From ola.spjuth at farmbio.uu.se Wed Apr 2 10:43:13 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Wed, 2 Apr 2008 16:43:13 +0200 Subject: [MOBY-l] Versioning of Moby objects Message-ID: <155FD762-7D7E-435D-A5A7-AC5935F94FF5@farmbio.uu.se> Hi, We in the Bioclipse project (www.bioclipse.net) are working for as much Moby interoperability as possible in our next version. As Bioclipse is a workbench where people can download and edit resources, we had an interesting discussion today how Moby objects (with ID and NAMESPACE) are treated with respect to modifications. Let's say I download a sequence from Genbank, and store it on my local computer. The question was how a modification to this resource should be handled. We considered having some sort of flag for this, or maybe a 'revision' or 'version' parameter, but wanted to hear your view on this matter. I'd also like to make a humble request that someone elaborated on the use of LSID in Moby, and related this to the REST approach when it comes to services, resources, and versioning of these. Cheers, .../Ola From ola.spjuth at farmbio.uu.se Wed Apr 2 11:06:25 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Wed, 2 Apr 2008 17:06:25 +0200 Subject: [MOBY-l] Services accepting multiple inputs Message-ID: Hi, Is there a way to see if services accept multiple inputs? I tried to feed the "MOBYSHoundGetGenBankff" with a MobyDataObject[] containing two simple objects with id and namespace. The result (as far as I can see) was only one 'file', and the other input object seems to have been omitted. Have I done something wrong or does this service only accept a single input? In that case, how can this be deducted from the service in jMoby? Cheers, .../Ola From markw at illuminae.com Wed Apr 2 11:10:38 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 02 Apr 2008 08:10:38 -0700 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: References: Message-ID: The service accepts a single input; however, as with all Moby services, you can send multiple requests (mobyData blocks) per invocation message. Mark On Wed, 02 Apr 2008 08:06:25 -0700, Ola Spjuth wrote: > Hi, > > Is there a way to see if services accept multiple inputs? I tried to > feed the "MOBYSHoundGetGenBankff" with a MobyDataObject[] containing two > simple objects with id and namespace. The result (as far as I can see) > was only one 'file', and the other input object seems to have been > omitted. Have I done something wrong or does this service only accept a > single input? In that case, how can this be deducted from the service in > jMoby? > > Cheers, > > .../Ola > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From edward.kawas at gmail.com Wed Apr 2 11:31:22 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 2 Apr 2008 08:31:22 -0700 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: References: Message-ID: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> Hi Ola, If you do a findService on the service that you would like to invoke, then you can see how many inputs there are. For instance (something like the following), CentralImpl central = new CentralImpl(); MobyService service = central.findService(new MobyService("MOBYSHoundGetGenBankff"))[0]; // get the input count int count = Service.getPrimaryInputs().length; Eddie -----Original Message----- From: moby-l-bounces at lists.open-bio.org [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Ola Spjuth Sent: April-02-08 8:06 AM To: moby-l at lists.open-bio.org Subject: [MOBY-l] Services accepting multiple inputs Hi, Is there a way to see if services accept multiple inputs? I tried to feed the "MOBYSHoundGetGenBankff" with a MobyDataObject[] containing two simple objects with id and namespace. The result (as far as I can see) was only one 'file', and the other input object seems to have been omitted. Have I done something wrong or does this service only accept a single input? In that case, how can this be deducted from the service in jMoby? Cheers, .../Ola _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l From markw at illuminae.com Wed Apr 2 12:19:53 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 02 Apr 2008 09:19:53 -0700 Subject: [MOBY-l] Versioning of Moby objects In-Reply-To: <155FD762-7D7E-435D-A5A7-AC5935F94FF5@farmbio.uu.se> References: <155FD762-7D7E-435D-A5A7-AC5935F94FF5@farmbio.uu.se> Message-ID: I don't think we have really considered objects to be anything more than "containers", so the idea of versioning an object when the data inside it changes has never come up. Certainly we do version our Object's as defined by the ontology (i.e. if the nature of the "container" changes, then that Object is re-versioned) but Moby objects really don't pay any attention to the data that is passed around inside of them. If you think this is a useful and missing feature, please feel free to submit an RFC :-) M On Wed, 02 Apr 2008 07:43:13 -0700, Ola Spjuth wrote: > Hi, > > We in the Bioclipse project (www.bioclipse.net) are working for as much > Moby interoperability as possible in our next version. As Bioclipse is a > workbench where people can download and edit resources, we had an > interesting discussion today how Moby objects (with ID and NAMESPACE) > are treated with respect to modifications. Let's say I download a > sequence from Genbank, and store it on my local computer. The question > was how a modification to this resource should be handled. We considered > having some sort of flag for this, or maybe a 'revision' or 'version' > parameter, but wanted to hear your view on this matter. > > I'd also like to make a humble request that someone elaborated on the > use of LSID in Moby, and related this to the REST approach when it comes > to services, resources, and versioning of these. > > Cheers, > > .../Ola > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l -- -- Mark Wilkinson iCAPTURE Centre From ola.spjuth at farmbio.uu.se Thu Apr 3 02:40:22 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Thu, 3 Apr 2008 08:40:22 +0200 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> References: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> Message-ID: <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> Hi Eddie, Thanks for the snippet. As the MobyRequest acceps a MobyDataInstance [] I thought this would be handled by the MobyRequest but reading the source reveals that in this case if too many inputs, only one will be used . Anyway, what does a service respond with if it accepts multiple inputs, for example a list of objects with undefined size? And could you please show how I pass in mutliple MobyData objects, as Mark described it, in the same MobyRequest invocation? Instead of doing as below (which obviously was wrong). MobyService templateService = new MobyService ("MOBYSHoundGetGenBankff"); MobyService[] validServices = worker.findService(templateService); MobyRequest mr = new MobyRequest(worker); mr.setService(validServices[0]); MobyDataObject[] input=new MobyDataObject[2]; input[0]=new MobyDataObject("NCBI_gi", "111076"); input[1]=new MobyDataObject("NCBI_gi", "111077"); mr.setInput(input); mr.invokeService(this); Cheers, .../Ola On Apr 2, 2008, at 17:31 , Edward Kawas wrote: > Hi Ola, > > If you do a findService on the service that you would like to > invoke, then > you can see how many inputs there are. > > For instance (something like the following), > > CentralImpl central = new CentralImpl(); > MobyService service = central.findService(new > MobyService("MOBYSHoundGetGenBankff"))[0]; > // get the input count > int count = Service.getPrimaryInputs().length; > > Eddie > > -----Original Message----- > From: moby-l-bounces at lists.open-bio.org > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Ola Spjuth > Sent: April-02-08 8:06 AM > To: moby-l at lists.open-bio.org > Subject: [MOBY-l] Services accepting multiple inputs > > Hi, > > Is there a way to see if services accept multiple inputs? I tried to > feed the "MOBYSHoundGetGenBankff" with a MobyDataObject[] containing > two simple objects with id and namespace. The result (as far as I can > see) was only one 'file', and the other input object seems to have > been omitted. Have I done something wrong or does this service only > accept a single input? In that case, how can this be deducted from > the service in jMoby? > > Cheers, > > .../Ola > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > From groscurt at mpiz-koeln.mpg.de Thu Apr 3 04:47:56 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 03 Apr 2008 10:47:56 +0200 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> References: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> Message-ID: <47F499BC.5040909@mpiz-koeln.mpg.de> Hi Ola, when i understand it correctly you want to call a service which takes one input for several inputs and expect MobyRequest to handle those several inputs. For me this approach does not make any sense and MobyRequest works correct as it is... it calls a service and returns it result. If you want to call the same service more often with different inputs you have to call the service more often and not giving the request all inputs... MobyService templateService = new MobyService("MOBYSHoundGetGenBankff"); MobyService[] validServices = worker.findService(templateService); MobyRequest mr = new MobyRequest(worker); mr.setService(validServices[0]); // simple example of iterating over all inputs for(String[] input : inputs) { mr.setInput(new MobyDataObject(input[0], input[1]); mr.setInput(input); mr.invokeService(this); } what do you expect to get back in your case ? it would mean you have a number of xmls, one for each input you give... how to know which input returned which output ? maybe there is a way, as Mark apparently indicates, but i cant see how shall work.... best andreas Ola Spjuth wrote: > Hi Eddie, > > Thanks for the snippet. As the MobyRequest acceps a MobyDataInstance[] > I thought this would be handled by the MobyRequest but reading the > source reveals that in this case if too many inputs, only one will be > used . Anyway, what does a service respond with if it accepts multiple > inputs, for example a list of objects with undefined size? And could > you please show how I pass in mutliple MobyData objects, as Mark > described it, in the same MobyRequest invocation? Instead of doing as > below (which obviously was wrong). > > MobyService templateService = new > MobyService("MOBYSHoundGetGenBankff"); > MobyService[] validServices = worker.findService(templateService); > MobyRequest mr = new MobyRequest(worker); > mr.setService(validServices[0]); > > MobyDataObject[] input=new MobyDataObject[2]; > input[0]=new MobyDataObject("NCBI_gi", "111076"); > input[1]=new MobyDataObject("NCBI_gi", "111077"); > > mr.setInput(input); > mr.invokeService(this); > > Cheers, > > .../Ola > > On Apr 2, 2008, at 17:31 , Edward Kawas wrote: > >> Hi Ola, >> >> If you do a findService on the service that you would like to invoke, >> then >> you can see how many inputs there are. >> >> For instance (something like the following), >> >> CentralImpl central = new CentralImpl(); >> MobyService service = central.findService(new >> MobyService("MOBYSHoundGetGenBankff"))[0]; >> // get the input count >> int count = Service.getPrimaryInputs().length; >> >> Eddie >> >> -----Original Message----- >> From: moby-l-bounces at lists.open-bio.org >> [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Ola Spjuth >> Sent: April-02-08 8:06 AM >> To: moby-l at lists.open-bio.org >> Subject: [MOBY-l] Services accepting multiple inputs >> >> Hi, >> >> Is there a way to see if services accept multiple inputs? I tried to >> feed the "MOBYSHoundGetGenBankff" with a MobyDataObject[] containing >> two simple objects with id and namespace. The result (as far as I can >> see) was only one 'file', and the other input object seems to have >> been omitted. Have I done something wrong or does this service only >> accept a single input? In that case, how can this be deducted from >> the service in jMoby? >> >> Cheers, >> >> .../Ola >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l >> > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From groscurt at mpiz-koeln.mpg.de Thu Apr 3 04:50:59 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 03 Apr 2008 10:50:59 +0200 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> References: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> Message-ID: <47F49A73.3080407@mpiz-koeln.mpg.de> Ola Spjuth wrote: > Hi Eddie, > > Thanks for the snippet. As the MobyRequest acceps a MobyDataInstance[] > I thought this would be handled by the MobyRequest i think here is the missunderstanding... of course the mobyrequest can handle MobyDataInstance[], but this is for service which have MORE primary inputs (like an identifier and a sequence), not for calling a service which has ONE primary input with several inputs.... From ola.spjuth at farmbio.uu.se Thu Apr 3 06:00:18 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Thu, 3 Apr 2008 12:00:18 +0200 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: <47F499BC.5040909@mpiz-koeln.mpg.de> References: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> <47F499BC.5040909@mpiz-koeln.mpg.de> Message-ID: <53CF0758-586E-4C86-8FDE-CAFACF85BD08@farmbio.uu.se> Hi, If a service accepts a single object as input, and delivers a single object as output (like MOBYSHoundGetGenBankff) it would be convenient if you were able to send a list of simple objects and get a list back with result objects. I understand if this is not possible (by design), and yes this was my question. I suppose it would be possible to set up another version of the service that accepted a MobyDataComposite containing an arbitrary number of wrapped MobyDataObject, and delivers a MobyDataComposite as output, containing an arbitrary number of objects? This means you need 2 different services to accommodate for the case of one input object and another for many inputs, and the situation is left to service providers and not handled by Moby. Is this a correct observation? On Apr 3, 2008, at 10:47 , Andreas