From gordonp at ucalgary.ca Mon Jun 1 17:52:24 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 01 Jun 2009 15:52:24 -0600 Subject: [MOBY-dev] New Moby app In-Reply-To: References: Message-ID: <4A244D98.7010208@ucalgary.ca> Hi all, I just put together a little video to introduce a new Moby application I'm hoping to release in the next couple of weeks, called Daggoo. It lets users create Moby services from existing Web Services via a drag 'n' drop interface. In case you are interested, the video is on SciVee, and is also embedded on the upcoming Daggoo Web site... http://www.daggoo.net/ Once I've committed the code, I'll follow up with more details. Cheers, Paul From dmitry.repchevski at bsc.es Tue Jun 2 14:47:32 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 02 Jun 2009 11:47:32 -0700 Subject: [MOBY-dev] New Moby app In-Reply-To: <4A244D98.7010208@ucalgary.ca> References: <4A244D98.7010208@ucalgary.ca> Message-ID: <4A2573C4.40805@bsc.es> Great! I have so many questions... I did the contrary conversion - represent Moby services as a doc-lit WSDL ones. http://inb.bsc.es/documents/java/nemus/index.html I also thought to do the similar thing (WSDL -> Moby), but didn't figure out what to do with limited Moby type system. Also there could be more then simple WSDL pattern (SOAP headers, swa, mtom...). If you have some spec. of such a conversion I would be able to provide a opposite side proxy based on your specs... ;-) Another issue is that Taverna yet to support schema type inheritance. (I don't blame them - it's a very tough task, I started to work on it, but have no time now, hopefully in July) Currently I have a core part implemented as an applet: http://inb.bsc.es/documents/java/nemus/executor/wsdl_executor.html By the way all our "inb.bsc.es" services have their proxy running at http://inb.bsc.es/gn6/proxy/SERVICE_NAME?wsdl (just to look how the result wsdl looks like) One thing I didn't understand from the presentation... Is this an application, API or some code generator. Is it possible to generate Taverna mixed workflow for moby/wsdl services? Well, expect to have more than your (nice) presentation, Best regards, Dmitry From soiland-reyes at cs.manchester.ac.uk Wed Jun 3 06:03:27 2009 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Wed, 3 Jun 2009 11:03:27 +0100 Subject: [MOBY-dev] New Moby app In-Reply-To: <4A2573C4.40805@bsc.es> References: <4A244D98.7010208@ucalgary.ca> <4A2573C4.40805@bsc.es> Message-ID: On Tue, Jun 2, 2009 at 19:47, Dmitry Repchevsky wrote: > Another issue is that Taverna yet to support schema type inheritance. > (I don't blame them - it's a very tough task, I started to work on it, but > have no time now, hopefully in July) It's in our plans, but yeah, it would require quite a bit of reworking and is hence not coming up immediately. We want to get rid of those XML splitters and do some more kind of wizard-y 'configuration' dialogue where you can tick the boxes for the granularity of inputs that you actually want. This could include drop-down boxes for abstract/subclassed types. You would then end up with a customized WSDL service with input and output ports per your specification which don't require any splitters in either end - comparable to how the BioMart services works in Taverna. As BioMoby deals with construction of data types a similar solution might be interesting for BioMoby services in Taverna, as many Moby workflows end up having various data object construction and parser 'processors' that are not really doing any execution - they are just shims like the XML splitters. > Is it possible to generate Taverna mixed workflow for moby/wsdl services? Yes, but you would probably have to dig down to individual strings on both sides with XML splitters and BioMoby objects/parsers. You might also need a few simple shims that do string joining etc. as WSDL services 'in the wild' expect sequences, gene identifiers etc. in many various kinds of syntactic formats. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From martin.senger at gmail.com Tue Jun 9 17:16:54 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 10 Jun 2009 05:16:54 +0800 Subject: [MOBY-dev] jMoby does not compile Message-ID: <4d93f07c0906091416x7b4881e7oaac2c6c1e5f5dcf8@mail.gmail.com> compile: [javac] Compiling 367 source files to /home/senger/moby-live/Java/build/classes [javac] /home/senger/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:327: cannot find symbol [javac] symbol : class Desktop [javac] location: class ca.ucalgary.seahawk.gui.MobyContentPane [javac] Desktop desktop = Desktop.getDesktop(); [javac] ^ [javac] /home/senger/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:327: cannot find symbol [javac] symbol : variable Desktop [javac] location: class ca.ucalgary.seahawk.gui.MobyContentPane [javac] Desktop desktop = Desktop.getDesktop(); [javac] ^ [javac] /home/senger/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:328: package Desktop does not exist [javac] if(!desktop.isSupported(Desktop.Action.BROWSE)) { [javac] ^ [javac] /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java:554: incompatible types [javac] found : java.lang.Object [javac] required: java.util.Map.Entry [javac] for(Map.Entry servicetype: gui.getMobyCentralImpl().getServiceTypes().entrySet()){ [javac] ^ [javac] Note: /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 4 errors BUILD FAILED /home/senger/moby-live/Java/build.xml:329: Compile failed; see the compiler error output for details. -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Tue Jun 9 17:59:49 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 09 Jun 2009 15:59:49 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0906091427p1424a819n80c8444925281de3@mail.gmail.com> References: <4d93f07c0906091416x7b4881e7oaac2c6c1e5f5dcf8@mail.gmail.com> <4A2ED2A1.1030803@ucalgary.ca> <4d93f07c0906091427p1424a819n80c8444925281de3@mail.gmail.com> Message-ID: <4A2EDB55.2010106@ucalgary.ca> I can't find a JDIC maven artifact anywhere...this is what java.awt.Desktop was before Java SE 6. Does anyone else have better luck? From gordonp at ucalgary.ca Tue Jun 9 18:02:15 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 09 Jun 2009 16:02:15 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4A2EDB55.2010106@ucalgary.ca> References: <4d93f07c0906091416x7b4881e7oaac2c6c1e5f5dcf8@mail.gmail.com> <4A2ED2A1.1030803@ucalgary.ca> <4d93f07c0906091427p1424a819n80c8444925281de3@mail.gmail.com> <4A2EDB55.2010106@ucalgary.ca> Message-ID: <4A2EDBE7.6000401@ucalgary.ca> Never mind...found a recent version finally, and am adding the dependency. Paul Gordon wrote: > I can't find a JDIC maven artifact anywhere...this is what > java.awt.Desktop was before Java SE 6. Does anyone else have better > luck? > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > From martin.senger at gmail.com Tue Jun 9 18:27:56 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 10 Jun 2009 06:27:56 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4A2EDBE7.6000401@ucalgary.ca> References: <4d93f07c0906091416x7b4881e7oaac2c6c1e5f5dcf8@mail.gmail.com> <4A2ED2A1.1030803@ucalgary.ca> <4d93f07c0906091427p1424a819n80c8444925281de3@mail.gmail.com> <4A2EDB55.2010106@ucalgary.ca> <4A2EDBE7.6000401@ucalgary.ca> Message-ID: <4d93f07c0906091527y47342dd0r1e8f0900a356b9b3@mail.gmail.com> Better, but it still does not compile: compile: [javac] Compiling 367 source files to /home/senger/moby-live/Java/build/classes [javac] /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java:554: incompatible types [javac] found : java.lang.Object [javac] required: java.util.Map.Entry [javac] for(Map.Entry servicetype: gui.getMobyCentralImpl().getServiceTypes().entrySet()){ [javac] ^ [javac] Note: /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 error BUILD FAILED /home/senger/moby-live/Java/build.xml:329: Compile failed; see the compiler error output for details. -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Jun 10 18:52:43 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 11 Jun 2009 06:52:43 +0800 Subject: [MOBY-dev] jMoby does not compile Message-ID: <4d93f07c0906101552v37240835re0bb216289a97819@mail.gmail.com> I still cannot compile jMoby. My problem now is that the new required maven repository (which was added to xmls/project.pom) - and which is this: http://ftp.kysoh.com/maven2/ - cannot be reached. Is this just my problem or also occurring elsewhere? Thanks, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenge From gordonp at ucalgary.ca Wed Jun 10 18:57:47 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 10 Jun 2009 16:57:47 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0906101552v37240835re0bb216289a97819@mail.gmail.com> References: <4d93f07c0906101552v37240835re0bb216289a97819@mail.gmail.com> Message-ID: <4A303A6B.2050605@ucalgary.ca> It seems to be down for me too. I can't find a recent jdic JAR file anywhere else though...if you can, we can replace this repo. Martin Senger wrote: > I still cannot compile jMoby. My problem now is that the new required maven > repository (which was added to xmls/project.pom) - and which is this: > http://ftp.kysoh.com/maven2/ - cannot be reached. > > Is this just my problem or also occurring elsewhere? > > Thanks, > Martin > > From martin.senger at gmail.com Wed Jun 10 19:26:19 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 11 Jun 2009 07:26:19 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4A303A6B.2050605@ucalgary.ca> References: <4d93f07c0906101552v37240835re0bb216289a97819@mail.gmail.com> <4A303A6B.2050605@ucalgary.ca> Message-ID: <4d93f07c0906101626n76d13246x344cfebb6fbb506b@mail.gmail.com> > It seems to be down for me too. I can't find a recent jdic JAR file > anywhere else though...if you can, we can replace this repo. Just send me the jar file and its pom file (you probabbly have it already in your local maven .mv) and I can deploy it to our biomoby maven repository. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From sneumann at ipb-halle.de Thu Jun 11 07:47:18 2009 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Thu, 11 Jun 2009 13:47:18 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? Message-ID: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> Hi, There is an itch I have since I got to know Moby: I'd like to *quickly* browse available services without fireing up the Dashboard. Or, maybe I'd like to tell someone "we have written this super-cool BioMoby service", and point them to a URL with a nicely formatted Name and Description of the service. * The serviceList is missing the both the description and some to point to our services http://biomoby.org/cgi-bin/serviceList, same with http://moby.ucalgary.ca/moby/ValidateService * The WSDL at e.g. http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks is not really human readable. * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances is neither human readable, nor can I point to my service * GBwrose can't easily be linked to with any search parameters, and anyway offers way too much functionality for my purpose Did I miss anything obvious ? I'd expect that a nicely formatted web accessible registry overview (with occasional visits by google et al) could boost public visibility of BioMoby. Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 From carole.goble at manchester.ac.uk Thu Jun 11 08:40:36 2009 From: carole.goble at manchester.ac.uk (Carole Goble) Date: Thu, 11 Jun 2009 13:40:36 +0100 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4A30FB44.8050307@manchester.ac.uk> Steffen http://beta.biocatalogue.org/services/search?q=biomoby has 181 biomoby services registered. we would welcome updates to the metadata!!! we launch the biocatalogue at ISMB Carole > Hi, > > There is an itch I have since I got to know Moby: > I'd like to *quickly* browse available services > without fireing up the Dashboard. Or, maybe > I'd like to tell someone "we have written > this super-cool BioMoby service", and point them > to a URL with a nicely formatted Name and Description > of the service. > > * The serviceList is missing the both the description > and some to point to our services > http://biomoby.org/cgi-bin/serviceList, same with > http://moby.ucalgary.ca/moby/ValidateService > > * The WSDL at e.g. > http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks > is not really human readable. > > * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances > is neither human readable, nor can I point to my service > > * GBwrose can't easily be linked to with any search parameters, > and anyway offers way too much functionality for my purpose > > Did I miss anything obvious ? I'd expect that a nicely formatted > web accessible registry overview (with occasional visits > by google et al) could boost public visibility of BioMoby. > > Yours, > Steffen > > From Sebastien.Carrere at toulouse.inra.fr Thu Jun 11 08:44:30 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 11 Jun 2009 14:44:30 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4A30FC2E.6080803@toulouse.inra.fr> Hi Steffen, In Toulouse, we use a cgi that we wrote to browse Moby registries: http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi To directly access to a service description in the public central, you have to provide 2 parameters : service and auth_uri. Here is an example: http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr As you can see on this example, for simple services (just one input), a direct link to Remora is provided in order to test the service. Hope this helps, Sebastien Steffen Neumann wrote: > Hi, > > There is an itch I have since I got to know Moby: > I'd like to *quickly* browse available services > without fireing up the Dashboard. Or, maybe > I'd like to tell someone "we have written > this super-cool BioMoby service", and point them > to a URL with a nicely formatted Name and Description > of the service. > > * The serviceList is missing the both the description > and some to point to our services > http://biomoby.org/cgi-bin/serviceList, same with > http://moby.ucalgary.ca/moby/ValidateService > > * The WSDL at e.g. > http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks > is not really human readable. > > * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances > is neither human readable, nor can I point to my service > > * GBwrose can't easily be linked to with any search parameters, > and anyway offers way too much functionality for my purpose > > Did I miss anything obvious ? I'd expect that a nicely formatted > web accessible registry overview (with occasional visits > by google et al) could boost public visibility of BioMoby. > > Yours, > Steffen > > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From jits at cs.man.ac.uk Thu Jun 11 09:24:05 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Jun 2009 14:24:05 +0100 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A30FB44.8050307@manchester.ac.uk> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FB44.8050307@manchester.ac.uk> Message-ID: <4A310575.2040307@cs.man.ac.uk> Hi Steffen, Just to add to Carole's email - what you'll see now is the beta site that we are preparing for a public launch at ISMB at the end of this month. So far, we have harvested some BioMoby services from SeekDa, but we intend to have better integration and harvesting of BioMoby services by Q4 of this year. Check out our roadmap (http://www.biocatalogue.org/wiki/doku.php?id=public:roadmap) and get in touch, if you're interested :-) Thanks, Jits Carole Goble wrote: > Steffen > > http://beta.biocatalogue.org/services/search?q=biomoby > > has 181 biomoby services registered. we would welcome updates to the > metadata!!! > we launch the biocatalogue at ISMB > > Carole > >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services without fireing up >> the Dashboard. Or, maybe I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them to a URL with a >> nicely formatted Name and Description of the service. >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From mgerlich at ipb-halle.de Thu Jun 11 09:44:07 2009 From: mgerlich at ipb-halle.de (Michael Gerlich) Date: Thu, 11 Jun 2009 15:44:07 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A30FC2E.6080803@toulouse.inra.fr> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> Message-ID: <4A310A27.2000001@ipb-halle.de> Hi, does this cgi script check for dead services? I noticed that all of our (ipb-halle.de) services are currently marked as dead services (including a whole bunch of other services - too many for my understanding...): http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Might this be causing empty entries in your registry when tried for our services? http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de I checked and all our services are working, and both Taverna and Dashboard have no problems with them. I guess the lookup if and how a service is marked as "dead" should be revised, or perhaps someone could point some information to me so I can assure that our services are not marked as dead (would this require rdf-editing?). Regards, Michael Sebastien Carrere wrote: > Hi Steffen, > > In Toulouse, we use a cgi that we wrote to browse Moby registries: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi > > To directly access to a service description in the public central, you > have to provide 2 parameters : service and auth_uri. > > Here is an example: > > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr > > > As you can see on this example, for simple services (just one input), > a direct link to Remora is provided in order to test the service. > > Hope this helps, > > Sebastien > > > > Steffen Neumann wrote: >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services without fireing up >> the Dashboard. Or, maybe I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them to a URL with a >> nicely formatted Name and Description of the service. >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany From edward.kawas at gmail.com Thu Jun 11 10:04:47 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 11 Jun 2009 07:04:47 -0700 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A310A27.2000001@ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> Message-ID: <4a310f0c.1bbc720a.31b7.0dee@mx.google.com> Hi Michael, What the service checker does is that it tries to ping the service by sending an empty moby message. If the service responds (basically echoes) then it is considered alive. What service are you trying? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich Sent: June-11-09 6:44 AM To: Core developer announcements Subject: Re: [MOBY-dev] Human Readable Registry on the Web ? Hi, does this cgi script check for dead services? I noticed that all of our (ipb-halle.de) services are currently marked as dead services (including a whole bunch of other services - too many for my understanding...): http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Might this be causing empty entries in your registry when tried for our services? http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_ser vice¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle. de I checked and all our services are working, and both Taverna and Dashboard have no problems with them. I guess the lookup if and how a service is marked as "dead" should be revised, or perhaps someone could point some information to me so I can assure that our services are not marked as dead (would this require rdf-editing?). Regards, Michael Sebastien Carrere wrote: > Hi Steffen, > > In Toulouse, we use a cgi that we wrote to browse Moby registries: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi > > To directly access to a service description in the public central, you > have to provide 2 parameters : service and auth_uri. > > Here is an example: > > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTN etBlast&auth_uri=iant.toulouse.inra.fr > > > As you can see on this example, for simple services (just one input), > a direct link to Remora is provided in order to test the service. > > Hope this helps, > > Sebastien > > > > Steffen Neumann wrote: >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services without fireing up >> the Dashboard. Or, maybe I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them to a URL with a >> nicely formatted Name and Description of the service. >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Jun 11 10:08:43 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 11 Jun 2009 07:08:43 -0700 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A310A27.2000001@ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> Message-ID: <4a310ff7.1921720a.56e4.0e8a@mx.google.com> Sorry, Check out the page at http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator Enter ipb-halle.de from the service provider drop down and hit the 'check my services' button. You will see why the server thinks that your services are dead. If they die because of the empty message, let me know, and I can help you fix your services so that they don't die on empty messages. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich Sent: June-11-09 6:44 AM To: Core developer announcements Subject: Re: [MOBY-dev] Human Readable Registry on the Web ? Hi, does this cgi script check for dead services? I noticed that all of our (ipb-halle.de) services are currently marked as dead services (including a whole bunch of other services - too many for my understanding...): http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Might this be causing empty entries in your registry when tried for our services? http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_ser vice¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle. de I checked and all our services are working, and both Taverna and Dashboard have no problems with them. I guess the lookup if and how a service is marked as "dead" should be revised, or perhaps someone could point some information to me so I can assure that our services are not marked as dead (would this require rdf-editing?). Regards, Michael Sebastien Carrere wrote: > Hi Steffen, > > In Toulouse, we use a cgi that we wrote to browse Moby registries: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi > > To directly access to a service description in the public central, you > have to provide 2 parameters : service and auth_uri. > > Here is an example: > > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTN etBlast&auth_uri=iant.toulouse.inra.fr > > > As you can see on this example, for simple services (just one input), > a direct link to Remora is provided in order to test the service. > > Hope this helps, > > Sebastien > > > > Steffen Neumann wrote: >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services without fireing up >> the Dashboard. Or, maybe I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them to a URL with a >> nicely formatted Name and Description of the service. >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From ytanoh at cs.man.ac.uk Thu Jun 11 09:59:03 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 11 Jun 2009 14:59:03 +0100 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A310575.2040307@cs.man.ac.uk> Message-ID: Hello everybody, The BioCatalogue (www.biocatalogue.org) team is proud to announce that the main portal for the project will be launched during ISMB/ECCB 2009, which takes place in Stockholm, Sweden between June 28 - July 2nd. (Please see: http://www.iscb.org/ismbeccb2009/). There