From martin.senger at gmail.com Mon Jul 2 09:13:47 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 2 Jul 2007 14:13:47 +0100 Subject: [MOBY-dev] jMoby add a parameter into a message In-Reply-To: <4667C73B.7050604@bsc.es> References: <4667C73B.7050604@bsc.es> Message-ID: <4d93f07c0707020613j53426821x2b53b6bf0a9ff166@mail.gmail.com> Hi, looking into jMoby code I found different basic moby types (i.e. > MobyDataBoolean and MobyBoolean) There are two ways how to do things in jMoby. And both of them share some data types, but also have their own ones. Your code snippet uses Moses data types, therefore, your data type for Boolean would be org.biomoby.shared.datatypes.MobyBoolean. , but can't find a way to construct a > message: What is your error messages? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From groscurt at mpiz-koeln.mpg.de Tue Jul 3 08:46:19 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 3 Jul 2007 14:46:19 +0200 Subject: [MOBY-dev] Get Information from the XML / bug in MobyContentInstance ? In-Reply-To: References: <1140939448@web.de> Message-ID: <200707031446.19706.groscurt@mpiz-koeln.mpg.de> Hi all, i need your help again.... its still java ;-) I called the service, retrieved an XML and now ? how do i get to the information ? I use Pauls 'client' MobyRequest request = new MobyRequest(central); request.setService(service); request.setInput(new MobyDataObject("Global_Keyword", keyword)); MobyContentInstance queries = request.invokeService(); on the docu it is written, that MobyContentInstance is a Map and I could retrieve information from the map... mhm... I cant printing it out with System.out.println i get the correct xml. This service retrieves all AGI_Locus Codes related to a given keyword via BioRS from MAtDB (MIPS Arabidopsis thaliana database) as far as I can see through this the following code should be responsible for that -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From groscurt at mpiz-koeln.mpg.de Tue Jul 3 08:51:33 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 3 Jul 2007 14:51:33 +0200 Subject: [MOBY-dev] Getting out from XML.... Bug in MobyContentInstance ? In-Reply-To: References: <1140939448@web.de> Message-ID: <200707031451.33339.groscurt@mpiz-koeln.mpg.de> Hi all, I call a service with Pauls 'client' MobyRequest request = new MobyRequest(central); request.setService(service); request.setInput(new MobyDataObject("Global_Keyword", keyword)); MobyContentInstance instance = request.invokeService(); in the docu it says via MobyContentInstance I can retrieve my data... but it doesnt. printling the object via println i get the following xml This service retrieves all AGI_Locus Codes related to a given keyword via BioRS from MAtDB (MIPS Arabidopsis thaliana database) I debugged the MobyContentInstance and apparently in the line NodeList collections = MobyPrefixResolver.getChildElements(dataGroupTag, "Collection"); and after, it should parse the collection - put it doesnt.... the result is -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From groscurt at mpiz-koeln.mpg.de Tue Jul 3 08:55:58 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 3 Jul 2007 14:55:58 +0200 Subject: [MOBY-dev] get data from XML... or MobyContentInstance... bug ? In-Reply-To: References: <1140939448@web.de> Message-ID: <200707031455.58449.groscurt@mpiz-koeln.mpg.de> Hi all, I call a service via Pauls 'Client' MobyRequest request = new MobyRequest(central); request.setService(service); request.setInput(new MobyDataObject("Global_Keyword", keyword)); MobyContentInstance instance = request.invokeService(); using println on the MobyContentInstance I get the xml This service retrieves all AGI_Locus Codes related to a given keyword via BioRS from MAtDB (MIPS Arabidopsis thaliana database) but using the Java Api methods for MobyConstentInstance - there is nothing.... The map, which should give me my data, looks the following: {result_codes=Name: result_codes Elements in collection: } So... as far as I can see - something failes while parsing ?! Is this a bug or somewhere my fault ? And anyway... is there another way to get data from the XML besides parsing it by myself ? Thanks Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From groscurt at mpiz-koeln.mpg.de Tue Jul 3 08:57:19 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 3 Jul 2007 14:57:19 +0200 Subject: [MOBY-dev] Get Information from the XML / bug in MobyContentInstance ? In-Reply-To: <200707031446.19706.groscurt@mpiz-koeln.mpg.de> References: <1140939448@web.de> <200707031446.19706.groscurt@mpiz-koeln.mpg.de> Message-ID: <200707031457.19264.groscurt@mpiz-koeln.mpg.de> Hi... grrrrr... due to some problems with Kmail - you will get the same Bug-MobyContentInstance Mail several times :-( sorry for that... the last one "get data from XML... or MobyContentInstance... bug ?" is the correct and complete one :( Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From gordonp at ucalgary.ca Tue Jul 3 09:46:47 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 03 Jul 2007 07:46:47 -0600 Subject: [MOBY-dev] Get Information from the XML / bug in MobyContentInstance ? In-Reply-To: <200707031457.19264.groscurt@mpiz-koeln.mpg.de> References: <1140939448@web.de> <200707031446.19706.groscurt@mpiz-koeln.mpg.de> <200707031457.19264.groscurt@mpiz-koeln.mpg.de> Message-ID: <468A5347.5040504@ucalgary.ca> Hi Andreas, The issue is that you have 2 "modes" for toXML() in the package. Please see the "org.biomoby.shared.data Package In Anger" http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAnger.html This should explain how to do what you want succinctly. If not, let me know what's not clear, and I'll update the docs. Cheers! Paul > Hi... > > grrrrr... due to some problems with Kmail - you will get the same > Bug-MobyContentInstance Mail several times :-( > sorry for that... > > the last one "get data from XML... or MobyContentInstance... bug ?" is the > correct and complete one > > :( > Andreas > > From markw at illuminae.com Tue Jul 3 14:00:23 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 03 Jul 2007 11:00:23 -0700 Subject: [MOBY-dev] PLoS ONE Decision Message-ID: There was a single reviewer, who decided that the manuscript required major revisions. It's probably worthwhile discussing as a group what our response to the review will be. Here is the review: ==================== The manuscript ?Interoperability with Moby 1.0? deals in standardizing methodologies to facilitate information exchange and access to analytical resources. The manuscript provides the detailed development that has occurred in BioMoby. The authors present and discuss why BioMoby is a distinct from other semantic web services. Major Compulsory Revisions (that author must respond to before decision on publication is reached) To Authors: To begin with the paper is well written in terms of technical and implementation aspects. What I see is that author?s do not clearly present difference between the earlier versions with the current version of BioMoby. It would be really helpful if the authors could explain this using a concrete example to understand the functioning of the BioMoby framework. The paper looks more like a user manual with technical specification rather than any scientific implication to the readers. The authors could improve the paper by providing a strong biological input as motivation for developing such a framework. As I read through the paper I see the author?s speak about semantic web services. It would be interesting for the readers to know what the other semantic web services and how BioMoby is better. Is it possible for u to demonstrate it with an example? In the results section the author?s speak about Namespaces Ontology wherein there are 300 different Namespaces that includes prominent public data resources. It would be interesting to know weather BioMoby also supports PSI MI, MAGE standards that are also coming in from prominent databases. In the Object Ontology the author?s specify BioMoby framework can receive any data-type and it does not re-define the legacy of the data type. Please provide a more concrete example for this point. In BioMoby web services Second Paragraph the author?s say: ?The providers do not need to be concerned about the exact structure of incoming data and do not need to query the ever- changing BioMoby ontology?. 1. Justify this statement. 2. Summaries what are the BioMoby?s ontology?s that was present in the earlier and in the current version. 3. How can you compare it with the other semantic web services ontology?s? Justify how SOAP concept implemented in BioMoby is better than the others service providers that could improve the interoperability of the framework. Through out the paper the author?s have introduced various terms as ontology. It is quite misleading for me to associate these different ontology under one roof of BioMoby. [[does anyone understand what this comment means??]] Finally, I feel that BioMoby is one of the most prominent approaches in the bioinformatics community. The paper contains less scientific inputs and more technical inputs. The paper does not contain strong examples to validate various arguments. Hence the paper cannot be accepted in the current form. If the author?s could answer some of the question raised, that could make the paper more interesting and more relevant to the PLoS ONE readers. ============================ -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From groscurt at mpiz-koeln.mpg.de Wed Jul 4 02:42:43 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 4 Jul 2007 08:42:43 +0200 Subject: [MOBY-dev] Get Information from the XML / bug in MobyContentInstance ? In-Reply-To: <468A5347.5040504@ucalgary.ca> References: <1140939448@web.de> <200707031457.19264.groscurt@mpiz-koeln.mpg.de> <468A5347.5040504@ucalgary.ca> Message-ID: <200707040842.43828.groscurt@mpiz-koeln.mpg.de> Hi Paul and all, thanks... after some coding / testing and so on - I finally found it out :-) My problem now was the getValue / getID methods in the case of an Simple-Object... getValue of course does not return something... but getID does.... wonderful :) thanks Andreas On Tuesday 03 July 2007 15:46, Paul Gordon wrote: > Hi Andreas, > > The issue is that you have 2 "modes" for toXML() in the package. > > Please see the "org.biomoby.shared.data Package In Anger" > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAn >ger.html > > This should explain how to do what you want succinctly. If not, let me > know what's not clear, and I'll update the docs. > > Cheers! > > Paul > > > Hi... > > > > grrrrr... due to some problems with Kmail - you will get the same > > Bug-MobyContentInstance Mail several times :-( > > sorry for that... > > > > the last one "get data from XML... or MobyContentInstance... bug ?" is > > the correct and complete one > > > > :( > > > > Andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From duncan.hull at cs.man.ac.uk Wed Jul 4 06:08:13 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 04 Jul 2007 11:08:13 +0100 Subject: [MOBY-dev] PLoS ONE Decision: A nightmare on SOAP street In-Reply-To: References: Message-ID: <468B718D.3060605@cs.man.ac.uk> Mark Wilkinson wrote: > Justify how SOAP concept implemented in BioMoby is better than the > others service providers that could improve the interoperability of the > framework. SOAP intereroperability is a nightmare for everyone, you might need to be more specific about what you mean: http://www.cs.man.ac.uk/~hulld/q2007-02-06.html Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From duncan.hull at cs.man.ac.uk Wed Jul 4 05:56:33 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 04 Jul 2007 10:56:33 +0100 Subject: [MOBY-dev] PLoS ONE Decision: Semantic Web Services In-Reply-To: References: Message-ID: <468B6ED1.9040004@cs.man.ac.uk> Hello Mark Mark Wilkinson wrote: > 3. How can you compare it with the other semantic web services ontology?s? > I haven't seen the BioMOBY Plos One manuscipt recently but it sounds like it might benefit from an explanation of how BioMOBY is different to myGrid and AI-systems like WSMO and OWL-S: For example: 1. How is BioMOBYs approach is different to myGrid? I think the key differentiator here is tagging (BioMOBY style) vs. curation (myGrid style). Each approach has its own strengths and limitations, which we are familiar with... 2. How is BioMOBY different to OWL-S and WSMO for example? I think the key differentiator here is reasoning. Neither BioMOBY or myGrid currently use description logic reasoning in a way originally envisioned by the AI community: http://dx.doi.org/10.1109/5254.920599 http://eprints.ecs.soton.ac.uk/7606/ In these approaches, reasoning is used to improve matching (better precision and recall) and ranking (a query for a service produces hundreds of hits, how do you rank them?) Just my $0.02 HTH Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From duncan.hull at cs.man.ac.uk Wed Jul 4 05:56:33 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 04 Jul 2007 10:56:33 +0100 Subject: [MOBY-dev] PLoS ONE Decision: Semantic Web Services In-Reply-To: References: Message-ID: <468B6ED1.9040004@cs.man.ac.uk> Hello Mark Mark Wilkinson wrote: > 3. How can you compare it with the other semantic web services ontology?s? > I haven't seen the BioMOBY Plos One manuscipt recently but it sounds like it might benefit from an explanation of how BioMOBY is different to myGrid and AI-systems like WSMO and OWL-S: For example: 1. How is BioMOBYs approach is different to myGrid? I think the key differentiator here is tagging (BioMOBY style) vs. curation (myGrid style). Each approach has its own strengths and limitations, which we are familiar with... 2. How is BioMOBY different to OWL-S and WSMO for example? I think the key differentiator here is reasoning. Neither BioMOBY or myGrid currently use description logic reasoning in a way originally envisioned by the AI community: http://dx.doi.org/10.1109/5254.920599 http://eprints.ecs.soton.ac.uk/7606/ In these approaches, reasoning is used to improve matching (better precision and recall) and ranking (a query for a service produces hundreds of hits, how do you rank them?) Just my $0.02 HTH Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From groscurt at mpiz-koeln.mpg.de Wed Jul 4 07:28:20 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 4 Jul 2007 13:28:20 +0200 Subject: [MOBY-dev] caching data from MobyRequest In-Reply-To: <468A5347.5040504@ucalgary.ca> References: <1140939448@web.de> <200707031457.19264.groscurt@mpiz-koeln.mpg.de> <468A5347.5040504@ucalgary.ca> Message-ID: <200707041328.21160.groscurt@mpiz-koeln.mpg.de> Hi all, again paul, thanks for the answer, it works nicely. Just one interesst: everytime I call the service I get the following log ERROR [STDERR] Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/Objects ERROR [STDERR] ... done ERROR [STDERR] Fetching namespace ontology from http://biomoby.org/RESOURCES/MOBY-S/Namespaces ERROR [STDERR] There are 1 collections in response 1 is there a way to cache these data, so that the application does not need fetch it everytime ? Thanks Andreas On Tuesday 03 July 2007 15:46, Paul Gordon wrote: > Hi Andreas, > > The issue is that you have 2 "modes" for toXML() in the package. > > Please see the "org.biomoby.shared.data Package In Anger" > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAn >ger.html > > This should explain how to do what you want succinctly. If not, let me > know what's not clear, and I'll update the docs. > > Cheers! > > Paul > > > Hi... > > > > grrrrr... due to some problems with Kmail - you will get the same > > Bug-MobyContentInstance Mail several times :-( > > sorry for that... > > > > the last one "get data from XML... or MobyContentInstance... bug ?" is > > the correct and complete one > > > > :( > > > > Andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From gordonp at ucalgary.ca Wed Jul 4 09:50:26 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 04 Jul 2007 07:50:26 -0600 Subject: [MOBY-dev] caching data from MobyRequest In-Reply-To: <200707041328.21160.groscurt@mpiz-koeln.mpg.de> References: <1140939448@web.de> <200707031457.19264.groscurt@mpiz-koeln.mpg.de> <468A5347.5040504@ucalgary.ca> <200707041328.21160.groscurt@mpiz-koeln.mpg.de> Message-ID: <468BA5A2.3010801@ucalgary.ca> Hi Andreas, Yes, there is a class that allows you to cache these... *org.biomoby.registry.meta.RegistryCache* You can see how I use it in the source code for * ca.ucalgary.seahawk.gui.MobyContentGUI *Though I should probably add a doc about that too :-)* * > Hi all, > > again paul, thanks for the answer, it works nicely. > > Just one interesst: > > everytime I call the service I get the following log > > ERROR [STDERR] Fetching data type ontology from > http://biomoby.org/RESOURCES/MOBY-S/Objects > ERROR [STDERR] ... done > ERROR [STDERR] Fetching namespace ontology from > http://biomoby.org/RESOURCES/MOBY-S/Namespaces > ERROR [STDERR] There are 1 collections in response 1 > > is there a way to cache these data, so that the application does not need > fetch it everytime ? > > Thanks > Andreas > > > On Tuesday 03 July 2007 15:46, Paul Gordon wrote: > >> Hi Andreas, >> >> The issue is that you have 2 "modes" for toXML() in the package. >> >> Please see the "org.biomoby.shared.data Package In Anger" >> >> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAn >> ger.html >> >> This should explain how to do what you want succinctly. If not, let me >> know what's not clear, and I'll update the docs. >> >> Cheers! >> >> Paul >> >> >>> Hi... >>> >>> grrrrr... due to some problems with Kmail - you will get the same >>> Bug-MobyContentInstance Mail several times :-( >>> sorry for that... >>> >>> the last one "get data from XML... or MobyContentInstance... bug ?" is >>> the correct and complete one >>> >>> :( >>> >>> Andreas >>> >> _______________________________________________ >> 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 Wed Jul 4 11:45:51 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 04 Jul 2007 08:45:51 -0700 Subject: [MOBY-dev] URGENT! affiliations required Message-ID: Hi all, PLoS ONE has requested that we add all affiliations for all members of the consortium, despite them not being explicitly listed as authors. Please, to save me having to look-up and type this all myself, could everyone please do the following for everyone that is on the author list of the paper: in the following format: Surname, Initial, institution, address, email. Please send me the info for every author in your "domain". Thanks! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From duncan.hull at cs.man.ac.uk Wed Jul 4 12:03:36 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 04 Jul 2007 17:03:36 +0100 Subject: [MOBY-dev] BioMOBY and myGrid In-Reply-To: <468B6ED1.9040004@cs.man.ac.uk> References: <468B6ED1.9040004@cs.man.ac.uk> Message-ID: <468BC4D8.70508@cs.man.ac.uk> Hello Duncan Hull wrote: > 1. How is BioMOBYs approach is different to myGrid? I think the key > differentiator here is tagging (BioMOBY style) vs. curation (myGrid > style). Each approach has its own strengths and limitations, which we > are familiar with... > ...but the journal reviewers are probably not familiar with these strengths and limitations, so they would be worth stating. They are fairly obvious, but if you want my list, I'm happy to pass it on. Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From markw at illuminae.com Wed Jul 4 13:02:12 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 04 Jul 2007 10:02:12 -0700 Subject: [MOBY-dev] BioMOBY and myGrid In-Reply-To: <468BC4D8.70508@cs.man.ac.uk> References: <468B6ED1.9040004@cs.man.ac.uk> <468BC4D8.70508@cs.man.ac.uk> Message-ID: Hi Duncan, Thanks for the offer! If you could provide that list I will incorporate it into the text and add you as an "author" :-) (actually, NOT having you as an author was a bit of an embarrassing oversight anyway, given that you have now done two graduate degrees studying meta-Moby!) M On Wed, 04 Jul 2007 09:03:36 -0700, Duncan Hull wrote: > Hello > > Duncan Hull wrote: >> 1. How is BioMOBYs approach is different to myGrid? I think the key >> differentiator here is tagging (BioMOBY style) vs. curation (myGrid >> style). Each approach has its own strengths and limitations, which we >> are familiar with... >> > > ...but the journal reviewers are probably not familiar with these > strengths and limitations, so they would be worth stating. > > They are fairly obvious, but if you want my list, I'm happy to pass it > on. > > Duncan > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From Pieter.Neerincx at wur.nl Wed Jul 4 15:16:08 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Wed, 04 Jul 2007 21:16:08 +0200 Subject: [MOBY-dev] PLoS ONE Decision In-Reply-To: References: Message-ID: Hi, On 03 Jul 2007, at 20:00, Mark Wilkinson wrote: > There was a single reviewer, Huh, a single reviewer? That doesn't sound very professional :(. I thought they called it PLoS *One* for different reasons :) > who decided that the manuscript required > major revisions. It's probably worthwhile discussing as a group > what our > response to the review will be. Here's my ? 