Groscurth wrote: > [snip] > maybe there is a way, as Mark apparently indicates, but i cant see > how shall work.... > Yes, I am also curious to hear about that! Cheers, .../Ola From groscurt at mpiz-koeln.mpg.de Thu Apr 3 06:47:41 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 03 Apr 2008 12:47:41 +0200 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: <53CF0758-586E-4C86-8FDE-CAFACF85BD08@farmbio.uu.se> References: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> <47F499BC.5040909@mpiz-koeln.mpg.de> <53CF0758-586E-4C86-8FDE-CAFACF85BD08@farmbio.uu.se> Message-ID: <47F4B5CD.7090902@mpiz-koeln.mpg.de> Ola Spjuth wrote: > I suppose it would be possible to set up another version of the > service that accepted a MobyDataComposite containing an arbitrary > number of wrapped MobyDataObject, and delivers a MobyDataComposite as > output, containing an arbitrary number of objects? no - because MobyDataComposite is the represent of complex data types, NOT for an arbtrary number of inputs. A service can accept one MobyDataObject (a single Object), one MobyDataComposite (a single complex type, like AminoAcidSequence) or more of them or a combination of them... but its not for using a collection of intputs just because it could be convenient to call a service with several different inputs ! just use for each input object a differnent cal - that would mobyrequest have also to do... becaus a service which defines one input can not take more inputs... > This means you need 2 different services to accommodate for the case > of one input object and another for many inputs, and the situation is > left to service providers and not handled by Moby. Is this a correct > observation? Why 2 different services ? Either your service takes e.g. one GI to do something, or takes a collection... Of course its up to the service provider to know what his services does and therefore to offer one of either possibilities. And if the services takes a collection of input - of course you can set more than one input (like 3 GIs), BUT if the service is registered with only one input - you have to stick to its rules. Best andreas > > On Apr 3, 2008, at 10:47 , Andreas Groscurth wrote: > > >> [snip] >> maybe there is a way, as Mark apparently indicates, but i cant see >> how shall work.... >> > > Yes, I am also curious to hear about that! > > Cheers, > > .../Ola > From ola.spjuth at farmbio.uu.se Thu Apr 3 08:23:49 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Thu, 3 Apr 2008 14:23:49 +0200 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: <47F4B5CD.7090902@mpiz-koeln.mpg.de> References: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> <47F499BC.5040909@mpiz-koeln.mpg.de> <53CF0758-586E-4C86-8FDE-CAFACF85BD08@farmbio.uu.se> <47F4B5CD.7090902@mpiz-koeln.mpg.de> Message-ID: <94BE9199-4F10-4C6B-A688-54D70D7884EA@farmbio.uu.se> Andreas, Thanks a lot for the explanation. Cheers, /Ola On Apr 3, 2008, at 12:47 , Andreas Groscurth wrote: > Ola Spjuth wrote: >> I suppose it would be possible to set up another version of the >> service that accepted a MobyDataComposite containing an arbitrary >> number of wrapped MobyDataObject, and delivers a MobyDataComposite >> as output, containing an arbitrary number of objects? > no - because MobyDataComposite is the represent of complex data > types, NOT for an arbtrary number of inputs. > > A service can accept one MobyDataObject (a single Object), one > MobyDataComposite (a single complex type, like AminoAcidSequence) > or more of them or a combination of them... but its not for using a > collection of intputs just because it could be convenient to call a > service with several different inputs ! > > just use for each input object a differnent cal - that would > mobyrequest have also to do... becaus a service which defines one > input can not take more inputs... > >> This means you need 2 different services to accommodate for the >> case of one input object and another for many inputs, and the >> situation is left to service providers and not handled by Moby. Is >> this a correct observation? > Why 2 different services ? Either your service takes e.g. one GI to > do something, or takes a collection... Of course its up to the > service provider to know what his services does and therefore to > offer one of either possibilities. And if the services takes a > collection of input - of course you can set more than one input > (like 3 GIs), BUT if the service is registered with only one input > - you have to stick to its rules. > > Best > andreas >> >> On Apr 3, 2008, at 10:47 , Andreas Groscurth wrote: >> >> >>> [snip] >>> maybe there is a way, as Mark apparently indicates, but i cant >>> see how shall work.... >>> >> >> Yes, I am also curious to hear about that! >> >> Cheers, >> >> .../Ola >> > From edward.kawas at gmail.com Thu Apr 3 08:54:39 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 3 Apr 2008 05:54:39 -0700 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: <94BE9199-4F10-4C6B-A688-54D70D7884EA@farmbio.uu.se> References: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> <47F499BC.5040909@mpiz-koeln.mpg.de> <53CF0758-586E-4C86-8FDE-CAFACF85BD08@farmbio.uu.se> <47F4B5CD.7090902@mpiz-koeln.mpg.de> <94BE9199-4F10-4C6B-A688-54D70D7884EA@farmbio.uu.se> Message-ID: <47f4d3aa.12da600a.65e1.2c86@mx.google.com> Just so that I get the last word ;-) I am not sure how to use MobyDataInstance/etc, but in the moby world if a service receives multiple mobyData blocks, then the service iterates over each of them and then returns a response. http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InputMessa ge.html (the part 'How to invoke a service with a Simple Article' describes this). Eddie -----Original Message----- From: moby-l-bounces at lists.open-bio.org [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Ola Spjuth Sent: April-03-08 5:24 AM To: Andreas Groscurth Cc: moby-l at lists.open-bio.org Subject: Re: [MOBY-l] Services accepting multiple inputs Andreas, Thanks a lot for the explanation. Cheers, /Ola On Apr 3, 2008, at 12:47 , Andreas Groscurth wrote: > Ola Spjuth wrote: >> I suppose it would be possible to set up another version of the >> service that accepted a MobyDataComposite containing an arbitrary >> number of wrapped MobyDataObject, and delivers a MobyDataComposite >> as output, containing an arbitrary number of objects? > no - because MobyDataComposite is the represent of complex data > types, NOT for an arbtrary number of inputs. > > A service can accept one MobyDataObject (a single Object), one > MobyDataComposite (a single complex type, like AminoAcidSequence) > or more of them or a combination of them... but its not for using a > collection of intputs just because it could be convenient to call a > service with several different inputs ! > > just use for each input object a differnent cal - that would > mobyrequest have also to do... becaus a service which defines one > input can not take more inputs... > >> This means you need 2 different services to accommodate for the >> case of one