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3D-EM DAS

3D-EM DAS. Extending DAS to 3D-EM and Molecular Fitting. http://biocomp.cnb.uam.es/das/ http://biocomp.cnb.uam.es:9000/das/. jrmacias@cnb.uam.es. What’s DAS ? D istributed A nnotation S ystem Distributed Annotation System - Entity feature relationships.

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3D-EM DAS

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  1. 3D-EM DAS Extending DAS to 3D-EM and Molecular Fitting http://biocomp.cnb.uam.es/das/ http://biocomp.cnb.uam.es:9000/das/ jrmacias@cnb.uam.es

  2. What’s DAS ? • Distributed Annotation System • Distributed Annotation System • - Entity feature relationships. • Distributed Annotation System • Made of distant, independent data sources. • Distributed Annotation System • Client/Server paradigm • One Client and many Servers • www.biodas.org : “(…)The distributed annotation system (DAS) is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up genome annotation information from multiple distant web sites, collate the information, and display it to the user in a single view.” jrmacias@cnb.uam.es

  3. Geographic Annotation System jrmacias@cnb.uam.es

  4. Is DAS a Web Service ? • REST-like Web Service • Representational State Transfer • Described by Roy Fielding in his PhD thesis. • http://www.ics.uci.edu/~fielding/pubs/dissertation/top.htm • Properties: • A resource is anything that has an identity. • Every resource has a URI. • A URI is “opaque” - exposes no details of implementation. • All Interactions are stateless. • Data and metadata formats are documented. • Data is available in multiple formats. • Representations include links to other resources. • Use available standards and technology. • Simple architecture. jrmacias@cnb.uam.es

  5. Genomic / Protein DAS • Structural DAS (SPICE) • 3D-EM DAS • Servers • 3DEM, Reference server • 3DEM_Fitting, Fitting results server • 3DEM_EMDB, Annotation server • Client • PeppeR jrmacias@cnb.uam.es

  6. Genomic / Proteomic DAS • Uses a DAS protocol to query remote data sources about what sequences and annotations they know about a particular biology entity (gene, protein). • Distributed : • - Servers • One Reference server: • Entry-points = Identifier + start / end points • Many Annotation servers: • Features, relative to an entry-point • - Clients • Web-based: Ensembl Genome Browser (http://www.ensembl.org/) • Flash-based: Dasty (http://www.ebi.ac.uk/das-srv/uniprot/dasty/) • Dowell RD, Jokerst RM, Day A, Eddy ST, Stein L. (2001). The Distributed Annotation System. BMC Bioinformatics 2:7. • Olason PI. (2005). Integrating protein annotation resources through theDistributed Annotation System. Nucleic Acids Res. 33: W468-W470. jrmacias@cnb.uam.es

  7. Reference Servers Client HTML query XML responses Annotation Servers jrmacias@cnb.uam.es

  8. DAS specification: Commands dsnreturns the list of data sources that are available from the server entry-pointsreturns the list of entry points available from the server sequencereturns the sequence (nucleotides or amino acids) corresponding to the requested segment typesreturns the annotation types available from the server featuresreturns all the known annotations relative for the requested segment Feature-by-id component supercomponent link stylesheet jrmacias@cnb.uam.es

  9. DAS specification: Query format server_prefix /source /command [?param=value] http://biocomp.cnb.uam.es:9000/das /dsn http://biocomp.cnb.uam.es:9000/das http://biocomp.cnb.uam.es:9000/das /3DEM /3DEM /3DEM_EMDB /3DEM_EMDB /3DEM_Fitting /3DEM_Fitting /3DEM_Fitting /entry_points /volmap ?query=EMD1017 http://biocomp.cnb.uam.es:9000/das http://biocomp.cnb.uam.es:9000/das /types /features ?segment=EMD1017 http://biocomp.cnb.uam.es:9000/das http://biocomp.cnb.uam.es:9000/das http://biocomp.cnb.uam.es:9000/das /entry_points /types /features ?segmet=FFT0005 jrmacias@cnb.uam.es

  10. List of available data sources: http://biocomp.cnb.uam.es:9000/das/dsn <?xml version="1.0" standalone="no"?> <!DOCTYPE DASDSN SYSTEM 'http://www.biodas.org/dtd/dasdsn.dtd' > <DASDSN> <DSN> <SOURCE id="3DEM_EMDB" version="1.02.20060508">3DEM_EMDB</SOURCE> <MAPMASTER>http://bioweb:9000/das/3DEM_EMDB/</MAPMASTER> <DESCRIPTION> Annotation server for 3D-EM volume data. Most textual data parsed from EMDB. </DESCRIPTION> </DSN> <DSN> <SOURCE id="3DEM_Fitting" version="1.02.20060503">3DEM_Fitting</SOURCE> <MAPMASTER>http://bioweb:9000/das/3DEM_Fitting/</MAPMASTER> <DESCRIPTION>Annotation server for fitting experiments (PDB structures into 3D-EM volumes).</DESCRIPTION> </DSN> <DSN> <SOURCE id="3DEM" version="1.02.20060503">3DEM</SOURCE> <MAPMASTER>http://bioweb:9000/das/3DEM/</MAPMASTER> <DESCRIPTION>Reference server for 3D-EM volume map data from EMDB.</DESCRIPTION> </DSN> </DASDSN> jrmacias@cnb.uam.es