will be a demo for the BioCatalogue during Technical Track session TT41, which will take place on Wednesday July 1st from 2:45pm - 3:10 pm in Room C8. There will also be a poster which will be presented during the poster session of the conference. The BioCatalogue will provide a centralised registry of curated Life Science web services. BioCatalogue will also act as a place where the community can find contacts and meet the experts and maintainers of these services. For more information about the project: http://www.biocatalogue.org/wiki If you are a developer or a consumer of Web Services, this is one session you shouldn't miss during ISMB/ECCB 2009. BioCatalogue is a BBSRC funded project [BB/F01046X/1, BB/F010540/1] and has been running since 1st June 2008. The project is a joint venture between the EMBL-EBI (led by Rodrigo Lopez) and the myGrid project at the University of Manchester (led by Carole Goble). The BioCatalogue team -----Original Message----- From: owner-biocatalogue at listserv.manchester.ac.uk [mailto:owner-biocatalogue at listserv.manchester.ac.uk] On Behalf Of Jiten Bhagat Sent: 11 June 2009 14:24 To: Core developer announcements Cc: BIOCATALOGUE at listserv.manchester.ac.uk Subject: Re: [MOBY-dev] Human Readable Registry on the Web ? Hi Steffen, Just to add to Carole's email - what you'll see now is the beta site that we are preparing for a public launch at ISMB at the end of this month. So far, we have harvested some BioMoby services from SeekDa, but we intend to have better integration and harvesting of BioMoby services by Q4 of this year. Check out our roadmap (http://www.biocatalogue.org/wiki/doku.php?id=public:roadmap) and get in touch, if you're interested :-) Thanks, Jits Carole Goble wrote: > Steffen > > http://beta.biocatalogue.org/services/search?q=biomoby > > has 181 biomoby services registered. we would welcome updates to the > metadata!!! > we launch the biocatalogue at ISMB > > Carole > >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services without fireing up >> the Dashboard. Or, maybe I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them to a URL with a >> nicely formatted Name and Description of the service. >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Sebastien.Carrere at toulouse.inra.fr Thu Jun 11 10:29:46 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 11 Jun 2009 16:29:46 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A310A27.2000001@ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> Message-ID: <4A3114DA.1030904@toulouse.inra.fr> This cgi does not check for dead services. It browses the whole registry. The problem with your service was related to Collection Input (we don't have a lot of services dealing with collections in our lab, that's why I had never seen this bug ...). I fixed it. Now, the following url is ok: http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de Sebastien. Michael Gerlich wrote: > Hi, > > does this cgi script check for dead services? > > I noticed that all of our (ipb-halle.de) services are currently marked > as dead services (including a whole bunch of other services - too many > for my understanding...): > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Might this be causing empty entries in your registry when tried for > our services? > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de > > > I checked and all our services are working, and both Taverna and > Dashboard have no problems with them. I guess the lookup if and how a > service is marked as "dead" should be revised, or perhaps someone > could point some information to me so I can assure that our services > are not marked as dead (would this require rdf-editing?). > > Regards, > Michael > > > Sebastien Carrere wrote: >> Hi Steffen, >> >> In Toulouse, we use a cgi that we wrote to browse Moby registries: >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi >> >> To directly access to a service description in the public central, >> you have to provide 2 parameters : service and auth_uri. >> >> Here is an example: >> >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr >> >> >> As you can see on this example, for simple services (just one input), >> a direct link to Remora is provided in order to test the service. >> >> Hope this helps, >> >> Sebastien >> >> >> >> Steffen Neumann wrote: >>> Hi, >>> >>> There is an itch I have since I got to know Moby: >>> I'd like to *quickly* browse available services without fireing up >>> the Dashboard. Or, maybe I'd like to tell someone "we have written >>> this super-cool BioMoby service", and point them to a URL with a >>> nicely formatted Name and Description of the service. >>> * The serviceList is missing the both the description >>> and some to point to our services >>> http://biomoby.org/cgi-bin/serviceList, same with >>> http://moby.ucalgary.ca/moby/ValidateService >>> >>> * The WSDL at e.g. >>> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >>> is not really human readable. >>> >>> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >>> is neither human readable, nor can I point to my service >>> >>> * GBwrose can't easily be linked to with any search parameters, >>> and anyway offers way too much functionality for my purpose >>> >>> Did I miss anything obvious ? I'd expect that a nicely formatted >>> web accessible registry overview (with occasional visits >>> by google et al) could boost public visibility of BioMoby. >>> >>> Yours, >>> Steffen >>> >>> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From mgerlich at ipb-halle.de Thu Jun 11 10:38:48 2009 From: mgerlich at ipb-halle.de (Michael Gerlich) Date: Thu, 11 Jun 2009 16:38:48 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A3114DA.1030904@toulouse.inra.fr> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> <4A3114DA.1030904@toulouse.inra.fr> Message-ID: <4A3116F8.8000407@ipb-halle.de> Thanks for that. Michael Sebastien Carrere wrote: > > This cgi does not check for dead services. It browses the whole registry. > > The problem with your service was related to Collection Input (we > don't have a lot of services dealing with collections in our lab, > that's why I had never seen this bug ...). > I fixed it. > > Now, the following url is ok: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de > > > > Sebastien. > > > > > Michael Gerlich wrote: >> Hi, >> >> does this cgi script check for dead services? >> >> I noticed that all of our (ipb-halle.de) services are currently >> marked as dead services (including a whole bunch of other services - >> too many for my understanding...): >> http://moby.ucalgary.ca/moby/ValidateService?getDeadServices >> >> Might this be causing empty entries in your registry when tried for >> our services? >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de >> >> >> I checked and all our services are working, and both Taverna and >> Dashboard have no problems with them. I guess the lookup if and how a >> service is marked as "dead" should be revised, or perhaps someone >> could point some information to me so I can assure that our services >> are not marked as dead (would this require rdf-editing?). >> >> Regards, >> Michael >> >> >> Sebastien Carrere wrote: >>> Hi Steffen, >>> >>> In Toulouse, we use a cgi that we wrote to browse Moby registries: >>> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi >>> >>> To directly access to a service description in the public central, >>> you have to provide 2 parameters : service and auth_uri. >>> >>> Here is an example: >>> >>> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr >>> >>> >>> As you can see on this example, for simple services (just one >>> input), a direct link to Remora is provided in order to test the >>> service. >>> >>> Hope this helps, >>> >>> Sebastien >>> >>> >>> >>> Steffen Neumann wrote: >>>> Hi, >>>> >>>> There is an itch I have since I got to know Moby: >>>> I'd like to *quickly* browse available services without fireing up >>>> the Dashboard. Or, maybe I'd like to tell someone "we have written >>>> this super-cool BioMoby service", and point them to a URL with a >>>> nicely formatted Name and Description of the service. >>>> * The serviceList is missing the both the description >>>> and some to point to our services >>>> http://biomoby.org/cgi-bin/serviceList, same with >>>> http://moby.ucalgary.ca/moby/ValidateService >>>> >>>> * The WSDL at e.g. >>>> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >>>> is not really human readable. >>>> >>>> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >>>> is neither human readable, nor can I point to my service >>>> >>>> * GBwrose can't easily be linked to with any search parameters, >>>> and anyway offers way too much functionality for my purpose >>>> >>>> Did I miss anything obvious ? I'd expect that a nicely formatted >>>> web accessible registry overview (with occasional visits >>>> by google et al) could boost public visibility of BioMoby. >>>> >>>> Yours, >>>> Steffen >>>> >>>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany From dmitry.repchevski at bsc.es Thu Jun 11 19:43:27 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Thu, 11 Jun 2009 16:43:27 -0700 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4A31969F.204@bsc.es> We (INB) have one: http://inab.org/MOWServ/ Cheers, Dmitry From srramirez at uma.es Fri Jun 12 05:02:21 2009 From: srramirez at uma.es (Sergio Ramirez Ramirez) Date: Fri, 12 Jun 2009 11:02:21 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4A32199D.4070104@uma.es> Hello Steffen, Is not exactly for browsing services, but you can search for services and datatypes in several registries at the same time using Magallanes. You can find a web client in http://chirimoyo.ac.uma.es/magallanes-web I hope you find it useful Best regards, Sergio Steffen Neumann wrote: > Hi, > > There is an itch I have since I got to know Moby: > I'd like to *quickly* browse available services > without fireing up the Dashboard. Or, maybe > I'd like to tell someone "we have written > this super-cool BioMoby service", and point them > to a URL with a nicely formatted Name and Description > of the service. > > * The serviceList is missing the both the description > and some to point to our services > http://biomoby.org/cgi-bin/serviceList, same with > http://moby.ucalgary.ca/moby/ValidateService > > * The WSDL at e.g. > http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks > is not really human readable. > > * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances > is neither human readable, nor can I point to my service > > * GBwrose can't easily be linked to with any search parameters, > and anyway offers way too much functionality for my purpose > > Did I miss anything obvious ? I'd expect that a nicely formatted > web accessible registry overview (with occasional visits > by google et al) could boost public visibility of BioMoby. > > Yours, > Steffen > > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 7236 "The first step in developing a new genetic analysis algorithm is to decide how to make the input data file format different from all pre-existing analysis data file formats. The second step in developing a new genetic analysis algorithm is to decide how to make the output data file format incompatible with all pre-existing analysis data file input formats." Andy Law "The third step is use mAPI to make them compatible" Sergio Ram?rez "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From sneumann at ipb-halle.de Fri Jun 12 05:24:26 2009 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Fri, 12 Jun 2009 11:24:26 +0200 Subject: [MOBY-dev] [SPAM_ipb] Re: Human Readable Registry on the Web ? In-Reply-To: <4A3114DA.1030904@toulouse.inra.fr> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> <4A3114DA.1030904@toulouse.inra.fr> Message-ID: <1244798666.14765.10.camel@lathan.ipb-sub.ipb-halle.de> On Thu, 2009-06-11 at 16:29 +0200, Sebastien Carrere wrote: > Now, the following url is ok: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de Hm, I wonder whether something like that could be integrated into (or at least linked from !!) the "official" biomoby.org site. One more comment: Should the servicetype view show the corresponding services ? http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_servicetype¢ral=mobycentral&servicetype=Retrieval This is currently empty, although I know at least one matching service ;-) Does the registry allow multiple service types for one service ? I could imagine to tag our MassBank service both "retrieval" *and* "Metabolomics". Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 From Sebastien.Carrere at toulouse.inra.fr Fri Jun 12 07:50:21 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Fri, 12 Jun 2009 13:50:21 +0200 Subject: [MOBY-dev] [SPAM_ipb] Re: Human Readable Registry on the Web ? In-Reply-To: <1244798666.14765.10.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> <4A3114DA.1030904@toulouse.inra.fr> <1244798666.14765.10.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4A3240FD.8030505@toulouse.inra.fr> Steffen Neumann wrote: > On Thu, 2009-06-11 at 16:29 +0200, Sebastien Carrere wrote: > >> Now, the following url is ok: >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de >> > > Hm, I wonder whether something like that > could be integrated into (or at least linked from !!) > the "official" biomoby.org site. > It's ok for me. Let see with the biomoby.org team. > One more comment: > Should the servicetype view show the corresponding services ? > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_servicetype¢ral=mobycentral&servicetype=Retrieval > This is currently empty, although I know at least > one matching service ;-) > Added to my TODO list. I'll do it ASAP. Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Fri Jun 12 11:31:08 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 12 Jun 2009 08:31:08 -0700 Subject: [MOBY-dev] [SPAM_ipb] Re: Human Readable Registry on the Web ? In-Reply-To: <1244798666.14765.10.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> <4A3114DA.1030904@toulouse.inra.fr> <1244798666.14765.10.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4a3274cb.1437720a.2f4b.fffff314@mx.google.com> I saw the subtle suggestion, "link from 'official' biomoby.org site", and added a blurb to the end-user-biomoby-application page on the site[1]. If the blurb is incorrect please send me what it is you prefer to have written instead and I will change it! Thanks, Eddie [1] http://biomoby.open-bio.org/index.php/browser_clients/end-user-biomoby-appli cations/#registrybrowser -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Steffen Neumann Sent: June-12-09 2:24 AM To: Core developer announcements Subject: Re: [MOBY-dev] [SPAM_ipb] Re: Human Readable Registry on the Web ? On Thu, 2009-06-11 at 16:29 +0200, Sebastien Carrere wrote: > Now, the following url is ok: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_ser vice¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle. de Hm, I wonder whether something like that could be integrated into (or at least linked from !!) the "official" biomoby.org site. One more comment: Should the servicetype view show the corresponding services ? http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_ser vicetype¢ral=mobycentral&servicetype=Retrieval This is currently empty, although I know at least one matching service ;-) Does the registry allow multiple service types for one service ? I could imagine to tag our MassBank service both "retrieval" *and* "Metabolomics". Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Fri Jun 12 12:38:49 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 12 Jun 2009 09:38:49 -0700 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A30FC2E.6080803@toulouse.inra.fr> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> Message-ID: There's also the Moby Encyclopedia, written by Ken many many many years ago: http://moby.ucalgary.ca/cgi-bin/list.services.cgi M On Thu, 11 Jun 2009 05:44:30 -0700, Sebastien Carrere wrote: > Hi Steffen, > > In Toulouse, we use a cgi that we wrote to browse Moby registries: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi > > To directly access to a service description in the public central, you > have to provide 2 parameters : service and auth_uri. > > Here is an example: > > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr > > As you can see on this example, for simple services (just one input), a > direct link to Remora is provided in order to test the service. > > Hope this helps, > > Sebastien > > > > Steffen Neumann wrote: >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services >> without fireing up the Dashboard. Or, maybe >> I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them >> to a URL with a nicely formatted Name and Description >> of the service. >> >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From markw at illuminae.com Fri Jun 12 13:00:34 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 12 Jun 2009 10:00:34 -0700 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> Message-ID: see links here: http://biomoby.open-bio.org/index.php/for-developers/registry_clients M On Fri, 12 Jun 2009 09:38:49 -0700, Mark Wilkinson wrote: > There's also the Moby Encyclopedia, written by Ken many many many years > ago: > > http://moby.ucalgary.ca/cgi-bin/list.services.cgi > > M > > > > > On Thu, 11 Jun 2009 05:44:30 -0700, Sebastien Carrere > wrote: > >> Hi Steffen, >> >> In Toulouse, we use a cgi that we wrote to browse Moby registries: >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi >> >> To directly access to a service description in the public central, you >> have to provide 2 parameters : service and auth_uri. >> >> Here is an example: >> >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr >> >> As you can see on this example, for simple services (just one input), a >> direct link to Remora is provided in order to test the service. >> >> Hope this helps, >> >> Sebastien >> >> >> >> Steffen Neumann wrote: >>> Hi, >>> >>> There is an itch I have since I got to know Moby: >>> I'd like to *quickly* browse available services >>> without fireing up the Dashboard. Or, maybe >>> I'd like to tell someone "we have written >>> this super-cool BioMoby service", and point them >>> to a URL with a nicely formatted Name and Description >>> of the service. >>> >>> * The serviceList is missing the both the description >>> and some to point to our services >>> http://biomoby.org/cgi-bin/serviceList, same with >>> http://moby.ucalgary.ca/moby/ValidateService >>> >>> * The WSDL at e.g. >>> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >>> is not really human readable. >>> >>> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >>> is neither human readable, nor can I point to my service >>> >>> * GBwrose can't easily be linked to with any search parameters, >>> and anyway offers way too much functionality for my purpose >>> >>> Did I miss anything obvious ? I'd expect that a nicely formatted >>> web accessible registry overview (with occasional visits >>> by google et al) could boost public visibility of BioMoby. >>> >>> Yours, >>> Steffen >>> >>> >> > > > -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From markw at illuminae.com Mon Jun 15 15:50:58 2009 From: markw at illuminae.com (markw at illuminae.com) Date: Mon, 15 Jun 2009 19:50:58 +0000 Subject: [MOBY-dev] Opinions from the group regarding curation of Moby Central Message-ID: <2011315558-1245095553-cardhu_decombobulator_blackberry.rim.net-1275707756-@bxe1266.bisx.prod.on.blackberry> Hi all! I'm writing to ask for opinions about the curation of the Vancouver Moby-Central registry. The specific question relates to services that are mis-registered in the registry, but where the service itself is functional and API-compliant. There are a few services I have discovered in the past few days that don't do what their registration says they do, but the service also hosts their own RDF signature document. Even if we update the registry manually to reflect the true service behaviour, the MOBY RDF Agent will always re-register what is in their RDF, so manual curation isn't an option. I'm hoping to hear-back from the original provider soon, but I'm interested in the "community consensus" about what should be done in this case. Eddie and I feel that the best way to proceed is to download the service provider's RDF, fix it, and then host that RDF ourselves until the original host can find the time and/or person who will take-charge of the services. Again, it isn't the *service* that is wrong, it is the *registration* that is wrong. Does this sound reasonable? Mark On the Road! From Usadel at mpimp-golm.mpg.de Mon Jun 15 17:43:15 2009 From: Usadel at mpimp-golm.mpg.de (Bjoern Usadel) Date: Mon, 15 Jun 2009 23:43:15 +0200 Subject: [MOBY-dev] Opinions from the group regarding curation of Moby Central Message-ID: <3C6529856AC10C4E843BE21F6B9356DA80CE9982CA@MAIL01.mpimp-golm.mpg.de> Dear Mark I always favor any manual curation as long as it is done carefully and sensibly. But it would be nice to warn the service maintainer a few times and give them some time to respond. I think however it will be important to know what does 'they don't do what they say' mean? Can this be a based on an ambiguity? Cheers, Bjoern --------------------- Bjoern Usadel Max Planck Institute of Molecular Plant Physiology Integrative Carbon Biology Am Muehlenberg 1 14476 Potsdam Golm Fon +493315678153 Fax +493315678134 --------------------------- ----- Originalnachricht ----- Von: moby-dev-bounces at lists.open-bio.org An: moby-dev at biomoby.org Gesendet: Mon Jun 15 21:50:58 2009 Betreff: [MOBY-dev] Opinions from the group regarding curation of Moby Central Hi all! I'm writing to ask for opinions about the curation of the Vancouver Moby-Central registry. The specific question relates to services that are mis-registered in the registry, but where the service itself is functional and API-compliant. There are a few services I have discovered in the past few days that don't do what their registration says they do, but the service also hosts their own RDF signature document. Even if we update the registry manually to reflect the true service behaviour, the MOBY RDF Agent will always re-register what is in their RDF, so manual curation isn't an option. I'm hoping to hear-back from the original provider soon, but I'm interested in the "community consensus" about what should be done in this case. Eddie and I feel that the best way to proceed is to download the service provider's RDF, fix it, and then host that RDF ourselves until the original host can find the time and/or person who will take-charge of the services. Again, it isn't the *service* that is wrong, it is the *registration* that is wrong. Does this sound reasonable? Mark On the Road! _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Jun 1 21:52:24 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 01 Jun 2009 15:52:24 -0600 Subject: [MOBY-dev] New Moby app In-Reply-To: References: Message-ID: <4A244D98.7010208@ucalgary.ca> Hi all, I just put together a little video to introduce a new Moby application I'm hoping to release in the next couple of weeks, called Daggoo. It lets users create Moby services from existing Web Services via a drag 'n' drop interface. In case you are interested, the video is on SciVee, and is also embedded on the upcoming Daggoo Web site... http://www.daggoo.net/ Once I've committed the code, I'll follow up with more