input object and another for many inputs, and the >> situation is left to service providers and not handled by Moby. Is >> this a correct observation? > Why 2 different services ? Either your service takes e.g. one GI to > do something, or takes a collection... Of course its up to the > service provider to know what his services does and therefore to > offer one of either possibilities. And if the services takes a > collection of input - of course you can set more than one input > (like 3 GIs), BUT if the service is registered with only one input > - you have to stick to its rules. > > Best > andreas >> >> On Apr 3, 2008, at 10:47 , Andreas Groscurth wrote: >> >> >>> [snip] >>> maybe there is a way, as Mark apparently indicates, but i cant >>> see how shall work.... >>> >> >> Yes, I am also curious to hear about that! >> >> Cheers, >> >> .../Ola >> > _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l From ola.spjuth at farmbio.uu.se Thu Apr 3 09:26:20 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Thu, 3 Apr 2008 15:26:20 +0200 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: <47f4d3aa.12da600a.65e1.2c86@mx.google.com> References: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> <47F499BC.5040909@mpiz-koeln.mpg.de> <53CF0758-586E-4C86-8FDE-CAFACF85BD08@farmbio.uu.se> <47F4B5CD.7090902@mpiz-koeln.mpg.de> <94BE9199-4F10-4C6B-A688-54D70D7884EA@farmbio.uu.se> <47f4d3aa.12da600a.65e1.2c86@mx.google.com> Message-ID: <2C330EBB-B486-4884-A855-A3BEFE3CFDFF@farmbio.uu.se> Interesting. It seems I want to use the Collection article to provide multiple simple objects (was not aware of its existence). I guess the service would need to be explicitly written with a Collection as PrimaryInput in order to support this? Cheers, /Ola On Apr 3, 2008, at 14:54 , Edward Kawas wrote: > Just so that I get the last word ;-) > > I am not sure how to use MobyDataInstance/etc, but in the moby > world if a > service receives multiple mobyData blocks, then the service > iterates over > each of them and then returns a response. > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/ > InputMessa > ge.html (the part 'How to invoke a service with a Simple Article' > describes > this). > > Eddie > > -----Original Message----- > From: moby-l-bounces at lists.open-bio.org > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Ola Spjuth > Sent: April-03-08 5:24 AM > To: Andreas Groscurth > Cc: moby-l at lists.open-bio.org > Subject: Re: [MOBY-l] Services accepting multiple inputs > > Andreas, > > Thanks a lot for the explanation. > > Cheers, > > /Ola > > On Apr 3, 2008, at 12:47 , Andreas Groscurth wrote: > >> Ola Spjuth wrote: >>> I suppose it would be possible to set up another version of the >>> service that accepted a MobyDataComposite containing an arbitrary >>> number of wrapped MobyDataObject, and delivers a MobyDataComposite >>> as output, containing an arbitrary number of objects? >> no - because MobyDataComposite is the represent of complex data >> types, NOT for an arbtrary number of inputs. >> >> A service can accept one MobyDataObject (a single Object), one >> MobyDataComposite (a single complex type, like AminoAcidSequence) >> or more of them or a combination of them... but its not for using a >> collection of intputs just because it could be convenient to call a >> service with several different inputs ! >> >> just use for each input object a differnent cal - that would >> mobyrequest have also to do... becaus a service which defines one >> input can not take more inputs... >> >>> This means you need 2 different services to accommodate for the >>> case of one input object and another for many inputs, and the >>> situation is left to service providers and not handled by Moby. Is >>> this a correct observation? >> Why 2 different services ? Either your service takes e.g. one GI to >> do something, or takes a collection... Of course its up to the >> service provider to know what his services does and therefore to >> offer one of either possibilities. And if the services takes a >> collection of input - of course you can set more than one input >> (like 3 GIs), BUT if the service is registered with only one input >> - you have to stick to its rules. >> >> Best >> andreas >>> >>> On Apr 3, 2008, at 10:47 , Andreas Groscurth wrote: >>> >>> >>>> [snip] >>>> maybe there is a way, as Mark apparently indicates, but i cant >>>> see how shall work.... >>>> >>> >>> Yes, I am also curious to hear about that! >>> >>> Cheers, >>> >>> .../Ola >>> >> > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > From groscurt at mpiz-koeln.mpg.de Thu Apr 3 09:44:28 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 03 Apr 2008 15:44:28 +0200 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: <47f4d3aa.12da600a.65e1.2c86@mx.google.com> References: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> <47F499BC.5040909@mpiz-koeln.mpg.de> <53CF0758-586E-4C86-8FDE-CAFACF85BD08@farmbio.uu.se> <47F4B5CD.7090902@mpiz-koeln.mpg.de> <94BE9199-4F10-4C6B-A688-54D70D7884EA@farmbio.uu.se> <47f4d3aa.12da600a.65e1.2c86@mx.google.com> Message-ID: <47F4DF3C.3070802@mpiz-koeln.mpg.de> guess this wont be the last words... i didnt know that, so based on the article in the moby world it is possible what Ola wants to do... so guess we have to wait till Paul can comment on that to clearify how MobyRequest etc working with that.. so it can be that its working somehow... grml andreas Edward Kawas wrote: > Just so that I get the last word ;-) > > I am not sure how to use MobyDataInstance/etc, but in the moby world if a > service receives multiple mobyData blocks, then the service iterates over > each of them and then returns a response. > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InputMessa > ge.html (the part 'How to invoke a service with a Simple Article' describes > this). > > Eddie > > -----Original Message----- > From: moby-l-bounces at lists.open-bio.org > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Ola Spjuth > Sent: April-03-08 5:24 AM > To: Andreas Groscurth > Cc: moby-l at lists.open-bio.org > Subject: Re: [MOBY-l] Services accepting multiple inputs > > Andreas, > > Thanks a lot for the explanation. > > Cheers, > > /Ola > > On Apr 3, 2008, at 12:47 , Andreas Groscurth wrote: > > >> Ola Spjuth wrote: >> >>> I suppose it would be possible to set up another version of the >>> service that accepted a MobyDataComposite containing an arbitrary >>> number of wrapped MobyDataObject, and delivers a MobyDataComposite >>> as output, containing an arbitrary number of objects? >>> >> no - because MobyDataComposite is the represent of complex data >> types, NOT for an arbtrary number of inputs. >> >> A service can accept one MobyDataObject (a single Object), one >> MobyDataComposite (a single complex type, like AminoAcidSequence) >> or more of them or a combination of them... but its not for using a >> collection of intputs just because it could be convenient to call a >> service with several different inputs ! >> >> just use for each input object a differnent cal - that would >> mobyrequest have also to do... becaus a service which defines one >> input can not take more inputs... >> >> >>> This means you need 2 different services to accommodate for the >>> case of one input object and another for many inputs, and the >>> situation is left to service providers and not handled by Moby. Is >>> this a correct observation? >>> >> Why 2 different services ? Either your service takes e.g. one GI to >> do something, or takes a collection... Of course its up to the >> service provider to know what his services does and therefore to >> offer one of either possibilities. And if the services takes a >> collection of input - of course you can set more than one input >> (like 3 GIs), BUT if the service is registered with only one input >> - you have to stick to its rules. >> >> Best >> andreas >> >>> On Apr 3, 2008, at 10:47 , Andreas Groscurth wrote: >>> >>> >>> >>>> [snip] >>>> maybe there is a way, as Mark apparently indicates, but i cant >>>> see how shall work.... >>>> >>>> >>> Yes, I am also curious to hear about that! >>> >>> Cheers, >>> >>> .../Ola >>> >>> > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > > From markw at illuminae.com Thu Apr 3 10:18:30 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 03 Apr 2008 07:18:30 -0700 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: <2C330EBB-B486-4884-A855-A3BEFE3CFDFF@farmbio.uu.se> References: <47f3a6e1.1def600a.2e2c.6198@mx.google.com> <449C7D0E-45C3-4A4A-990A-25901CA97EED@farmbio.uu.se> <47F499BC.5040909@mpiz-koeln.mpg.de> <53CF0758-586E-4C86-8FDE-CAFACF85BD08@farmbio.uu.se> <47F4B5CD.7090902@mpiz-koeln.mpg.de> <94BE9199-4F10-4C6B-A688-54D70D7884EA@farmbio.uu.se> <47f4d3aa.12da600a.65e1.2c86@mx.google.com> <2C330EBB-B486-4884-A855-A3BEFE3CFDFF@farmbio.uu.se> Message-ID: That's correct. A collection is a SINGLE input. e.g. lets say I want to create a BLAST service, where I provide both the DNA Sequence database, as well as the DNA Sequence that I want to blast against it. The database goes into a Collection of DNASEwquence objects, the query sequence goes into a Simple, and both of these go into a mobyData block as a SINGLE input to the service. M On Thu, 03 Apr 2008 06:26:20 -0700, Ola Spjuth wrote: > Interesting. It seems I want to use the Collection article to provide > multiple simple objects (was not aware of its existence). I guess the > service would need to be explicitly written with a Collection as > PrimaryInput in order to support this? > > Cheers, > > /Ola > > > On Apr 3, 2008, at 14:54 , Edward Kawas wrote: > >> Just so that I get the last word ;-) >> >> I am not sure how to use MobyDataInstance/etc, but in the moby world if >> a >> service receives multiple mobyData blocks, then the service iterates >> over >> each of them and then returns a response. >> >> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/ >> InputMessa >> ge.html (the part 'How to invoke a service with a Simple Article' >> describes >> this). >> >> Eddie >> >> -----Original Message----- >> From: moby-l-bounces at lists.open-bio.org >> [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Ola Spjuth >> Sent: April-03-08 5:24 AM >> To: Andreas Groscurth >> Cc: moby-l at lists.open-bio.org >> Subject: Re: [MOBY-l] Services accepting multiple inputs >> >> Andreas, >> >> Thanks a lot for the explanation. >> >> Cheers, >> >> /Ola >> >> On Apr 3, 2008, at 12:47 , Andreas Groscurth wrote: >> >>> Ola Spjuth wrote: >>>> I suppose it would be possible to set up another version of the >>>> service that accepted a MobyDataComposite containing an arbitrary >>>> number of wrapped MobyDataObject, and delivers a MobyDataComposite >>>> as output, containing an arbitrary number of objects? >>> no - because MobyDataComposite is the represent of complex data >>> types, NOT for an arbtrary number of inputs. >>> >>> A service can accept one MobyDataObject (a single Object), one >>> MobyDataComposite (a single complex type, like AminoAcidSequence) >>> or more of them or a combination of them... but its not for using a >>> collection of intputs just because it could be convenient to call a >>> service with several different inputs ! >>> >>> just use for each input object a differnent cal - that would >>> mobyrequest have also to do... becaus a service which defines one >>> input can not take more inputs... >>> >>>> This means you need 2 different services to accommodate for the >>>> case of one input object and another for many inputs, and the >>>> situation is left to service providers and not handled by Moby. Is >>>> this a correct observation? >>> Why 2 different services ? Either your service takes e.g. one GI to >>> do something, or takes a collection... Of course its up to the >>> service provider to know what his services does and therefore to >>> offer one of either possibilities. And if the services takes a >>> collection of input - of course you can set more than one input >>> (like 3 GIs), BUT if the service is registered with only one input >>> - you have to stick to its rules. >>> >>> Best >>> andreas >>>> >>>> On Apr 3, 2008, at 10:47 , Andreas Groscurth wrote: >>>> >>>> >>>>> [snip] >>>>> maybe there is a way, as Mark apparently indicates, but i cant >>>>> see how shall work.... >>>>> >>>> >>>> Yes, I am also curious to hear about that! >>>> >>>> Cheers, >>>> >>>> .../Ola >>>> >>> >> >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l >> > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From haase_dirk at web.de Thu Apr 3 09:55:24 2008 From: haase_dirk at web.de (Dirk Haase) Date: Thu, 03 Apr 2008 15:55:24 +0200 Subject: [MOBY-l] Services accepting multiple inputs Message-ID: <994911619@web.de> Hi Ola, > Interesting. It seems I want to use the Collection article to provide > multiple simple objects (was not aware of its existence). To be honest: I don't think so. For a service which does a 1-1 ID mapping it makes no sense to use a Collection Input. The most important reason is that it would not be clear which of the input IDs maps to which output... What you most probably want - and what Mark and Eddie tried to point you to - is to use multiple elements within a single invocation message. The queryID lets the client know how to map inputs and outputs. You get the idea? Best, dirk From groscurt at mpiz-koeln.mpg.de Thu Apr 3 10:36:34 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 03 Apr 2008 16:36:34 +0200 Subject: [MOBY-l] Services accepting multiple inputs In-Reply-To: <994911619@web.de> References: <994911619@web.de> Message-ID: <47F4EB72.9050200@mpiz-koeln.mpg.de> Dirk Haase wrote: > Hi Ola, > > >> Interesting. It seems I want to use the Collection article to provide >> multiple simple objects (was not aware of its existence). >> > > To be honest: I don't think so. For a service which does a 1-1 ID mapping > it makes no sense to use a Collection Input. The most important > reason is that it would not be clear which of the input IDs maps to which > output... > > What you most probably want - and what Mark and Eddie tried > to point you to - is to