From ljgarcia at ebi.ac.uk Mon Oct 17 08:43:32 2011 From: ljgarcia at ebi.ac.uk (Leyla Garcia) Date: Mon, 17 Oct 2011 13:43:32 +0100 Subject: [DAS] Multiple methods for a feature In-Reply-To: <30073ABE-515C-4951-9F38-A7D22435AE6C@cs.uct.ac.za> References: <30073ABE-515C-4951-9F38-A7D22435AE6C@cs.uct.ac.za> Message-ID: <4E9C22F4.8010001@ebi.ac.uk> Hi all, At UniProt, we can have more than one method for a feature. It could be the same method but from different sources, for instance "Experimental evidence ECO:0000006" could refer to experiments from Ensembl and InterPro, or totally different methods, for instance "Experimental evidence ECO:0000006" and "Sequence similarity ECO:0000044". Currently in DAS 1.6, it is only possible to have one method for each feature. Why? Is there any other DAS server facing a similar situation as UniProt? If there is, how have you solved this problem? Cheers, Leyla From jw12 at sanger.ac.uk Thu Oct 20 05:27:56 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 20 Oct 2011 10:27:56 +0100 Subject: [DAS] DAS Down Time- Registry and some sources down this weekend Message-ID: <378F234A-259A-41BF-A050-D3E9DCF5680F@sanger.ac.uk> The DAS registry and Sanger DAS sources will be unavailable from Friday midday (GMT) through the weekend. This is because the Sanger Data Centre is being shut down for essential maintenance. I'm pretty sure this will affect the EBI DAS sources also. But someone from the EBI may want to confirm this? We are working on a solution so that a read only version of the Sanger DAS data and Registry will be available when there are future shutdowns, but this facility is not currently available. Sorry for any inconvenience caused. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jw12 at sanger.ac.uk Thu Oct 20 07:26:15 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 20 Oct 2011 12:26:15 +0100 Subject: [DAS] Workshop 2012 Message-ID: <3A2BC093-E884-4DF5-A91F-77BD1886FB48@sanger.ac.uk> Hi I've started a wiki page for the DAS workshop 2012 preliminarily scheduled for 27-29th Feb 2012. Subject to funding. http://www.biodas.org/wiki/DASWorkshop2012 The page is currently split into 3 sections 1)Recent developments since the last DAS workshop 2) Suggestions for Developer Discussions on Developers Day 3) Possible DAS related talks. To kick things off I've added to some of those topics. Please feel free to add some suggestions and/or email to the list. I'd also be very interested in hearing from people who would be interested in attending, either as a new user for the tutorials or a seasoned DAS developer. This will enable us to make informed decisions about how the 2012 workshop should be organised. For the last couple of years the workshop has been a 3 day event with the first day consisting of tutorials, the second had talks and the third a developer discussions day. As many of last years talks are available on the web we may change the format so there are a reduced number of talks. Links to videos are available next to the talks here: http://www.biodas.org/wiki/DASWorkshop2011#Day_2 As a taster here are some of the new things that are available for use by the community since the last DAS workshop: DAS write-back (MyDAS), DAS search (MyDAS), Registry CRUD via web service (get, post, put, delete, authentication headers), Registry supports JSON for all requests and responses, new DAS Registry architecture (client-server), I'm sure there is more......? Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From andy.jenkinson at ebi.ac.uk Mon Oct 24 10:49:14 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Mon, 24 Oct 2011 15:49:14 +0100 Subject: [DAS] Multiple methods for a feature In-Reply-To: <4E9C22F4.8010001@ebi.ac.uk> References: <30073ABE-515C-4951-9F38-A7D22435AE6C@cs.uct.ac.za> <4E9C22F4.8010001@ebi.ac.uk> Message-ID: Hi Leyla, Quite simply, I imagine this is just unique to UniProt. Most peoples' DAS sources are for data generated from a single source, i.e. primary data. But really I think your problem is that you are wanting to use the method to describe how the data behind your annotations is derived (e.g. an experiment, or publication) NOT how the annotation itself was derived (i.e. inferred by a curator). The semantics are a little fuzzy here, but if you were