details. Cheers, Paul From dmitry.repchevski at bsc.es Tue Jun 2 18:47:32 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 02 Jun 2009 11:47:32 -0700 Subject: [MOBY-dev] New Moby app In-Reply-To: <4A244D98.7010208@ucalgary.ca> References: <4A244D98.7010208@ucalgary.ca> Message-ID: <4A2573C4.40805@bsc.es> Great! I have so many questions... I did the contrary conversion - represent Moby services as a doc-lit WSDL ones. http://inb.bsc.es/documents/java/nemus/index.html I also thought to do the similar thing (WSDL -> Moby), but didn't figure out what to do with limited Moby type system. Also there could be more then simple WSDL pattern (SOAP headers, swa, mtom...). If you have some spec. of such a conversion I would be able to provide a opposite side proxy based on your specs... ;-) Another issue is that Taverna yet to support schema type inheritance. (I don't blame them - it's a very tough task, I started to work on it, but have no time now, hopefully in July) Currently I have a core part implemented as an applet: http://inb.bsc.es/documents/java/nemus/executor/wsdl_executor.html By the way all our "inb.bsc.es" services have their proxy running at http://inb.bsc.es/gn6/proxy/SERVICE_NAME?wsdl (just to look how the result wsdl looks like) One thing I didn't understand from the presentation... Is this an application, API or some code generator. Is it possible to generate Taverna mixed workflow for moby/wsdl services? Well, expect to have more than your (nice) presentation, Best regards, Dmitry From soiland-reyes at cs.manchester.ac.uk Wed Jun 3 10:03:27 2009 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Wed, 3 Jun 2009 11:03:27 +0100 Subject: [MOBY-dev] New Moby app In-Reply-To: <4A2573C4.40805@bsc.es> References: <4A244D98.7010208@ucalgary.ca> <4A2573C4.40805@bsc.es> Message-ID: On Tue, Jun 2, 2009 at 19:47, Dmitry Repchevsky wrote: > Another issue is that Taverna yet to support schema type inheritance. > (I don't blame them - it's a very tough task, I started to work on it, but > have no time now, hopefully in July) It's in our plans, but yeah, it would require quite a bit of reworking and is hence not coming up immediately. We want to get rid of those XML splitters and do some more kind of wizard-y 'configuration' dialogue where you can tick the boxes for the granularity of inputs that you actually want. This could include drop-down boxes for abstract/subclassed types. You would then end up with a customized WSDL service with input and output ports per your specification which don't require any splitters in either end - comparable to how the BioMart services works in Taverna. As BioMoby deals with construction of data types a similar solution might be interesting for BioMoby services in Taverna, as many Moby workflows end up having various data object construction and parser 'processors' that are not really doing any execution - they are just shims like the XML splitters. > Is it possible to generate Taverna mixed workflow for moby/wsdl services? Yes, but you would probably have to dig down to individual strings on both sides with XML splitters and BioMoby objects/parsers. You might also need a few simple shims that do string joining etc. as WSDL services 'in the wild' expect sequences, gene identifiers etc. in many various kinds of syntactic formats. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From martin.senger at gmail.com Tue Jun 9 21:16:54 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 10 Jun 2009 05:16:54 +0800 Subject: [MOBY-dev] jMoby does not compile Message-ID: <4d93f07c0906091416x7b4881e7oaac2c6c1e5f5dcf8@mail.gmail.com> compile: [javac] Compiling 367 source files to /home/senger/moby-live/Java/build/classes [javac] /home/senger/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:327: cannot find symbol [javac] symbol : class Desktop [javac] location: class ca.ucalgary.seahawk.gui.MobyContentPane [javac] Desktop desktop = Desktop.getDesktop(); [javac] ^ [javac] /home/senger/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:327: cannot find symbol [javac] symbol : variable Desktop [javac] location: class ca.ucalgary.seahawk.gui.MobyContentPane [javac] Desktop desktop = Desktop.getDesktop(); [javac] ^ [javac] /home/senger/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:328: package Desktop does not exist [javac] if(!desktop.isSupported(Desktop.Action.BROWSE)) { [javac] ^ [javac] /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java:554: incompatible types [javac] found : java.lang.Object [javac] required: java.util.Map.Entry [javac] for(Map.Entry servicetype: gui.getMobyCentralImpl().getServiceTypes().entrySet()){ [javac] ^ [javac] Note: /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 4 errors BUILD FAILED /home/senger/moby-live/Java/build.xml:329: Compile failed; see the compiler error output for details. -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Tue Jun 9 21:59:49 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 09 Jun 2009 15:59:49 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0906091427p1424a819n80c8444925281de3@mail.gmail.com> References: <4d93f07c0906091416x7b4881e7oaac2c6c1e5f5dcf8@mail.gmail.com> <4A2ED2A1.1030803@ucalgary.ca> <4d93f07c0906091427p1424a819n80c8444925281de3@mail.gmail.com> Message-ID: <4A2EDB55.2010106@ucalgary.ca> I can't find a JDIC maven artifact anywhere...this is what java.awt.Desktop was before Java SE 6. Does anyone else have better luck? From gordonp at ucalgary.ca Tue Jun 9 22:02:15 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 09 Jun 2009 16:02:15 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4A2EDB55.2010106@ucalgary.ca> References: <4d93f07c0906091416x7b4881e7oaac2c6c1e5f5dcf8@mail.gmail.com> <4A2ED2A1.1030803@ucalgary.ca> <4d93f07c0906091427p1424a819n80c8444925281de3@mail.gmail.com> <4A2EDB55.2010106@ucalgary.ca> Message-ID: <4A2EDBE7.6000401@ucalgary.ca> Never mind...found a recent version finally, and am adding the dependency. Paul Gordon wrote: > I can't find a JDIC maven artifact anywhere...this is what > java.awt.Desktop was before Java SE 6. Does anyone else have better > luck? > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > From martin.senger at gmail.com Tue Jun 9 22:27:56 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 10 Jun 2009 06:27:56 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4A2EDBE7.6000401@ucalgary.ca> References: <4d93f07c0906091416x7b4881e7oaac2c6c1e5f5dcf8@mail.gmail.com> <4A2ED2A1.1030803@ucalgary.ca> <4d93f07c0906091427p1424a819n80c8444925281de3@mail.gmail.com> <4A2EDB55.2010106@ucalgary.ca> <4A2EDBE7.6000401@ucalgary.ca> Message-ID: <4d93f07c0906091527y47342dd0r1e8f0900a356b9b3@mail.gmail.com> Better, but it still does not compile: compile: [javac] Compiling 367 source files to /home/senger/moby-live/Java/build/classes [javac] /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java:554: incompatible types [javac] found : java.lang.Object [javac] required: java.util.Map.Entry [javac] for(Map.Entry servicetype: gui.getMobyCentralImpl().getServiceTypes().entrySet()){ [javac] ^ [javac] Note: /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 error BUILD FAILED /home/senger/moby-live/Java/build.xml:329: Compile failed; see the compiler error output for details. -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Jun 10 22:52:43 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 11 Jun 2009 06:52:43 +0800 Subject: [MOBY-dev] jMoby does not compile Message-ID: <4d93f07c0906101552v37240835re0bb216289a97819@mail.gmail.com> I still cannot compile jMoby. My problem now is that the new required maven repository (which was added to xmls/project.pom) - and which is this: http://ftp.kysoh.com/maven2/ - cannot be reached. Is this just my problem or also occurring elsewhere? Thanks, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenge From gordonp at ucalgary.ca Wed Jun 10 22:57:47 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 10 Jun 2009 16:57:47 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0906101552v37240835re0bb216289a97819@mail.gmail.com> References: <4d93f07c0906101552v37240835re0bb216289a97819@mail.gmail.com> Message-ID: <4A303A6B.2050605@ucalgary.ca> It seems to be down for me too. I can't find a recent jdic JAR file anywhere else though...if you can, we can replace this repo. Martin Senger wrote: > I still cannot compile jMoby. My problem now is that the new required maven > repository (which was added to xmls/project.pom) - and which is this: > http://ftp.kysoh.com/maven2/ - cannot be reached. > > Is this just my problem or also occurring elsewhere? > > Thanks, > Martin > > From martin.senger at gmail.com Wed Jun 10 23:26:19 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 11 Jun 2009 07:26:19 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4A303A6B.2050605@ucalgary.ca> References: <4d93f07c0906101552v37240835re0bb216289a97819@mail.gmail.com> <4A303A6B.2050605@ucalgary.ca> Message-ID: <4d93f07c0906101626n76d13246x344cfebb6fbb506b@mail.gmail.com> > It seems to be down for me too. I can't find a recent jdic JAR file > anywhere else though...if you can, we can replace this repo. Just send me the jar file and its pom file (you probabbly have it already in your local maven .mv) and I can deploy it to our biomoby maven repository. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From sneumann at ipb-halle.de Thu Jun 11 11:47:18 2009 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Thu, 11 Jun 2009 13:47:18 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? Message-ID: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> Hi, There is an itch I have since I got to know Moby: I'd like to *quickly* browse available services without fireing up the Dashboard. Or, maybe I'd like to tell someone "we have written this super-cool BioMoby service", and point them to a URL with a nicely formatted Name and Description of the service. * The serviceList is missing the both the description and some to point to our services http://biomoby.org/cgi-bin/serviceList, same with http://moby.ucalgary.ca/moby/ValidateService * The WSDL at e.g. http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks is not really human readable. * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances is neither human readable, nor can I point to my service * GBwrose can't easily be linked to with any search parameters, and anyway offers way too much functionality for my purpose Did I miss anything obvious ? I'd expect that a nicely formatted web accessible registry overview (with occasional visits by google et al) could boost public visibility of BioMoby. Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 From carole.goble at manchester.ac.uk Thu Jun 11 12:40:36 2009 From: carole.goble at manchester.ac.uk (Carole Goble) Date: Thu, 11 Jun 2009 13:40:36 +0100 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4A30FB44.8050307@manchester.ac.uk> Steffen http://beta.biocatalogue.org/services/search?q=biomoby has 181 biomoby services registered. we would welcome updates to the metadata!!! we launch the biocatalogue at ISMB Carole > Hi, > > There is an itch I have since I got to know Moby: > I'd like to *quickly* browse available services > without fireing up the Dashboard. Or, maybe > I'd like to tell someone "we have written > this super-cool BioMoby service", and point them > to a URL with a nicely formatted Name and Description > of the service. > > * The serviceList is missing the both the description > and some to point to our services > http://biomoby.org/cgi-bin/serviceList, same with > http://moby.ucalgary.ca/moby/ValidateService > > * The WSDL at e.g. > http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks > is not really human readable. > > * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances > is neither human readable, nor can I point to my service > > * GBwrose can't easily be linked to with any search parameters, > and anyway offers way too much functionality for my purpose > > Did I miss anything obvious ? I'd expect that a nicely formatted > web accessible registry overview (with occasional visits > by google et al) could boost public visibility of BioMoby. > > Yours, > Steffen > > From Sebastien.Carrere at toulouse.inra.fr Thu Jun 11 12:44:30 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 11 Jun 2009 14:44:30 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4A30FC2E.6080803@toulouse.inra.fr> Hi Steffen, In Toulouse, we use a cgi that we wrote to browse Moby registries: http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi To directly access to a service description in the public central, you have to provide 2 parameters : service and auth_uri. Here is an example: http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr As you can see on this example, for simple services (just one input), a direct link to Remora is provided in order to test the service. Hope this helps, Sebastien Steffen Neumann wrote: > Hi, > > There is an itch I have since I got to know Moby: > I'd like to *quickly* browse available services > without fireing up the Dashboard. Or, maybe > I'd like to tell someone "we have written > this super-cool BioMoby service", and point them > to a URL with a nicely formatted Name and Description > of the service. > > * The serviceList is missing the both the description > and some to point to our services > http://biomoby.org/cgi-bin/serviceList, same with > http://moby.ucalgary.ca/moby/ValidateService > > * The WSDL at e.g. > http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks > is not really human readable. > > * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances > is neither human readable, nor can I point to my service > > * GBwrose can't easily be linked to with any search parameters, > and anyway offers way too much functionality for my purpose > > Did I miss anything obvious ? I'd expect that a nicely formatted > web accessible registry overview (with occasional visits > by google et al) could boost public visibility of BioMoby. > > Yours, > Steffen > > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From jits at cs.man.ac.uk Thu Jun 11 13:24:05 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Jun 2009 14:24:05 +0100 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A30FB44.8050307@manchester.ac.uk> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FB44.8050307@manchester.ac.uk> Message-ID: <4A310575.2040307@cs.man.ac.uk> Hi Steffen, Just to add to Carole's email - what you'll see now is the beta site that we are preparing for a public launch at ISMB at the end of this month. So far, we have harvested some BioMoby services from SeekDa, but we intend to have better integration and harvesting of BioMoby services by Q4 of this year. Check out our roadmap (http://www.biocatalogue.org/wiki/doku.php?id=public:roadmap) and get in touch, if you're interested :-) Thanks, Jits Carole Goble wrote: > Steffen > > http://beta.biocatalogue.org/services/search?q=biomoby > > has 181 biomoby services registered. we would welcome updates to the > metadata!!! > we launch the biocatalogue at ISMB > > Carole > >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services without fireing up >> the Dashboard. Or, maybe I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them to a URL with a >> nicely formatted Name and Description of the service. >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From mgerlich at ipb-halle.de Thu Jun 11 13:44:07 2009 From: mgerlich at ipb-halle.de (Michael Gerlich) Date: Thu, 11 Jun 2009 15:44:07 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A30FC2E.6080803@toulouse.inra.fr> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> Message-ID: <4A310A27.2000001@ipb-halle.de> Hi, does this cgi script check for dead services? I noticed that all of our (ipb-halle.de) services are currently marked as dead services (including a whole bunch of other services - too many for my understanding...): http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Might this be causing empty entries in your registry when tried for our services? http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de I checked and all our services are working, and both Taverna and Dashboard have no problems with them. I guess the lookup if and how a service is marked as "dead" should be revised, or perhaps someone could point some information to me so I can assure that our services are not marked as dead (would this require rdf-editing?). Regards, Michael Sebastien Carrere wrote: > Hi Steffen, > > In Toulouse, we use a cgi that we wrote to browse Moby registries: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi > > To directly access to a service description in the public central, you > have to provide 2 parameters : service and auth_uri. > > Here is an example: > > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr > > > As you can see on this example, for simple services (just one input), > a direct link to Remora is provided in order to test the service. > > Hope this helps, > > Sebastien > > > > Steffen Neumann wrote: >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services without fireing up >> the Dashboard. Or, maybe I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them to a URL with a >> nicely formatted Name and Description of the service. >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany From edward.kawas at gmail.com Thu Jun 11 14:04:47 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 11 Jun 2009 07:04:47 -0700 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A310A27.2000001@ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> Message-ID: <4a310f0c.1bbc720a.31b7.0dee@mx.google.com> Hi Michael, What the service checker does is that it tries to ping the service by sending an empty moby message. If the service responds (basically echoes) then it is considered alive. What service are you trying? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich Sent: June-11-09 6:44 AM To: Core developer announcements Subject: Re: [MOBY-dev] Human Readable Registry on the Web ? Hi, does this cgi script check for dead services? I noticed that all of our (ipb-halle.de) services are currently marked as dead services (including a whole bunch of other services - too many for my understanding...): http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Might this be causing empty entries in your registry when tried for our services? http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_ser vice¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle. de I checked and all our services are working, and both Taverna and Dashboard have no problems with them. I guess the lookup if and how a service is marked as "dead" should be revised, or perhaps someone could point some information to me so I can assure that our services are not marked as dead (would this require rdf-editing?). Regards, Michael Sebastien Carrere wrote: > Hi Steffen, > > In Toulouse, we use a cgi that we wrote to browse Moby registries: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi > > To directly access to a service description in the public central, you > have to provide 2 parameters : service and auth_uri. > > Here is an example: > > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTN etBlast&auth_uri=iant.toulouse.inra.fr > > > As you can see on this example, for simple services (just one input), > a direct link to Remora is provided in order to test the service. > > Hope this helps, > > Sebastien > > > > Steffen Neumann wrote: >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services without fireing up >> the Dashboard. Or, maybe I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them to a URL with a >> nicely formatted Name and Description of the service. >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Jun 11 14:08:43 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 11 Jun 2009 07:08:43 -0700 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A310A27.2000001@ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> Message-ID: <4a310ff7.1921720a.56e4.0e8a@mx.google.com> Sorry, Check out the page at http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator Enter ipb-halle.de from the service provider drop down and hit the 'check my services' button. You will see why the server thinks that your services are dead. If they die because of the empty message, let me know, and I can help you fix your services so that they don't die on empty messages. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich Sent: June-11-09 6:44 AM To: Core developer announcements Subject: Re: [MOBY-dev] Human Readable Registry on the Web ? Hi, does this cgi script check for dead services? I noticed that all of our (ipb-halle.de) services are currently marked as dead services (including a whole bunch of other services - too many for my understanding...): http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Might this be causing empty entries in your registry when tried for our services? http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_ser vice¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle. de I checked and all our services are working, and both Taverna and Dashboard have no problems with them. I guess the lookup if and how a service is marked as "dead" should be revised, or perhaps someone could point some information to me so I can assure that our services are not marked as dead (would this require rdf-editing?). Regards, Michael Sebastien Carrere wrote: > Hi Steffen, > > In Toulouse, we use a cgi that we wrote to browse Moby registries: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi > > To directly access to a service description in the public central, you > have to provide 2 parameters : service and auth_uri. > > Here is an example: > > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTN etBlast&auth_uri=iant.toulouse.inra.fr > > > As you can see on this example, for simple services (just one input), > a direct link to Remora is provided in order to test the service. > > Hope this helps, > > Sebastien > > > > Steffen Neumann wrote: >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services without fireing up >> the Dashboard. Or, maybe I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them to a URL with a >> nicely formatted Name and Description of the service. >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From ytanoh at cs.man.ac.uk Thu Jun 11 13:59:03 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 11 Jun 2009 14:59:03 +0100 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A310575.2040307@cs.man.ac.uk> Message-ID: Hello everybody, The BioCatalogue (www.biocatalogue.org) team is proud to announce that the main portal for the project will be launched during ISMB/ECCB 2009, which takes place in Stockholm, Sweden between June 28 - July 2nd. (Please see: http://www.iscb.org/ismbeccb2009/). There will be a demo for the BioCatalogue during Technical Track session TT41, which will take place on Wednesday July 1st from 2:45pm - 3:10 pm in Room C8. There will also be a poster which will be presented during the poster session of the conference. The BioCatalogue will provide a centralised registry of curated Life Science web services. BioCatalogue will also act as a place where the community can find contacts and meet the experts and maintainers of these services. For more information about the project: http://www.biocatalogue.org/wiki If you are a developer or a consumer of Web Services, this is one session you shouldn't miss during