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DAS and Ensembl The 7 year itch!

DAS and Ensembl The 7 year itch!. DAS and Ensembl The 7 year itch!. A brief history DAS ist gut Issues Some proposals. DAS & Ensembl a brief history. Ensembl was one of the earliest adopters for the DAS Protocol; Initially just a client;

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DAS and Ensembl The 7 year itch!

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  1. DAS and EnsemblThe 7 year itch!

  2. DAS and EnsemblThe 7 year itch! A brief history DAS ist gut Issues Some proposals

  3. DAS & Ensembl a brief history Ensembl was one of the earliest adopters for the DAS Protocol; Initially just a client; Introduced data upload which created DAS sources (LDAS, ProServer, ensembls own server); Extended itself to a server.

  4. DAS ist gut! Ensembl does not have to “assimiliate” all data to make it available with in Ensembl. Allows discovery of sources available; Allows client to retrieve only the data they need; Allows server to inform client how the data should be grouped/rendered/.../ etc

  5. Issues DAS is a vague standard Grouping; Stylesheet "zoom" levels; What does each style mean… DAS isn't an enforced standard Feature ids not unique; Missing values; DAS falls short in a number of places Returning other information about features; Same source multiple viewing approaches; Proliferation of sources in multi-sample world; Very verbose: Dealing with "sub-feature" structure. e.g. HSPs in an alignment. Dealing with large amount of "numeric" date; e.g. continuous score data.

  6. Proposals DAS is a vague standard Grouping; Stylesheet "zoom" levels; What does each style mean… DAS isn't an enforced standard Feature ids not unique; Missing values; DAS falls short in a number of places Returning other information about features; Same source multiple viewing approaches; Proliferation of sources in multi-sample world; Very verbose: Dealing with "sub-feature" structure. e.g. HSPs in an alignment. Dealing with large amount of "numeric" date; e.g. continuous score data.

  7. Proposal: Attributes • /das/attributes command alternative/extension of types command <attributes><attribute code="tissue" type="fixed">    <caption>Tissue Type</caption>    <value>Heart</value>    <value>Lung</value></attribute><attribute code="percent_identity" type="numeric" min="0" max="100">    <caption>Percentage Identity</caption></attribute><attribute code="trait" type="string">    <caption>Trait</caption></attribute> </attributes> • Filtering via /das/features?attribute:tissue=;attribute:trait=; • ORs attributes of same type; AND attributes of different types. • Addition of <ATTRIBUTE type="X"></ATTRIBUTE> entries on features. <feature id=“”> <attribute type="tissue">Heart</attribute> <attribute type="stage">Embryonic</attribute> <attribute type="trait">Breast Cancer</attribute> <…> </feature>

  8. Proposals DAS is a vague standard Grouping; Stylesheet "zoom" levels; What does each style mean… DAS isn't an enforced standard Feature ids not unique; Missing values; DAS falls short in a number of places Returning other information about features; Same source multiple viewing approaches; Proliferation of sources in multi-sample world; Very verbose: Dealing with "sub-feature" structure. e.g. HSPs in an alignment. Dealing with large amount of "numeric" date; e.g. continuous score data.

  9. Proposal: internal structure CIGAR string or similar structure attribute, e.g. <alignment type="cigar">20M10I30MD30M2I30M</alignment> or BED/PSL style: <subparts start=“1,100,200,400” length=“90,50,50,100” /> Structured score data, similar to “WIG” data: <scores step="10">0.9 1.0 0.8 0.7</scores> <scores step="variable">10 0.9 20 1 30 0.8 40 0.7</scores>

  10. Proposals DAS is a vague standard Grouping; Stylesheet "zoom" levels; What does each style mean… DAS isn't an enforced standard Feature ids not unique; Missing values; DAS falls short in a number of places Returning other information about features; Same source multiple viewing approaches; Proliferation of sources in multi-sample world;a Very verbose: Dealing with "sub-feature" structure. e.g. HSPs in an alignment. Dealing with large amount of "numeric" date; e.g. continuous score data.

  11. Proposal: alternate stylesheets • Alternative stylesheets: • "Replacement" for zoom • Server can suggest alternative stylesheets so same data can be rendered in alternative - but under the control of the server - different view.Similar to HTML alternative stylesheets. • User can be given the option which one to render.

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