being pedantic about it you should consider the accuracy of this - is your annotation actually fully expressed by each of the evidence codes you are using? For a contrived example, a curator comes to a conclusion that protein X is involved in a pathway A via these pieces of evidence: Experiment 1 says protein X interacts with protein Y. Experiment 2 says protein X interacts with protein Z. Paper 3 says proteins Y and Z are part of pathway A. So in this case, would you use the evidence codes of "inferred by experiment" and "inferred from publication", or whatever they are called, to support an annotation of "protein X is involved in pathway B"? These are not really several methods of producing the annotation - the actual method was the curator's ability to combine the conclusions of the other methods. So would you use "inferred by curator" instead? Cheers, Andy On 17 Oct 2011, at 13:43, Leyla Garcia wrote: > Hi all, > > At UniProt, we can have more than one method for a feature. It could be the same method but from different sources, for instance "Experimental evidence ECO:0000006" could refer to experiments from Ensembl and InterPro, or totally different methods, for instance "Experimental evidence ECO:0000006" and "Sequence similarity ECO:0000044". > > Currently in DAS 1.6, it is only possible to have one method for each feature. Why? Is there any other DAS server facing a similar situation as UniProt? If there is, how have you solved this problem? > > Cheers, > > Leyla > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das From jprocter at compbio.dundee.ac.uk Mon Oct 24 11:17:53 2011 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Mon, 24 Oct 2011 16:17:53 +0100 Subject: [DAS] Workshop 2012 In-Reply-To: <3A2BC093-E884-4DF5-A91F-77BD1886FB48@sanger.ac.uk> References: <3A2BC093-E884-4DF5-A91F-77BD1886FB48@sanger.ac.uk> Message-ID: <4EA581A1.1010006@compbio.dundee.ac.uk> Hi Jon.. On 20/10/2011 12:26, Jonathan Warren wrote: > I'd also be very interested in hearing from people who would be > interested in attending, either as a new user for the tutorials or a > seasoned DAS developer. This will enable us to make informed decisions > about how the 2012 workshop should be organised. I'll be there, notwithstanding the usual caveats about buses, suns going nova, etc.. > For the last couple of years the workshop has been a 3 day event with > the first day consisting of tutorials, the second had talks and the > third a developer discussions day. As many of last years talks are > available on the web we may change the format so there are a reduced > number of talks. Links to videos are available next to the talks here: > http://www.biodas.org/wiki/DASWorkshop2011#Day_2 > > As a taster here are some of the new things that are available for use > by the community since the last DAS workshop: > DAS write-back (MyDAS), DAS search (MyDAS), Registry CRUD via web > service (get, post, put, delete, authentication headers), Registry > supports JSON for all requests and responses, new DAS Registry > architecture (client-server), I'm sure there is more......? It'd be nice to hear about any new DAS client libraries (particularly if they are accessible from Java ;) ). Perhaps it would be good to remind those of us on the list about what outstanding (if any) community development targets remain since last years meeting ? I'd personally also be really interested to hear about case studies - where DAS works and where it should (but doesn't). Jim. ps. re java das libraries. I'll be in Hinxton on 1st December 2011. Is anyone interested in a one day java DAS client code sprint ? From mc at manuelcorpas.com Mon Oct 31 18:23:57 2011 From: mc at manuelcorpas.com (Manuel Corpas) Date: Mon, 31 Oct 2011 22:23:57 +0000 Subject: [DAS] myKaryoView Paper Out Message-ID: Dear Colleagues, on behalf of the other co-authors, I am pleased to announce that the paper describing myKaryoView, a light weight client for visualization of personal genomics data, is now published in PLoS One. The article is open access and we welcome any feedback. You can access it here: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026345 Best wishes, Manuel Manuel Corpas, PhD Tel:? ? ? +44.122349.2372 Web: ? ?http://manuelcorpas.com/about/ Twitter: @manuelcorpas