astrodas : sharing assertions across astronomy catalogues through distributed annotation
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
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)
Outline
1. Astronomy catalogues and existing OpenSkyQuery system
2. Custom cross-matching algorithms: AstroDAS
3. How AstroDAS compares to other annotation systems
SDSS (Visual)
TWOMASS (Infrared)
SDSS (Visual)
TWOMASS (Infrared)
AstroDAS: Astronomy Distributed Annotation SystemExample astronomy catalogue schema
SDSS:Sky node
TWOMASS:Sky node
USNOB:Sky node
:OpenSky Query client
OpenSkyQuery Portal
OpenSkyQuery
SELECTs.objid, t.objid, u.objid,s.ra, s.dec, s.type,t.ra, t.dec,u.ra, u.decFROMSDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary uWHEREXMATCH(s,t,u)<3.5 ANDRegion(’CircleJ2000 200 -1 0.02’) ANDs.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 sigmawhich encodes tolerance of match
AstroDAS: Astronomy Distributed Annotation SystemExisting OpenSkyQuery system for astronomy catalogue access
National Virtual Observatory. (2006). Open SkyQuery Help: The XMatch Algorithm <http://openskyquery.net/Sky/SkySite/help/algo.asp>
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
AstroDAS: Astronomy Distributed Annotation SystemExisting OpenSkyQuery system for astronomy catalogue access
http://openskyquery.net/
SDSS:Sky node
TWOMASS:Sky node
USNOB:Sky node
:OpenSky Query client
OpenSkyQuery Portal
OpenSkyQuery
SELECTs.objid, t.objid, u.objid,s.ra, s.dec, s.type,t.ra, t.dec,u.ra, u.decFROMSDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary uWHEREXMATCH(s,t,u)<3.5 ANDRegion(’CircleJ2000 200 -1 0.02’) ANDs.type=3 AND
ADQL query
AstroDAS: Astronomy Distributed Annotation System
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Existing OpenSkyQuery system provides X-Match results based on proximity
SDSS:Sky node
TWOMASS:Sky node
USNOB:Sky node
:OpenSky Query client
OpenSkyQuery Portal
OpenSkyQuery
SELECTs.objid, t.objid, u.objid,s.ra, s.dec, s.type,t.ra, t.dec,u.ra, u.decFROMSDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary uWHEREXMATCH(s,t,u)<3.5 ANDRegion(’CircleJ2000 200 -1 0.02’) ANDs.type=3 AND
ADQL query
AstroDAS: Astronomy Distributed Annotation System
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
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
OpenSkyQuery
SELECTs.objid, t.objid, u.objid,s.ra, s.dec, s.type,t.ra, t.dec,u.ra, u.decFROMSDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary uWHEREXMATCH(s,t,u)<3.5 ANDRegion(’CircleJ2000 200 -1 0.02’) ANDs.type=3 AND
ADQL query
AstroDAS: Astronomy Distributed Annotation System
UEdinburgh:<SDSS, 58778470> ↔ <TWOMASS, 35773478><SDSS, 58778470> ↔ <USNOB, 13317280><SDSS, 58777039> ↔ <USNOB, 13317184>
URome:<SDSS, 58778583> ↔ <TWOMASS, 35777512>
So group produces its own cross-match results
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:<SDSS, 58778470> ↔ <TWOMASS, 35773478><SDSS, 58778470> ↔ <USNOB, 13317280><SDSS, 58777039> ↔ <USNOB, 13317184>
URome:<SDSS, 58778583> ↔ <TWOMASS, 35777512>
SELECTs.objid, t.objid, u.objid,s.ra, s.dec, s.type,t.ra, t.dec,u.ra, u.decFROMSDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary uWHEREXMATCH(s,t,u)<3.5 ANDRegion(’CircleJ2000 200 -1 0.02’) ANDs.type=3 AND
ADQL query
Storing annotations to map database objects
AstroDAS: Astronomy Distributed Annotation SystemStoring annotations to map database objects
db_object db_object
SDSS_58778470 TWOMASS_35773478
annote1 author annote_sourceSAME OBJECT
(algorithm1) researcher1
(algorithm1) researcher1
… … … … ……
id
1
2
3
SDSS_58778470 USNOB_13317280
UEdinburgh:<SDSS, 58778470> ↔ <TWOMASS, 35773478><SDSS, 58778470> ↔ <USNOB, 13317280><SDSS, 58777039> ↔ <USNOB, 13317184>
