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DASxVO

DASxVO. DAS for Visual Omics. Jose Ramon Macias Biocomputing Unit, CNB-CSIC jrmacias@cnb.csic.es. Visual Omics. Visualizing Functional Genomics Visual, as (some) techniques for obtaining primary data are image-based: In situ hybridization (ISH) Immunohistochemistry Omics, because...

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DASxVO

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  1. DASxVO DAS for Visual Omics Jose Ramon Macias Biocomputing Unit, CNB-CSIC jrmacias@cnb.csic.es 2009 DAS Workshop

  2. Visual Omics Visualizing Functional Genomics Visual, as (some) techniques for obtaining primary data are image-based: • In situ hybridization (ISH) • Immunohistochemistry Omics, because... ...well everything is –omics nowadays ;-)

  3. aGEM • anatomical Gene Expression Mapping • Integrates spatial and temporal gene expression data from different sources. • Analyze data to find biological relation between genes or structures with similar profiles. • Represents data in a summarized view.

  4. Not only DAS... • A tool for biologists, not for bioinformaticians • to make easier the access to information related to the anatomical pattern of gene expression in model organisms • An integrative tool • Should include “any” data source of interest

  5. ...but DAS DAS has proven as a successful data sharing platform. Annotations from other genome or proteome sources would be directly integrated.

  6. Pcna Vax1 Acty Cblc Pcna Vax1 Acty Cblc Mif Pkia Biological meaning • We started addressing two questions: • Given a certain anatomical component (retina)... • ...what genes are expressed during development?

  7. Biological meaning • We started addressing two questions: • Given a certain anatomical component (retina)... • ...what genes are expressed during development? • Given a set of genes... • ...in what anatomical structures they are expressed during development? Calcr Coch Rgs4 …

  8. Querying aGEM http://biocomp.cnb.csic.es/VisualOmics/aGEM/

  9. Querying aGEM http://biocomp.cnb.csic.es/VisualOmics/aGEM/

  10. Querying aGEM http://biocomp.cnb.csic.es/VisualOmics/aGEM/

  11. Querying aGEM http://biocomp.cnb.csic.es/VisualOmics/aGEM/

  12. Querying aGEM http://biocomp.cnb.csic.es/VisualOmics/aGEM/

  13. Querying aGEM http://biocomp.cnb.csic.es/VisualOmics/aGEM/

  14. Querying aGEM http://biocomp.cnb.csic.es/VisualOmics/aGEM/

  15. Querying aGEM http://biocomp.cnb.csic.es/VisualOmics/aGEM/

  16. Querying aGEM http://biocomp.cnb.csic.es/VisualOmics/aGEM/

  17. Querying aGEM http://biocomp.cnb.csic.es/VisualOmics/aGEM/

  18. aGEM DASxVO Architecture DASxVO EMAP_Reference MGI_Reference Annotation servers Statistics Analysis Client (Web browser) EMAGE MGI-GXD GENSAT MTB OMIM Annotations SymAtlas KEGG BAMS

  19. FOREBRAIN MA0000171 EMAP for embryo MA adult MGI GENE IDs PROSENCEPHALON Reference system Anatomic term in data base A ReferenceSystem Anatomic term reference system ID Anatomic term in data base B

  20. Theiler Stage 26 Long whiskers TS26, BRAIN EMAP11619 Reference system

  21. DAS: entry_points http://biocomp.cnb.csic.es:9090/das/EMAP_Reference/entry_points/ <?xml version="1.0" standalone="no"?> <?xml-stylesheet type="text/xsl" href="http://biocomp.cnb.csic.es:9090/das/xsl=EMAP_entry_points.xsl"?> <!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd"> <DASEP> <ENTRY_POINTS href="http://biocomp.cnb.csic.es:9090/das/EMAP_Reference/entry_points" version="1.03.20070516"> EMAP Reference server <SEGMENT id="EMAP0" description="Mouse_anatomy_by_time_xproduct" class="Ontology term" type="Anatomic Term" subparts="Yes" superparts="No"/> <SEGMENT id="EMAP1" description="TS1,first polar body" class="Ontology term" type="Anatomic Term" subparts="No" superparts="Yes"/> <SEGMENT id="EMAP2" description="TS1,one-cell stage" class="Ontology term" type="Anatomic Term" subparts="No" superparts="Yes"/> <SEGMENT id="EMAP3" description="TS1,second polar body" class="Ontology term" type="Anatomic Term" subparts="No" superparts="Yes"/> <SEGMENT id="EMAP4" description="TS1,zona pellucida" class="Ontology term" type="Anatomic Term" subparts="No" superparts="Yes"/> <SEGMENT id="EMAP5" description="TS2,second polar body" class="Ontology term" type="Anatomic Term" subparts="No" superparts="Yes"/> <SEGMENT id="EMAP6" description="TS2,two-cell stage" class="Ontology term" type="Anatomic Term" subparts="No" superparts="Yes"/> <SEGMENT id="EMAP7" description="TS2,zona pellucida" class="Ontology term" type="Anatomic Term" subparts="No" superparts="Yes"/> ... </ENTRY_POINTS> </DASEP>