From ljgarcia at ebi.ac.uk Mon Oct 17 12:43:32 2011 From: ljgarcia at ebi.ac.uk (Leyla Garcia) Date: Mon, 17 Oct 2011 13:43:32 +0100 Subject: [DAS] Multiple methods for a feature In-Reply-To: <30073ABE-515C-4951-9F38-A7D22435AE6C@cs.uct.ac.za> References: <30073ABE-515C-4951-9F38-A7D22435AE6C@cs.uct.ac.za> Message-ID: <4E9C22F4.8010001@ebi.ac.uk> Hi all, At UniProt, we can have more than one method for a feature. It could be the same method but from different sources, for instance "Experimental evidence ECO:0000006" could refer to experiments from Ensembl and InterPro, or totally different methods, for instance "Experimental evidence ECO:0000006" and "Sequence similarity ECO:0000044". Currently in DAS 1.6, it is only possible to have one method for each feature. Why? Is there any other DAS server facing a similar situation as UniProt? If there is, how have you solved this problem? Cheers, Leyla From jw12 at sanger.ac.uk Thu Oct 20 09:27:56 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 20 Oct 2011 10:27:56 +0100 Subject: [DAS] DAS Down Time- Registry and some sources down this weekend Message-ID: <378F234A-259A-41BF-A050-D3E9DCF5680F@sanger.ac.uk> The DAS registry and Sanger DAS sources will be unavailable from Friday midday (GMT) through the weekend. This is because the Sanger Data Centre is being shut down for essential maintenance. I'm pretty sure this will affect the EBI DAS sources also. But someone from the EBI may want to confirm this? We are working on a solution so that a read only version of the Sanger DAS data and Registry will be available when there are future shutdowns, but this facility is not currently available. Sorry for any inconvenience caused. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jw12 at sanger.ac.uk Thu Oct 20 11:26:15 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 20 Oct 2011 12:26:15 +0100 Subject: [DAS] Workshop 2012 Message-ID: <3A2BC093-E884-4DF5-A91F-77BD1886FB48@sanger.ac.uk> Hi I've started a wiki page for the DAS workshop 2012 preliminarily scheduled for 27-29th Feb 2012. Subject to funding. http://www.biodas.org/wiki/DASWorkshop2012 The page is currently split into 3 sections 1)Recent developments since the last DAS workshop 2) Suggestions for Developer Discussions on Developers Day 3) Possible DAS related talks. To kick things off I've added to some of those topics. Please feel free to add some suggestions and/or email to the list. I'd also be very interested in hearing from people who would be interested in attending, either as a new user for the tutorials or a seasoned DAS developer. This will enable us to make informed decisions about how the 2012 workshop should be organised. For the last couple of years the workshop has been a 3 day event with the first day consisting of tutorials, the second had talks and the third a developer discussions day. As many of last years talks are available on the web we may change the format so there are a reduced number of talks. Links to videos are available next to the talks here: http://www.biodas.org/wiki/DASWorkshop2011#Day_2 As a taster here are some of the new things that are available for use by the community since the last DAS workshop: DAS write-back (MyDAS), DAS search (MyDAS), Registry CRUD via web service (get, post, put, delete, authentication headers), Registry supports JSON for all requests and responses, new DAS Registry architecture (client-server), I'm sure there is more......? Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From andy.jenkinson at ebi.ac.uk Mon Oct 24 14:49:14 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Mon, 24 Oct 2011 15:49:14 +0100 Subject: [DAS] Multiple methods for a feature In-Reply-To: <4E9C22F4.8010001@ebi.ac.uk> References: <30073ABE-515C-4951-9F38-A7D22435AE6C@cs.uct.ac.za> <4E9C22F4.8010001@ebi.ac.uk> Message-ID: Hi Leyla, Quite simply, I imagine this is just unique to UniProt. Most peoples' DAS sources are for data generated from a single source, i.e. primary data. But really I think your problem is that you are wanting to use the method to describe how the data behind your annotations is derived (e.g. an experiment, or publication) NOT how the annotation itself was derived (i.e. inferred by a curator). The semantics are a little fuzzy here, but if you were