0.02... > Here is the review: > > ==================== > The manuscript ?Interoperability with Moby 1.0? deals in standardizing > methodologies to facilitate information exchange and access to > analytical > resources. The manuscript provides the detailed development that has > occurred in BioMoby. The authors present and discuss why BioMoby is a > distinct from other semantic web services. > > Major Compulsory Revisions (that author must respond to before > decision > on publication is reached) > > To Authors: > > To begin with the paper is well written in terms of technical and > implementation aspects. > > What I see is that author?s do not clearly present difference > between the > earlier versions with the current version of BioMoby. Well this is officially the first version as in 1.0 isn't it?. This is a first "milestone" release, so there is not much to compare it with. Of course BioMOBY has been slowly evolving as a beta in several labs, but which CVS date should we compare against? Compared to version 0.0 every feature in BioMOBY is a new feature: so it's a major improvement :). Doesn't make much sense to me... If they insist on a comparison we might compare the current state of art with what was described in "BioMOBY: an open-source biological web services proposal" by Wilkinson, MD, Links, M. (2002). That's the oldest publication on BioMOBY a.f.a.i.k. > It would be really > helpful if the authors could explain this using a concrete example to > understand the functioning of the BioMoby framework. > > The paper looks more like a user manual with technical > specification rather > than any scientific implication to the readers. The authors could > improve > the > paper by providing a strong biological input as motivation for > developing > such a framework. > > As I read through the paper I see the author?s speak about semantic > web > services. It would be interesting for the readers to know what the > other > semantic web services and how BioMoby is better. Is it possible for > u to > demonstrate it with an example? If I understand the items above correctly, what the reviewer wants to see is basically a good example case, that clearly shows the advantages of BioMOBY and the differences between BioMOBY and other web service technology. When I read this I'm thinking of the graph on the front page: the one that says "Tired of this? ... Try This!". Maybe we can make such a comparison between the way too many Biologist in the lab have their work slowly flowing and the kind of workflow you can make with BioMOBY. > In the results section the author?s speak about Namespaces Ontology > wherein there are 300 different Namespaces that includes prominent > public > data resources. It would be interesting to know weather BioMoby also > supports PSI MI, MAGE standards that are also coming in from prominent > databases. Correct me if I'm wrong, but as far as I know we support any namespace: just register thing if it wasn't already. Maybe it is not clear enough though that BioMOBY allows you to support *any* namespace or kind of data format you like. Whether or not datatypes and/or namespaces for a certain standard have already been registered or not is not crucially important in my opinion, but if PLoS insists certain standards must be there to make BioMOBY interesting enough for their readers, I can easily create a small script that registers them... (Just hope they do not insist there are also services that actually use those objects and namespaces, because that will be a lot more work.) > In the Object Ontology the author?s specify BioMoby framework can > receive any data-type and it does not re-define the legacy of the data > type. > Please provide a more concrete example for this point. > In BioMoby web services Second Paragraph the author?s say: > ?The providers do not need to be concerned about the exact > structure of > incoming data and do not need to query the ever- changing BioMoby > ontology?. > > 1. Justify this statement. > > 2. Summaries what are the BioMoby?s ontology?s that was present in the > earlier and in the current version. > > 3. How can you compare it with the other semantic web services > ontology?s? > > Justify how SOAP concept implemented in BioMoby is better than the > others service providers that could improve the interoperability of > the > framework. > > Through out the paper the author?s have introduced various terms as > ontology. It is quite misleading for me to associate these different > ontology > under one roof of BioMoby. [[does anyone understand what this > comment > means??]] For me BioMOBY is a collection of several tools, frameworks/ libraries, concepts, a community and several ontologies. We have a namespace ontology, an object ontology and a service ontology. Although these are strongly related they do not share the same root. Maybe it's not clear to the reviewer what BioMOBY exactly is. To be honest it's not a bad question... According to "What is BioMOBY from the website BioMOBY: "The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next." Hence it's a messaging standard. That does not include the ontologies, the libraries, etc. It's only the standard, so the part labelled on the website as "Latest MOBY Services API". Maybe we should be more clear on what is all included when we talk about BioMOBY... Not sure if this is what the reviewer was complaining about, but it's the best I can make from the comment... > Finally, I feel that BioMoby is one of the most prominent > approaches in the > bioinformatics community. The paper contains less scientific inputs > and > more technical inputs. The paper does not contain strong examples to > validate various arguments. > > Hence the paper cannot be accepted in the current form. If the > author?s > could > answer some of the question raised, that could make the paper more > interesting and more relevant to the PLoS ONE readers. Cheers, Pi > ============================ > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have > received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From duncan.hull at cs.man.ac.uk Thu Jul 5 11:02:58 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Thu, 05 Jul 2007 16:02:58 +0100 Subject: [MOBY-dev] BioMOBY and myGrid: my $0.02 In-Reply-To: References: <468B6ED1.9040004@cs.man.ac.uk> <468BC4D8.70508@cs.man.ac.uk> Message-ID: <468D0822.4010506@cs.man.ac.uk> Hi Mark Mark Wilkinson wrote: > Thanks for the offer! If you could provide that list I will > incorporate it into the text and add you as an "author" :-) Well you've probably thought of all these already, but in case you missed any, here they are: (Your mileage may vary of course...) Pros for tagging, BioMOBY style: ======================== + Low barrier to adoption + Allows many people to annotate services + Wisdom of crowds, potentially captures more consensual knowledge Cons for tagging, BioMOBY style ======================== + The wisdom of crowds is always "close to madness" [1], you can cite Alcuin on that one! + Can produce a large quantity of low quality metadata, what the Flickr people call "noisy metadata" [2] + Difficult to precisely and accurately query registry Pros for curation, myGrid style ====================== + Less noise in service metadata + Potentially more coherent unified view + Higher quality (?), lower coverage Cons for curation, myGrid style ====================== - Services not annotated by default, as with BioMOBY - Restricts the number of people who can annotate services - Labour intensive - Time consuming - Expensive - Captures a smaller world view, the "wisdom of the curator" rather than the "wisdom of the service provider" > (actually, NOT having you as an author was a bit of an embarrassing > oversight anyway, given that you have now done two graduate degrees > studying meta-Moby!) The third degree isn't in the bag just yet ;) While we're at it... Pros for DL reasoning during service discovery ================================= + More intelligent matchmaking e.g. + Better precision + Better recall + Ability to rank services which are otherwise unrankable (without invading users privacy). + Rank by degree of match between request and advertisement [3]) + Analagous to an "Advanced Search" http://www.google.co.uk/advanced_search?hl=en Cons for DL reasoning during service discovery ================================= - Queries have to be written either in SPARQL or as OWL class expressions - Few people used "Advanced Search" features - Requires detailed annotation of services using OWL - Issues with scaling If any of this doesn't make sense, let me know and I can clarify. Duncan [1] http://www.cs.man.ac.uk/~hulld/q2004-02-11.html [2] http://dx.doi.org/10.1145/1125451.1125462 [3] http://eprints.ecs.soton.ac.uk/7606/ -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From Usadel at mpimp-golm.mpg.de Thu Jul 5 12:55:59 2007 From: Usadel at mpimp-golm.mpg.de (Bjoern Usadel) Date: Thu, 5 Jul 2007 18:55:59 +0200 Subject: [MOBY-dev] BioMOBY PLOS One: comparison to earlier releases References: <468B6ED1.9040004@cs.man.ac.uk> <468BC4D8.70508@cs.man.ac.uk> <468D0822.4010506@cs.man.ac.uk> Message-ID: <8233DF2244998040848283889E22DBA0864C04@MAIL.mpimp-golm.mpg.de> Hi All, concerning the comparison to earlier versions, one could also consider a comparison to Biomoby 0.8.2 which is the latest (at least) perl release available as a tarball and which I am always tempted to get :-) Cheers, Bjoern -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 2673 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20070705/0195da2f/attachment.bin From groscurt at mpiz-koeln.mpg.de Fri Jul 6 08:58:35 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 6 Jul 2007 14:58:35 +0200 Subject: [MOBY-dev] Another Java API question In-Reply-To: <001701c7ba4e$b5d2e060$6400a8c0@notebook> References: <467AD616.2010806@ucalgary.ca> <200706291505.27668.groscurt@mpiz-koeln.mpg.de> <001701c7ba4e$b5d2e060$6400a8c0@notebook> Message-ID: <200707061458.35954.groscurt@mpiz-koeln.mpg.de> Hi all, based on eddies answer below... I just wanted to know if I understood it correctly MobyDataObjectSet set = new MobyDataObjectSet(""); set.add(data); s.addOutput(set); with this I get all services which returns a collection... right ? if i write s.addOutput(data) I get only services which exactly return one object... right ? and if I want all services which return both - object and collection - can I write s.addOutput(set); s.addOutput(data) ? thanks for helping me through the jungel Andreas On Friday 29 June 2007 15:09, Edward Kawas wrote: > Hi Andreas, > > Hopefully this helps you out! > CentralImpl central = new CentralImpl(); > MobyService s = new MobyService(); > s.setCategory(""); > MobyDataObject data = new MobyDataObject(""); > data.setDataType(new MobyDataType("Object")); > data.addNamespace(new MobyNamespace("NCBI_gi")); > MobyDataObjectSet set = new MobyDataObjectSet(""); > set.add(data); > s.addOutput((set)); > MobyService[] services = central.findService(s,null,true,false); > > Eddie > > > -----Original Message----- > > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > > Sent: Friday, June 29, 2007 6:05 AM > > To: Core developer announcements > > Subject: [MOBY-dev] Another Java API question > > > > Hi all again, > > > > I couldnt find anything about this, so I hope you can help me with this > > simple > > one: > > > > Actually I only want to find services with specific informations, e.g. I > > want > > to find all services with a specific input or output namespace and so on. > > > > I fail by creating a service with my needs. > > > > The way I thought of doing it is to create a Central instance and call > > the findService method with a MobyService as parameter. > > My current problem is how to tell the Mobyservice which inputs it has to > > consume ? > > > > E.g. how to tell that I want an GenBank identifier as input ? > > > > The MobyService has the method setInput, which requires MobyData... and i > > couldnt get any connection from MobyData to MobyObject (to set the > > namespace > > then to GenBank or whatsoever). > > > > So how can I tell the service which MobyObjects I want to use or how can > > I find services with a given input and / or ouput ? > > > > Thanks > > obedient Andreas > > > > -- > > Andreas Groscurth > > Diplom Bioinformatik - PhD Student > > Max Planck Institute for Plant Breeding Research > > Carl-von-Linn?-Weg 10 > > 50829 Cologne > > Germany > > E-mail: ? ?groscurt at mpiz-koeln.mpg.de > > Phone: ? ?+49(0)221-5062-447 > > > > _______________________________________________ > > 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 -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From groscurt at mpiz-koeln.mpg.de Fri Jul 6 09:47:27 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 6 Jul 2007 15:47:27 +0200 Subject: [MOBY-dev] findService... how to ? In-Reply-To: <200707061458.35954.groscurt@mpiz-koeln.mpg.de> References: <467AD616.2010806@ucalgary.ca> <001701c7ba4e$b5d2e060$6400a8c0@notebook> <200707061458.35954.groscurt@mpiz-koeln.mpg.de> Message-ID: <200707061547.27461.groscurt@mpiz-koeln.mpg.de> Hi, i keep the list busy ;-) its just... I dont quite understand the findservice method.... as far as I understood it - with the following I get all services which has an image as output and an AGI Locuscode as input MobyDataObject object = new MobyDataObject( "" ); object.setPrimaryNamespace( new MobyNamespace( "AGI_LocusCode" ) ); service.addInput( object ); MobyDataObject dataObject = new MobyDataObject( "SimpleAnnotatedJPEGImage" ); MobyDataObjectSet set = new MobyDataObjectSet( "" ); set.add( dataObject ); service.addOutput( set ); MobyService[] services = central.findService( service, null, false, false ); this is an extract of what I get back Service getTairRefsByAgi Service getGOAccsByAGICode Service genefarmGetGeneIDByAGI Service PhytoprotGetByAGICode Service getReporterImageByAGI_dev Service getPMCIDsByAGI why getPMCIDsByAGI ? why getGOAccsByAGICode ? and so on both das not have any SimpleAnnotatedJPEGImage anywhere written.... Thanks Andreas From edward.kawas at gmail.com Fri Jul 6 10:39:45 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 6 Jul 2007 07:39:45 -0700 Subject: [MOBY-dev] findService... how to ? In-Reply-To: <200707061547.27461.groscurt@mpiz-koeln.mpg.de> References: <467AD616.2010806@ucalgary.ca><001701c7ba4e$b5d2e060$6400a8c0@notebook><200707061458.35954.groscurt@mpiz-koeln.mpg.de> <200707061547.27461.groscurt@mpiz-koeln.mpg.de> Message-ID: <000e01c7bfdb$7f85b2c0$6400a8c0@notebook> Hi Andreas, I am not sure of the problem, but when you look at the debugger, the inputs and outputs are not being set up properly and so I think that is why the results are as you are seeing them. Perhaps Paul or Martin can comment. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: Friday, July 06, 2007 6:47 AM > To: Core developer announcements > Subject: [MOBY-dev] findService... how to ? > > Hi, > > i keep the list busy ;-) > > its just... I dont quite understand the findservice method.... > > as far as I understood it - with the following I get all services which > has an > image as output and an AGI Locuscode as input > > MobyDataObject object = new MobyDataObject( "" ); > object.setPrimaryNamespace( new MobyNamespace( "AGI_LocusCode" ) ); > service.addInput( object ); > MobyDataObject dataObject = new MobyDataObject( "SimpleAnnotatedJPEGImage" > ); > MobyDataObjectSet set = new MobyDataObjectSet( "" ); > set.add( dataObject ); > service.addOutput( set ); > > MobyService[] services = central.findService( service, null, false, false > ); > > this is an extract of what I get back > > Service getTairRefsByAgi > Service getGOAccsByAGICode > Service genefarmGetGeneIDByAGI > Service PhytoprotGetByAGICode > Service getReporterImageByAGI_dev > Service getPMCIDsByAGI > > why getPMCIDsByAGI ? why getGOAccsByAGICode ? and so on > both das not have any SimpleAnnotatedJPEGImage anywhere written.... > > Thanks > Andreas > _______________________________________________ > 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 Fri Jul 6 14:37:26 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 06 Jul 2007 12:37:26 -0600 Subject: [MOBY-dev] findService... how to ? In-Reply-To: <200707061547.27461.groscurt@mpiz-koeln.mpg.de> References: <467AD616.2010806@ucalgary.ca> <001701c7ba4e$b5d2e060$6400a8c0@notebook> <200707061458.35954.groscurt@mpiz-koeln.mpg.de> <200707061547.27461.groscurt@mpiz-koeln.mpg.de> Message-ID: <468E8BE6.2080409@ucalgary.ca> Hi Andreas, For the returned object, you are asking for any object at all (you happen to name it "SimpleAnnotatedJPEGImage". MobyDataObject is ONLY for base objects. The constructor you want is the one for non-primitives of the ontology, MobyDataComposite... MobyDataObject dataObject = new MobyDataComposite("SimpleAnnotatedJPEGImage"); > Hi, > > i keep the list busy ;-) > > its just... I dont quite understand the findservice method.... > > as far as I understood it - with the following I get all services which has an > image as output and an AGI Locuscode as input > > MobyDataObject object = new MobyDataObject( "" ); > object.setPrimaryNamespace( new MobyNamespace( "AGI_LocusCode" ) ); > service.addInput( object ); > MobyDataObject dataObject = new MobyDataObject( "SimpleAnnotatedJPEGImage" ); > MobyDataObjectSet set = new MobyDataObjectSet( "" ); > set.add( dataObject ); > service.addOutput( set ); > > MobyService[] services = central.findService( service, null, false, false ); > > this is an extract of what I get back > > Service getTairRefsByAgi > Service getGOAccsByAGICode > Service genefarmGetGeneIDByAGI > Service PhytoprotGetByAGICode > Service getReporterImageByAGI_dev > Service getPMCIDsByAGI > > why getPMCIDsByAGI ? why getGOAccsByAGICode ? and so on > both das not have any SimpleAnnotatedJPEGImage anywhere written.... > > Thanks > Andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,468e4685802139014536! > > > > From markw at illuminae.com Sat Jul 7 20:32:30 2007 From: markw at illuminae.com (mark wilkinson) Date: Sun, 8 Jul 2007 00:32:30 +0000 GMT Subject: [MOBY-dev] Urgent re-request Message-ID: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> So far I have only 5 responses from the ~40 "authors" on the paper. I need your affiliation information ASAP please!!! Thanks! Mark -- Mark Wilkinson ...on the road! From usadel at mpimp-golm.mpg.de Mon Jul 9 05:42:12 2007 From: usadel at mpimp-golm.mpg.de (=?ISO-8859-1?Q?Bj=F6rn_Usadel?=) Date: Mon, 09 Jul 2007 11:42:12 +0200 Subject: [MOBY-dev] Urgent re-request In-Reply-To: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> References: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> Message-ID: <469202F4.7010109@mpimp-golm.mpg.de> Hi Mark, if nothing happens, why don't you just post the missing authors here, and we share the affiliation finding work? Cheers, Bj?rn mark wilkinson wrote: > So far I have only 5 responses from the ~40 "authors" on the paper. > > I need your affiliation information ASAP please!!! > > Thanks! > > Mark > -- > Mark Wilkinson > ...on the road! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From Pieter.Neerincx at wur.nl Mon Jul 9 07:20:36 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 9 Jul 2007 13:20:36 +0200 Subject: [MOBY-dev] Urgent re-request In-Reply-To: <469202F4.7010109@mpimp-golm.mpg.de> References: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> <469202F4.7010109@mpimp-golm.mpg.de> Message-ID: <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> On 9-Jul-2007, at 11:42 AM, Bj?rn Usadel wrote: > Hi Mark, > > if nothing happens, why don't you just post the missing authors here, > and we share the affiliation finding work? Good plan. In large parts of Europe the summer holiday periods have started so some of the authors missing might be unplugged for a while... Cheers, Pi > > Cheers, > Bj?rn > > mark wilkinson wrote: >> So far I have only 5 responses from the ~40 "authors" on the paper. >> >> I need your affiliation information ASAP please!!! >> >> Thanks! >> >> Mark >> -- >> Mark Wilkinson >> ...on the road! >> _______________________________________________ >> 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 ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Pieter.Neerincx at wur.nl Mon Jul 9 09:02:00 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 9 Jul 2007 15:02:00 +0200 Subject: [MOBY-dev] BioMOBY at ISMB 2007 Vienna? In-Reply-To: <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> References: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> <469202F4.7010109@mpimp-golm.mpg.de> <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> Message-ID: <78625869-CC68-4DF8-B21C-DB81BACA12A5@wur.nl> Hi, I was wondering who's joining for ISMB this year. I heard from a reliable source Mark will be missing again :(, but Martin will represent BioMOBY at BOSC again :) (one of the SIGs that precede ISMB/ ECCB). Furthermore I know there will be at least one poster at ISMB with a big BioMOBY logo :) as my pipeline heavily relies on this technology, but I expect there will be 800+ posters, so it would be great if there are more to advertise BioMOBY! If there are others joining either for one of the SIGs or the main conference we might organise a small informal BioMOBY gathering... Cheers, Pi ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From martin.senger at gmail.com Mon Jul 9 17:44:39 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 9 Jul 2007 22:44:39 +0100 Subject: [MOBY-dev] BioMOBY at ISMB 2007 Vienna? In-Reply-To: <78625869-CC68-4DF8-B21C-DB81BACA12A5@wur.nl> References: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> <469202F4.7010109@mpimp-golm.mpg.de> <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> <78625869-CC68-4DF8-B21C-DB81BACA12A5@wur.nl> Message-ID: <4d93f07c0707091444i239f676k8fa3d56aaa775a4c@mail.gmail.com> > Mark will be missing again :(, but Martin will > represent BioMOBY at BOSC again :) I confirm that your source has a correct information :-) Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Mon Jul 9 19:11:20 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 09 Jul 2007 16:11:20 -0700 Subject: [MOBY-dev] Urgent re-request In-Reply-To: <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> References: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> <469202F4.7010109@mpimp-golm.mpg.de> <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> Message-ID: >> if nothing happens, why don't you just post the missing authors here, >> and we share the affiliation finding work? Okay, that's a good idea. I'll compile what I have and then put the rest of them out to the community for help. I'm still struggling with writing a response to this review. There are a few valid points where we clearly missed talking about some issue or another, but most of it is... very very odd! I find myself writing and re-writing paragraphs trying to understand what the question is, and eventually find myself simply copy/pasting quotes out of the manuscript itself! Case in point - the reviewer asks for a concrete example of BioMoby passing a legacy data-type, in a comment where they refer to the paragraph about the object ontology. Well... in that EXACT paragraph there is not only a concrete example in the text of that paragraph (EMBL), but there is also a reference to a figure where the concrete XML for an EMBL object is written-out longhand! I am not usually defensive when I get reviews, but this one has me completely baffled! I simply don't understand what the reviewer is asking/expecting us to change... I don't suppose it is sufficient to say "in response to your comments and questions, please read the manuscript again" ;-) ;-) I am, however, tempted to ask PLoS ONE to try harder to get a second reviewer, since I don't think this reviewer represents our intended target-audience... (and being reviewed by one person isn't really a robust review, in my opinion) Anyway, I'm going to try to have a polite and attentive response finished