storing annotations to map database objects AstroDAS :AstroDAS client AstroDAS Portal UEdinburgh:AstroDAS Server URome:AstroDAS Server SDSS:Sky node TWOMASS:Sky node USNOB:Sky node :OpenSky Query client OpenSkyQuery Portal ADQL query 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 OpenSkyQuery UEdinburgh: <SDSS, 58778470> ↔ <TWOMASS, 35773478> <SDSS, 58778470> ↔ <USNOB, 13317280> <SDSS, 58777039> ↔ <USNOB, 13317184> URome: <SDSS, 58778583> ↔ <TWOMASS, 35777512>

  12. AstroDAS: Astronomy Distributed Annotation System Storing annotations to map database objects annote1 db_object db_object id author annote_source SAME OBJECT (algorithm1) 1 SDSS_58778470 TWOMASS_35773478 researcher1 SAME OBJECT 2 (algorithm1) USNOB_13317280 SDSS_58778470 researcher1 NOT SAME OBJECT TWOMASS_35773478 (algorithm2) 3 SDSS_58778470 researcher2 … … … … … … UEdinburgh: <SDSS, 58778470> ↔ <TWOMASS, 35773478> <SDSS, 58778470> ↔ <USNOB, 13317280> <SDSS, 58777039> ↔ <USNOB, 13317184> URome: <SDSS, 58778583> ↔ <TWOMASS, 35777512>

  13. AstroDAS: Astronomy Distributed Annotation System Querying annotations on astronomy catalogues mapping table created dynamically from annotations AstroDAS SDSS TWOMASS USNOB 58778470 35773478 13317280 58777039 null 13317184 58778583 35777512 null 3 :AstroDAS client AstroDAS Portal 1 4 2 UEdinburgh:AstroDAS Server URome:AstroDAS Server SDSS:Sky node TWOMASS:Sky node USNOB:Sky node :OpenSky Query client OpenSkyQuery Portal DSQL query 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’ OpenSkyQuery

  14. AstroDAS: Astronomy Distributed Annotation System Creating a mapping table from stored annotations: inference mapping table created dynamically from annotations AstroDAS SDSS TWOMASS USNOB 58778470 35773478 13317280 58777039 null 13317184 58778583 35777512 null 3 :AstroDAS client AstroDAS Portal 1 4 2 UEdinburgh:AstroDAS Server URome:AstroDAS Server SDSS:Sky node TWOMASS:Sky node USNOB:Sky node :OpenSky Query client OpenSkyQuery Portal DSQL query 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’ OpenSkyQuery UEdinburgh: <SDSS, 58778470> ↔ <TWOMASS, 35773478> <SDSS, 58778470> ↔ <USNOB, 13317280> <SDSS, 58777039> ↔ <USNOB, 13317184> URome: <SDSS, 58778583> ↔ <TWOMASS, 35777512>

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

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

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

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

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

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

  21. Example 1: Genome annotation and BioDAS Annotation of the Malaria Mosquito Anopheles gambiae genome sequence 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

  22. Example 1: Genome annotation and BioDAS Annotation of the Malaria Mosquito Anopheles gambiae genome sequence 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

  23. Example 1: Genome annotation and BioDAS Annotation of the Malaria Mosquito Anopheles gambiae genome sequence 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. Example 1: Genome annotation and BioDAS Example of genome annotation from the biological literature 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

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

  26. Example 2: Medical image annotation Human Brain Project (HBP) image annotation (Gertz 2002, 2003) • 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).

  27. Example 2: Medical image annotation Edinburgh Mouse Atlas Project (EMAP) (Baldock 1999) • 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/)

  28. AstroDAS: Astronomy Distributed Annotation System Storing annotations to map database objects annote1 db_object db_object id annote2 annote_source SAME OBJECT (algorithm1) 1 SDSS_112233 TWOMASS_445566 GROUP1 NOT SAME OBJECT 2 TWOMASS_445566 (algorithm2) SDSS_112233 GROUP2 NOT SAME OBJECT (algorithm1) 3 TWOMASS_778899 SDSS_112233 GROUP1 … … … … … …

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