being pedantic about it you should consider the accuracy of this - is your annotation actually fully expressed by each of the evidence codes you are using? For a contrived example, a curator comes to a conclusion that protein X is involved in a pathway A via these pieces of evidence: Experiment 1 says protein X interacts with protein Y. Experiment 2 says protein X interacts with protein Z. Paper 3 says proteins Y and Z are part of pathway A. So in this case, would you use the evidence codes of "inferred by experiment" and "inferred from publication", or whatever they are called, to support an annotation of "protein X is involved in pathway B"? These are not really several methods of producing the annotation - the actual method was the curator's ability to combine the conclusions of the other methods. So would you use "inferred by curator" instead? Cheers, Andy On 17 Oct 2011, at 13:43, Leyla Garcia wrote: > Hi all, > > At UniProt, we can have more than one method for a feature. It could be the same method but from different sources, for instance "Experimental evidence ECO:0000006" could refer to experiments from Ensembl and InterPro, or totally different methods, for instance "Experimental evidence ECO:0000006" and "Sequence similarity ECO:0000044". > > Currently in DAS 1.6, it is only possible to have one method for each feature. Why? Is there any other DAS server facing a similar situation as UniProt? If there is, how have you solved this problem? > > Cheers, > > Leyla > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das From jprocter at compbio.dundee.ac.uk Mon Oct 24 15:17:53 2011 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Mon, 24 Oct 2011 16:17:53 +0100 Subject: [DAS] Workshop 2012 In-Reply-To: <3A2BC093-E884-4DF5-A91F-77BD1886FB48@sanger.ac.uk> References: <3A2BC093-E884-4DF5-A91F-77BD1886FB48@sanger.ac.uk> Message-ID: <4EA581A1.1010006@compbio.dundee.ac.uk> Hi Jon.. On 20/10/2011 12:26, Jonathan Warren wrote: > I'd also be very interested in hearing from people who would be > interested in attending, either as a new user for the tutorials or a > seasoned DAS developer. This will enable us to make informed decisions > about how the 2012 workshop should be organised. I'll be there, notwithstanding the usual caveats about buses, suns going nova, etc.. > For the last couple of years the workshop has been a 3 day event with > the first day consisting of tutorials, the second had talks and the > third a developer discussions day. As many of last years talks are > available on the web we may change the format so there are a reduced > number of talks. Links to videos are available next to the talks here: > http://www.biodas.org/wiki/DASWorkshop2011#Day_2 > > As a taster here are some of the new things that are available for use > by the community since the last DAS workshop: > DAS write-back (MyDAS), DAS search (MyDAS), Registry CRUD via web > service (get, post, put, delete, authentication headers), Registry > supports JSON for all requests and responses, new DAS Registry > architecture (client-server), I'm sure there is more......? It'd be nice to hear about any new DAS client libraries (particularly if they are accessible from Java ;) ). Perhaps it would be good to remind those of us on the list about what outstanding (if any) community development targets remain since last years meeting ? I'd personally also be really interested to hear about case studies - where DAS works and where it should (but doesn't). Jim. ps. re java das libraries. I'll be in Hinxton on 1st December 2011. Is anyone interested in a one day java DAS client code sprint ? From mc at manuelcorpas.com Mon Oct 31 22:23:57 2011 From: mc at manuelcorpas.com (Manuel Corpas) Date: Mon, 31 Oct 2011 22:23:57 +0000 Subject: [DAS] myKaryoView Paper Out Message-ID: Dear Colleagues, on behalf of the other co-authors, I am pleased to announce that the paper describing myKaryoView, a light weight client for visualization of personal genomics data, is now published in PLoS One. The article is open access and we welcome any feedback. You can access it here: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026345 Best wishes, Manuel Manuel Corpas, PhD Tel:? ? ? +44.122349.2372 Web: ? ?http://manuelcorpas.com/about/ Twitter: @manuelcorpas