Difference between revisions of "DASworkshop200903Day3"

Revision as of 15:52, 16 March 2009

Doodle Poll: poll

This page is for people attending day 3 of the workshop to put down their ideas and volunteer to host a session on a topic or write some minutes of the meeting on the biodas wiki site, so we have a record of what was discussed and what the outcomes were or ideally some code to work with.

• My current suggestion for the format would be to have the 1.6 spec and the DAS1/DAS2 merger topics discussed in the first 2 hrs of the day and be open to everybody. Then have groups split up into the remainder of the topics?

DAS 1.6 spec and where to go with the Registry

Host: Jonathan Warren and Andy Jenkinson Secretary: Jonathan Warren and Andy Jenkinson

1.6_Examples

DAS1/DAS2 merger

DAS writeback

Adapting Java DAS client libraries for alignment and PDB file retrieval for clients that dont use BioJava

Javascript das client/server library (allow DAS server discovery and retrieval on the browser page)

Meeting held on Thursday as relevant people were available after workshop:

MINUTES Attendees: Bernat, Greg, Andy, Jonathan, Gustavo and Rafael

On Thursday 12 we talked about JavaScript DAS client libraries. We identified three different ways to create user interfaces using javascript.

• 1.- Clients based on the google maps idea. Creating images on the server and using javascript on the client to manage tailing images. Victor de la Torre show a nice example on his presentation "collaborative annotation tool (MaDAS)"

• 2.- Clients drawing graphics using canvas. Canvas is a new HTML element which can be used to draw graphics using scripting (usually JavaScript). Following this idea the client collects the information to render it on the canvas. Bernat Gel gave some examples with his genome viewer "DASgenexp".

• 3.- Client creating graphics using HTML elements and transparent shaped images. In this case the client creates graphic representations creating HTML elements through the DOM and javascript. We can find an example in Dasty2 and the Karyotype Viewer.

To be able to share javascript on web DAS clients rendering graphics on the client side we proposed to create a standard javascript library. On a web client we can identify three general stages: Request, Parsing and Visualization. Since visualization it is more up to the developer and the necessities of the project we proposed to create this standard library for requests and parsing. Rafael agreed to create the first prototype for this library.

DAS interfaces to sequence analysis tools

Not discussed as a group due to time constraints

BioSapiens ontology lookup and general Ontologies

How to represent the ontology in DAS, e.g. JR Macias' "term" command

• http://biocomp.cnb.csic.es/VisualOmics

DAS vs. ontologies, how and why

This topic was suggeseted because I'd like to understand how 'ontologies' (in general) are implemented in DAS and how this relates to the feature annotation models in Chado or GFF3, for example. How should an annotator use an ontology? How should the use of an ontology be reflected in the client behaviour? What about DAS ontology servers (and the 'term' DAS command)? This topic dosn't really fit with the idea of a 'hackathon', but is a very interesting aspect of DAS. i.e.

What are:

• Ontodas
• DAS Protein Ontology
• Ontology Lookup Service
• The BioSapians (feature type?) ontology
• The ontology of 'input filters' from EMBRACE This is an effort by the EMBRACE project to define ontologies for use in registering web services in the EMBRACE registry and later in the BioCatalogue registry. The ontology will cover the terms used in EMBRACE servcies, including BioMart and EMBOSS - both of which already have well-defined terms which will be used to populate the ontology. This will be contributed to the OBO foundry (like the other ontologies used in DAS) and can be extended to cover algorithms to give a better description of a service, its inputs, parameters and outputs. Contact Peter Rice pmr@ebi.ac.uk for more information.

???

Discussion group notes

• similar to attribute, but includes hierachical structure

• if treated like coordsys, but additional layers hidden

• use case: anatomical ontology, uses "term" as query command;

but more general terms return too much data, response needs to be cut

-> proposed solution: use "maxbins"-like functionality

-> For DAS 1.6: adopt ontology from 1.53E as cvID and method

a) Sequence Feature Ontology (SFO)

add terms if necessary, other ontology may need to be added for anatomical eg.

b) evidence codes

example: <TYPE id="exon SO:0000147" category="inferred from RT-PCR experiment (ECO:0000109)">exon</TYPE>

• Add to Registry: Cache Ontology, add links to master ontology files (PSI?) and ontology browser (EBI?)

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