use multiple > elements within a single invocation message. The queryID lets the > client know how to map inputs and outputs. You get the idea? > > I think so - the question i think is now is... how does this work with the MobyRequest API from Paul. From jason.e.stewart at gmail.com Fri Apr 4 06:50:28 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Fri, 4 Apr 2008 16:20:28 +0530 Subject: [MOBY-l] Hours of work, money, accounting stuff In-Reply-To: References: <41c1ade50803040953k354d6c29ob6e5ca98e03a309f@mail.gmail.com> <41c1ade50804030627v17b25fceucccee863f7ef05ea@mail.gmail.com> Message-ID: <41c1ade50804040350g169ecdbat75cb7a698a5f0c78@mail.gmail.com> Hey, On 03/04/2008, Mark Wilkinson wrote: > > > I tried using CommonSubs.pm but the online docs for making a client > > were not helpful, so in the end I stole a bunch of code from moses to > > make the service call with a MOBY payload, but with my proxy server > > set. > > CommonSubs is really just there for legacy reasons. Install MOSES::MOBY > from CPAN and use that for your services instead. OK. I am using MOSES:MOBY now, but I was hoping to just whip something quick and dirty, and the Perl tutorial pointed to CommonSubs... Cheers, jas. From markw at illuminae.com Fri Apr 11 13:00:36 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 11 Apr 2008 10:00:36 -0700 Subject: [MOBY-l] MOby Central back up Message-ID: Sorry about that - mysql went into some "maintenance" mode and I didn't know how to get it to come back up from there. Got hold of Paul G this morning and he had sufficient knowledge to solve the problem :-) thanks Paul! Mark -- -- Mark Wilkinson iCAPTURE Centre From maliha.aziz at yahoo.com Fri Apr 11 15:19:21 2008 From: maliha.aziz at yahoo.com (maliha aziz) Date: Fri, 11 Apr 2008 12:19:21 -0700 (PDT) Subject: [MOBY-l] MOby Central back up In-Reply-To: Message-ID: <694746.46545.qm@web57412.mail.re1.yahoo.com> Hi The BioMoby APIs are taking forever to respond. ( have been waiting for half an hour now for "fetching service type ontology from http://moby.ucalgary.ca/RESOURCE/MOBY-S/Services" to complete). Is there an issue at the server again? thanks maliha --- On Fri, 4/11/08, Mark Wilkinson wrote: From: Mark Wilkinson Subject: [MOBY-l] MOby Central back up To: "moby-l at lists.open-bio.org" Date: Friday, April 11, 2008, 10:00 PM Sorry about that - mysql went into some "maintenance" mode and I didn't know how to get it to come back up from there. Got hold of Paul G this morning and he had sufficient knowledge to solve the problem :-) thanks Paul! Mark -- -- Mark Wilkinson iCAPTURE Centre _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From markw at illuminae.com Fri Apr 11 17:17:01 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 11 Apr 2008 14:17:01 -0700 Subject: [MOBY-l] MOby Central back up In-Reply-To: <694746.46545.qm@web57412.mail.re1.yahoo.com> References: <694746.46545.qm@web57412.mail.re1.yahoo.com> Message-ID: yes, we're having terrible problems with Moby today - running out of memory on the Central server every few hours. I'm trying to figure out what/who is hammering on it. M On Fri, 11 Apr 2008 12:19:21 -0700, maliha aziz wrote: > Hi > > The BioMoby APIs are taking forever to respond. ( have been waiting for > half an > hour now for "fetching service type ontology from > http://moby.ucalgary.ca/RESOURCE/MOBY-S/Services" > to complete). > Is there an issue at the server again? > > thanks > > maliha > > --- On Fri, 4/11/08, Mark Wilkinson wrote: > > From: Mark Wilkinson > Subject: [MOBY-l] MOby Central back up > To: "moby-l at lists.open-bio.org" > Date: Friday, April 11, 2008, 10:00 PM > > Sorry about that - mysql went into some "maintenance" mode and I > didn't > know how to get it to come back up from there. Got hold of Paul G this > morning and he had sufficient knowledge to solve the problem :-) > > thanks Paul! > > Mark > > > -- -- Mark Wilkinson iCAPTURE Centre From jason.e.stewart at gmail.com Sat Apr 12 07:12:01 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Sat, 12 Apr 2008 16:42:01 +0530 Subject: [MOBY-l] document/literal format in Perl Message-ID: <41c1ade50804120412p1d4cbf71t3f50b7b3a36a200a@mail.gmail.com> Hey All, I am wanting to test out the XML::Compile module for Perl support of doc/lit format in Perl. I was chatting with Martin and he indicated a problem in my thinking. XML::Compile uses WSDL files to generate on the fly code generators... That means that we would need a WSDL file for any service... Martin also indicated that moby is not using XML schema for it's service inputs and outputs... That surprised me. I think there is maybe a *lot* that I'm not understanding :-( Cheers, jas. From markw at illuminae.com Sat Apr 12 13:26:58 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 12 Apr 2008 10:26:58 -0700 Subject: [MOBY-l] document/literal format in Perl In-Reply-To: <41c1ade50804120412p1d4cbf71t3f50b7b3a36a200a@mail.gmail.com> References: <41c1ade50804120412p1d4cbf71t3f50b7b3a36a200a@mail.gmail.com> Message-ID: Hi Jas, That's correct, Moby doesn't use XML Schema, though I wish we could because it would make so many people so much happier! Unfortunately,the way the Object ontology is serialized into it's instances creates XML structures that cannot be represented in W3C Schema for a variety of reasons. Others can give you the details if you're interested but suffice to say that it is not possible for many of the same reasons that it is not possible to represent an RDF individual of an OWL Class in XML Schema - just too much flexibility/possibility to fit into a rigid schema. Moby Central creates WSDL as best it can - it creates on-the-fly a WSDL file representing an endpoint, where the inputs and outputs are simply xsd:anyType (or mabey xsd:xml? I can't remember how that discussion ended as there was a conflict between the Perl and Java stacks on this issue if I recall correctly). In Perl, the client libraries (SOAP::Lite) use that WSDL to create the stubs for their connection. My understanding is that the Java Moby libraries don't bother with the WSDL at all (is that correct?) though I have asked Eddie to put an extra call into the jMoby stack to retrieve the WSDL of the called service, since it helps us with another project we are doing - registry mining to improve search results! One thing that I really SHOULD do is put a REST-like interface into MOBY Central where the WSDLs can be retrieved from a predictable URL... I really must do that! Hope you're not TOO disappointed!! We're doing our best, but getting RDF/Semantic-Web-like behaviours without using RDF/OWL is causing all sorts of problems... >>sigh<< if I could go back in time to 2001! M On Sat, 12 Apr 2008 04:12:01 -0700, Jason Stewart wrote: > Hey All, > > I am wanting to test out the XML::Compile module for Perl support of > doc/lit format in Perl. > > I was chatting with Martin and he indicated a problem in my thinking. > XML::Compile uses WSDL files to generate on the fly code generators... > That means that we would need a WSDL file for any service... > > Martin also indicated that moby is not using XML schema for it's > service inputs and outputs... That surprised me. > > I think there is maybe a *lot* that I'm not understanding :-( > > Cheers, jas. > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From Pieter.Neerincx at wur.nl Sun Apr 13 12:54:06 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Sun, 13 Apr 2008 18:54:06 +0200 Subject: [MOBY-l] BioMOBY namespaces for EntrezGene Message-ID: <822B9414-4ABF-4D66-AA6A-1CFE4E6E93F7@wur.nl> Hi Frank, I want to use some BioMOBY objects with EntrezGene identifiers and saw you already registered a namespace for EntrezGene IDs. There are 2 though with exactly the same description: EntrezGene_EntrezGeneID EntrezGene_ID So I was wondering if one of them might by the result of a typo or maybe depreciated for whatever reason. Which one should I recycle? Cheers, Pi ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: +31 (0)317-483 060 fax: +31 (0)317-483 584 mobile: +31 (0)6-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From jason.e.stewart at gmail.com Mon Apr 14 06:34:41 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Mon, 14 Apr 2008 16:04:41 +0530 Subject: [MOBY-l] questions about doc/literal support in Moby Message-ID: <41c1ade50804140334x23791df1n6a878cb29ee79b6b@mail.gmail.com> Hey all, I've been chatting with martin trying to get my head around what is needed for doc/literal support in MOBY. Not quite there yet, but slowly beginning to understand. I found this piece of information while reading an article: "This example also highlights one area where rpc/encoded is actually more capable than document/literal today. The SOAP encoding rules facilitate the representation of object graphs in XML such as the cyclical reference shown in Figure 4. Since there is no way to represent this with just XML Schema, the document/literal example will throw an exception if you try to return something that cannot be represented as a natural tree structure. This issue will probably be solved by defining a standard way to represent object graphs in conjunction with XML Schema." from: http://msdn2.microsoft.com/en-us/magazine/cc164152.aspx How do people feel about that? Isn't that a pretty big limitation? I would think that a lot of biological data has cyclical relations, but maybe that's incorrect. Just checking. Cheers, jas. From phillip.lord at newcastle.ac.uk Mon Apr 14 08:32:26 2008 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Mon, 14 Apr 2008 13:32:26 +0100 Subject: [MOBY-l] CFP: Bio-Ontologies 2008: Knowledge in Biology Message-ID: <87k5j0hb1h.fsf@dinley.ncl.ac.uk> ** Call for Papers Submissions are now invited Bio-Ontologies 2008: Knowledge in Biology, a SIG at Intelligent Systems for Molecular Biology 2008. *** Key Dates - Submission due: **Friday 2nd May** - Notifications: **Friday 23rd May** - Final Version Due: **Friday 30th May** - Workshop: **Sunday 20th July** *** Introduction Bio-Ontologies has existed as a SIG at ISMB (http://www.iscb.org/ismb2008) for more than a decade, making it one of the longest running. For this time, Bio-Ontologies has provided a forum for discussion on the latest and most cutting edge research on ontologies. In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. Following on from last year's reflective look, this year we are broadening the scope of SIG; we are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology. So, for example: - Semantic and/or Scientific wikis. - Multimedia blogs - Folksonomies - Tag Clouds - Collaborative Curation Platforms - Collaborative Ontology Authoring and Peer-Review Mechanisms are topics which will be of relevance to the SIG, in addition to the more traditional areas for bio-ontologies. - Biological Applications of Ontologies - Reports on Newly Developed or Existing Bio-Ontologies - Tools for Developing Ontologies - Use of Ontologies in Data Communication Standards - Use of Semantic Web technologies in Bioinformatics - Implications of Bio-Ontologies or the Semantic Web for drug discovery - Current Research In Ontology Languages and its implication for Bio-Ontologies Please note, that this year ISCB have made an innovative schedule, holding some of the SIGs **DURING** ISMB. Bio-Ontologies is on the Sunday parallel to the main conference. ** Programme This year's keynote speaker will be Professor **Philip E. Bourne**, from the Skaggs School of Pharmacy & Pharmaceutical Sciences, UCSD. Our panel session will the following members: - Philip E. Bourne, UCSD - Helen Parkinson, European Bioinformatics Institute - Matt Cockerill, BioMed Central - Mark Wilkinson, University of British Columbia *** Submissions Submissions are now open and can be submitted through easychair (http://www.easychair.org/conferences/?conf=bioontologies2008). *** Instructions to Authors We are inviting two types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1/2 page. Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the day for at least one poster session. Unsuccesful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic. The best papers from Bio-Ontologies 2008: Knowledge in Biology will be published in BMC Bioinformatics. *** Organisers Phillip Lord, Newcastle University Susanna-Assunta Sansone, EBI Nigam Shah, Stanford Matt Cockerill, BioMedCentral *** Programme Committee The programme committee, organised alphabetically is: Mike Bada, University of Colorado Judith Blake, Jackson Laboratory Frank Gibson, Newcastle University Cliff Joslyn, Pacific National Laboratory Wacek Kusnierczyk, Norwegian University of Science and Technology Robin MacEntire, GSK Helen Parkinson, EBI Daniel Rubin, Stanford University Alan Ruttenberg, Science Commons Susie M. Stephens, Eli Lilly Robert Stevens, University of Manchester and the conference organisers. *** Templates Submission templates are available from the website (http://bio-ontologies.org.uk). -- Phillip Lord, Phone: +44 (0) 191 222 7827 Lecturer in Bioinformatics, Email: phillip.lord at newcastle.ac.uk School of Computing Science, http://homepages.cs.ncl.ac.uk/phillip.lord Claremont Tower Room 909, skype: russet_apples Newcastle University, msn: msn at russet.org.uk NE1 7RU From edward.kawas at gmail.com Tue Apr 15 15:05:41 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 15 Apr 2008 12:05:41 -0700 Subject: [MOBY-l] tools for registering items into mobycentral Message-ID: <4804fc92.1bbc720a.5a00.ffff9710@mx.google.com> A long time ago, I created some java applets that aided in the registration of datatypes, namespaces, services, and service types into mobycentral. They were a good first crack at things, but had many flaws. Recently, I have removed them and replaced them with pure javascript versions located at: http://bioinfo.icapture.ubc.ca:8090/MobyRegistrationPages. The new version is lacking documentation, but doc is in the works. I am posting the url for people to try and to provide feedback for me to improve them. Right now, there are some style sheet issues, but the pages are functional. I know that they work in the most recent