Difference between revisions of "Talk:DAS/2"
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(New page: Does anyone know if the Biopackages DAS2 server is defunct? I have not had any luck connecting to it, and I think it ought to be removed from this page as a resource if it no longer operat...) |
(Link to a post from Gregg on DAS/2 grant reflections) |
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| + | == Biopackages DAS/2 server == | ||
| + | * http://das.biopackages.net/das/genome - DAS/2 server reference implementation | ||
Does anyone know if the Biopackages DAS2 server is defunct? I have not had any luck connecting to it, and I think it ought to be removed from this page as a resource if it no longer operates as advertised. [[User:Mbrauer|Mbrauer]] 23:22, 2 February 2009 (UTC) | Does anyone know if the Biopackages DAS2 server is defunct? I have not had any luck connecting to it, and I think it ought to be removed from this page as a resource if it no longer operates as advertised. [[User:Mbrauer|Mbrauer]] 23:22, 2 February 2009 (UTC) | ||
| + | : I've contacted Allen Day (author) about it. We may be able to revive it, stay tuned. In the meantime, I'd be OK if it was delisted from the page. [[User:SteveC|sac]] 19:34, 3 February 2009 (UTC) | ||
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| + | == Why not using a format compatible with RDF == | ||
| + | |||
| + | Hi all, | ||
| + | I was wondering how the DAS protocol can be used to retrieve the semantic of the annotation ? | ||
| + | Why not using a XML schema compatible with [http://www.w3.org/RDF/ RDF] ? | ||
| + | |||
| + | --[[User:Lindenb|Lindenb]] 15:12, 26 May 2009 (UTC) | ||
| + | : '''Short answer''': No, but there's definitely interest in this sort of thing. '''Long answer''': The original DAS/2 grant proposed to explore this possibility (ca. 2004), noting that "''there have been a number of proposals to add a general mechanism to DAS to attach arbitrary attributes to sequences and sequence features, and also to allow for describing arbitrary relationships between features and/or sequences. Both of these could be achieved by using an RDF XML syntax that references the URIs of the features.''" There were discussions about how to pass arbitrary RDF via the DAS/2 spec, but it didn't make it into the spec. The DAS/2 spec scratches the surface of richer semantics by having improved feature classification via ontology referencing ([[DAS/2.1/Spec/Get-Genomic/Types#TYPES_element|noted here]]), and the DAS 1.6 series has something similar. DAS/2 has also been used to provide a RESTful framework around [[DAS/2.1/Spec#Ontology_Retrievals|ontology terms (placeholder)]]. How to best use DAS to provide richer semantics between and among sequences, features, and ontology terms is an area deserving more thought. It's also worth questioning whether it makes sense to use DAS to channel richer semantic info (my sense: yes) and what implications might this have for the evolution of the DAS spec and existing clients and servers. [[User:SteveC|SteveC]] 00:38, 27 May 2009 (UTC) | ||
| + | ::Thanks a lot for this answser Steve. FYI, this subject was discussed on FriendFeed [http://friendfeed.com/cassj/dffceeeb/ensembl-lies-setting-up-das-server-is-not-easy http://friendfeed.com/cassj/dffceeeb/ensembl-lies-setting-up-das-server-is-not-easy] , [http://friendfeed.com/the-life-scientists/97c3ea28/main-page-biodas http://friendfeed.com/the-life-scientists/97c3ea28/main-page-biodas] --[[User:Lindenb|Lindenb]] 05:48, 27 May 2009 (UTC) | ||
| + | |||
| + | == DAS/2 Grant History == | ||
| + | |||
| + | Some DAS/2 grant reflections from Gregg Helt on 2008-10-29: http://article.gmane.org/gmane.science.biology.biodas/81 | ||
Latest revision as of 01:00, 14 July 2009
Biopackages DAS/2 server
- http://das.biopackages.net/das/genome - DAS/2 server reference implementation
Does anyone know if the Biopackages DAS2 server is defunct? I have not had any luck connecting to it, and I think it ought to be removed from this page as a resource if it no longer operates as advertised. Mbrauer 23:22, 2 February 2009 (UTC)
- I've contacted Allen Day (author) about it. We may be able to revive it, stay tuned. In the meantime, I'd be OK if it was delisted from the page. sac 19:34, 3 February 2009 (UTC)
Why not using a format compatible with RDF
Hi all, I was wondering how the DAS protocol can be used to retrieve the semantic of the annotation ? Why not using a XML schema compatible with RDF ?
--Lindenb 15:12, 26 May 2009 (UTC)
- Short answer: No, but there's definitely interest in this sort of thing. Long answer: The original DAS/2 grant proposed to explore this possibility (ca. 2004), noting that "there have been a number of proposals to add a general mechanism to DAS to attach arbitrary attributes to sequences and sequence features, and also to allow for describing arbitrary relationships between features and/or sequences. Both of these could be achieved by using an RDF XML syntax that references the URIs of the features." There were discussions about how to pass arbitrary RDF via the DAS/2 spec, but it didn't make it into the spec. The DAS/2 spec scratches the surface of richer semantics by having improved feature classification via ontology referencing (noted here), and the DAS 1.6 series has something similar. DAS/2 has also been used to provide a RESTful framework around ontology terms (placeholder). How to best use DAS to provide richer semantics between and among sequences, features, and ontology terms is an area deserving more thought. It's also worth questioning whether it makes sense to use DAS to channel richer semantic info (my sense: yes) and what implications might this have for the evolution of the DAS spec and existing clients and servers. SteveC 00:38, 27 May 2009 (UTC)
- Thanks a lot for this answser Steve. FYI, this subject was discussed on FriendFeed http://friendfeed.com/cassj/dffceeeb/ensembl-lies-setting-up-das-server-is-not-easy , http://friendfeed.com/the-life-scientists/97c3ea28/main-page-biodas --Lindenb 05:48, 27 May 2009 (UTC)
DAS/2 Grant History
Some DAS/2 grant reflections from Gregg Helt on 2008-10-29: http://article.gmane.org/gmane.science.biology.biodas/81
