Thanks for the encouragement Andy! Yup, I need to look in detail at the DAS writeback specification.
I remember Gustavo talking a couple of years back, asking people to work together on features like these (rather than all competing on similar but probably mutually exclusive methods). I really value that sentiment. Cheers, Dan. On 2 November 2010 13:07, Andy Jenkinson <[email protected]> wrote: > Hi Dan, > > Now I see what you mean - basically the wiki and DAS source have the same > data/comments, and there are two ways to enter it (writeback inside the > client OR the wiki itself). This sounds good and certainly feasible. I guess > there will be details about the format the comments take in the Wiki, but I'm > sure it would work. I agree that the great thing about an approach like this > (and DAS writeback's "independent" architecture) is the open model. This, and > the fact that it would also be possible to have the comments propagated into > multiple clients (the usual DAS distributed approach) make things much more > appealing than just a single isolated database of user comments. > > It's probably worth looking at the provenance/users aspect of the wiki > integration to see how this can work with writeback. Gustavo can say more > about how writeback handles user tracking I expect, but authentication is > often the most difficult thing when it comes to implementing these things, I > find. Specifically in this case: "when I edit something in the client, can > people see who made the edit on the wiki itself, and if so is the process by > which that happens secure?" > > I definitely encourage you to look further into it and am keen to find out > how you get on. > > Cheers, > Andy > > On 2 Nov 2010, at 10:14, Dan Bolser wrote: > >> Here is how I thought it would work (please let me know if this sounds >> about right, or if I made some mistakes in my understanding of the way >> DAS writeback will work): >> >> 1) I was thinking that the ProServer DAS server should (or at least >> could) implement the DAS writeback extension. >> >> 2) The genome browser client (or some other client) would talk to the >> DAS server using the DAS writeback protocol once a comment was added >> (i.e. I'm relying on a sensible client that can 'properly' handle >> comments). >> >> 3) I expect that ProServer will offload the job of actually storing >> the comment on a datasource adaptor. >> >> 4) I thought I'd extend the MediaWiki adaptor that I wrote for reading >> feature data from the wiki to also write feature data there too. >> (Comments are just features right?) >> >> 5) You could then use either the genome browser client (or some other >> client) or the wiki directly to add and/or edit comments. i.e. the >> wiki is just another feature editing client / DAS datasource. >> >> >> I like this solution because I think 'community annotation' should be >> in the 'community', not on some server behind closed doors somewhere >> (somehow a wiki 'feels' more 'open' to me than some bespoke database >> x). There are plenty of wikis that could be used as back ends, and >> 'wiki' is a good way to do community annotation. They handle issues >> related to provenance, QC, versioning, authorship, motivation, >> publicising, publication, etc., etc. Again, MediaWiki is a good >> choice, because their is a lot of development for that platform, and I >> can easily imagine tagging, 'micro-publication' and syndication >> extensions being leveraged for this kind of data. >> >> >> Does it sound reasonable? >> >> >> Cheers, >> Dan. >> >> BioWiki conference: >> http://www.nettab.org/2010/ >> >> >> On 30 October 2010 12:41, Andy Jenkinson <[email protected]> wrote: >>> Hi Dan, >>> >>> Sounds interesting. How do you see that working? >>> >>> Cheers, >>> Andy >>> >>> On 29 Oct 2010, at 16:28, Dan Bolser wrote: >>> >>>> My thinking was that the DASWiki approach could also support the DAS >>>> writeback extension. >>>> >>>> On 29 October 2010 11:58, Gustavo Adolfo Salazar Orejuela >>>> <[email protected]> wrote: >>>>> Hello There, >>>>> >>>>> I have been working in an extension to DAS1.6 called >>>>> writeback(http://www.biodas.org/wiki/DAS1.6E#DAS_writeback), this will >>>>> allow >>>>> to create new versions of an existing feature. So, putting new notes into >>>>> a >>>>> feature is just a creation of a new version of the feature. The server >>>>> implementation of the writeback extends MyDas >>>>> (http://code.google.com/p/mydas/) and you can get a mydas+writebackk >>>>> datasource by SVN (https://mydas.googlecode.com/svn/writeback-datasource). >>>>> We are close to release the plugin for Dasty3 to use the writeback server, >>>>> however this first client is a protein client, and so far there is not a >>>>> development for a genome client with DAS writeback capability, but I am >>>>> quite interested in this. >>>>> I hope to be able to announce the release of the writeback client in >>>>> Dasty3 >>>>> in a few days, so you will be able to see it working and see if this >>>>> approach goes in the same direction of what you are looking for. >>>>> >>>>> Regards, >>>>> >>>>> Gustavo. >>>>> >>>>> 2010/10/29 Dan Bolser <[email protected]> >>>>>> >>>>>> Hi Bob, >>>>>> >>>>>> This is a nice idea. In my spare time I've been working on running a >>>>>> DAS server from a MediaWiki data source. (MediaWiki is the wiki that >>>>>> runs Wikipedia). >>>>>> >>>>>> In theory, you could have a comments track that was pulled in from the >>>>>> 'DASWiki', and clicking the details link would take you to the wiki >>>>>> page to edit the comment. Going back to the GBrowse, you would then >>>>>> see the updated data from the wiki page. It wouldn't be too hard to >>>>>> have a similar workflow for adding new comments. >>>>>> >>>>>> I saw a talk from some people at KeyGene who are doing something >>>>>> similar (loading DAS into a wiki and linking it to GBrowse to generate >>>>>> query reports for specific regions). You can see the talk here: >>>>>> >>>>>> SMWCon Fall 2010 / Sunday / Rudi van Bavel >>>>>> * http://semantic-mediawiki.org/wiki/SMWCon_Fall_2010#Program >>>>>> ** https://docs.google.com/present/view?id=dg56kh6m_344gh2dg72g >>>>>> ** >>>>>> http://srv-hrl-32.web.pwo.ou.nl//informatica/SMWCon/Van%20Bavel%20bulk%20loading.wmv >>>>>> >>>>>> >>>>>> If anyone wants to take what I have done so far, my (sadly neglected) >>>>>> prototype is here: >>>>>> >>>>>> http://das.referata.com/wiki/Main_Page >>>>>> >>>>>> >>>>>> Kick me a few times and I'll get the underlying code into shape. A >>>>>> year or two back I did have a working prototype based on a MediaWiki >>>>>> ProServer adaptor. >>>>>> >>>>>> >>>>>> If you are interested in community annotation should think about >>>>>> attending >>>>>> this: >>>>>> >>>>>> Joint NETTAB 2010 and BBCC 2010 workshops focused on Biological Wikis: >>>>>> http://www.nettab.org/2010/ >>>>>> >>>>>> >>>>>> Cheers, >>>>>> Dan. >>>>>> >>>>>> On 26 October 2010 20:31, Bob Muller <[email protected]> wrote: >>>>>>> We are working with a small research project that doesn't have funds for >>>>>>> a full-scale database for features, so they want to know: >>>>>>> >>>>>>> How difficult would it be to add a comment section editable by users to >>>>>>> gbrowse? When you click on a feature in gbrowse it shows a detail page >>>>>>> for >>>>>>> that feature, is there any way we could enable edits that could be >>>>>>> written >>>>>>> back to the underlying mysql database that gbrowse runs on? >>>>>>> >>>>>>> Their idea is to use the SeqFeature::Store database to hold "comments" >>>>>>> entered through GBrowse as a way to annotate their genome. I'd be >>>>>>> interested >>>>>>> in whether this is possible in GBrowse 1.7 or in 2.x. >>>>>>> >>>>>>> --Bob Muller, TAIR (www.arabidopsis.org) >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America >>>>>>> contest >>>>>>> Create new apps & games for the Nokia N8 for consumers in U.S. and >>>>>>> Canada >>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in >>>>>>> marketing >>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store >>>>>>> http://p.sf.net/sfu/nokia-dev2dev >>>>>>> _______________________________________________ >>>>>>> Gmod-gbrowse mailing list >>>>>>> [email protected] >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> DAS mailing list >>>>>> [email protected] >>>>>> http://lists.open-bio.org/mailman/listinfo/das >>>>> >>>>> >>>>> >>>>> -- >>>>> Gustavo Adolfo Salazar Orejuela >>>>> >>>> >>>> _______________________________________________ >>>> DAS mailing list >>>> [email protected] >>>> http://lists.open-bio.org/mailman/listinfo/das >>> >>> > > _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