URome:<SDSS, 58778583> ↔ <TWOMASS, 35777512>
SAME OBJECT
NOT SAME OBJECT
(algorithm2) researcher2SDSS_58778470 TWOMASS_35773478
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
USNOBTWOMASSSDSSAstroDAS
OpenSkyQuery
mapping table created dynamically from annotations
12
3
4
AstroDAS: Astronomy Distributed Annotation SystemQuerying annotations on astronomy catalogues
SELECTs.objid, s.ra, s.dec, s.type,t.objid, t.ra, t.decu.objid, u.ra, u.decFROMSDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary uAS:UEdinburgh e, AS:URome rWHERERegion(’CircleJ2000 200 -1 0.02’) ANDs.type=3 ANDe.author=’algorithm1’ ANDr.author=’algorithm2’
DSQL query
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
USNOBTWOMASSSDSSAstroDAS
OpenSkyQuery
mapping table created dynamically from annotations
12
3
4
AstroDAS: Astronomy Distributed Annotation SystemCreating a mapping table from stored annotations: inference
SELECTs.objid, s.ra, s.dec, s.type,t.objid, t.ra, t.decu.objid, u.ra, u.decFROMSDSS:photoprimary s, TWOMASS:photoprimary t, USNOB:photoprimary uAS:UEdinburgh e, AS:URome rWHERERegion(’CircleJ2000 200 -1 0.02’) ANDs.type=3 ANDe.author=’algorithm1’ ANDr.author=’algorithm2’
DSQL query
UEdinburgh:<SDSS, 58778470> ↔ <TWOMASS, 35773478><SDSS, 58778470> ↔ <USNOB, 13317280><SDSS, 58777039> ↔ <USNOB, 13317184>
URome:<SDSS, 58778583> ↔ <TWOMASS, 35777512>
Outline
1. Astronomy catalogues and existing OpenSkyQuery system
2. Custom cross-matching algorithms: AstroDAS
3. How AstroDAS compares to other annotation systems
http://www.wormbase.org/db/das/elegans/features?segment=Ihttp:// <server> /das/<source>/<command>?<args>
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).
Ensembl system which includes BioDAS functionalityExample 1: Genome annotation and BioDAS
http://www.ensembl.org
Ensembl system which includes BioDAS functionalityExample 1: Genome annotation and BioDAS
http://www.ensembl.org
Outline
1. Astronomy catalogues and existing OpenSkyQuery system
2. Custom cross-matching algorithms: AstroDAS
3. How AstroDAS compares to other annotation systems
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)
Annotation of the Malaria Mosquito Anopheles gambiae genome sequenceExample 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
Annotation of the Malaria Mosquito Anopheles gambiae genome sequenceExample 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
Annotation of the Malaria Mosquito Anopheles gambiae genome sequenceExample 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
Lauer, Kim P., Llorente, Isabel, Blair, Eric, Seto, Jason, Krasnov, Vladimir, Purkayastha, Anjan, Ditty, Susan E., Hadfield, Ted L., Buck, Charles, Tibbetts, Clark, Seto, DonaldNatural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1J Gen Virol 2004 85: 2615-2625http://intl-vir.sgmjournals.org/cgi/citmgr?gca=vir;85/9/2615
Example of genome annotation from the biological literatureExample 1: Genome annotation and BioDAS
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Human Brain Project (HBP) image annotation (Gertz 2002, 2003)Example 2: Medical image annotation
http://neuroscience.ucdavis.edu/hbp/viewer.html
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).
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/)
AstroDAS: Astronomy Distributed Annotation SystemStoring annotations to map database objects
db_object db_object
SDSS_112233 TWOMASS_445566
annote1 annote2 annote_sourceSAME OBJECT
(algorithm1) GROUP1
NOT SAME OBJECT
(algorithm2) GROUP2
NOT SAME OBJECT
(algorithm1) GROUP1
… … … … ……
id
1
2
3
SDSS_112233
SDSS_112233 TWOMASS_778899
TWOMASS_445566