by Wednesday to send out to you all for comment. Cheers! M On Mon, 09 Jul 2007 04:20:36 -0700, Pieter Neerincx wrote: > > On 9-Jul-2007, at 11:42 AM, Bj?rn Usadel wrote: > >> Hi Mark, >> > > Good plan. In large parts of Europe the summer holiday periods have > started so some of the authors missing might be unplugged for a while... > > Cheers, > > Pi > >> >> Cheers, >> Bj?rn >> >> mark wilkinson wrote: >>> So far I have only 5 responses from the ~40 "authors" on the paper. >>> >>> I need your affiliation information ASAP please!!! >>> >>> Thanks! >>> >>> Mark >>> -- >>> Mark Wilkinson >>> ...on the road! >>> _______________________________________________ >>> 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 > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From gordonp at ucalgary.ca Wed Jul 11 15:59:10 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 11 Jul 2007 13:59:10 -0600 Subject: [MOBY-dev] Experimental applet Message-ID: <4695368E.7070702@ucalgary.ca> Hi all, I've redeployed Seahawk using a Java 1.5 technology called pack200 (thanks to Dmitry Repchevski for the tip). Now the applet is 1.3MB instead of 4.4MB. I've posted it at http://moby.ucalgary.ca/seahawk/pack.html. Please let me know if you have any issues launching it. If not, I'll update the main Seahawk site on Monday. Regards, Paul From groscurt at mpiz-koeln.mpg.de Mon Jul 16 09:14:11 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 16 Jul 2007 15:14:11 +0200 Subject: [MOBY-dev] SOAPException while calling a service In-Reply-To: <4695368E.7070702@ucalgary.ca> References: <4695368E.7070702@ucalgary.ca> Message-ID: <200707161514.11642.groscurt@mpiz-koeln.mpg.de> hi, I try to call the SUBA_AGI2Publications webservice, which works fine via the dashboard, with the basic Java client MobyRequest request = new MobyRequest( central ); request.setService( service ); request.setInput( new MobyDataObject( "AGI_LocusCode", "At1g01040" ) ); MobyContentInstance contents = request.invokeService(); // .... in the last line i get an exception: Exception in thread "main" org.biomoby.shared.SOAPException: While invoking SOAP Call: Call to a member function attributes() on a non-object at org.biomoby.client.MobyRequest.performSOAPRequest(MobyRequest.java:532) what exactly does it mean and what do I do wrong ? Thanks Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From gordonp at ucalgary.ca Tue Jul 17 12:09:25 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 17 Jul 2007 10:09:25 -0600 Subject: [MOBY-dev] SOAPException while calling a service In-Reply-To: <200707161514.11642.groscurt@mpiz-koeln.mpg.de> References: <4695368E.7070702@ucalgary.ca> <200707161514.11642.groscurt@mpiz-koeln.mpg.de> Message-ID: <469CE9B5.2080804@ucalgary.ca> Hi Andreas, The error seems to be in Axis parsing the XML message returned by the service. How is this service being provided? > hi, > > I try to call the SUBA_AGI2Publications webservice, which works fine via the > dashboard, with the basic Java client > > MobyRequest request = new MobyRequest( central ); > request.setService( service ); > request.setInput( new MobyDataObject( "AGI_LocusCode", "At1g01040" ) ); > MobyContentInstance contents = request.invokeService(); > // .... > > in the last line i get an exception: > > Exception in thread "main" org.biomoby.shared.SOAPException: While invoking > SOAP Call: Call to a member function attributes() on a non-object > at org.biomoby.client.MobyRequest.performSOAPRequest(MobyRequest.java:532) > > what exactly does it mean and what do I do wrong ? > > Thanks > Andreas > > From groscurt at mpiz-koeln.mpg.de Thu Jul 19 03:07:09 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Thu, 19 Jul 2007 09:07:09 +0200 (CEST) Subject: [MOBY-dev] SOAPException while calling a service In-Reply-To: <469CE9B5.2080804@ucalgary.ca> References: <4695368E.7070702@ucalgary.ca> <200707161514.11642.groscurt@mpiz-koeln.mpg.de> <469CE9B5.2080804@ucalgary.ca> Message-ID: <2248.217.19.47.130.1184828829.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi Paul, what exactly you mean with 'how is this service being provided' ? As far as I know its a PHP Webservice normally registered at the production central. As I mentioned, calling in dashboard it works, strangely not in the basic Java client.... Thanks Andreas > Hi Andreas, > > The error seems to be in Axis parsing the XML message returned by the > service. > How is this service being provided? >> hi, >> >> I try to call the SUBA_AGI2Publications webservice, which works fine via >> the >> dashboard, with the basic Java client >> >> MobyRequest request = new MobyRequest( central ); >> request.setService( service ); >> request.setInput( new MobyDataObject( "AGI_LocusCode", "At1g01040" ) ); >> MobyContentInstance contents = request.invokeService(); >> // .... >> >> in the last line i get an exception: >> >> Exception in thread "main" org.biomoby.shared.SOAPException: While >> invoking >> SOAP Call: Call to a member function attributes() on a non-object >> at >> org.biomoby.client.MobyRequest.performSOAPRequest(MobyRequest.java:532) >> >> what exactly does it mean and what do I do wrong ? >> >> Thanks >> Andreas >> >> > > _______________________________________________ > 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 Thu Jul 19 08:58:52 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 19 Jul 2007 06:58:52 -0600 Subject: [MOBY-dev] SOAPException while calling a service In-Reply-To: <2248.217.19.47.130.1184828829.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <4695368E.7070702@ucalgary.ca> <200707161514.11642.groscurt@mpiz-koeln.mpg.de> <469CE9B5.2080804@ucalgary.ca> <2248.217.19.47.130.1184828829.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <469F600C.4090402@ucalgary.ca> Hi Andreas, What I mean it, is it a MoSeS service? A MobyServlet? A straight Perl MOBY Service? The error is happening when Axis parses the response message from the service. This is strange that it works in Dashboard, since it uses Axis too I thought (though maybe it uses a different version??) > Hi Paul, > > what exactly you mean with 'how is this service being provided' ? > > As far as I know its a PHP Webservice normally registered at the > production central. As I mentioned, calling in dashboard it works, > strangely not in the basic Java client.... > > Thanks > Andreas > > > >> Hi Andreas, >> >> The error seems to be in Axis parsing the XML message returned by the >> service. >> How is this service being provided? >> >>> hi, >>> >>> I try to call the SUBA_AGI2Publications webservice, which works fine via >>> the >>> dashboard, with the basic Java client >>> >>> MobyRequest request = new MobyRequest( central ); >>> request.setService( service ); >>> request.setInput( new MobyDataObject( "AGI_LocusCode", "At1g01040" ) ); >>> MobyContentInstance contents = request.invokeService(); >>> // .... >>> >>> in the last line i get an exception: >>> >>> Exception in thread "main" org.biomoby.shared.SOAPException: While >>> invoking >>> SOAP Call: Call to a member function attributes() on a non-object >>> at >>> org.biomoby.client.MobyRequest.performSOAPRequest(MobyRequest.java:532) >>> >>> what exactly does it mean and what do I do wrong ? >>> >>> Thanks >>> Andreas >>> >>> >>> >> _______________________________________________ >> 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 > > !DSPAM:60005,469f15368021626625063! > > > > From aloraine at gmail.com Fri Jul 27 12:23:57 2007 From: aloraine at gmail.com (Ann Loraine) Date: Fri, 27 Jul 2007 11:23:57 -0500 Subject: [MOBY-dev] can you help? need to cite Message-ID: <83722dde0707270923t25937dc9n9b1770870ed37565@mail.gmail.com> Dear all, I'm being a bit lazy by asking for your help rather than doing a lit search - my apologies! I'm writing an article which mentions BioMoby, and I would like to cite some publications that discuss applications that use BioMoby. I of course thought immediately of the Taverna software, and I found some citations for Taverna, but I wonder if you could point me to articles describing service aggregators or other applications utlizing BioMoby. (If these are not yet published in a traditional journals, that is fine...URLs will probably work just as well!) Thank you very much for your time. Yours, Ann From markw at illuminae.com Fri Jul 27 13:03:31 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 27 Jul 2007 10:03:31 -0700 Subject: [MOBY-dev] can you help? need to cite In-Reply-To: <83722dde0707270923t25937dc9n9b1770870ed37565@mail.gmail.com> References: <83722dde0707270923t25937dc9n9b1770870ed37565@mail.gmail.com> Message-ID: http://biomoby.open-bio.org/index.php/what-is-moby/publications this is a pretty comprehensive list... Hope that helps! :-) M On Fri, 27 Jul 2007 09:23:57 -0700, Ann Loraine wrote: > Dear all, > > I'm being a bit lazy by asking for your help rather than doing a lit > search - my apologies! > > I'm writing an article which mentions BioMoby, and I would like to > cite some publications that discuss applications that use BioMoby. I > of course thought immediately of the Taverna software, and I found > some citations for Taverna, but I wonder if you could point me to > articles describing service aggregators or other applications utlizing > BioMoby. (If these are not yet published in a traditional journals, > that is fine...URLs will probably work just as well!) > > Thank you very much for your time. > > Yours, > > Ann > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From aloraine at gmail.com Fri Jul 27 13:30:35 2007 From: aloraine at gmail.com (Ann Loraine) Date: Fri, 27 Jul 2007 12:30:35 -0500 Subject: [MOBY-dev] can you help? need to cite In-Reply-To: References: <83722dde0707270923t25937dc9n9b1770870ed37565@mail.gmail.com> Message-ID: <83722dde0707271030s44c72339hdb380957a7b5090d@mail.gmail.com> Yes it does - thanks! -Ann On 7/27/07, Mark Wilkinson wrote: > http://biomoby.open-bio.org/index.php/what-is-moby/publications > > this is a pretty comprehensive list... > > Hope that helps! :-) > > M > > > > On Fri, 27 Jul 2007 09:23:57 -0700, Ann Loraine wrote: > > > Dear all, > > > > I'm being a bit lazy by asking for your help rather than doing a lit > > search - my apologies! > > > > I'm writing an article which mentions BioMoby, and I would like to > > cite some publications that discuss applications that use BioMoby. I > > of course thought immediately of the Taverna software, and I found > > some citations for Taverna, but I wonder if you could point me to > > articles describing service aggregators or other applications utlizing > > BioMoby. (If these are not yet published in a traditional journals, > > that is fine...URLs will probably work just as well!) > > > > Thank you very much for your time. > > > > Yours, > > > > Ann > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Ann Loraine Assistant Professor University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From haase_dirk at web.de Fri Jul 27 15:34:13 2007 From: haase_dirk at web.de (Dirk Haase) Date: Fri, 27 Jul 2007 21:34:13 +0200 Subject: [MOBY-dev] can you help? need to cite Message-ID: <1148697625@web.de> Hi Ann, > Dear all, > > I'm being a bit lazy by asking for your help rather than doing a lit > search - my apologies! > > I'm writing an article which mentions BioMoby, and I would like to > cite some publications that discuss applications that use BioMoby. I > of course thought immediately of the Taverna software, and I found > some citations for Taverna, but I wonder if you could point me to > articles describing service aggregators or other applications utlizing > BioMoby. (If these are not yet published in a traditional journals, > that is fine...URLs will probably work just as well!) Just because you asked specifically for aggregators, I'd like to point you to the applications linked on http://bioinfo.mpiz-koeln.mpg.de/araws/searchtools/searchtoolsoverview which unfortunately did not work when I tried a minute ago :-| Mark, is there a problem with MOBY Central? It seems the aggregators don't find any service. Best, dirk From markw at illuminae.com Fri Jul 27 18:36:53 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 27 Jul 2007 15:36:53 -0700 Subject: [MOBY-dev] can you help? need to cite In-Reply-To: <1148697625@web.de> References: <1148697625@web.de> Message-ID: I'm not aware of anything wrong with M.C. it's been working for me all day...??? I just checked the encyclopaedia and the services you are asking for are not registered (in fact, there are *no* services registered to mips.gsf.de!!) ??? perhaps the agent couldn't access your RDF ??? M On Fri, 27 Jul 2007 12:34:13 -0700, Dirk Haase wrote: > Hi Ann, > >> Dear all, >> >> I'm being a bit lazy by asking for your help rather than doing a lit >> search - my apologies! >> >> I'm writing an article which mentions BioMoby, and I would like to >> cite some publications that discuss applications that use BioMoby. I >> of course thought immediately of the Taverna software, and I found >> some citations for Taverna, but I wonder if you could point me to >> articles describing service aggregators or other applications utlizing >> BioMoby. (If these are not yet published in a traditional journals, >> that is fine...URLs will probably work just as well!) > > Just because you asked specifically for aggregators, I'd like to point > you to the applications linked on > http://bioinfo.mpiz-koeln.mpg.de/araws/searchtools/searchtoolsoverview > > which unfortunately did not work when I tried a minute ago :-| > > Mark, is there a problem with MOBY Central? It seems the aggregators > don't find any service. > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From haase_dirk at web.de Sat Jul 28 09:09:23 2007 From: haase_dirk at web.de (Dirk Haase) Date: Sat, 28 Jul 2007 15:09:23 +0200 Subject: [MOBY-dev] can you help? need to cite Message-ID: <1148851010@web.de> Hi Mark, > I'm not aware of anything wrong with M.C. it's been working for me all > day...??? > > I just checked the encyclopaedia and the services you are asking for are > not registered (in fact, there are *no* services registered to > mips.gsf.de!!) Oh, that's bad. Thanks for investigation! > ??? perhaps the agent couldn't access your RDF ??? No, the RDFs are still accessible. Don't know what's going on. I'll try to find someone in charge on Monday. The loss of all MIPS services would be a serious pity :-| Thanks for help. Cheers, dirk From groscurt at mpiz-koeln.mpg.de Mon Jul 30 05:49:53 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 30 Jul 2007 11:49:53 +0200 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: <1148851010@web.de> References: <1148851010@web.de> Message-ID: <200707301149.53557.groscurt@mpiz-koeln.mpg.de> Hi, yes all the services are gone :( Any progress in recovering them ? Cheers Andreas On Saturday 28 July 2007 15:09, Dirk Haase wrote: > Hi Mark, > > > I'm not aware of anything wrong with M.C. it's been working for me all > > day...??? > > > > I just checked the encyclopaedia and the services you are asking for are > > not registered (in fact, there are *no* services registered to > > mips.gsf.de!!) > > Oh, that's bad. Thanks for investigation! > > > ??? perhaps the agent couldn't access your RDF ??? > > No, the RDFs are still accessible. Don't know what's going on. I'll try to > find someone in charge on Monday. The loss of all MIPS services would > be a serious pity :-| > > Thanks for help. > > Cheers, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From markw at illuminae.com Mon Jul 30 07:23:17 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 30 Jul 2007 04:23:17 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: <200707301149.53557.groscurt@mpiz-koeln.mpg.de> References: <1148851010@web.de> <200707301149.53557.groscurt@mpiz-koeln.mpg.de> Message-ID: Eddie, is the agent able to see the MIPS Signature RDF? M On Mon, 30 Jul 2007 02:49:53 -0700, Andreas Groscurth wrote: > Hi, > > yes all the services are gone :( > > Any progress in recovering them ? > > Cheers > Andreas > > On Saturday 28 July 2007 15:09, Dirk Haase wrote: >> Hi Mark, >> >> > I'm not aware of anything wrong with M.C. it's been working for me >> all >> > day...??? >> > >> > I just checked the encyclopaedia and the services you are asking for >> are >> > not registered (in fact, there are *no* services registered to >> > mips.gsf.de!!) >> >> Oh, that's bad. Thanks for investigation! >> >> > ??? perhaps the agent couldn't access your RDF ??? >> >> No, the RDFs are still accessible. Don't know what's going on. I'll try >> to >> find someone in charge on Monday. The loss of all MIPS services would >> be a serious pity :-| >> >> Thanks for help. >> >> Cheers, >> dirk >> _______________________________________________ >> 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 Mon Jul 30 08:22:50 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 05:22:50 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: References: <1148851010@web.de> <200707301149.53557.groscurt@mpiz-koeln.mpg.de> Message-ID: <000601c7d2a4$58b33ec0$6400a8c0@notebook> I don't think that it was able to ... What is the URL to their document and I will tell the agent to try again. Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson > Sent: Monday, July 30, 2007 4:23 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] MIPS Services are lost > > Eddie, is the agent able to see the MIPS Signature RDF? > > M > > > > > On Mon, 30 Jul 2007 02:49:53 -0700, Andreas Groscurth > wrote: > > > Hi, > > > > yes all the services are gone :( > > > > Any progress in recovering them ? > > > > Cheers > > Andreas > > > > On Saturday 28 July 2007 15:09, Dirk Haase wrote: > >> Hi Mark, > >> > >> > I'm not aware of anything wrong with M.C. it's been working for me > >> all > >> > day...??? > >> > > >> > I just checked the encyclopaedia and the services you are asking for > >> are > >> > not registered (in fact, there are *no* services registered to > >> > mips.gsf.de!!) > >> > >> Oh, that's bad. Thanks for investigation! > >> > >> > ??? perhaps the agent couldn't access your RDF ??? > >> > >> No, the RDFs are still accessible. Don't know what's going on. I'll try > >> to > >> find someone in charge on Monday. The loss of all MIPS services would > >> be a serious pity :-| > >> > >> Thanks for help. > >> > >> Cheers, > >> dirk > >> _______________________________________________ > >> 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 From haase_dirk at web.de Mon Jul 30 08:46:52 2007 From: haase_dirk at web.de (Dirk Haase) Date: Mon, 30 Jul 2007 14:46:52 +0200 Subject: [MOBY-dev] MIPS Services are lost Message-ID: <1149221085@web.de> > I don't think that it was able to ... > > What is the URL to their document and I will tell the agent to try again. For the major part of the services there are separate RDFs with URLs following the pattern http://mips.gsf.de/proj/planet/moby/RDF/.rdf However, I'm not able to give a listing of services, sorry! I guess nobody from MIPS is currently looking at this list :-( Another multi-service RDF is accessible under http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf Eddie, can you see the original reason for de-registration, I mean if it was due to the RDFs not being accessible or if somebody did something about it? Best, dirk From edward.kawas at gmail.com Mon Jul 30 09:40:57 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 06:40:57 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: <1149221085@web.de> References: <1149221085@web.de> Message-ID: <000701c7d2af$42c401c0$6400a8c0@notebook> Hi, The agent deleted the services because there 'was a problem processing the url'. It couldn't read from it (or something like that). Anyways, I found the following urls: http://mips.gsf.de/proj/planet/moby/RDF/getSplicedSequence.rdf http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf http://mips.gsf.de/proj/planet/moby/RDF/getElement.rdf http://mips.gsf.de/proj/planet/moby/RDF/getMIPSArabidopsisAnnotationAsGFF3.r df http://mips.gsf.de/proj/planet/moby/RDF/getElementsByName.rdf http://mips.gsf.de/proj/planet/moby/RDF/getClonesByName.rdf http://mips.gsf.de/proj/planet/moby/RDF/getClonesByFreeText.rdf http://mips.gsf.de/proj/planet/moby/RDF/getElementsOfType.rdf http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementNameByFreeText.rdf http://mips.gsf.de/proj/planet/moby/RDF/getJICGeneTrapImageByAgi.rdf http://mips.gsf.de/proj/planet/moby/RDF/getProteinSequence.rdf http://mips.gsf.de/proj/planet/moby/RDF/getElementAnnotation.rdf http://mips.gsf.de/proj/planet/moby/RDF/getClonesForChromosome.rdf http://mips.gsf.de/proj/planet/moby/RDF/getAllGeneticElements.rdf http://mips.gsf.de/proj/planet/moby/RDF/getUnsplicedSequence.rdf http://mips.gsf.de/proj/planet/moby/RDF/getElementsForContig.rdf http://mips.gsf.de/proj/planet/moby/RDF/getElementsByFreeText.rdf http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementsOfType.rdf http://mips.gsf.de/proj/planet/moby/RDF/getContigsByName.rdf http://mips.gsf.de/proj/planet/moby/RDF/getContigsByFreeText.rdf and the agent has been called on all of them. If some are missing, please let me know. After I processed them I looked into the log and the agent was able to read and process the contents of the files ... Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Monday, July 30, 2007 5:47 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] MIPS Services are lost > > > I don't think that it was able to ... > > > > What is the URL to their document and I will tell the agent to try > again. > > For the major part of the services there are separate RDFs with URLs > following the pattern > http://mips.gsf.de/proj/planet/moby/RDF/.rdf > > However, I'm not able to give a listing of services, sorry! I guess > nobody from MIPS is currently looking at this list :-( > > Another multi-service RDF is accessible under > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > > Eddie, can you see the original reason for de-registration, I mean if > it was due to the RDFs not being accessible or if somebody > did something about it? > > Best, > dirk > _______________________________________________ > 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 Mon Jul 30 09:43:45 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 30 Jul 2007 06:43:45 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: <000701c7d2af$42c401c0$6400a8c0@notebook> References: <1149221085@web.de> <000701c7d2af$42c401c0$6400a8c0@notebook> Message-ID: The agent normally sends an email to the owner of the service to tell them what happened... who is the contact for these services? They should have been alerted that the agent couldn't find the RDF for several days before it actually deleted them from the registry... M On Mon, 30 Jul 2007 06:40:57 -0700, Edward Kawas wrote: > Hi, > > The agent deleted the services because there 'was a problem processing > the > url'. It couldn't read from it (or something like that). > > Anyways, I found the following urls: > http://mips.gsf.de/proj/planet/moby/RDF/getSplicedSequence.rdf > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getElement.