1. Ensembl DAS and Ensembl The 7 year itch!

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

3. Ensembl 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. Ensembl 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. Ensembl 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. Ensembl 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. Ensembl Proposal: Attributes /das/attributes command alternative/extension of types command Tissue Type Heart Lung Percentage Identity Trait Filtering via /das/features?attribute:tissue=;attribute:trait=; –ORs attributes of same type; AND attributes of different types. Addition of entries on features. Heart Embryonic Breast Cancer

8. Ensembl 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. Ensembl Proposal: internal structure CIGAR string or similar structure attribute, e.g. 20M10I30MD30M2I30M or BED/PSL style: Structured score data, similar to “WIG” data: 0.9 1.0 0.8 0.7 10 0.9 20 1 30 0.8 40 0.7

10. Ensembl 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. Ensembl 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.