  11. List of available entry points in a data source: http://biocomp.cnb.uam.es:9000/das/3DEM/entry_points <?xml version="1.0" standalone="no"?> <!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd"> <DASEP> <ENTRY_POINTS href="http://bioweb:9000/das/3DEM/entry_points" version="1.0.2"> <SEGMENT id="EMD1001" class="volume_map" type="ccp4" release_date="20/06/2002">EMD1001</SEGMENT> <SEGMENT id="EMD1003" class="volume_map" type="ccp4" release_date="22/08/2002">EMD1003</SEGMENT> <SEGMENT id="EMD1004" class="volume_map" type="ccp4" release_date="29/08/2003">EMD1004</SEGMENT> <SEGMENT id="EMD1005" class="volume_map" type="ccp4" release_date="30/08/2003">EMD1005</SEGMENT> <SEGMENT id="EMD1006" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1006</SEGMENT> <SEGMENT id="EMD1007" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1007</SEGMENT> <SEGMENT id="EMD1008" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1008</SEGMENT> <SEGMENT id="EMD1009" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1009</SEGMENT> <SEGMENT id="EMD1010" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1010</SEGMENT> <SEGMENT id="EMD1011" class="volume_map" type="ccp4" release_date="09/10/2002">EMD1011</SEGMENT> <SEGMENT id="EMD1012" class="volume_map" type="ccp4" release_date="10/10/2002">EMD1012</SEGMENT> <SEGMENT id="EMD1013" class="volume_map" type="ccp4" release_date="10/10/2002">EMD1013</SEGMENT> … <SEGMENT id="EMD1212" class="volume_map" type="ccp4" release_date="03/04/2007">EMD1212</SEGMENT> <SEGMENT id="EMD1213" class="volume_map" type="ccp4" release_date="03/04/2006">EMD1213</SEGMENT> </ENTRY_POINTS> </DASEP> jrmacias@cnb.uam.es

  12. Known annotations for an entry point: http://biocomp.cnb.uam.es:9000/das/3DEM/features?segment=emd_1017 <?xml version='1.0' standalone='yes'?> <!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd"> <DASGFF> <GFF version="1.5" href="http://bioweb:9000/das/3DEM_EMDB/features"> <SEGMENT id="EMD1017" version="1.0" start="1" stop=""> <FEATURE id="1017" label="1017"> <TYPE id="Description" reference="no" subparts="no" superparts="no">Description</TYPE> <START>1</START> <END>0</END> <SCORE>-</SCORE> <ORIENTATION>0</ORIENTATION> <PHASE>-</PHASE> <NOTE>Sample: "DnaB.DnaC complex from Escherichia coli "; Author: "M.Barcena,T.Ruiz,L.E.Donate,S.E.Brown,N.E.Dixon,M.Radermacher,J.M.Carazo"</NOTE> <LINK href="ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/emd-1017/map/emd_1017.map.gz">Retrive 17/10/2003 from EMDB</LINK> <GROUP id="1" type="Summary" /> </FEATURE> </SEGMENT> </GFF> </DASGFF> jrmacias@cnb.uam.es

  13. jrmacias@cnb.uam.es

  14. DAS Registry: jrmacias@cnb.uam.es

  15. Genomic / Protein DAS • Structural DAS (SPICE) • 3D-EM DAS • Servers • 3DEM, Reference server • 3DEM_Fitting, Fitting results server • 3DEM_EMDB, Annotation server • Client • PeppeR jrmacias@cnb.uam.es

  16. Structural DAS: • Servers • Reference • Uniprot • PDB • Alignment server • MSD • Client • SPICE • Prlic A, Down A, Hubbard TJ (2005). Adding some SPICE to DAS. Bioinformatics, 2005, 21 Suppl 2, ii40-ii41 jrmacias@cnb.uam.es

  17. Structural DAS Genomic DAS Sequences (reference) Structures (reference) Alignment server Features / Annotations SPICE Structural Client jrmacias@cnb.uam.es

  18. SPICE http://www.efamily.org.uk/software/dasclients/spice/ jrmacias@cnb.uam.es

  19. Genomic / Protein DAS • Structural DAS (SPICE) • 3D-EM DAS • Servers • 3DEM, Reference server • 3DEM_Fitting, Fitting results server • 3DEM_EMDB, Annotation server • Client • PeppeR jrmacias@cnb.uam.es

  20. Crystallography RMN, etc. 3D Electron Microscopy Molecular Fitting: Medium to Low-resolution Techniques High-resolution Techniques Hybrid Model jrmacias@cnb.uam.es

  21. Genomic DAS Structure DAS 3D-EM DAS New Sequences (reference) Structures (reference) 3D-EM volume maps (reference) Alignment server New Features / Annotations Fitting results New New EMDB annotations PeppeR 3D-EM DAS Client jrmacias@cnb.uam.es

  22. 3D-EM DAS client: PeppeR • Java implementation • - Architecture independent • Windows • Unix / Linux • Mac • - Java Web Start deployment • launched directly from a web link • AstexViewer for map / pdb structures display • Features (annotations) panels from SPICE library jrmacias@cnb.uam.es

  23. http://biocomp.cnb.uam.es/das/PeppeR/ jrmacias@cnb.uam.es

  24. jrmacias@cnb.uam.es

  25. jrmacias@cnb.uam.es

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