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getMIPSArabidopsisAnnotationAsGFF3.r > df > http://mips.gsf.de/proj/planet/moby/RDF/getElementsByName.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getClonesByName.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getClonesByFreeText.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getElementsOfType.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementNameByFreeText.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getJICGeneTrapImageByAgi.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getProteinSequence.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getElementAnnotation.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getClonesForChromosome.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getAllGeneticElements.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getUnsplicedSequence.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getElementsForContig.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getElementsByFreeText.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementsOfType.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getContigsByName.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getContigsByFreeText.rdf > > and the agent has been called on all of them. If some are missing, please > let me know. > > After I processed them I looked into the log and the agent was able to > read > and process the contents of the files ... > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Dirk Haase >> Sent: Monday, July 30, 2007 5:47 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] MIPS Services are lost >> >> > I don't think that it was able to ... >> > >> > What is the URL to their document and I will tell the agent to try >> again. >> >> For the major part of the services there are separate RDFs with URLs >> following the pattern >> http://mips.gsf.de/proj/planet/moby/RDF/.rdf >> >> However, I'm not able to give a listing of services, sorry! I guess >> nobody from MIPS is currently looking at this list :-( >> >> Another multi-service RDF is accessible under >> http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf >> >> Eddie, can you see the original reason for de-registration, I mean if >> it was due to the RDFs not being accessible or if somebody >> did something about it? >> >> Best, >> dirk >> _______________________________________________ >> 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 From edward.kawas at gmail.com Mon Jul 30 09:45:22 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 06:45:22 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: References: <1149221085@web.de> <000701c7d2af$42c401c0$6400a8c0@notebook> Message-ID: <000b01c7d2af$e0d20b00$6400a8c0@notebook> The address most prevalent is: Octave.Noubibou at gsf.de Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson > Sent: Monday, July 30, 2007 6:44 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] MIPS Services are lost > > The agent normally sends an email to the owner of the service to tell them > what happened... who is the contact for these services? They should have > been alerted that the agent couldn't find the RDF for several days before > it actually deleted them from the registry... > > M > > > > On Mon, 30 Jul 2007 06:40:57 -0700, Edward Kawas > wrote: > > > Hi, > > > > The agent deleted the services because there 'was a problem processing > > the > > url'. It couldn't read from it (or something like that). > > > > Anyways, I found the following urls: > > http://mips.gsf.de/proj/planet/moby/RDF/getSplicedSequence.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getElement.rdf > > > http://mips.gsf.de/proj/planet/moby/RDF/getMIPSArabidopsisAnnotationAsGFF3 > .r > > df > > http://mips.gsf.de/proj/planet/moby/RDF/getElementsByName.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getClonesByName.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getClonesByFreeText.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getElementsOfType.rdf > > > http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementNameByFreeText.rd > f > > http://mips.gsf.de/proj/planet/moby/RDF/getJICGeneTrapImageByAgi.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getProteinSequence.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getElementAnnotation.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getClonesForChromosome.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getAllGeneticElements.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getUnsplicedSequence.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getElementsForContig.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getElementsByFreeText.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementsOfType.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getContigsByName.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getContigsByFreeText.rdf > > > > and the agent has been called on all of them. If some are missing, > please > > let me know. > > > > After I processed them I looked into the log and the agent was able to > > read > > and process the contents of the files ... > > > > Eddie > > > > > >> -----Original Message----- > >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > >> bounces at lists.open-bio.org] On Behalf Of Dirk Haase > >> Sent: Monday, July 30, 2007 5:47 AM > >> To: Core developer announcements > >> Subject: Re: [MOBY-dev] MIPS Services are lost > >> > >> > I don't think that it was able to ... > >> > > >> > What is the URL to their document and I will tell the agent to try > >> again. > >> > >> For the major part of the services there are separate RDFs with URLs > >> following the pattern > >> http://mips.gsf.de/proj/planet/moby/RDF/.rdf > >> > >> However, I'm not able to give a listing of services, sorry! I guess > >> nobody from MIPS is currently looking at this list :-( > >> > >> Another multi-service RDF is accessible under > >> http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > >> > >> Eddie, can you see the original reason for de-registration, I mean if > >> it was due to the RDFs not being accessible or if somebody > >> did something about it? > >> > >> Best, > >> dirk > >> _______________________________________________ > >> 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 > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From haase_dirk at web.de Mon Jul 30 10:00:29 2007 From: haase_dirk at web.de (Dirk Haase) Date: Mon, 30 Jul 2007 16:00:29 +0200 Subject: [MOBY-dev] MIPS Services are lost Message-ID: <1149242476@web.de> > The address most prevalent is: > > Octave.Noubibou at gsf.de Yes and Octave left MIPS several weeks ago. So either the mails were ignored or not even delivered. Could the latter be the reason for the instant de-registration? In the meantime I managed to talk to the responsible person at MIPS and he is not aware of any longer offline periods. However I asked him to replace the contact mail addresses in the RDFs with something more useful. Best, dirk From edward.kawas at gmail.com Mon Jul 30 10:02:58 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 07:02:58 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: <1149242476@web.de> References: <1149242476@web.de> Message-ID: <000c01c7d2b2$5613d360$6400a8c0@notebook> The messages returned undeliverable, but that wouldn't cause the agent to deregister them instantaneously. In the meantime, I will keep an eye on the mips services. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Monday, July 30, 2007 7:00 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] MIPS Services are lost > > > The address most prevalent is: > > > > Octave.Noubibou at gsf.de > > Yes and Octave left MIPS several weeks ago. So either the mails were > ignored or not even delivered. Could the latter be the reason for the > instant de-registration? In the meantime I managed to talk to the > responsible person at MIPS and he is not aware of any longer > offline periods. > > However I asked him to replace the contact mail addresses in the > RDFs with something more useful. > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Mon Jul 30 10:38:49 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 30 Jul 2007 16:38:49 +0200 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <000c01c7d2b2$5613d360$6400a8c0@notebook> References: <1149242476@web.de> <000c01c7d2b2$5613d360$6400a8c0@notebook> Message-ID: <200707301638.49459.groscurt@mpiz-koeln.mpg.de> Hi, I would like to address an issue we had discussed a little at the meeting in Vancouver, namely to enable the possibility for service providers to add their url (to their homepage) and a logo. This was based on the suggestions from the Tigr workshop, where the people wanted to have that, so if one is aggregating their service, is possible to link to the origin of the service. Actually there are two ways to do so (in my opinion): 1. Add the url to the homepage and the url to a logo into the service notes for each service result 2. Give the opportunity to enter this information while registering a service In case of 1. there are no changes needed in the API (neither perl nor java), if somewant wants to use this information they have to parse it from the service notes. in case of 2. the api has to change (and also all registration clients and probably the database....) to have methods to access these information and to enter or store them in the service objects (or however this is done with perl services) Intuitively - from a developer - I would suggest 2. because it sounds much more clearer to access and to store this information. Putting it into the service notes sounds more like a workaround ('ah... everything else is put there') - are there any other information in there ? how it is represented there ? and so on.. but I think I can see that point 1 is easier and sooner to use.... But I'm open for discussion. I can live with all ways :-) Best Andreas From edward.kawas at gmail.com Mon Jul 30 10:46:59 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 07:46:59 -0700 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <200707301638.49459.groscurt@mpiz-koeln.mpg.de> References: <1149242476@web.de> <000c01c7d2b2$5613d360$6400a8c0@notebook> <200707301638.49459.groscurt@mpiz-koeln.mpg.de> Message-ID: <000d01c7d2b8$7c460ed0$6400a8c0@notebook> Another way of doing this would be to modify the RDF metadata for a particular service. I haven't thought about this too deeply, but as a service provider, if I wish to augment the information in the RDF with extra information regarding my service, I am free to do so. So for example, imagine that we agree on a predicate like 'hasLogoURL'. Anybody wishing to show logos would only have to check for existence of that predicate in the RDF and behave accordingly. This wouldn't change the api. Having said that, I, being the fence sitter moby java developers know and love ;-), agree with Andreas and think that this information should be recorded at registration time. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: Monday, July 30, 2007 7:39 AM > To: Core developer announcements > Subject: [MOBY-dev] ServiceProvider URL and Logo > > Hi, > > I would like to address an issue we had discussed a little at the meeting > in > Vancouver, namely to enable the possibility for service providers to add > their url (to their homepage) and a logo. > This was based on the suggestions from the Tigr workshop, where the people > wanted to have that, so if one is aggregating their service, is possible > to > link to the origin of the service. > > Actually there are two ways to do so (in my opinion): > > 1. Add the url to the homepage and the url to a logo into the service > notes > for each service result > > 2. Give the opportunity to enter this information while registering a > service > > > In case of 1. there are no changes needed in the API (neither perl nor > java), > if somewant wants to use this information they have to parse it from the > service notes. > > in case of 2. the api has to change (and also all registration clients and > probably the database....) to have methods to access these information > and > to enter or store them in the service objects (or however this is done > with > perl services) > > Intuitively - from a developer - I would suggest 2. because it sounds much > more clearer to access and to store this information. Putting it into the > service notes sounds more like a workaround ('ah... everything else is put > there') - are there any other information in there ? how it is represented > there ? and so on.. but I think I can see that point 1 is easier and > sooner > to use.... > > But I'm open for discussion. I can live with all ways :-) > > Best > Andreas > _______________________________________________ > 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 Jul 30 10:49:03 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 30 Jul 2007 08:49:03 -0600 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <200707301638.49459.groscurt@mpiz-koeln.mpg.de> References: <1149242476@web.de> <000c01c7d2b2$5613d360$6400a8c0@notebook> <200707301638.49459.groscurt@mpiz-koeln.mpg.de> Message-ID: <46ADFA5F.6030204@ucalgary.ca> I am personally in favour of the serviceNotes option, since this gives you the flexibility to put any HTML you like (e.g. the SeqHound services display the citation to use). Of course, you could have both the free-form HTML and the logo protocol, but maybe client software would be less likely to show the former if the latter is a requirement... > Hi, > > I would like to address an issue we had discussed a little at the meeting in > Vancouver, namely to enable the possibility for service providers to add > their url (to their homepage) and a logo. > This was based on the suggestions from the Tigr workshop, where the people > wanted to have that, so if one is aggregating their service, is possible to > link to the origin of the service. > > Actually there are two ways to do so (in my opinion): > > 1. Add the url to the homepage and the url to a logo into the service notes > for each service result > > 2. Give the opportunity to enter this information while registering a service > > > In case of 1. there are no changes needed in the API (neither perl nor java), > if somewant wants to use this information they have to parse it from the > service notes. > > in case of 2. the api has to change (and also all registration clients and > probably the database....) to have methods to access these information and > to enter or store them in the service objects (or however this is done with > perl services) > > Intuitively - from a developer - I would suggest 2. because it sounds much > more clearer to access and to store this information. Putting it into the > service notes sounds more like a workaround ('ah... everything else is put > there') - are there any other information in there ? how it is represented > there ? and so on.. but I think I can see that point 1 is easier and sooner > to use.... > > But I'm open for discussion. I can live with all ways :-) > > Best > Andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,46adf68680211809920332! > > > > From gordonp at ucalgary.ca Mon Jul 30 10:52:58 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 30 Jul 2007 08:52:58 -0600 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <000d01c7d2b8$7c460ed0$6400a8c0@notebook> References: <1149242476@web.de> <000c01c7d2b2$5613d360$6400a8c0@notebook> <200707301638.49459.groscurt@mpiz-koeln.mpg.de> <000d01c7d2b8$7c460ed0$6400a8c0@notebook> Message-ID: <46ADFB4A.9070401@ucalgary.ca> I like the RDF metadata idea, Eddie! The registration process should only really include data required to run the service. A logo is definitely not core to running a service. If we start including things like the logo, we will be thinking of things to add to the registration process for years... > Another way of doing this would be to modify the RDF metadata for a > particular service. I haven't thought about this too deeply, but as a > service provider, if I wish to augment the information in the RDF with extra > information regarding my service, I am free to do so. So for example, > imagine that we agree on a predicate like 'hasLogoURL'. > > Anybody wishing to show logos would only have to check for existence of that > predicate in the RDF and behave accordingly. This wouldn't change the api. > > Having said that, I, being the fence sitter moby java developers know and > love ;-), agree with Andreas and think that this information should be > recorded at registration time. > > Eddie > > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth >> Sent: Monday, July 30, 2007 7:39 AM >> To: Core developer announcements >> Subject: [MOBY-dev] ServiceProvider URL and Logo >> >> Hi, >> >> I would like to address an issue we had discussed a little at the meeting >> in >> Vancouver, namely to enable the possibility for service providers to add >> their url (to their homepage) and a logo. >> This was based on the suggestions from the Tigr workshop, where the people >> wanted to have that, so if one is aggregating their service, is possible >> to >> link to the origin of the service. >> >> Actually there are two ways to do so (in my opinion): >> >> 1. Add the url to the homepage and the url to a logo into the service >> notes >> for each service result >> >> 2. Give the opportunity to enter this information while registering a >> service >> >> >> In case of 1. there are no changes needed in the API (neither perl nor >> java), >> if somewant wants to use this information they have to parse it from the >> service notes. >> >> in case of 2. the api has to change (and also all registration clients and >> probably the database....) to have methods to access these information >> and >> to enter or store them in the service objects (or however this is done >> with >> perl services) >> >> Intuitively - from a developer - I would suggest 2. because it sounds much >> more clearer to access and to store this information. Putting it into the >> service notes sounds more like a workaround ('ah... everything else is put >> there') - are there any other information in there ? how it is represented >> there ? and so on.. but I think I can see that point 1 is easier and >> sooner >> to use.... >> >> But I'm open for discussion. I can live with all ways :-) >> >> Best >> Andreas >> _______________________________________________ >> 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 > > !DSPAM:60005,46adf85f8021244901854! > > > > From edward.kawas at gmail.com Mon Jul 30 11:22:45 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 08:22:45 -0700 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <46ADFB4A.9070401@ucalgary.ca> References: <1149242476@web.de><000c01c7d2b2$5613d360$6400a8c0@notebook> <200707301638.49459.groscurt@mpiz-koeln.mpg.de><000d01c7d2b8$7c460ed0$6400a8c0@notebook> <46ADFB4A.9070401@ucalgary.ca> Message-ID: <000e01c7d2bd$7aec8000$6400a8c0@notebook> > A logo is definitely not core to running a service. If we start > including things like the logo, we will be thinking of things to add to > the > registration process for years... I thought about this, and I was going to comment on it. I am glad that you brought this up Paul. Eddie From groscurt at mpiz-koeln.mpg.de Mon Jul 30 11:37:01 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 30 Jul 2007 17:37:01 +0200 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <000e01c7d2bd$7aec8000$6400a8c0@notebook> References: <1149242476@web.de> <46ADFB4A.9070401@ucalgary.ca> <000e01c7d2bd$7aec8000$6400a8c0@notebook> Message-ID: <200707301737.02105.groscurt@mpiz-koeln.mpg.de> havent thought of this... thats right. but anyhow this should be done in an easy fashion for the service registration, so that service providers dont have to edit the rdf manually... and if its easily possible for a client to access these information - then... I like the idea :D Best Andreas On Monday 30 July 2007 17:22, Edward Kawas wrote: > > A logo is definitely not core to running a service. If we start > > including things like the logo, we will be thinking of things to add to > > the > > registration process for years... > > I thought about this, and I was going to comment on it. I am glad that you > brought this up Paul. > > Eddie > > _______________________________________________ > 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 Mon Jul 30 11:39:56 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 08:39:56 -0700 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <200707301737.02105.groscurt@mpiz-koeln.mpg.de> References: <1149242476@web.de> <46ADFB4A.9070401@ucalgary.ca><000e01c7d2bd$7aec8000$6400a8c0@notebook> <200707301737.02105.groscurt@mpiz-koeln.mpg.de> Message-ID: <000f01c7d2bf$e1fa6b20$6400a8c0@notebook> > and if its easily possible for a client to access these information - > then... > I like the idea :D If you resolve the LSID for a particular service, there is a service provider 'port' that has an HTTP "Get'able url that is the signatureURL for a service. So the information is reachable. Eddie From dmitry.repchevski at bsc.es Tue Jul 31 10:56:16 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 31 Jul 2007 16:56:16 +0200 Subject: [MOBY-dev] parameter name should not be namespace qualified Message-ID: <46AF4D90.3040309@bsc.es> Hello! I found the strange thing with Axis (tried v1.2.1 and 1.4). It puts a namespace onto a parameter. <*ns1:*arg0 xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" xsi:type="soapenc:string"> ... According guys from JBoss team this goes against the specification - they look for the parameter without any namespace so the service fails by not finding it. Guys from GlassFish also follows the same rule. I'm not sure does it matter now when we suppose to move into doc/literal encoding (away from axis)... Axis used to be very relaxed to the errors. For example it can call the service even if the parameter name doesn't match. I mean that perl client calls the request parameter "data", but DashBoard "arg0"... The question is can namespace for parameters be fixed easy? Dmitry From martin.senger at gmail.com Mon Jul 2 13:13:47 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 2 Jul 2007 14:13:47 +0100 Subject: [MOBY-dev] jMoby add a parameter into a message In-Reply-To: <4667C73B.7050604@bsc.es> References: <4667C73B.7050604@bsc.es> Message-ID: <4d93f07c0707020613j53426821x2b53b6bf0a9ff166@mail.gmail.com> Hi, looking into jMoby code I found different basic moby types (i.e. > MobyDataBoolean and MobyBoolean) There are two ways how to do things in jMoby. And both of them share some data types, but also have their own ones. Your code snippet uses Moses data types, therefore, your data type for Boolean would be org.biomoby.shared.datatypes.MobyBoolean. , but can't find a way to construct a > message: What is your error messages? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From groscurt at mpiz-koeln.mpg.de Tue Jul 3 12:46:19 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 3 Jul 2007 14:46:19 +0200 Subject: [MOBY-dev] Get Information from the XML / bug in MobyContentInstance ? In-Reply-To: References: <1140939448@web.de> Message-ID: <200707031446.19706.groscurt@mpiz-koeln.mpg.de> Hi all, i need your help again.... its still java ;-) I called the service, retrieved an XML and now ? how do i get to the information ? I use Pauls 'client' MobyRequest request = new MobyRequest(central); request.setService(service); request.setInput(new MobyDataObject("Global_Keyword", keyword)); MobyContentInstance queries = request.invokeService(); on the docu it is written, that MobyContentInstance is a Map and I could retrieve information from the map... mhm... I cant printing it out with System.out.println i get the correct xml. This service retrieves all AGI_Locus Codes related to a given keyword via BioRS from MAtDB (MIPS Arabidopsis thaliana database) as far as I can see through this the following code should be responsible for that -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From groscurt at mpiz-koeln.mpg.de Tue Jul 3 12:51:33 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 3 Jul 2007 14:51:33 +0200 Subject: [MOBY-dev] Getting out from XML.... Bug in MobyContentInstance ? In-Reply-To: References: <1140939448@web.de> Message-ID: <200707031451.33339.groscurt@mpiz-koeln.mpg.de> Hi all, I call a service with Pauls 'client' MobyRequest request = new MobyRequest(central); request.setService(service); request.setInput(new MobyDataObject("Global_Keyword", keyword)); MobyContentInstance instance = request.invokeService(); in the docu it says via MobyContentInstance I can retrieve my data... but it doesnt. printling the object via println i get the following xml This service retrieves all AGI_Locus Codes related to a given keyword via BioRS from MAtDB (MIPS Arabidopsis thaliana database) I debugged the MobyContentInstance and apparently in the line NodeList collections = MobyPrefixResolver.getChildElements(dataGroupTag, "Collection"); and after, it should parse the collection - put it doesnt.... the result is -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From groscurt at mpiz-koeln.mpg.de Tue Jul 3 12:55:58 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 3 Jul 2007 14:55:58 +0200 Subject: [MOBY-dev] get data from XML... or MobyContentInstance... bug ? In-Reply-To: References: <1140939448@web.de> Message-ID: <200707031455.58449.groscurt@mpiz-koeln.mpg.de> Hi all, I call a service via Pauls 'Client' MobyRequest request = new MobyRequest(central); request.setService(service); request.setInput(new MobyDataObject("Global_Keyword", keyword)); MobyContentInstance instance = request.invokeService(); using println on the MobyContentInstance I get the xml This service retrieves all AGI_Locus Codes related to a given keyword via BioRS from MAtDB (MIPS Arabidopsis thaliana database) but using the Java Api methods for MobyConstentInstance - there is nothing.... The map, which should give me my data, looks the following: {result_codes=Name: result_codes Elements in collection: } So... as far as I can see - something failes while parsing ?! Is this a bug or somewhere my fault ? And anyway... is there another way to get data from the XML besides parsing it by myself ? Thanks Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From groscurt at mpiz-koeln.mpg.de Tue Jul 3 12:57:19 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 3 Jul 2007 14:57:19 +0200 Subject: [MOBY-dev] Get Information from the XML / bug in MobyContentInstance ? In-Reply-To: <200707031446.19706.groscurt@mpiz-koeln.mpg.de> References: <1140939448@web.de> <200707031446.19706.groscurt@mpiz-koeln.mpg.de> Message-ID: <200707031457.19264.groscurt@mpiz-koeln.mpg.de> Hi... grrrrr... due to some problems with Kmail - you will get the same Bug-MobyContentInstance Mail several times :-( sorry for that... the last one "get data from XML... or MobyContentInstance... bug ?" is the correct and complete one :( Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From gordonp at ucalgary.ca Tue Jul 3 13:46:47 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 03 Jul 2007 07:46:47 -0600 Subject: [MOBY-dev] Get Information from the XML / bug in MobyContentInstance ? In-Reply-To: <200707031457.19264.groscurt@mpiz-koeln.mpg.de> References: <1140939448@web.de> <200707031446.19706.groscurt@mpiz-koeln.mpg.de> <200707031457.19264.groscurt@mpiz-koeln.mpg.de> Message-ID: <468A5347.5040504@ucalgary.ca> Hi Andreas, The issue is that you have 2 "modes" for toXML() in the package. Please see the "org.biomoby.shared.data Package In Anger" http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAnger.html This should explain how to do what you want succinctly. If not, let me know what's not clear, and I'll update the docs. Cheers! Paul > Hi... > > grrrrr... due to some problems with Kmail - you will get the same > Bug-MobyContentInstance Mail several times :-( > sorry for that... > > the last one "get data from XML... or MobyContentInstance... bug ?" is the > correct and complete one > > :( > Andreas > > From markw at illuminae.com Tue Jul 3 18:00:23 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 03 Jul 2007 11:00:23 -0700 Subject: [MOBY-dev] PLoS ONE Decision Message-ID: There was a single reviewer, who decided that the manuscript required major revisions. It's probably worthwhile discussing as a group what our response to the review will be. Here is the review: ==================== The manuscript ?Interoperability with Moby 1.0? deals in standardizing methodologies to facilitate information exchange and access to analytical resources. The manuscript provides the detailed development that has occurred in BioMoby. The authors present and discuss why BioMoby is a distinct from other semantic web services. Major Compulsory Revisions (that author must respond to before decision on publication is reached) To Authors: To begin with the paper is well written in terms of technical and implementation aspects. What I see is that author?s do not clearly present difference between the earlier versions with the current version of BioMoby. It would be really helpful if the authors could explain this using a concrete example to understand the functioning of the BioMoby framework. The paper looks more like a user manual with technical specification rather than any scientific implication to the readers. The authors could improve the paper by providing a strong biological input as motivation for developing such a framework. As I read through the paper I see the author?s speak about semantic web services. It would be interesting for the readers to know what the other semantic web services and how BioMoby is better. Is it possible for u to demonstrate it with an example? In the results section the author?s speak about Namespaces Ontology wherein there are 300 different Namespaces that includes prominent public data resources. It would be interesting to know weather BioMoby also supports PSI MI, MAGE standards that are also coming in from prominent databases. In the Object Ontology the author?s specify BioMoby framework can receive any data-type and it does not re-define the legacy of the data type. Please provide a more concrete example for this point. In BioMoby web services Second Paragraph the author?s say: ?The providers do not need to be concerned about the exact structure of incoming data and do not need to query the ever- changing BioMoby ontology?. 1. Justify this statement. 2. Summaries what are the BioMoby?s ontology?s that was present in the earlier and in the current version. 3. How can you compare it with the other semantic web services ontology?s? Justify how SOAP concept implemented in BioMoby is better than the others service providers that could improve the interoperability of the framework. Through out the paper the author?s have introduced various terms as ontology. It is quite misleading for me to associate these different ontology under one roof of BioMoby. [[does anyone understand what this comment means??]] Finally, I feel that BioMoby is one of the most prominent approaches in the bioinformatics community. The paper contains less scientific inputs and more technical inputs. The paper does not contain strong examples to validate various arguments. Hence the paper cannot be accepted in the current form. If the author?s could answer some of the question raised, that could make the paper more interesting and more relevant to the PLoS ONE readers. ============================ -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From groscurt at mpiz-koeln.mpg.de Wed Jul 4 06:42:43 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 4 Jul 2007 08:42:43 +0200 Subject: [MOBY-dev] Get Information from the XML / bug in MobyContentInstance ? In-Reply-To: <468A5347.5040504@ucalgary.ca> References: <1140939448@web.de> <200707031457.19264.groscurt@mpiz-koeln.mpg.de> <468A5347.5040504@ucalgary.ca> Message-ID: <200707040842.43828.groscurt@mpiz-koeln.mpg.de> Hi Paul and all, thanks... after some coding / testing and so on - I finally found it out :-) My problem now was the getValue / getID methods in the case of an Simple-Object... getValue of course does not return something... but getID does.... wonderful :) thanks Andreas On Tuesday 03 July 2007 15:46, Paul Gordon wrote: > Hi Andreas, > > The issue is that you have 2 "modes" for toXML() in the package. > > Please see the "org.biomoby.shared.data Package In Anger" > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAn >ger.html > > This should explain how to do what you want succinctly. If not, let me > know what's not clear, and I'll update the docs. > > Cheers! > > Paul > > > Hi... > > > > grrrrr... due to some problems with Kmail - you will get the same > > Bug-MobyContentInstance Mail several times :-( > > sorry for that... > > > > the last one "get data from XML... or MobyContentInstance... bug ?" is > > the correct and complete one > > > > :( > > > > Andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From duncan.hull at cs.man.ac.uk Wed Jul 4 10:08:13 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 04 Jul 2007 11:08:13 +0100 Subject: [MOBY-dev] PLoS ONE Decision: A nightmare on SOAP street In-Reply-To: References: Message-ID: <468B718D.3060605@cs.man.ac.uk> Mark Wilkinson wrote: > Justify how SOAP concept implemented in BioMoby is better than the > others service providers that could improve the interoperability of the > framework. SOAP intereroperability is a nightmare for everyone, you might need to be more specific about what you mean: http://www.cs.man.ac.uk/~hulld/q2007-02-06.html Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From duncan.hull at cs.man.ac.uk Wed Jul 4 09:56:33 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 04 Jul 2007 10:56:33 +0100 Subject: [MOBY-dev] PLoS ONE Decision: Semantic Web Services In-Reply-To: References: Message-ID: <468B6ED1.9040004@cs.man.ac.uk> Hello Mark Mark Wilkinson wrote: > 3. How can you compare it with the other semantic web services ontology?s? > I haven't seen the BioMOBY Plos One manuscipt recently but it sounds like it might benefit from an explanation of how BioMOBY is different to myGrid and AI-systems like WSMO and OWL-S: For example: 1. How is BioMOBYs approach is different to myGrid? I think the key differentiator here is tagging (BioMOBY style) vs. curation (myGrid style). Each approach has its own strengths and limitations, which we are familiar with... 2. How is BioMOBY different to OWL-S and WSMO for example? I think the key differentiator here is reasoning. Neither BioMOBY or myGrid currently use description logic reasoning in a way originally envisioned by the AI community: http://dx.doi.org/10.1109/5254.920599 http://eprints.ecs.soton.ac.uk/7606/ In these approaches, reasoning is used to improve matching (better precision and recall) and ranking (a query for a service produces hundreds of hits, how do you rank them?) Just my $0.02 HTH Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From duncan.hull at cs.man.ac.uk Wed Jul 4 09:56:33 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 04 Jul 2007 10:56:33 +0100 Subject: [MOBY-dev] PLoS ONE Decision: Semantic Web Services In-Reply-To: References: Message-ID: <468B6ED1.9040004@cs.man.ac.uk> Hello Mark Mark Wilkinson wrote: > 3. How can you compare it with the other semantic web services ontology?s? > I haven't seen the BioMOBY Plos One manuscipt recently but it sounds like it might benefit from an explanation of how BioMOBY is different to myGrid and AI-systems like WSMO and OWL-S: For example: 1. How is BioMOBYs approach is different to myGrid? I think the key differentiator here is tagging (BioMOBY style) vs. curation (myGrid style). Each approach has its own strengths and limitations, which we are familiar with... 2. How is BioMOBY different to OWL-S and WSMO for example? I think the key differentiator here is reasoning. Neither BioMOBY or myGrid currently use description logic reasoning in a way originally envisioned by the AI community: http://dx.doi.org/10.1109/5254.920599 http://eprints.ecs.soton.ac.uk/7606/ In these approaches, reasoning is used to improve matching (better precision and recall) and ranking (a query for a service produces hundreds of hits, how do you rank them?) Just my $0.02 HTH Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From groscurt at mpiz-koeln.mpg.de Wed Jul 4 11:28:20 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 4 Jul 2007 13:28:20 +0200 Subject: [MOBY-dev] caching data from MobyRequest In-Reply-To: <468A5347.5040504@ucalgary.ca> References: <1140939448@web.de> <200707031457.19264.groscurt@mpiz-koeln.mpg.de> <468A5347.5040504@ucalgary.ca> Message-ID: <200707041328.21160.groscurt@mpiz-koeln.mpg.de> Hi all, again paul, thanks for the answer, it works nicely. Just one interesst: everytime I call the service I get the following log ERROR [STDERR] Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/Objects ERROR [STDERR] ... done ERROR [STDERR] Fetching namespace ontology from http://biomoby.org/RESOURCES/MOBY-S/Namespaces ERROR [STDERR] There are 1 collections in response 1 is there a way to cache these data, so that the application does not need fetch it everytime ? Thanks Andreas On Tuesday 03 July 2007 15:46, Paul Gordon wrote: > Hi Andreas, > > The issue is that you have 2 "modes" for toXML() in the package. > > Please see the "org.biomoby.shared.data Package In Anger" > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAn >ger.html > > This should explain how to do what you want succinctly. If not, let me > know what's not clear, and I'll update the docs. > > Cheers! > > Paul > > > Hi... > > > > grrrrr... due to some problems with Kmail - you will get the same > > Bug-MobyContentInstance Mail several times :-( > > sorry for that... > > > > the last one "get data from XML... or MobyContentInstance... bug ?" is > > the correct and complete one > > > > :( > > > > Andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From gordonp at ucalgary.ca Wed Jul 4 13:50:26 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 04 Jul 2007 07:50:26 -0600 Subject: [MOBY-dev] caching data from MobyRequest In-Reply-To: <200707041328.21160.groscurt@mpiz-koeln.mpg.de> References: <1140939448@web.de> <200707031457.19264.groscurt@mpiz-koeln.mpg.de> <468A5347.5040504@ucalgary.ca> <200707041328.21160.groscurt@mpiz-koeln.mpg.de> Message-ID: <468BA5A2.3010801@ucalgary.ca> Hi Andreas, Yes, there is a class that allows you to cache these... *org.biomoby.registry.meta.RegistryCache* You can see how I use it in the source code for * ca.ucalgary.seahawk.gui.MobyContentGUI *Though I should probably add a doc about that too :-)* * > Hi all, > > again paul, thanks for the answer, it works nicely. > > Just one interesst: > > everytime I call the service I get the following log > > ERROR [STDERR] Fetching data type ontology from > http://biomoby.org/RESOURCES/MOBY-S/Objects > ERROR [STDERR] ... done > ERROR [STDERR] Fetching namespace ontology from > http://biomoby.org/RESOURCES/MOBY-S/Namespaces > ERROR [STDERR] There are 1 collections in response 1 > > is there a way to cache these data, so that the application does not need > fetch it everytime ? > > Thanks > Andreas > > > On Tuesday 03 July 2007 15:46, Paul Gordon wrote: > >> Hi Andreas, >> >> The issue is that you have 2 "modes" for toXML() in the package. >> >> Please see the "org.biomoby.shared.data Package In Anger" >> >> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAn >> ger.html >> >> This should explain how to do what you want succinctly. If not, let me >> know what's not clear, and I'll update the docs. >> >> Cheers! >> >> Paul >> >> >>> Hi... >>> >>> grrrrr... due to some problems with Kmail - you will get the same >>> Bug-MobyContentInstance Mail several times :-( >>> sorry for that... >>> >>> the last one "get data from XML... or MobyContentInstance... bug ?" is >>> the correct and complete one >>> >>> :( >>> >>> Andreas >>> >> _______________________________________________ >> 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 Wed Jul 4 15:45:51 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 04 Jul 2007 08:45:51 -0700 Subject: [MOBY-dev] URGENT! affiliations required Message-ID: Hi all, PLoS ONE has requested that we add all affiliations for all members of the consortium, despite them not being explicitly listed as authors. Please, to save me having to look-up and type this all myself, could everyone please do the following for everyone that is on the author list of the paper: in the following format: Surname, Initial, institution, address, email. Please send me the info for every author in your "domain". Thanks! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From duncan.hull at cs.man.ac.uk Wed Jul 4 16:03:36 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 04 Jul 2007 17:03:36 +0100 Subject: [MOBY-dev] BioMOBY and myGrid In-Reply-To: <468B6ED1.9040004@cs.man.ac.uk> References: <468B6ED1.9040004@cs.man.ac.uk> Message-ID: <468BC4D8.70508@cs.man.ac.uk> Hello Duncan Hull wrote: > 1. How is BioMOBYs approach is different to myGrid? I think the key > differentiator here is tagging (BioMOBY style) vs. curation (myGrid > style). Each approach has its own strengths and limitations, which we > are familiar with... > ...but the journal reviewers are probably not familiar with these strengths and limitations, so they would be worth stating. They are fairly obvious, but if you want my list, I'm happy to pass it on. Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From markw at illuminae.com Wed Jul 4 17:02:12 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 04 Jul 2007 10:02:12 -0700 Subject: [MOBY-dev] BioMOBY and myGrid In-Reply-To: <468BC4D8.70508@cs.man.ac.uk> References: <468B6ED1.9040004@cs.man.ac.uk> <468BC4D8.70508@cs.man.ac.uk> Message-ID: Hi Duncan, Thanks for the offer! If you could provide that list I will incorporate it into the text and add you as an "author" :-) (actually, NOT having you as an author was a bit of an embarrassing oversight anyway, given that you have now done two graduate degrees studying meta-Moby!) M On Wed, 04 Jul 2007 09:03:36 -0700, Duncan Hull wrote: > Hello > > Duncan Hull wrote: >> 1. How is BioMOBYs approach is different to myGrid? I think the key >> differentiator here is tagging (BioMOBY style) vs. curation (myGrid >> style). Each approach has its own strengths and limitations, which we >> are familiar with... >> > > ...but the journal reviewers are probably not familiar with these > strengths and limitations, so they would be worth stating. > > They are fairly obvious, but if you want my list, I'm happy to pass it > on. > > Duncan > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From Pieter.Neerincx at wur.nl Wed Jul 4 19:16:08 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Wed, 04 Jul 2007 21:16:08 +0200 Subject: [MOBY-dev] PLoS ONE Decision In-Reply-To: References: Message-ID: Hi, On 03 Jul 2007, at 20:00, Mark Wilkinson wrote: > There was a single reviewer, Huh, a single reviewer? That doesn't sound very professional :(. I thought they called it PLoS *One* for different reasons :) > who decided that the manuscript required > major revisions. It's probably worthwhile discussing as a group > what our > response to the review will be. Here's my ? 