ISMB/ECCB 2009. BioCatalogue is a BBSRC funded project [BB/F01046X/1, BB/F010540/1] and has been running since 1st June 2008. The project is a joint venture between the EMBL-EBI (led by Rodrigo Lopez) and the myGrid project at the University of Manchester (led by Carole Goble). The BioCatalogue team -----Original Message----- From: owner-biocatalogue at listserv.manchester.ac.uk [mailto:owner-biocatalogue at listserv.manchester.ac.uk] On Behalf Of Jiten Bhagat Sent: 11 June 2009 14:24 To: Core developer announcements Cc: BIOCATALOGUE at listserv.manchester.ac.uk Subject: Re: [MOBY-dev] Human Readable Registry on the Web ? Hi Steffen, Just to add to Carole's email - what you'll see now is the beta site that we are preparing for a public launch at ISMB at the end of this month. So far, we have harvested some BioMoby services from SeekDa, but we intend to have better integration and harvesting of BioMoby services by Q4 of this year. Check out our roadmap (http://www.biocatalogue.org/wiki/doku.php?id=public:roadmap) and get in touch, if you're interested :-) Thanks, Jits Carole Goble wrote: > Steffen > > http://beta.biocatalogue.org/services/search?q=biomoby > > has 181 biomoby services registered. we would welcome updates to the > metadata!!! > we launch the biocatalogue at ISMB > > Carole > >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services without fireing up >> the Dashboard. Or, maybe I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them to a URL with a >> nicely formatted Name and Description of the service. >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Sebastien.Carrere at toulouse.inra.fr Thu Jun 11 14:29:46 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 11 Jun 2009 16:29:46 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A310A27.2000001@ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> Message-ID: <4A3114DA.1030904@toulouse.inra.fr> This cgi does not check for dead services. It browses the whole registry. The problem with your service was related to Collection Input (we don't have a lot of services dealing with collections in our lab, that's why I had never seen this bug ...). I fixed it. Now, the following url is ok: http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de Sebastien. Michael Gerlich wrote: > Hi, > > does this cgi script check for dead services? > > I noticed that all of our (ipb-halle.de) services are currently marked > as dead services (including a whole bunch of other services - too many > for my understanding...): > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Might this be causing empty entries in your registry when tried for > our services? > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de > > > I checked and all our services are working, and both Taverna and > Dashboard have no problems with them. I guess the lookup if and how a > service is marked as "dead" should be revised, or perhaps someone > could point some information to me so I can assure that our services > are not marked as dead (would this require rdf-editing?). > > Regards, > Michael > > > Sebastien Carrere wrote: >> Hi Steffen, >> >> In Toulouse, we use a cgi that we wrote to browse Moby registries: >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi >> >> To directly access to a service description in the public central, >> you have to provide 2 parameters : service and auth_uri. >> >> Here is an example: >> >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr >> >> >> As you can see on this example, for simple services (just one input), >> a direct link to Remora is provided in order to test the service. >> >> Hope this helps, >> >> Sebastien >> >> >> >> Steffen Neumann wrote: >>> Hi, >>> >>> There is an itch I have since I got to know Moby: >>> I'd like to *quickly* browse available services without fireing up >>> the Dashboard. Or, maybe I'd like to tell someone "we have written >>> this super-cool BioMoby service", and point them to a URL with a >>> nicely formatted Name and Description of the service. >>> * The serviceList is missing the both the description >>> and some to point to our services >>> http://biomoby.org/cgi-bin/serviceList, same with >>> http://moby.ucalgary.ca/moby/ValidateService >>> >>> * The WSDL at e.g. >>> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >>> is not really human readable. >>> >>> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >>> is neither human readable, nor can I point to my service >>> >>> * GBwrose can't easily be linked to with any search parameters, >>> and anyway offers way too much functionality for my purpose >>> >>> Did I miss anything obvious ? I'd expect that a nicely formatted >>> web accessible registry overview (with occasional visits >>> by google et al) could boost public visibility of BioMoby. >>> >>> Yours, >>> Steffen >>> >>> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From mgerlich at ipb-halle.de Thu Jun 11 14:38:48 2009 From: mgerlich at ipb-halle.de (Michael Gerlich) Date: Thu, 11 Jun 2009 16:38:48 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A3114DA.1030904@toulouse.inra.fr> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> <4A3114DA.1030904@toulouse.inra.fr> Message-ID: <4A3116F8.8000407@ipb-halle.de> Thanks for that. Michael Sebastien Carrere wrote: > > This cgi does not check for dead services. It browses the whole registry. > > The problem with your service was related to Collection Input (we > don't have a lot of services dealing with collections in our lab, > that's why I had never seen this bug ...). > I fixed it. > > Now, the following url is ok: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de > > > > Sebastien. > > > > > Michael Gerlich wrote: >> Hi, >> >> does this cgi script check for dead services? >> >> I noticed that all of our (ipb-halle.de) services are currently >> marked as dead services (including a whole bunch of other services - >> too many for my understanding...): >> http://moby.ucalgary.ca/moby/ValidateService?getDeadServices >> >> Might this be causing empty entries in your registry when tried for >> our services? >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de >> >> >> I checked and all our services are working, and both Taverna and >> Dashboard have no problems with them. I guess the lookup if and how a >> service is marked as "dead" should be revised, or perhaps someone >> could point some information to me so I can assure that our services >> are not marked as dead (would this require rdf-editing?). >> >> Regards, >> Michael >> >> >> Sebastien Carrere wrote: >>> Hi Steffen, >>> >>> In Toulouse, we use a cgi that we wrote to browse Moby registries: >>> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi >>> >>> To directly access to a service description in the public central, >>> you have to provide 2 parameters : service and auth_uri. >>> >>> Here is an example: >>> >>> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr >>> >>> >>> As you can see on this example, for simple services (just one >>> input), a direct link to Remora is provided in order to test the >>> service. >>> >>> Hope this helps, >>> >>> Sebastien >>> >>> >>> >>> Steffen Neumann wrote: >>>> Hi, >>>> >>>> There is an itch I have since I got to know Moby: >>>> I'd like to *quickly* browse available services without fireing up >>>> the Dashboard. Or, maybe I'd like to tell someone "we have written >>>> this super-cool BioMoby service", and point them to a URL with a >>>> nicely formatted Name and Description of the service. >>>> * The serviceList is missing the both the description >>>> and some to point to our services >>>> http://biomoby.org/cgi-bin/serviceList, same with >>>> http://moby.ucalgary.ca/moby/ValidateService >>>> >>>> * The WSDL at e.g. >>>> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >>>> is not really human readable. >>>> >>>> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >>>> is neither human readable, nor can I point to my service >>>> >>>> * GBwrose can't easily be linked to with any search parameters, >>>> and anyway offers way too much functionality for my purpose >>>> >>>> Did I miss anything obvious ? I'd expect that a nicely formatted >>>> web accessible registry overview (with occasional visits >>>> by google et al) could boost public visibility of BioMoby. >>>> >>>> Yours, >>>> Steffen >>>> >>>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany From dmitry.repchevski at bsc.es Thu Jun 11 23:43:27 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Thu, 11 Jun 2009 16:43:27 -0700 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4A31969F.204@bsc.es> We (INB) have one: http://inab.org/MOWServ/ Cheers, Dmitry From srramirez at uma.es Fri Jun 12 09:02:21 2009 From: srramirez at uma.es (Sergio Ramirez Ramirez) Date: Fri, 12 Jun 2009 11:02:21 +0200 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4A32199D.4070104@uma.es> Hello Steffen, Is not exactly for browsing services, but you can search for services and datatypes in several registries at the same time using Magallanes. You can find a web client in http://chirimoyo.ac.uma.es/magallanes-web I hope you find it useful Best regards, Sergio Steffen Neumann wrote: > Hi, > > There is an itch I have since I got to know Moby: > I'd like to *quickly* browse available services > without fireing up the Dashboard. Or, maybe > I'd like to tell someone "we have written > this super-cool BioMoby service", and point them > to a URL with a nicely formatted Name and Description > of the service. > > * The serviceList is missing the both the description > and some to point to our services > http://biomoby.org/cgi-bin/serviceList, same with > http://moby.ucalgary.ca/moby/ValidateService > > * The WSDL at e.g. > http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks > is not really human readable. > > * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances > is neither human readable, nor can I point to my service > > * GBwrose can't easily be linked to with any search parameters, > and anyway offers way too much functionality for my purpose > > Did I miss anything obvious ? I'd expect that a nicely formatted > web accessible registry overview (with occasional visits > by google et al) could boost public visibility of BioMoby. > > Yours, > Steffen > > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 7236 "The first step in developing a new genetic analysis algorithm is to decide how to make the input data file format different from all pre-existing analysis data file formats. The second step in developing a new genetic analysis algorithm is to decide how to make the output data file format incompatible with all pre-existing analysis data file input formats." Andy Law "The third step is use mAPI to make them compatible" Sergio Ram?rez "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From sneumann at ipb-halle.de Fri Jun 12 09:24:26 2009 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Fri, 12 Jun 2009 11:24:26 +0200 Subject: [MOBY-dev] [SPAM_ipb] Re: Human Readable Registry on the Web ? In-Reply-To: <4A3114DA.1030904@toulouse.inra.fr> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> <4A3114DA.1030904@toulouse.inra.fr> Message-ID: <1244798666.14765.10.camel@lathan.ipb-sub.ipb-halle.de> On Thu, 2009-06-11 at 16:29 +0200, Sebastien Carrere wrote: > Now, the following url is ok: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de Hm, I wonder whether something like that could be integrated into (or at least linked from !!) the "official" biomoby.org site. One more comment: Should the servicetype view show the corresponding services ? http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_servicetype¢ral=mobycentral&servicetype=Retrieval This is currently empty, although I know at least one matching service ;-) Does the registry allow multiple service types for one service ? I could imagine to tag our MassBank service both "retrieval" *and* "Metabolomics". Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 From Sebastien.Carrere at toulouse.inra.fr Fri Jun 12 11:50:21 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Fri, 12 Jun 2009 13:50:21 +0200 Subject: [MOBY-dev] [SPAM_ipb] Re: Human Readable Registry on the Web ? In-Reply-To: <1244798666.14765.10.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> <4A3114DA.1030904@toulouse.inra.fr> <1244798666.14765.10.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4A3240FD.8030505@toulouse.inra.fr> Steffen Neumann wrote: > On Thu, 2009-06-11 at 16:29 +0200, Sebastien Carrere wrote: > >> Now, the following url is ok: >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_service¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle.de >> > > Hm, I wonder whether something like that > could be integrated into (or at least linked from !!) > the "official" biomoby.org site. > It's ok for me. Let see with the biomoby.org team. > One more comment: > Should the servicetype view show the corresponding services ? > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_servicetype¢ral=mobycentral&servicetype=Retrieval > This is currently empty, although I know at least > one matching service ;-) > Added to my TODO list. I'll do it ASAP. Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Fri Jun 12 15:31:08 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 12 Jun 2009 08:31:08 -0700 Subject: [MOBY-dev] [SPAM_ipb] Re: Human Readable Registry on the Web ? In-Reply-To: <1244798666.14765.10.camel@lathan.ipb-sub.ipb-halle.de> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> <4A310A27.2000001@ipb-halle.de> <4A3114DA.1030904@toulouse.inra.fr> <1244798666.14765.10.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <4a3274cb.1437720a.2f4b.fffff314@mx.google.com> I saw the subtle suggestion, "link from 'official' biomoby.org site", and added a blurb to the end-user-biomoby-application page on the site[1]. If the blurb is incorrect please send me what it is you prefer to have written instead and I will change it! Thanks, Eddie [1] http://biomoby.open-bio.org/index.php/browser_clients/end-user-biomoby-appli cations/#registrybrowser -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Steffen Neumann Sent: June-12-09 2:24 AM To: Core developer announcements Subject: Re: [MOBY-dev] [SPAM_ipb] Re: Human Readable Registry on the Web ? On Thu, 2009-06-11 at 16:29 +0200, Sebastien Carrere wrote: > Now, the following url is ok: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_ser vice¢ral=mobycentral&service=MassBank_unique_DBLinks&auth_uri=ipb-halle. de Hm, I wonder whether something like that could be integrated into (or at least linked from !!) the "official" biomoby.org site. One more comment: Should the servicetype view show the corresponding services ? http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?form=more_ser vicetype¢ral=mobycentral&servicetype=Retrieval This is currently empty, although I know at least one matching service ;-) Does the registry allow multiple service types for one service ? I could imagine to tag our MassBank service both "retrieval" *and* "Metabolomics". Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Fri Jun 12 16:38:49 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 12 Jun 2009 09:38:49 -0700 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: <4A30FC2E.6080803@toulouse.inra.fr> References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> Message-ID: There's also the Moby Encyclopedia, written by Ken many many many years ago: http://moby.ucalgary.ca/cgi-bin/list.services.cgi M On Thu, 11 Jun 2009 05:44:30 -0700, Sebastien Carrere wrote: > Hi Steffen, > > In Toulouse, we use a cgi that we wrote to browse Moby registries: > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi > > To directly access to a service description in the public central, you > have to provide 2 parameters : service and auth_uri. > > Here is an example: > > http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr > > As you can see on this example, for simple services (just one input), a > direct link to Remora is provided in order to test the service. > > Hope this helps, > > Sebastien > > > > Steffen Neumann wrote: >> Hi, >> >> There is an itch I have since I got to know Moby: >> I'd like to *quickly* browse available services >> without fireing up the Dashboard. Or, maybe >> I'd like to tell someone "we have written >> this super-cool BioMoby service", and point them >> to a URL with a nicely formatted Name and Description >> of the service. >> >> * The serviceList is missing the both the description >> and some to point to our services >> http://biomoby.org/cgi-bin/serviceList, same with >> http://moby.ucalgary.ca/moby/ValidateService >> >> * The WSDL at e.g. >> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >> is not really human readable. >> >> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >> is neither human readable, nor can I point to my service >> >> * GBwrose can't easily be linked to with any search parameters, >> and anyway offers way too much functionality for my purpose >> >> Did I miss anything obvious ? I'd expect that a nicely formatted >> web accessible registry overview (with occasional visits >> by google et al) could boost public visibility of BioMoby. >> >> Yours, >> Steffen >> >> > -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From markw at illuminae.com Fri Jun 12 17:00:34 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 12 Jun 2009 10:00:34 -0700 Subject: [MOBY-dev] Human Readable Registry on the Web ? In-Reply-To: References: <1244720838.7735.12.camel@lathan.ipb-sub.ipb-halle.de> <4A30FC2E.6080803@toulouse.inra.fr> Message-ID: see links here: http://biomoby.open-bio.org/index.php/for-developers/registry_clients M On Fri, 12 Jun 2009 09:38:49 -0700, Mark Wilkinson wrote: > There's also the Moby Encyclopedia, written by Ken many many many years > ago: > > http://moby.ucalgary.ca/cgi-bin/list.services.cgi > > M > > > > > On Thu, 11 Jun 2009 05:44:30 -0700, Sebastien Carrere > wrote: > >> Hi Steffen, >> >> In Toulouse, we use a cgi that we wrote to browse Moby registries: >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi >> >> To directly access to a service description in the public central, you >> have to provide 2 parameters : service and auth_uri. >> >> Here is an example: >> >> http://lipm-bioinfo.toulouse.inra.fr/registry/cgi/registry.cgi?service=iANTNetBlast&auth_uri=iant.toulouse.inra.fr >> >> As you can see on this example, for simple services (just one input), a >> direct link to Remora is provided in order to test the service. >> >> Hope this helps, >> >> Sebastien >> >> >> >> Steffen Neumann wrote: >>> Hi, >>> >>> There is an itch I have since I got to know Moby: >>> I'd like to *quickly* browse available services >>> without fireing up the Dashboard. Or, maybe >>> I'd like to tell someone "we have written >>> this super-cool BioMoby service", and point them >>> to a URL with a nicely formatted Name and Description >>> of the service. >>> >>> * The serviceList is missing the both the description >>> and some to point to our services >>> http://biomoby.org/cgi-bin/serviceList, same with >>> http://moby.ucalgary.ca/moby/ValidateService >>> >>> * The WSDL at e.g. >>> http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_unique_DBLinks >>> is not really human readable. >>> >>> * The RDF at http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances >>> is neither human readable, nor can I point to my service >>> >>> * GBwrose can't easily be linked to with any search parameters, >>> and anyway offers way too much functionality for my purpose >>> >>> Did I miss anything obvious ? I'd expect that a nicely formatted >>> web accessible registry overview (with occasional visits >>> by google et al) could boost public visibility of BioMoby. >>> >>> Yours, >>> Steffen >>> >>> >> > > > -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From markw at illuminae.com Mon Jun 15 19:50:58 2009 From: markw at illuminae.com (markw at illuminae.com) Date: Mon, 15 Jun 2009 19:50:58 +0000 Subject: [MOBY-dev] Opinions from the group regarding curation of Moby Central Message-ID: <2011315558-1245095553-cardhu_decombobulator_blackberry.rim.net-1275707756-@bxe1266.bisx.prod.on.blackberry> Hi all! I'm writing to ask for opinions about the curation of the Vancouver Moby-Central registry. The specific question relates to services that are mis-registered in the registry, but where the service itself is functional and API-compliant. There are a few services I have discovered in the past few days that don't do what their registration says they do, but the service also hosts their own RDF signature document. Even if we update the registry manually to reflect the true service behaviour, the MOBY RDF Agent will always re-register what is in their RDF, so manual curation isn't an option. I'm hoping to hear-back from the original provider soon, but I'm interested in the "community consensus" about what should be done in this case. Eddie and I feel that the best way to proceed is to download the service provider's RDF, fix it, and then host that RDF ourselves until the original host can find the time and/or person who will take-charge of the services. Again, it isn't the *service* that is wrong, it is the *registration* that is wrong. Does this sound reasonable? Mark On the Road! From Usadel at mpimp-golm.mpg.de Mon Jun 15 21:43:15 2009 From: Usadel at mpimp-golm.mpg.de (Bjoern Usadel) Date: Mon, 15 Jun 2009 23:43:15 +0200 Subject: [MOBY-dev] Opinions from the group regarding curation of Moby Central Message-ID: <3C6529856AC10C4E843BE21F6B9356DA80CE9982CA@MAIL01.mpimp-golm.mpg.de> Dear Mark I always favor any manual curation as long as it is done carefully and sensibly. But it would be nice to warn the service maintainer a few times and give them some time to respond. I think however it will be important to know what does 'they don't do what they say' mean? Can this be a based on an ambiguity? Cheers, Bjoern --------------------- Bjoern Usadel Max Planck Institute of Molecular Plant Physiology Integrative Carbon Biology Am Muehlenberg 1 14476 Potsdam Golm Fon +493315678153 Fax +493315678134 --------------------------- ----- Originalnachricht ----- Von: moby-dev-bounces at lists.open-bio.org An: moby-dev at biomoby.org Gesendet: Mon Jun 15 21:50:58 2009 Betreff: [MOBY-dev] Opinions from the group regarding curation of Moby Central Hi all! I'm writing to ask for opinions about the curation of the Vancouver Moby-Central registry. The specific question relates to services that are mis-registered in the registry, but where the service itself is functional and API-compliant. There are a few services I have discovered in the past few days that don't do what their registration says they do, but the service also hosts their own RDF signature document. Even if we update the registry manually to reflect the true service behaviour, the MOBY RDF Agent will always re-register what is in their RDF, so manual curation isn't an option. I'm hoping to hear-back from the original provider soon, but I'm interested in the "community consensus" about what should be done in this case. Eddie and I feel that the best way to proceed is to download the service provider's RDF, fix it, and then host that RDF ourselves until the original host can find the time and/or person who will take-charge of the services. Again, it isn't the *service* that is wrong, it is the *registration* that is wrong. Does this sound reasonable? Mark On the Road! _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev