Ensembl DAS and Ensembl The 7 year itch!

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

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.

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

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.

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.

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

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.

Ensembl Proposal: internal structure CIGAR string or similar structure attribute, e.g. 20M10I30MD30M2I30M or BED/PSL style: Structured score data, similar to “WIG” data:

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.

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.