0.02... > Here is the review: > > ==================== > The manuscript ?Interoperability with Moby 1.0? deals in standardizing > methodologies to facilitate information exchange and access to > analytical > resources. The manuscript provides the detailed development that has > occurred in BioMoby. The authors present and discuss why BioMoby is a > distinct from other semantic web services. > > Major Compulsory Revisions (that author must respond to before > decision > on publication is reached) > > To Authors: > > To begin with the paper is well written in terms of technical and > implementation aspects. > > What I see is that author?s do not clearly present difference > between the > earlier versions with the current version of BioMoby. Well this is officially the first version as in 1.0 isn't it?. This is a first "milestone" release, so there is not much to compare it with. Of course BioMOBY has been slowly evolving as a beta in several labs, but which CVS date should we compare against? Compared to version 0.0 every feature in BioMOBY is a new feature: so it's a major improvement :). Doesn't make much sense to me... If they insist on a comparison we might compare the current state of art with what was described in "BioMOBY: an open-source biological web services proposal" by Wilkinson, MD, Links, M. (2002). That's the oldest publication on BioMOBY a.f.a.i.k. > It would be really > helpful if the authors could explain this using a concrete example to > understand the functioning of the BioMoby framework. > > The paper looks more like a user manual with technical > specification rather > than any scientific implication to the readers. The authors could > improve > the > paper by providing a strong biological input as motivation for > developing > such a framework. > > As I read through the paper I see the author?s speak about semantic > web > services. It would be interesting for the readers to know what the > other > semantic web services and how BioMoby is better. Is it possible for > u to > demonstrate it with an example? If I understand the items above correctly, what the reviewer wants to see is basically a good example case, that clearly shows the advantages of BioMOBY and the differences between BioMOBY and other web service technology. When I read this I'm thinking of the graph on the front page: the one that says "Tired of this? ... Try This!". Maybe we can make such a comparison between the way too many Biologist in the lab have their work slowly flowing and the kind of workflow you can make with BioMOBY. > In the results section the author?s speak about Namespaces Ontology > wherein there are 300 different Namespaces that includes prominent > public > data resources. It would be interesting to know weather BioMoby also > supports PSI MI, MAGE standards that are also coming in from prominent > databases. Correct me if I'm wrong, but as far as I know we support any namespace: just register thing if it wasn't already. Maybe it is not clear enough though that BioMOBY allows you to support *any* namespace or kind of data format you like. Whether or not datatypes and/or namespaces for a certain standard have already been registered or not is not crucially important in my opinion, but if PLoS insists certain standards must be there to make BioMOBY interesting enough for their readers, I can easily create a small script that registers them... (Just hope they do not insist there are also services that actually use those objects and namespaces, because that will be a lot more work.) > In the Object Ontology the author?s specify BioMoby framework can > receive any data-type and it does not re-define the legacy of the data > type. > Please provide a more concrete example for this point. > In BioMoby web services Second Paragraph the author?s say: > ?The providers do not need to be concerned about the exact > structure of > incoming data and do not need to query the ever- changing BioMoby > ontology?. > > 1. Justify this statement. > > 2. Summaries what are the BioMoby?s ontology?s that was present in the > earlier and in the current version. > > 3. How can you compare it with the other semantic web services > ontology?s? > > Justify how SOAP concept implemented in BioMoby is better than the > others service providers that could improve the interoperability of > the > framework. > > Through out the paper the author?s have introduced various terms as > ontology. It is quite misleading for me to associate these different > ontology > under one roof of BioMoby. [[does anyone understand what this > comment > means??]] For me BioMOBY is a collection of several tools, frameworks/ libraries, concepts, a community and several ontologies. We have a namespace ontology, an object ontology and a service ontology. Although these are strongly related they do not share the same root. Maybe it's not clear to the reviewer what BioMOBY exactly is. To be honest it's not a bad question... According to "What is BioMOBY from the website BioMOBY: "The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next." Hence it's a messaging standard. That does not include the ontologies, the libraries, etc. It's only the standard, so the part labelled on the website as "Latest MOBY Services API". Maybe we should be more clear on what is all included when we talk about BioMOBY... Not sure if this is what the reviewer was complaining about, but it's the best I can make from the comment... > Finally, I feel that BioMoby is one of the most prominent > approaches in the > bioinformatics community. The paper contains less scientific inputs > and > more technical inputs. The paper does not contain strong examples to > validate various arguments. > > Hence the paper cannot be accepted in the current form. If the > author?s > could > answer some of the question raised, that could make the paper more > interesting and more relevant to the PLoS ONE readers. Cheers, Pi > ============================ > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have > received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From duncan.hull at cs.man.ac.uk Thu Jul 5 15:02:58 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Thu, 05 Jul 2007 16:02:58 +0100 Subject: [MOBY-dev] BioMOBY and myGrid: my $0.02 In-Reply-To: References: <468B6ED1.9040004@cs.man.ac.uk> <468BC4D8.70508@cs.man.ac.uk> Message-ID: <468D0822.4010506@cs.man.ac.uk> Hi Mark Mark Wilkinson wrote: > Thanks for the offer! If you could provide that list I will > incorporate it into the text and add you as an "author" :-) Well you've probably thought of all these already, but in case you missed any, here they are: (Your mileage may vary of course...) Pros for tagging, BioMOBY style: ======================== + Low barrier to adoption + Allows many people to annotate services + Wisdom of crowds, potentially captures more consensual knowledge Cons for tagging, BioMOBY style ======================== + The wisdom of crowds is always "close to madness" [1], you can cite Alcuin on that one! + Can produce a large quantity of low quality metadata, what the Flickr people call "noisy metadata" [2] + Difficult to precisely and accurately query registry Pros for curation, myGrid style ====================== + Less noise in service metadata + Potentially more coherent unified view + Higher quality (?), lower coverage Cons for curation, myGrid style ====================== - Services not annotated by default, as with BioMOBY - Restricts the number of people who can annotate services - Labour intensive - Time consuming - Expensive - Captures a smaller world view, the "wisdom of the curator" rather than the "wisdom of the service provider" > (actually, NOT having you as an author was a bit of an embarrassing > oversight anyway, given that you have now done two graduate degrees > studying meta-Moby!) The third degree isn't in the bag just yet ;) While we're at it... Pros for DL reasoning during service discovery ================================= + More intelligent matchmaking e.g. + Better precision + Better recall + Ability to rank services which are otherwise unrankable (without invading users privacy). + Rank by degree of match between request and advertisement [3]) + Analagous to an "Advanced Search" http://www.google.co.uk/advanced_search?hl=en Cons for DL reasoning during service discovery ================================= - Queries have to be written either in SPARQL or as OWL class expressions - Few people used "Advanced Search" features - Requires detailed annotation of services using OWL - Issues with scaling If any of this doesn't make sense, let me know and I can clarify. Duncan [1] http://www.cs.man.ac.uk/~hulld/q2004-02-11.html [2] http://dx.doi.org/10.1145/1125451.1125462 [3] http://eprints.ecs.soton.ac.uk/7606/ -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From Usadel at mpimp-golm.mpg.de Thu Jul 5 16:55:59 2007 From: Usadel at mpimp-golm.mpg.de (Bjoern Usadel) Date: Thu, 5 Jul 2007 18:55:59 +0200 Subject: [MOBY-dev] BioMOBY PLOS One: comparison to earlier releases References: <468B6ED1.9040004@cs.man.ac.uk> <468BC4D8.70508@cs.man.ac.uk> <468D0822.4010506@cs.man.ac.uk> Message-ID: <8233DF2244998040848283889E22DBA0864C04@MAIL.mpimp-golm.mpg.de> Hi All, concerning the comparison to earlier versions, one could also consider a comparison to Biomoby 0.8.2 which is the latest (at least) perl release available as a tarball and which I am always tempted to get :-) Cheers, Bjoern -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 2673 bytes Desc: not available URL: From groscurt at mpiz-koeln.mpg.de Fri Jul 6 12:58:35 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 6 Jul 2007 14:58:35 +0200 Subject: [MOBY-dev] Another Java API question In-Reply-To: <001701c7ba4e$b5d2e060$6400a8c0@notebook> References: <467AD616.2010806@ucalgary.ca> <200706291505.27668.groscurt@mpiz-koeln.mpg.de> <001701c7ba4e$b5d2e060$6400a8c0@notebook> Message-ID: <200707061458.35954.groscurt@mpiz-koeln.mpg.de> Hi all, based on eddies answer below... I just wanted to know if I understood it correctly MobyDataObjectSet set = new MobyDataObjectSet(""); set.add(data); s.addOutput(set); with this I get all services which returns a collection... right ? if i write s.addOutput(data) I get only services which exactly return one object... right ? and if I want all services which return both - object and collection - can I write s.addOutput(set); s.addOutput(data) ? thanks for helping me through the jungel Andreas On Friday 29 June 2007 15:09, Edward Kawas wrote: > Hi Andreas, > > Hopefully this helps you out! > CentralImpl central = new CentralImpl(); > MobyService s = new MobyService(); > s.setCategory(""); > MobyDataObject data = new MobyDataObject(""); > data.setDataType(new MobyDataType("Object")); > data.addNamespace(new MobyNamespace("NCBI_gi")); > MobyDataObjectSet set = new MobyDataObjectSet(""); > set.add(data); > s.addOutput((set)); > MobyService[] services = central.findService(s,null,true,false); > > Eddie > > > -----Original Message----- > > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > > Sent: Friday, June 29, 2007 6:05 AM > > To: Core developer announcements > > Subject: [MOBY-dev] Another Java API question > > > > Hi all again, > > > > I couldnt find anything about this, so I hope you can help me with this > > simple > > one: > > > > Actually I only want to find services with specific informations, e.g. I > > want > > to find all services with a specific input or output namespace and so on. > > > > I fail by creating a service with my needs. > > > > The way I thought of doing it is to create a Central instance and call > > the findService method with a MobyService as parameter. > > My current problem is how to tell the Mobyservice which inputs it has to > > consume ? > > > > E.g. how to tell that I want an GenBank identifier as input ? > > > > The MobyService has the method setInput, which requires MobyData... and i > > couldnt get any connection from MobyData to MobyObject (to set the > > namespace > > then to GenBank or whatsoever). > > > > So how can I tell the service which MobyObjects I want to use or how can > > I find services with a given input and / or ouput ? > > > > Thanks > > obedient Andreas > > > > -- > > Andreas Groscurth > > Diplom Bioinformatik - PhD Student > > Max Planck Institute for Plant Breeding Research > > Carl-von-Linn?-Weg 10 > > 50829 Cologne > > Germany > > E-mail: ? ?groscurt at mpiz-koeln.mpg.de > > Phone: ? ?+49(0)221-5062-447 > > > > _______________________________________________ > > 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 -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From groscurt at mpiz-koeln.mpg.de Fri Jul 6 13:47:27 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 6 Jul 2007 15:47:27 +0200 Subject: [MOBY-dev] findService... how to ? In-Reply-To: <200707061458.35954.groscurt@mpiz-koeln.mpg.de> References: <467AD616.2010806@ucalgary.ca> <001701c7ba4e$b5d2e060$6400a8c0@notebook> <200707061458.35954.groscurt@mpiz-koeln.mpg.de> Message-ID: <200707061547.27461.groscurt@mpiz-koeln.mpg.de> Hi, i keep the list busy ;-) its just... I dont quite understand the findservice method.... as far as I understood it - with the following I get all services which has an image as output and an AGI Locuscode as input MobyDataObject object = new MobyDataObject( "" ); object.setPrimaryNamespace( new MobyNamespace( "AGI_LocusCode" ) ); service.addInput( object ); MobyDataObject dataObject = new MobyDataObject( "SimpleAnnotatedJPEGImage" ); MobyDataObjectSet set = new MobyDataObjectSet( "" ); set.add( dataObject ); service.addOutput( set ); MobyService[] services = central.findService( service, null, false, false ); this is an extract of what I get back Service getTairRefsByAgi Service getGOAccsByAGICode Service genefarmGetGeneIDByAGI Service PhytoprotGetByAGICode Service getReporterImageByAGI_dev Service getPMCIDsByAGI why getPMCIDsByAGI ? why getGOAccsByAGICode ? and so on both das not have any SimpleAnnotatedJPEGImage anywhere written.... Thanks Andreas From edward.kawas at gmail.com Fri Jul 6 14:39:45 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 6 Jul 2007 07:39:45 -0700 Subject: [MOBY-dev] findService... how to ? In-Reply-To: <200707061547.27461.groscurt@mpiz-koeln.mpg.de> References: <467AD616.2010806@ucalgary.ca><001701c7ba4e$b5d2e060$6400a8c0@notebook><200707061458.35954.groscurt@mpiz-koeln.mpg.de> <200707061547.27461.groscurt@mpiz-koeln.mpg.de> Message-ID: <000e01c7bfdb$7f85b2c0$6400a8c0@notebook> Hi Andreas, I am not sure of the problem, but when you look at the debugger, the inputs and outputs are not being set up properly and so I think that is why the results are as you are seeing them. Perhaps Paul or Martin can comment. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: Friday, July 06, 2007 6:47 AM > To: Core developer announcements > Subject: [MOBY-dev] findService... how to ? > > Hi, > > i keep the list busy ;-) > > its just... I dont quite understand the findservice method.... > > as far as I understood it - with the following I get all services which > has an > image as output and an AGI Locuscode as input > > MobyDataObject object = new MobyDataObject( "" ); > object.setPrimaryNamespace( new MobyNamespace( "AGI_LocusCode" ) ); > service.addInput( object ); > MobyDataObject dataObject = new MobyDataObject( "SimpleAnnotatedJPEGImage" > ); > MobyDataObjectSet set = new MobyDataObjectSet( "" ); > set.add( dataObject ); > service.addOutput( set ); > > MobyService[] services = central.findService( service, null, false, false > ); > > this is an extract of what I get back > > Service getTairRefsByAgi > Service getGOAccsByAGICode > Service genefarmGetGeneIDByAGI > Service PhytoprotGetByAGICode > Service getReporterImageByAGI_dev > Service getPMCIDsByAGI > > why getPMCIDsByAGI ? why getGOAccsByAGICode ? and so on > both das not have any SimpleAnnotatedJPEGImage anywhere written.... > > Thanks > Andreas > _______________________________________________ > 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 Fri Jul 6 18:37:26 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 06 Jul 2007 12:37:26 -0600 Subject: [MOBY-dev] findService... how to ? In-Reply-To: <200707061547.27461.groscurt@mpiz-koeln.mpg.de> References: <467AD616.2010806@ucalgary.ca> <001701c7ba4e$b5d2e060$6400a8c0@notebook> <200707061458.35954.groscurt@mpiz-koeln.mpg.de> <200707061547.27461.groscurt@mpiz-koeln.mpg.de> Message-ID: <468E8BE6.2080409@ucalgary.ca> Hi Andreas, For the returned object, you are asking for any object at all (you happen to name it "SimpleAnnotatedJPEGImage". MobyDataObject is ONLY for base objects. The constructor you want is the one for non-primitives of the ontology, MobyDataComposite... MobyDataObject dataObject = new MobyDataComposite("SimpleAnnotatedJPEGImage"); > Hi, > > i keep the list busy ;-) > > its just... I dont quite understand the findservice method.... > > as far as I understood it - with the following I get all services which has an > image as output and an AGI Locuscode as input > > MobyDataObject object = new MobyDataObject( "" ); > object.setPrimaryNamespace( new MobyNamespace( "AGI_LocusCode" ) ); > service.addInput( object ); > MobyDataObject dataObject = new MobyDataObject( "SimpleAnnotatedJPEGImage" ); > MobyDataObjectSet set = new MobyDataObjectSet( "" ); > set.add( dataObject ); > service.addOutput( set ); > > MobyService[] services = central.findService( service, null, false, false ); > > this is an extract of what I get back > > Service getTairRefsByAgi > Service getGOAccsByAGICode > Service genefarmGetGeneIDByAGI > Service PhytoprotGetByAGICode > Service getReporterImageByAGI_dev > Service getPMCIDsByAGI > > why getPMCIDsByAGI ? why getGOAccsByAGICode ? and so on > both das not have any SimpleAnnotatedJPEGImage anywhere written.... > > Thanks > Andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,468e4685802139014536! > > > > From markw at illuminae.com Sun Jul 8 00:32:30 2007 From: markw at illuminae.com (mark wilkinson) Date: Sun, 8 Jul 2007 00:32:30 +0000 GMT Subject: [MOBY-dev] Urgent re-request Message-ID: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> So far I have only 5 responses from the ~40 "authors" on the paper. I need your affiliation information ASAP please!!! Thanks! Mark -- Mark Wilkinson ...on the road! From usadel at mpimp-golm.mpg.de Mon Jul 9 09:42:12 2007 From: usadel at mpimp-golm.mpg.de (=?ISO-8859-1?Q?Bj=F6rn_Usadel?=) Date: Mon, 09 Jul 2007 11:42:12 +0200 Subject: [MOBY-dev] Urgent re-request In-Reply-To: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> References: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> Message-ID: <469202F4.7010109@mpimp-golm.mpg.de> Hi Mark, if nothing happens, why don't you just post the missing authors here, and we share the affiliation finding work? Cheers, Bj?rn mark wilkinson wrote: > So far I have only 5 responses from the ~40 "authors" on the paper. > > I need your affiliation information ASAP please!!! > > Thanks! > > Mark > -- > Mark Wilkinson > ...on the road! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From Pieter.Neerincx at wur.nl Mon Jul 9 11:20:36 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 9 Jul 2007 13:20:36 +0200 Subject: [MOBY-dev] Urgent re-request In-Reply-To: <469202F4.7010109@mpimp-golm.mpg.de> References: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> <469202F4.7010109@mpimp-golm.mpg.de> Message-ID: <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> On 9-Jul-2007, at 11:42 AM, Bj?rn Usadel wrote: > Hi Mark, > > if nothing happens, why don't you just post the missing authors here, > and we share the affiliation finding work? Good plan. In large parts of Europe the summer holiday periods have started so some of the authors missing might be unplugged for a while... Cheers, Pi > > Cheers, > Bj?rn > > mark wilkinson wrote: >> So far I have only 5 responses from the ~40 "authors" on the paper. >> >> I need your affiliation information ASAP please!!! >> >> Thanks! >> >> Mark >> -- >> Mark Wilkinson >> ...on the road! >> _______________________________________________ >> 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 ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Pieter.Neerincx at wur.nl Mon Jul 9 13:02:00 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 9 Jul 2007 15:02:00 +0200 Subject: [MOBY-dev] BioMOBY at ISMB 2007 Vienna? In-Reply-To: <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> References: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> <469202F4.7010109@mpimp-golm.mpg.de> <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> Message-ID: <78625869-CC68-4DF8-B21C-DB81BACA12A5@wur.nl> Hi, I was wondering who's joining for ISMB this year. I heard from a reliable source Mark will be missing again :(, but Martin will represent BioMOBY at BOSC again :) (one of the SIGs that precede ISMB/ ECCB). Furthermore I know there will be at least one poster at ISMB with a big BioMOBY logo :) as my pipeline heavily relies on this technology, but I expect there will be 800+ posters, so it would be great if there are more to advertise BioMOBY! If there are others joining either for one of the SIGs or the main conference we might organise a small informal BioMOBY gathering... Cheers, Pi ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From martin.senger at gmail.com Mon Jul 9 21:44:39 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 9 Jul 2007 22:44:39 +0100 Subject: [MOBY-dev] BioMOBY at ISMB 2007 Vienna? In-Reply-To: <78625869-CC68-4DF8-B21C-DB81BACA12A5@wur.nl> References: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> <469202F4.7010109@mpimp-golm.mpg.de> <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> <78625869-CC68-4DF8-B21C-DB81BACA12A5@wur.nl> Message-ID: <4d93f07c0707091444i239f676k8fa3d56aaa775a4c@mail.gmail.com> > Mark will be missing again :(, but Martin will > represent BioMOBY at BOSC again :) I confirm that your source has a correct information :-) Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Mon Jul 9 23:11:20 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 09 Jul 2007 16:11:20 -0700 Subject: [MOBY-dev] Urgent re-request In-Reply-To: <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> References: <2006130777-1183854770-cardhu_blackberry.rim.net-21991-@engine18-cell01> <469202F4.7010109@mpimp-golm.mpg.de> <1723BE26-857A-4908-941E-4010A86ADD58@wur.nl> Message-ID: >> if nothing happens, why don't you just post the missing authors here, >> and we share the affiliation finding work? Okay, that's a good idea. I'll compile what I have and then put the rest of them out to the community for help. I'm still struggling with writing a response to this review. There are a few valid points where we clearly missed talking about some issue or another, but most of it is... very very odd! I find myself writing and re-writing paragraphs trying to understand what the question is, and eventually find myself simply copy/pasting quotes out of the manuscript itself! Case in point - the reviewer asks for a concrete example of BioMoby passing a legacy data-type, in a comment where they refer to the paragraph about the object ontology. Well... in that EXACT paragraph there is not only a concrete example in the text of that paragraph (EMBL), but there is also a reference to a figure where the concrete XML for an EMBL object is written-out longhand! I am not usually defensive when I get reviews, but this one has me completely baffled! I simply don't understand what the reviewer is asking/expecting us to change... I don't suppose it is sufficient to say "in response to your comments and questions, please read the manuscript again" ;-) ;-) I am, however, tempted to ask PLoS ONE to try harder to get a second reviewer, since I don't think this reviewer represents our intended target-audience... (and being reviewed by one person isn't really a robust review, in my opinion) Anyway, I'm going to try to have a polite and attentive response finished by Wednesday to send out to you all for comment. Cheers! M On Mon, 09 Jul 2007 04:20:36 -0700, Pieter Neerincx wrote: > > On 9-Jul-2007, at 11:42 AM, Bj?rn Usadel wrote: > >> Hi Mark, >> > > Good plan. In large parts of Europe the summer holiday periods have > started so some of the authors missing might be unplugged for a while... > > Cheers, > > Pi > >> >> Cheers, >> Bj?rn >> >> mark wilkinson wrote: >>> So far I have only 5 responses from the ~40 "authors" on the paper. >>> >>> I need your affiliation information ASAP please!!! >>> >>> Thanks! >>> >>> Mark >>> -- >>> Mark Wilkinson >>> ...on the road! >>> _______________________________________________ >>> 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 > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From gordonp at ucalgary.ca Wed Jul 11 19:59:10 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 11 Jul 2007 13:59:10 -0600 Subject: [MOBY-dev] Experimental applet Message-ID: <4695368E.7070702@ucalgary.ca> Hi all, I've redeployed Seahawk using a Java 1.5 technology called pack200 (thanks to Dmitry Repchevski for the tip). Now the applet is 1.3MB instead of 4.4MB. I've posted it at http://moby.ucalgary.ca/seahawk/pack.html. Please let me know if you have any issues launching it. If not, I'll update the main Seahawk site on Monday. Regards, Paul From groscurt at mpiz-koeln.mpg.de Mon Jul 16 13:14:11 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 16 Jul 2007 15:14:11 +0200 Subject: [MOBY-dev] SOAPException while calling a service In-Reply-To: <4695368E.7070702@ucalgary.ca> References: <4695368E.7070702@ucalgary.ca> Message-ID: <200707161514.11642.groscurt@mpiz-koeln.mpg.de> hi, I try to call the SUBA_AGI2Publications webservice, which works fine via the dashboard, with the basic Java client MobyRequest request = new MobyRequest( central ); request.setService( service ); request.setInput( new MobyDataObject( "AGI_LocusCode", "At1g01040" ) ); MobyContentInstance contents = request.invokeService(); // .... in the last line i get an exception: Exception in thread "main" org.biomoby.shared.SOAPException: While invoking SOAP Call: Call to a member function attributes() on a non-object at org.biomoby.client.MobyRequest.performSOAPRequest(MobyRequest.java:532) what exactly does it mean and what do I do wrong ? Thanks Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From gordonp at ucalgary.ca Tue Jul 17 16:09:25 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 17 Jul 2007 10:09:25 -0600 Subject: [MOBY-dev] SOAPException while calling a service In-Reply-To: <200707161514.11642.groscurt@mpiz-koeln.mpg.de> References: <4695368E.7070702@ucalgary.ca> <200707161514.11642.groscurt@mpiz-koeln.mpg.de> Message-ID: <469CE9B5.2080804@ucalgary.ca> Hi Andreas, The error seems to be in Axis parsing the XML message returned by the service. How is this service being provided? > hi, > > I try to call the SUBA_AGI2Publications webservice, which works fine via the > dashboard, with the basic Java client > > MobyRequest request = new MobyRequest( central ); > request.setService( service ); > request.setInput( new MobyDataObject( "AGI_LocusCode", "At1g01040" ) ); > MobyContentInstance contents = request.invokeService(); > // .... > > in the last line i get an exception: > > Exception in thread "main" org.biomoby.shared.SOAPException: While invoking > SOAP Call: Call to a member function attributes() on a non-object > at org.biomoby.client.MobyRequest.performSOAPRequest(MobyRequest.java:532) > > what exactly does it mean and what do I do wrong ? > > Thanks > Andreas > > From groscurt at mpiz-koeln.mpg.de Thu Jul 19 07:07:09 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Thu, 19 Jul 2007 09:07:09 +0200 (CEST) Subject: [MOBY-dev] SOAPException while calling a service In-Reply-To: <469CE9B5.2080804@ucalgary.ca> References: <4695368E.7070702@ucalgary.ca> <200707161514.11642.groscurt@mpiz-koeln.mpg.de> <469CE9B5.2080804@ucalgary.ca> Message-ID: <2248.217.19.47.130.1184828829.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi Paul, what exactly you mean with 'how is this service being provided' ? As far as I know its a PHP Webservice normally registered at the production central. As I mentioned, calling in dashboard it works, strangely not in the basic Java client.... Thanks Andreas > Hi Andreas, > > The error seems to be in Axis parsing the XML message returned by the > service. > How is this service being provided? >> hi, >> >> I try to call the SUBA_AGI2Publications webservice, which works fine via >> the >> dashboard, with the basic Java client >> >> MobyRequest request = new MobyRequest( central ); >> request.setService( service ); >> request.setInput( new MobyDataObject( "AGI_LocusCode", "At1g01040" ) ); >> MobyContentInstance contents = request.invokeService(); >> // .... >> >> in the last line i get an exception: >> >> Exception in thread "main" org.biomoby.shared.SOAPException: While >> invoking >> SOAP Call: Call to a member function attributes() on a non-object >> at >> org.biomoby.client.MobyRequest.performSOAPRequest(MobyRequest.java:532) >> >> what exactly does it mean and what do I do wrong ? >> >> Thanks >> Andreas >> >> > > _______________________________________________ > 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 Thu Jul 19 12:58:52 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 19 Jul 2007 06:58:52 -0600 Subject: [MOBY-dev] SOAPException while calling a service In-Reply-To: <2248.217.19.47.130.1184828829.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <4695368E.7070702@ucalgary.ca> <200707161514.11642.groscurt@mpiz-koeln.mpg.de> <469CE9B5.2080804@ucalgary.ca> <2248.217.19.47.130.1184828829.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <469F600C.4090402@ucalgary.ca> Hi Andreas, What I mean it, is it a MoSeS service? A MobyServlet? A straight Perl MOBY Service? The error is happening when Axis parses the response message from the service. This is strange that it works in Dashboard, since it uses Axis too I thought (though maybe it uses a different version??) > Hi Paul, > > what exactly you mean with 'how is this service being provided' ? > > As far as I know its a PHP Webservice normally registered at the > production central. As I mentioned, calling in dashboard it works, > strangely not in the basic Java client.... > > Thanks > Andreas > > > >> Hi Andreas, >> >> The error seems to be in Axis parsing the XML message returned by the >> service. >> How is this service being provided? >> >>> hi, >>> >>> I try to call the SUBA_AGI2Publications webservice, which works fine via >>> the >>> dashboard, with the basic Java client >>> >>> MobyRequest request = new MobyRequest( central ); >>> request.setService( service ); >>> request.setInput( new MobyDataObject( "AGI_LocusCode", "At1g01040" ) ); >>> MobyContentInstance contents = request.invokeService(); >>> // .... >>> >>> in the last line i get an exception: >>> >>> Exception in thread "main" org.biomoby.shared.SOAPException: While >>> invoking >>> SOAP Call: Call to a member function attributes() on a non-object >>> at >>> org.biomoby.client.MobyRequest.performSOAPRequest(MobyRequest.java:532) >>> >>> what exactly does it mean and what do I do wrong ? >>> >>> Thanks >>> Andreas >>> >>> >>> >> _______________________________________________ >> 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 > > !DSPAM:60005,469f15368021626625063! > > > > From aloraine at gmail.com Fri Jul 27 16:23:57 2007 From: aloraine at gmail.com (Ann Loraine) Date: Fri, 27 Jul 2007 11:23:57 -0500 Subject: [MOBY-dev] can you help? need to cite Message-ID: <83722dde0707270923t25937dc9n9b1770870ed37565@mail.gmail.com> Dear all, I'm being a bit lazy by asking for your help rather than doing a lit search - my apologies! I'm writing an article which mentions BioMoby, and I would like to cite some publications that discuss applications that use BioMoby. I of course thought immediately of the Taverna software, and I found some citations for Taverna, but I wonder if you could point me to articles describing service aggregators or other applications utlizing BioMoby. (If these are not yet published in a traditional journals, that is fine...URLs will probably work just as well!) Thank you very much for your time. Yours, Ann From markw at illuminae.com Fri Jul 27 17:03:31 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 27 Jul 2007 10:03:31 -0700 Subject: [MOBY-dev] can you help? need to cite In-Reply-To: <83722dde0707270923t25937dc9n9b1770870ed37565@mail.gmail.com> References: <83722dde0707270923t25937dc9n9b1770870ed37565@mail.gmail.com> Message-ID: http://biomoby.open-bio.org/index.php/what-is-moby/publications this is a pretty comprehensive list... Hope that helps! :-) M On Fri, 27 Jul 2007 09:23:57 -0700, Ann Loraine wrote: > Dear all, > > I'm being a bit lazy by asking for your help rather than doing a lit > search - my apologies! > > I'm writing an article which mentions BioMoby, and I would like to > cite some publications that discuss applications that use BioMoby. I > of course thought immediately of the Taverna software, and I found > some citations for Taverna, but I wonder if you could point me to > articles describing service aggregators or other applications utlizing > BioMoby. (If these are not yet published in a traditional journals, > that is fine...URLs will probably work just as well!) > > Thank you very much for your time. > > Yours, > > Ann > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From aloraine at gmail.com Fri Jul 27 17:30:35 2007 From: aloraine at gmail.com (Ann Loraine) Date: Fri, 27 Jul 2007 12:30:35 -0500 Subject: [MOBY-dev] can you help? need to cite In-Reply-To: References: <83722dde0707270923t25937dc9n9b1770870ed37565@mail.gmail.com> Message-ID: <83722dde0707271030s44c72339hdb380957a7b5090d@mail.gmail.com> Yes it does - thanks! -Ann On 7/27/07, Mark Wilkinson wrote: > http://biomoby.open-bio.org/index.php/what-is-moby/publications > > this is a pretty comprehensive list... > > Hope that helps! :-) > > M > > > > On Fri, 27 Jul 2007 09:23:57 -0700, Ann Loraine wrote: > > > Dear all, > > > > I'm being a bit lazy by asking for your help rather than doing a lit > > search - my apologies! > > > > I'm writing an article which mentions BioMoby, and I would like to > > cite some publications that discuss applications that use BioMoby. I > > of course thought immediately of the Taverna software, and I found > > some citations for Taverna, but I wonder if you could point me to > > articles describing service aggregators or other applications utlizing > > BioMoby. (If these are not yet published in a traditional journals, > > that is fine...URLs will probably work just as well!) > > > > Thank you very much for your time. > > > > Yours, > > > > Ann > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Ann Loraine Assistant Professor University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From haase_dirk at web.de Fri Jul 27 19:34:13 2007 From: haase_dirk at web.de (Dirk Haase) Date: Fri, 27 Jul 2007 21:34:13 +0200 Subject: [MOBY-dev] can you help? need to cite Message-ID: <1148697625@web.de> Hi Ann, > Dear all, > > I'm being a bit lazy by asking for your help rather than doing a lit > search - my apologies! > > I'm writing an article which mentions BioMoby, and I would like to > cite some publications that discuss applications that use BioMoby. I > of course thought immediately of the Taverna software, and I found > some citations for Taverna, but I wonder if you could point me to > articles describing service aggregators or other applications utlizing > BioMoby. (If these are not yet published in a traditional journals, > that is fine...URLs will probably work just as well!) Just because you asked specifically for aggregators, I'd like to point you to the applications linked on http://bioinfo.mpiz-koeln.mpg.de/araws/searchtools/searchtoolsoverview which unfortunately did not work when I tried a minute ago :-| Mark, is there a problem with MOBY Central? It seems the aggregators don't find any service. Best, dirk From markw at illuminae.com Fri Jul 27 22:36:53 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 27 Jul 2007 15:36:53 -0700 Subject: [MOBY-dev] can you help? need to cite In-Reply-To: <1148697625@web.de> References: <1148697625@web.de> Message-ID: I'm not aware of anything wrong with M.C. it's been working for me all day...??? I just checked the encyclopaedia and the services you are asking for are not registered (in fact, there are *no* services registered to mips.gsf.de!!) ??? perhaps the agent couldn't access your RDF ??? M On Fri, 27 Jul 2007 12:34:13 -0700, Dirk Haase wrote: > Hi Ann, > >> Dear all, >> >> I'm being a bit lazy by asking for your help rather than doing a lit >> search - my apologies! >> >> I'm writing an article which mentions BioMoby, and I would like to >> cite some publications that discuss applications that use BioMoby. I >> of course thought immediately of the Taverna software, and I found >> some citations for Taverna, but I wonder if you could point me to >> articles describing service aggregators or other applications utlizing >> BioMoby. (If these are not yet published in a traditional journals, >> that is fine...URLs will probably work just as well!) > > Just because you asked specifically for aggregators, I'd like to point > you to the applications linked on > http://bioinfo.mpiz-koeln.mpg.de/araws/searchtools/searchtoolsoverview > > which unfortunately did not work when I tried a minute ago :-| > > Mark, is there a problem with MOBY Central? It seems the aggregators > don't find any service. > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From haase_dirk at web.de Sat Jul 28 13:09:23 2007 From: haase_dirk at web.de (Dirk Haase) Date: Sat, 28 Jul 2007 15:09:23 +0200 Subject: [MOBY-dev] can you help? need to cite Message-ID: <1148851010@web.de> Hi Mark, > I'm not aware of anything wrong with M.C. it's been working for me all > day...??? > > I just checked the encyclopaedia and the services you are asking for are > not registered (in fact, there are *no* services registered to > mips.gsf.de!!) Oh, that's bad. Thanks for investigation! > ??? perhaps the agent couldn't access your RDF ??? No, the RDFs are still accessible. Don't know what's going on. I'll try to find someone in charge on Monday. The loss of all MIPS services would be a serious pity :-| Thanks for help. Cheers, dirk From groscurt at mpiz-koeln.mpg.de Mon Jul 30 09:49:53 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 30 Jul 2007 11:49:53 +0200 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: <1148851010@web.de> References: <1148851010@web.de> Message-ID: <200707301149.53557.groscurt@mpiz-koeln.mpg.de> Hi, yes all the services are gone :( Any progress in recovering them ? Cheers Andreas On Saturday 28 July 2007 15:09, Dirk Haase wrote: > Hi Mark, > > > I'm not aware of anything wrong with M.C. it's been working for me all > > day...??? > > > > I just checked the encyclopaedia and the services you are asking for are > > not registered (in fact, there are *no* services registered to > > mips.gsf.de!!) > > Oh, that's bad. Thanks for investigation! > > > ??? perhaps the agent couldn't access your RDF ??? > > No, the RDFs are still accessible. Don't know what's going on. I'll try to > find someone in charge on Monday. The loss of all MIPS services would > be a serious pity :-| > > Thanks for help. > > Cheers, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From markw at illuminae.com Mon Jul 30 11:23:17 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 30 Jul 2007 04:23:17 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: <200707301149.53557.groscurt@mpiz-koeln.mpg.de> References: <1148851010@web.de> <200707301149.53557.groscurt@mpiz-koeln.mpg.de> Message-ID: Eddie, is the agent able to see the MIPS Signature RDF? M On Mon, 30 Jul 2007 02:49:53 -0700, Andreas Groscurth wrote: > Hi, > > yes all the services are gone :( > > Any progress in recovering them ? > > Cheers > Andreas > > On Saturday 28 July 2007 15:09, Dirk Haase wrote: >> Hi Mark, >> >> > I'm not aware of anything wrong with M.C. it's been working for me >> all >> > day...??? >> > >> > I just checked the encyclopaedia and the services you are asking for >> are >> > not registered (in fact, there are *no* services registered to >> > mips.gsf.de!!) >> >> Oh, that's bad. Thanks for investigation! >> >> > ??? perhaps the agent couldn't access your RDF ??? >> >> No, the RDFs are still accessible. Don't know what's going on. I'll try >> to >> find someone in charge on Monday. The loss of all MIPS services would >> be a serious pity :-| >> >> Thanks for help. >> >> Cheers, >> dirk >> _______________________________________________ >> 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 Mon Jul 30 12:22:50 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 05:22:50 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: References: <1148851010@web.de> <200707301149.53557.groscurt@mpiz-koeln.mpg.de> Message-ID: <000601c7d2a4$58b33ec0$6400a8c0@notebook> I don't think that it was able to ... What is the URL to their document and I will tell the agent to try again. Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson > Sent: Monday, July 30, 2007 4:23 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] MIPS Services are lost > > Eddie, is the agent able to see the MIPS Signature RDF? > > M > > > > > On Mon, 30 Jul 2007 02:49:53 -0700, Andreas Groscurth > wrote: > > > Hi, > > > > yes all the services are gone :( > > > > Any progress in recovering them ? > > > > Cheers > > Andreas > > > > On Saturday 28 July 2007 15:09, Dirk Haase wrote: > >> Hi Mark, > >> > >> > I'm not aware of anything wrong with M.C. it's been working for me > >> all > >> > day...??? > >> > > >> > I just checked the encyclopaedia and the services you are asking for > >> are > >> > not registered (in fact, there are *no* services registered to > >> > mips.gsf.de!!) > >> > >> Oh, that's bad. Thanks for investigation! > >> > >> > ??? perhaps the agent couldn't access your RDF ??? > >> > >> No, the RDFs are still accessible. Don't know what's going on. I'll try > >> to > >> find someone in charge on Monday. The loss of all MIPS services would > >> be a serious pity :-| > >> > >> Thanks for help. > >> > >> Cheers, > >> dirk > >> _______________________________________________ > >> 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 From haase_dirk at web.de Mon Jul 30 12:46:52 2007 From: haase_dirk at web.de (Dirk Haase) Date: Mon, 30 Jul 2007 14:46:52 +0200 Subject: [MOBY-dev] MIPS Services are lost Message-ID: <1149221085@web.de> > I don't think that it was able to ... > > What is the URL to their document and I will tell the agent to try again. For the major part of the services there are separate RDFs with URLs following the pattern http://mips.gsf.de/proj/planet/moby/RDF/.rdf However, I'm not able to give a listing of services, sorry! I guess nobody from MIPS is currently looking at this list :-( Another multi-service RDF is accessible under http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf Eddie, can you see the original reason for de-registration, I mean if it was due to the RDFs not being accessible or if somebody did something about it? Best, dirk From edward.kawas at gmail.com Mon Jul 30 13:40:57 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 06:40:57 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: <1149221085@web.de> References: <1149221085@web.de> Message-ID: <000701c7d2af$42c401c0$6400a8c0@notebook> Hi, The agent deleted the services because there 'was a problem processing the url'. It couldn't read from it (or something like that). Anyways, I found the following urls: http://mips.gsf.de/proj/planet/moby/RDF/getSplicedSequence.rdf http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf http://mips.gsf.de/proj/planet/moby/RDF/getElement.rdf http://mips.gsf.de/proj/planet/moby/RDF/getMIPSArabidopsisAnnotationAsGFF3.r df http://mips.gsf.de/proj/planet/moby/RDF/getElementsByName.rdf http://mips.gsf.de/proj/planet/moby/RDF/getClonesByName.rdf http://mips.gsf.de/proj/planet/moby/RDF/getClonesByFreeText.rdf http://mips.gsf.de/proj/planet/moby/RDF/getElementsOfType.rdf http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementNameByFreeText.rdf http://mips.gsf.de/proj/planet/moby/RDF/getJICGeneTrapImageByAgi.rdf http://mips.gsf.de/proj/planet/moby/RDF/getProteinSequence.rdf http://mips.gsf.de/proj/planet/moby/RDF/getElementAnnotation.rdf http://mips.gsf.de/proj/planet/moby/RDF/getClonesForChromosome.rdf http://mips.gsf.de/proj/planet/moby/RDF/getAllGeneticElements.rdf http://mips.gsf.de/proj/planet/moby/RDF/getUnsplicedSequence.rdf http://mips.gsf.de/proj/planet/moby/RDF/getElementsForContig.rdf http://mips.gsf.de/proj/planet/moby/RDF/getElementsByFreeText.rdf http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementsOfType.rdf http://mips.gsf.de/proj/planet/moby/RDF/getContigsByName.rdf http://mips.gsf.de/proj/planet/moby/RDF/getContigsByFreeText.rdf and the agent has been called on all of them. If some are missing, please let me know. After I processed them I looked into the log and the agent was able to read and process the contents of the files ... Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Monday, July 30, 2007 5:47 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] MIPS Services are lost > > > I don't think that it was able to ... > > > > What is the URL to their document and I will tell the agent to try > again. > > For the major part of the services there are separate RDFs with URLs > following the pattern > http://mips.gsf.de/proj/planet/moby/RDF/.rdf > > However, I'm not able to give a listing of services, sorry! I guess > nobody from MIPS is currently looking at this list :-( > > Another multi-service RDF is accessible under > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > > Eddie, can you see the original reason for de-registration, I mean if > it was due to the RDFs not being accessible or if somebody > did something about it? > > Best, > dirk > _______________________________________________ > 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 Mon Jul 30 13:43:45 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 30 Jul 2007 06:43:45 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: <000701c7d2af$42c401c0$6400a8c0@notebook> References: <1149221085@web.de> <000701c7d2af$42c401c0$6400a8c0@notebook> Message-ID: The agent normally sends an email to the owner of the service to tell them what happened... who is the contact for these services? They should have been alerted that the agent couldn't find the RDF for several days before it actually deleted them from the registry... M On Mon, 30 Jul 2007 06:40:57 -0700, Edward Kawas wrote: > Hi, > > The agent deleted the services because there 'was a problem processing > the > url'. It couldn't read from it (or something like that). > > Anyways, I found the following urls: > http://mips.gsf.de/proj/planet/moby/RDF/getSplicedSequence.rdf > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getElement.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getMIPSArabidopsisAnnotationAsGFF3.r > df > http://mips.gsf.de/proj/planet/moby/RDF/getElementsByName.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getClonesByName.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getClonesByFreeText.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getElementsOfType.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementNameByFreeText.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getJICGeneTrapImageByAgi.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getProteinSequence.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getElementAnnotation.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getClonesForChromosome.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getAllGeneticElements.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getUnsplicedSequence.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getElementsForContig.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getElementsByFreeText.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementsOfType.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getContigsByName.rdf > http://mips.gsf.de/proj/planet/moby/RDF/getContigsByFreeText.rdf > > and the agent has been called on all of them. If some are missing, please > let me know. > > After I processed them I looked into the log and the agent was able to > read > and process the contents of the files ... > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Dirk Haase >> Sent: Monday, July 30, 2007 5:47 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] MIPS Services are lost >> >> > I don't think that it was able to ... >> > >> > What is the URL to their document and I will tell the agent to try >> again. >> >> For the major part of the services there are separate RDFs with URLs >> following the pattern >> http://mips.gsf.de/proj/planet/moby/RDF/.rdf >> >> However, I'm not able to give a listing of services, sorry! I guess >> nobody from MIPS is currently looking at this list :-( >> >> Another multi-service RDF is accessible under >> http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf >> >> Eddie, can you see the original reason for de-registration, I mean if >> it was due to the RDFs not being accessible or if somebody >> did something about it? >> >> Best, >> dirk >> _______________________________________________ >> 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 From edward.kawas at gmail.com Mon Jul 30 13:45:22 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 06:45:22 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: References: <1149221085@web.de> <000701c7d2af$42c401c0$6400a8c0@notebook> Message-ID: <000b01c7d2af$e0d20b00$6400a8c0@notebook> The address most prevalent is: Octave.Noubibou at gsf.de Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson > Sent: Monday, July 30, 2007 6:44 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] MIPS Services are lost > > The agent normally sends an email to the owner of the service to tell them > what happened... who is the contact for these services? They should have > been alerted that the agent couldn't find the RDF for several days before > it actually deleted them from the registry... > > M > > > > On Mon, 30 Jul 2007 06:40:57 -0700, Edward Kawas > wrote: > > > Hi, > > > > The agent deleted the services because there 'was a problem processing > > the > > url'. It couldn't read from it (or something like that). > > > > Anyways, I found the following urls: > > http://mips.gsf.de/proj/planet/moby/RDF/getSplicedSequence.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getElement.rdf > > > http://mips.gsf.de/proj/planet/moby/RDF/getMIPSArabidopsisAnnotationAsGFF3 > .r > > df > > http://mips.gsf.de/proj/planet/moby/RDF/getElementsByName.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getClonesByName.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getClonesByFreeText.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getElementsOfType.rdf > > > http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementNameByFreeText.rd > f > > http://mips.gsf.de/proj/planet/moby/RDF/getJICGeneTrapImageByAgi.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getProteinSequence.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getElementAnnotation.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getClonesForChromosome.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getAllGeneticElements.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getUnsplicedSequence.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getElementsForContig.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getElementsByFreeText.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getGeneticElementsOfType.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getContigsByName.rdf > > http://mips.gsf.de/proj/planet/moby/RDF/getContigsByFreeText.rdf > > > > and the agent has been called on all of them. If some are missing, > please > > let me know. > > > > After I processed them I looked into the log and the agent was able to > > read > > and process the contents of the files ... > > > > Eddie > > > > > >> -----Original Message----- > >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > >> bounces at lists.open-bio.org] On Behalf Of Dirk Haase > >> Sent: Monday, July 30, 2007 5:47 AM > >> To: Core developer announcements > >> Subject: Re: [MOBY-dev] MIPS Services are lost > >> > >> > I don't think that it was able to ... > >> > > >> > What is the URL to their document and I will tell the agent to try > >> again. > >> > >> For the major part of the services there are separate RDFs with URLs > >> following the pattern > >> http://mips.gsf.de/proj/planet/moby/RDF/.rdf > >> > >> However, I'm not able to give a listing of services, sorry! I guess > >> nobody from MIPS is currently looking at this list :-( > >> > >> Another multi-service RDF is accessible under > >> http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > >> > >> Eddie, can you see the original reason for de-registration, I mean if > >> it was due to the RDFs not being accessible or if somebody > >> did something about it? > >> > >> Best, > >> dirk > >> _______________________________________________ > >> 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 > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From haase_dirk at web.de Mon Jul 30 14:00:29 2007 From: haase_dirk at web.de (Dirk Haase) Date: Mon, 30 Jul 2007 16:00:29 +0200 Subject: [MOBY-dev] MIPS Services are lost Message-ID: <1149242476@web.de> > The address most prevalent is: > > Octave.Noubibou at gsf.de Yes and Octave left MIPS several weeks ago. So either the mails were ignored or not even delivered. Could the latter be the reason for the instant de-registration? In the meantime I managed to talk to the responsible person at MIPS and he is not aware of any longer offline periods. However I asked him to replace the contact mail addresses in the RDFs with something more useful. Best, dirk From edward.kawas at gmail.com Mon Jul 30 14:02:58 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 07:02:58 -0700 Subject: [MOBY-dev] MIPS Services are lost In-Reply-To: <1149242476@web.de> References: <1149242476@web.de> Message-ID: <000c01c7d2b2$5613d360$6400a8c0@notebook> The messages returned undeliverable, but that wouldn't cause the agent to deregister them instantaneously. In the meantime, I will keep an eye on the mips services. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Monday, July 30, 2007 7:00 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] MIPS Services are lost > > > The address most prevalent is: > > > > Octave.Noubibou at gsf.de > > Yes and Octave left MIPS several weeks ago. So either the mails were > ignored or not even delivered. Could the latter be the reason for the > instant de-registration? In the meantime I managed to talk to the > responsible person at MIPS and he is not aware of any longer > offline periods. > > However I asked him to replace the contact mail addresses in the > RDFs with something more useful. > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Mon Jul 30 14:38:49 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 30 Jul 2007 16:38:49 +0200 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <000c01c7d2b2$5613d360$6400a8c0@notebook> References: <1149242476@web.de> <000c01c7d2b2$5613d360$6400a8c0@notebook> Message-ID: <200707301638.49459.groscurt@mpiz-koeln.mpg.de> Hi, I would like to address an issue we had discussed a little at the meeting in Vancouver, namely to enable the possibility for service providers to add their url (to their homepage) and a logo. This was based on the suggestions from the Tigr workshop, where the people wanted to have that, so if one is aggregating their service, is possible to link to the origin of the service. Actually there are two ways to do so (in my opinion): 1. Add the url to the homepage and the url to a logo into the service notes for each service result 2. Give the opportunity to enter this information while registering a service In case of 1. there are no changes needed in the API (neither perl nor java), if somewant wants to use this information they have to parse it from the service notes. in case of 2. the api has to change (and also all registration clients and probably the database....) to have methods to access these information and to enter or store them in the service objects (or however this is done with perl services) Intuitively - from a developer - I would suggest 2. because it sounds much more clearer to access and to store this information. Putting it into the service notes sounds more like a workaround ('ah... everything else is put there') - are there any other information in there ? how it is represented there ? and so on.. but I think I can see that point 1 is easier and sooner to use.... But I'm open for discussion. I can live with all ways :-) Best Andreas From edward.kawas at gmail.com Mon Jul 30 14:46:59 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 07:46:59 -0700 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <200707301638.49459.groscurt@mpiz-koeln.mpg.de> References: <1149242476@web.de> <000c01c7d2b2$5613d360$6400a8c0@notebook> <200707301638.49459.groscurt@mpiz-koeln.mpg.de> Message-ID: <000d01c7d2b8$7c460ed0$6400a8c0@notebook> Another way of doing this would be to modify the RDF metadata for a particular service. I haven't thought about this too deeply, but as a service provider, if I wish to augment the information in the RDF with extra information regarding my service, I am free to do so. So for example, imagine that we agree on a predicate like 'hasLogoURL'. Anybody wishing to show logos would only have to check for existence of that predicate in the RDF and behave accordingly. This wouldn't change the api. Having said that, I, being the fence sitter moby java developers know and love ;-), agree with Andreas and think that this information should be recorded at registration time. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: Monday, July 30, 2007 7:39 AM > To: Core developer announcements > Subject: [MOBY-dev] ServiceProvider URL and Logo > > Hi, > > I would like to address an issue we had discussed a little at the meeting > in > Vancouver, namely to enable the possibility for service providers to add > their url (to their homepage) and a logo. > This was based on the suggestions from the Tigr workshop, where the people > wanted to have that, so if one is aggregating their service, is possible > to > link to the origin of the service. > > Actually there are two ways to do so (in my opinion): > > 1. Add the url to the homepage and the url to a logo into the service > notes > for each service result > > 2. Give the opportunity to enter this information while registering a > service > > > In case of 1. there are no changes needed in the API (neither perl nor > java), > if somewant wants to use this information they have to parse it from the > service notes. > > in case of 2. the api has to change (and also all registration clients and > probably the database....) to have methods to access these information > and > to enter or store them in the service objects (or however this is done > with > perl services) > > Intuitively - from a developer - I would suggest 2. because it sounds much > more clearer to access and to store this information. Putting it into the > service notes sounds more like a workaround ('ah... everything else is put > there') - are there any other information in there ? how it is represented > there ? and so on.. but I think I can see that point 1 is easier and > sooner > to use.... > > But I'm open for discussion. I can live with all ways :-) > > Best > Andreas > _______________________________________________ > 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 Jul 30 14:49:03 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 30 Jul 2007 08:49:03 -0600 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <200707301638.49459.groscurt@mpiz-koeln.mpg.de> References: <1149242476@web.de> <000c01c7d2b2$5613d360$6400a8c0@notebook> <200707301638.49459.groscurt@mpiz-koeln.mpg.de> Message-ID: <46ADFA5F.6030204@ucalgary.ca> I am personally in favour of the serviceNotes option, since this gives you the flexibility to put any HTML you like (e.g. the SeqHound services display the citation to use). Of course, you could have both the free-form HTML and the logo protocol, but maybe client software would be less likely to show the former if the latter is a requirement... > Hi, > > I would like to address an issue we had discussed a little at the meeting in > Vancouver, namely to enable the possibility for service providers to add > their url (to their homepage) and a logo. > This was based on the suggestions from the Tigr workshop, where the people > wanted to have that, so if one is aggregating their service, is possible to > link to the origin of the service. > > Actually there are two ways to do so (in my opinion): > > 1. Add the url to the homepage and the url to a logo into the service notes > for each service result > > 2. Give the opportunity to enter this information while registering a service > > > In case of 1. there are no changes needed in the API (neither perl nor java), > if somewant wants to use this information they have to parse it from the > service notes. > > in case of 2. the api has to change (and also all registration clients and > probably the database....) to have methods to access these information and > to enter or store them in the service objects (or however this is done with > perl services) > > Intuitively - from a developer - I would suggest 2. because it sounds much > more clearer to access and to store this information. Putting it into the > service notes sounds more like a workaround ('ah... everything else is put > there') - are there any other information in there ? how it is represented > there ? and so on.. but I think I can see that point 1 is easier and sooner > to use.... > > But I'm open for discussion. I can live with all ways :-) > > Best > Andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,46adf68680211809920332! > > > > From gordonp at ucalgary.ca Mon Jul 30 14:52:58 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 30 Jul 2007 08:52:58 -0600 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <000d01c7d2b8$7c460ed0$6400a8c0@notebook> References: <1149242476@web.de> <000c01c7d2b2$5613d360$6400a8c0@notebook> <200707301638.49459.groscurt@mpiz-koeln.mpg.de> <000d01c7d2b8$7c460ed0$6400a8c0@notebook> Message-ID: <46ADFB4A.9070401@ucalgary.ca> I like the RDF metadata idea, Eddie! The registration process should only really include data required to run the service. A logo is definitely not core to running a service. If we start including things like the logo, we will be thinking of things to add to the registration process for years... > Another way of doing this would be to modify the RDF metadata for a > particular service. I haven't thought about this too deeply, but as a > service provider, if I wish to augment the information in the RDF with extra > information regarding my service, I am free to do so. So for example, > imagine that we agree on a predicate like 'hasLogoURL'. > > Anybody wishing to show logos would only have to check for existence of that > predicate in the RDF and behave accordingly. This wouldn't change the api. > > Having said that, I, being the fence sitter moby java developers know and > love ;-), agree with Andreas and think that this information should be > recorded at registration time. > > Eddie > > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth >> Sent: Monday, July 30, 2007 7:39 AM >> To: Core developer announcements >> Subject: [MOBY-dev] ServiceProvider URL and Logo >> >> Hi, >> >> I would like to address an issue we had discussed a little at the meeting >> in >> Vancouver, namely to enable the possibility for service providers to add >> their url (to their homepage) and a logo. >> This was based on the suggestions from the Tigr workshop, where the people >> wanted to have that, so if one is aggregating their service, is possible >> to >> link to the origin of the service. >> >> Actually there are two ways to do so (in my opinion): >> >> 1. Add the url to the homepage and the url to a logo into the service >> notes >> for each service result >> >> 2. Give the opportunity to enter this information while registering a >> service >> >> >> In case of 1. there are no changes needed in the API (neither perl nor >> java), >> if somewant wants to use this information they have to parse it from the >> service notes. >> >> in case of 2. the api has to change (and also all registration clients and >> probably the database....) to have methods to access these information >> and >> to enter or store them in the service objects (or however this is done >> with >> perl services) >> >> Intuitively - from a developer - I would suggest 2. because it sounds much >> more clearer to access and to store this information. Putting it into the >> service notes sounds more like a workaround ('ah... everything else is put >> there') - are there any other information in there ? how it is represented >> there ? and so on.. but I think I can see that point 1 is easier and >> sooner >> to use.... >> >> But I'm open for discussion. I can live with all ways :-) >> >> Best >> Andreas >> _______________________________________________ >> 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 > > !DSPAM:60005,46adf85f8021244901854! > > > > From edward.kawas at gmail.com Mon Jul 30 15:22:45 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 08:22:45 -0700 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <46ADFB4A.9070401@ucalgary.ca> References: <1149242476@web.de><000c01c7d2b2$5613d360$6400a8c0@notebook> <200707301638.49459.groscurt@mpiz-koeln.mpg.de><000d01c7d2b8$7c460ed0$6400a8c0@notebook> <46ADFB4A.9070401@ucalgary.ca> Message-ID: <000e01c7d2bd$7aec8000$6400a8c0@notebook> > A logo is definitely not core to running a service. If we start > including things like the logo, we will be thinking of things to add to > the > registration process for years... I thought about this, and I was going to comment on it. I am glad that you brought this up Paul. Eddie From groscurt at mpiz-koeln.mpg.de Mon Jul 30 15:37:01 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 30 Jul 2007 17:37:01 +0200 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <000e01c7d2bd$7aec8000$6400a8c0@notebook> References: <1149242476@web.de> <46ADFB4A.9070401@ucalgary.ca> <000e01c7d2bd$7aec8000$6400a8c0@notebook> Message-ID: <200707301737.02105.groscurt@mpiz-koeln.mpg.de> havent thought of this... thats right. but anyhow this should be done in an easy fashion for the service registration, so that service providers dont have to edit the rdf manually... and if its easily possible for a client to access these information - then... I like the idea :D Best Andreas On Monday 30 July 2007 17:22, Edward Kawas wrote: > > A logo is definitely not core to running a service. If we start > > including things like the logo, we will be thinking of things to add to > > the > > registration process for years... > > I thought about this, and I was going to comment on it. I am glad that you > brought this up Paul. > > Eddie > > _______________________________________________ > 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 Mon Jul 30 15:39:56 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Jul 2007 08:39:56 -0700 Subject: [MOBY-dev] ServiceProvider URL and Logo In-Reply-To: <200707301737.02105.groscurt@mpiz-koeln.mpg.de> References: <1149242476@web.de> <46ADFB4A.9070401@ucalgary.ca><000e01c7d2bd$7aec8000$6400a8c0@notebook> <200707301737.02105.groscurt@mpiz-koeln.mpg.de> Message-ID: <000f01c7d2bf$e1fa6b20$6400a8c0@notebook> > and if its easily possible for a client to access these information - > then... > I like the idea :D If you resolve the LSID for a particular service, there is a service provider 'port' that has an HTTP "Get'able url that is the signatureURL for a service. So the information is reachable. Eddie From dmitry.repchevski at bsc.es Tue Jul 31 14:56:16 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 31 Jul 2007 16:56:16 +0200 Subject: [MOBY-dev] parameter name should not be namespace qualified Message-ID: <46AF4D90.3040309@bsc.es> Hello! I found the strange thing with Axis (tried v1.2.1 and 1.4). It puts a namespace onto a parameter. <*ns1:*arg0 xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" xsi:type="soapenc:string"> ... According guys from JBoss team this goes against the specification - they look for the parameter without any namespace so the service fails by not finding it. Guys from GlassFish also follows the same rule. I'm not sure does it matter now when we suppose to move into doc/literal encoding (away from axis)... Axis used to be very relaxed to the errors. For example it can call the service even if the parameter name doesn't match. I mean that perl client calls the request parameter "data", but DashBoard "arg0"... The question is can namespace for parameters be fixed easy? Dmitry