version of Opera and firefox. They should also work in Internet explorer and Safari. Let me know if you find any errors and if/how you think I could improve the look and feel of the pages. I am by no means an expert in creating UIs or in html/javascript so your suggestions are welcomed! Thanks, Eddie From phillip.lord at newcastle.ac.uk Fri Apr 25 09:06:00 2008 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Fri, 25 Apr 2008 14:06:00 +0100 Subject: [MOBY-l] CFP: Bio-Ontologies: Knowledge in Biology 2008. *1 Week to submission deadline* Message-ID: **One Week to the Submission Deadline** ** Call for Papers Submissions are now invited Bio-Ontologies 2008: Knowledge in Biology, a SIG at Intelligent Systems for Molecular Biology 2008. *** Key Dates - Submission due: **Friday 2nd May** - Notifications: **Friday 23rd May** - Final Version Due: **Friday 30th May** - Workshop: **Sunday 20th July** *** Introduction Bio-Ontologies has existed as a SIG at ISMB (http://www.iscb.org/ismb2008) for more than a decade, making it one of the longest running. For this time, Bio-Ontologies has provided a forum for discussion on the latest and most cutting edge research on ontologies. In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. Following on from last year's reflective look, this year we are broadening the scope of SIG; we are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology. So, for example: - Semantic and/or Scientific wikis. - Multimedia blogs - Folksonomies - Tag Clouds - Collaborative Curation Platforms - Collaborative Ontology Authoring and Peer-Review Mechanisms are topics which will be of relevance to the SIG, in addition to the more traditional areas for bio-ontologies. - Biological Applications of Ontologies - Reports on Newly Developed or Existing Bio-Ontologies - Tools for Developing Ontologies - Use of Ontologies in Data Communication Standards - Use of Semantic Web technologies in Bioinformatics - Implications of Bio-Ontologies or the Semantic Web for drug discovery - Current Research In Ontology Languages and its implication for Bio-Ontologies Please note, that this year ISCB have made an innovative schedule, holding some of the SIGs **DURING** ISMB. Bio-Ontologies is on the Sunday parallel to the main conference. The best papers from Bio-Ontologies 2008: Knowledge in Biology will be published in BMC Bioinformatics. ** Programme This year's keynote speaker will be Professor **Philip E. Bourne**, from the Skaggs School of Pharmacy & Pharmaceutical Sciences, UCSD. Our panel session will the following members: - Philip E. Bourne, UCSD - Helen Parkinson, European Bioinformatics Institute - Matt Cockerill, BioMed Central - Mark Wilkinson, University of British Columbia *** Submissions Submissions are now open and can be submitted through easychair (http://www.easychair.org/conferences/?conf=bioontologies2008). *** Instructions to Authors We are inviting two types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1/2 page. Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the day for at least one poster session. Unsuccesful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic. The best papers from Bio-Ontologies 2008: Knowledge in Biology will be published in BMC Bioinformatics. *** Organisers Phillip Lord, Newcastle University Susanna-Assunta Sansone, EBI Nigam Shah, Stanford Matt Cockerill, BioMedCentral *** Programme Committee The programme committee, organised alphabetically is: Mike Bada, University of Colorado Judith Blake, Jackson Laboratory Frank Gibson, Newcastle University Cliff Joslyn, Pacific National Laboratory Wacek Kusnierczyk, Norwegian University of Science and Technology Robin MacEntire, GSK Helen Parkinson, EBI Daniel Rubin, Stanford University Alan Ruttenberg, Science Commons Susie M. Stephens, Eli Lilly Robert Stevens, University of Manchester and the conference organisers. *** Templates Submission templates are available from the website (http://bio-ontologies.org.uk). From jmfernandez at cnio.es Mon Apr 28 09:45:10 2008 From: jmfernandez at cnio.es (=?windows-1252?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Mon, 28 Apr 2008 15:45:10 +0200 Subject: [MOBY-l] [Fwd: Fwd: Final reminder: DEADLINE THIS WEEK for ESF programme in Functional Genomics - Call for Proposals] Message-ID: <4815D4E6.4080804@cnio.es> f.y.i. Begin forwarded message: > *From: *"cheryl smythe (BI)" > > *Date: *April 28, 2008 1:04:23 PM GMT+02:00 > *To: *"ffg-list" > > *Subject: **Final reminder: DEADLINE THIS WEEK for ESF programme in > Functional Genomics - Call for Proposals* > > > The ESF Programme/ Frontiers of Functional Genomics/ would like to > send you a final reminder of the > > *Call for Proposals for Science Meetings, Short Visit & Exchange > Grants in 2008* > > *Deadline 17:00 CET on Friday 2 May 2008* > > Applications must be made online. For further information, and access > to the online submission forms, please go to > _http://www.functionalgenomics.org.uk/sections/news/programme.htm_ or > _http://www.esf.org/ffg_. > > Applicants are asked to adhere to the guidelines found on the website > and are reminded that applications should have a clear connection with > the programme which covers many aspects of functional genomics. Any > informal enquiries can be made to Cheryl Smythe > (_cheryl.smythe__ at bbsrc.ac.uk_ ).* > The deadline for applications is 17:00 CET on 2 May 2008*. > > ???????????? > > *Registration is now open for the * > > */3rd ESF Conference on Functional Genomics & Disease/* > > */Innsbruck, Austria, 1-4 October 2008 > /* > > *Registration fee of only ?95 for graduate students* > > *Travel Bursaries Available!* > > Deadline for abstract submissions -* 30 May* 2008 > > Deadline for early registration -* 30 June* 2008 > > See _www.esffg2008.org_ for further details. > > Dr Cheryl Smythe > ESF Programme in Functional Genomics Co-ordinator > Babraham Bioscience Technologies > Babraham Research Campus > Cambridge CB22 3AT > UK > Tel: +44 1223 496246 > Fax: +44 1223 496045 > > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. 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From darin.london at duke.edu Tue Apr 29 12:56:35 2008 From: darin.london at duke.edu (darin.london at duke.edu) Date: Tue, 29 Apr 2008 12:56:35 -0400 Subject: [MOBY-l] BOSC 2008 Announcement and Call For Submissions Message-ID: <200804291656.m3TGuZVR020876@tenero.duhs.duke.edu> BOSC 2008 Call for Abstracts Reminder The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008). This is a reminder to submit your proposals for talks to the BOSC submission system before May 11. Submission Process: All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php). The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details) Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t Important Dates: May 11: Abstract submission deadline. June 2: Notification of accepted talks. June 4: Early registration discount cut-off. July 18-19: BOSC 2008! We hope to see you at BOSC 2008! Kam Dahlquist and Darin London BOSC 2008 Co-organizers