  22. DAS: term (new command) http://biocomp.cnb.csic.es:9090/das/EMAP_Reference/term?query=EMAP800 <?xml version="1.0" standalone="no"?> <?xml-stylesheet type="text/xsl" href="http://biocomp.cnb.csic.es:9090/das/xsl=EMAP_dasterm.xsl"?> EMAP Reference server <!DOCTYPE DASTERM SYSTEM "http://biocomp.cnb.uam.es/das/dtd/dasterm.dtd"> <DASTERM version="1.03.20070516"> <TERM id="EMAP800" class="Ontology Term" type="Anatomic Term" subparts="Yes" version="1.0"> <ID>EMAP800</ID> <DESCRIPTION>TS14,future midbrain</DESCRIPTION> <STAGE id="TS14" type="Theiler">14</STAGE> <CHILD id="EMAP801" description="TS14,floor plate" subparts="No" version="1.0" /> <CHILD id="EMAP802" description="TS14,lateral wall" subparts="No" version="1.0" /> <CHILD id="EMAP803" description="TS14,mesencephalic vesicle" subparts="No" version="1.0" /> <CHILD id="EMAP804" description="TS14,neural crest" subparts="No" version="1.0" /> <CHILD id="EMAP805" description="TS14,roof plate" subparts="No" version="1.0" /> <LINK href="http://genex.hgu.mrc.ac.uk/Databases/Anatomy/Diagrams/ts14"> http://genex.hgu.mrc.ac.uk/Databases/Anatomy/Diagrams/ts14 </LINK> </TERM> </TERM> </DASTERM> • Homolog to dna, sequence or volmap. • Retrieves a reference of the system

  23. DAS: features http://biocomp.cnb.csic.es:9090/das/EMAP_Reference/term?query=EMAP800 <?xml version='1.0' standalone='no'?> <?xml-stylesheet type="text/xsl" href="http://biocomp.cnb.csic.es:9090/das/xsl=EMAGE_Features.xsl"?> EMAP Reference server <!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd"> <DASGFF> <GFF version="1.5" href="http://biocomp.cnb.csic.es:9090/das/EMAGE_Features/features"> <SEGMENT id="EMAP800" version="1.0" start="1" stop="" label="TS14, future midbrain"> <FEATURE id="EMAGE:116-T0" label="Assay_Title"> <TYPE id="Assay header" category="title" reference="no" subparts="no" superparts="no">EMAGE assay</TYPE> <START>0</START> <END>0</END> <ORIENTATION>0</ORIENTATION> <TARGET id="EMAGE:116">ISH</TARGET> <LINK href="http://genex.hgu.mrc.ac.uk/das/jsp/submission.jsp?id=EMAGE:116">EMAGE:116</LINK> <GROUP id="EMAGE:116" type="GeneExpression" /> </FEATURE> <FEATURE id="EMAGE:116-G0" label="MGI_Gene_link"> <TYPE id="Assay header" category="link" reference="no" subparts="no" superparts="no">MGI gene link</TYPE> ... </FEATURE> </SEGMENT> </GFF> </DASGFF>

  24. Future work • Integration of new gene expression data sources: Allen Brain Atlas, Gene Paint. • Micro Array data integration. • Expansion to other model organisms: rat, zebrafish, Drosophila, and Human.

  25. The VO team Natalia Jimenez – natalia@cnb.csic.es Joan Segura - jsegura@cnb.csic.es National Institute for Bioinformatics (INB) Juan Jose Vega - jvega@cnb.csic.es CDTI-CENIT :CDTEAM Project Jose Ramon Macias - jrmacias@cnb.csic.es EMBRACE Group Leader Jose Maria Carazo – carazo@cnb.csic.es Biocomputing Unit CNB-CSIC, Madrid

  26. Thanks.

  27. DASxVO Architecture Other DAS systems DASx3DEM Other genomic Reference Servers Reference Server (PDB structures) Reference Server (EMDB data) Alignment Server (Hybrid models) Annotations Server (EMDB metadata) Annotations Servers Client

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