From aw3 at ebgm.jussieu.fr Thu Nov 4 09:09:23 2004 From: aw3 at ebgm.jussieu.fr (Apache) Date: Thu Nov 4 17:11:46 2004 Subject: [MOBY-dev] RDF ? Message-ID: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> Hi, Newbie in the concepts of biomoby, can someone explain me how the RDF is supposed to work exactly ? After having registered a service, how to unregister ? Is it sufficient to edit the local copy of the RDF ? Or is (will) it (be) necessary to re-post it ? Or is the RDF layer not fully functional yet ? Idem for modifying the service specification. Thanks by advance ! Pierre From mwilkinson at mrl.ubc.ca Thu Nov 4 17:49:44 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu Nov 4 17:29:40 2004 Subject: [spam] [MOBY-dev] RDF ? In-Reply-To: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> References: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> Message-ID: <1099608583.29632.45.camel@mobycentral.icapture.ubc.ca> On Thu, 2004-11-04 at 06:09, Apache wrote: > Newbie in the concepts of biomoby, can someone explain me how the > RDF is supposed to work exactly ? Don't worry about being a newbie - this is new to everyone... > After having registered a service, how to unregister ? Is it sufficient > to edit the local copy of the RDF ? Or is (will) it (be) necessary to > re-post it ? Or is the RDF layer not fully functional yet ? the RDF layer is not fully functional *yet*, but we will be switching it on soon. There have been problems with different versions of the Java libraries between the different developers, and that caused compilation problems and such. Apparently, that might be fixed now, so we should soon be able to switch on the agent "for real". Nina is just running some last-minute tests on it now to make sure that it is registering/deregistering services correctly. It will be sufficient to edit the RDF to change a service. It will also be sufficient to delete that sub-graph of the RDF document in order to delete your service. You can also do the same thing via the MOBY Central API as previously. I'll be sending out a message once the agent is running to let everyone know that they should keep an eye on their services just in case something goes wrong. I will do a complete backup of the database just beforehand in case there is an error. Cheers, M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Thu Nov 4 17:49:44 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu Nov 4 17:29:41 2004 Subject: [spam] [MOBY-dev] RDF ? In-Reply-To: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> References: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> Message-ID: <1099608583.29632.45.camel@mobycentral.icapture.ubc.ca> On Thu, 2004-11-04 at 06:09, Apache wrote: > Newbie in the concepts of biomoby, can someone explain me how the > RDF is supposed to work exactly ? Don't worry about being a newbie - this is new to everyone... > After having registered a service, how to unregister ? Is it sufficient > to edit the local copy of the RDF ? Or is (will) it (be) necessary to > re-post it ? Or is the RDF layer not fully functional yet ? the RDF layer is not fully functional *yet*, but we will be switching it on soon. There have been problems with different versions of the Java libraries between the different developers, and that caused compilation problems and such. Apparently, that might be fixed now, so we should soon be able to switch on the agent "for real". Nina is just running some last-minute tests on it now to make sure that it is registering/deregistering services correctly. It will be sufficient to edit the RDF to change a service. It will also be sufficient to delete that sub-graph of the RDF document in order to delete your service. You can also do the same thing via the MOBY Central API as previously. I'll be sending out a message once the agent is running to let everyone know that they should keep an eye on their services just in case something goes wrong. I will do a complete backup of the database just beforehand in case there is an error. Cheers, M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gss at ncgr.org Tue Nov 9 17:39:11 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue Nov 9 17:41:23 2004 Subject: [MOBY-dev] MOBY Meeting: Reminder & Details Message-ID: <4191470F.9010001@ncgr.org> This is a reminder that the MOBY autumn 2004 meeting is approaching quickly (11 days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register: Date : November 20-21 (Saturday & Sunday) Location : Santa Fe, New Mexico USA Venue : National Center for Genome Resources (www.ncgr.org) Fee : $50 USD/person (covers lunch and transportation between hotels and NCGR) The tentative agenda is as follows; please post any suggestions to the moby-l or moby-dev lists: Saturday, November 20, 2004: 8:30 am Bagels and coffee 9:00 am Semantic MOBY (Damian Gessler) 10:00 am Taverna (Martin Senger) 10:45 am Break 11:00 am MOBY Services (Mark Wilkinson) 12:00 pm Lunch provided 1:00 pm: Virtual Plant Network (Bill Beavis, discussion leader) 2:00 pm: Conceptual ways to merge S-MOBY, MOBY-S, and MyGrid in a real-world application (joined by Phil Lord via telecon [Manchester is seven hours ahead of Santa Fe]) 6:00pm Dinner Sunday, November 21, 2004 9:00 am Bagels and coffee 9:30 am Technical challenges to merging S-MOBY, MOBY-S, and MyGrid 11:30 am Next steps From letondal at pasteur.fr Wed Nov 10 11:47:01 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Wed Nov 10 11:43:07 2004 Subject: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? Message-ID: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Hi, I would have a question: how is the Moby-S branch of Biomoby connected to other efforts that seek to integrate Web services and Semantic Web? I mean groups, systems or forums such as: http://www.w3.org/2002/ws/swsig/ http://www.wsmo.org (Web service modelling Ontology) http://www.wsmo.org/wsml (Web Service Modeling Language) http://www.daml.org/services/owl-s (OWL-based Web service ontology) ...? BTW, I have just heard of this book: Developing Semantic Web Services (A. K. Peters) : http://www.akpeters.com/product.asp?ProdCode=2124 -- Catherine Letondal -- Institut Pasteur From letondal at pasteur.fr Fri Nov 12 04:48:21 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Fri Nov 12 04:44:47 2004 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Message-ID: On Nov 11, 2004, at 1:28 AM, Phillip Lord wrote: > > OWL-S/WSMO are trying to do a different thing to moby-s. The main aim > for these technologies is to use highly expressive logics to enable > automated composition and choreography of web services. This is a nice > idea, but, my own suspicion is that most biologists, or bioinformatics > service providers are not going to go to the effort to describe their > services logically. > > Moby-s on the other hand takes a more constrained view of > semantics. It's trying to produce semantic descriptions which are good > enough to reduce the problem for the biologist to selecting from one > or a short list, rather than then 500. > I meant S-Moby in fact, not Moby-S, sorry for this mistake. > There is a paper in this years ISWC (currently going on now!), which > you can get from here... > > http://www.cs.man.ac.uk/~phillord/download/publications/biomoby- > comparison-iswc2004.pdf > Thanks a lot for this information. I have read the paper, which indeed helped a lot to understand your underlying choices (BTW, I would be interested to know about the feedback it had at the ISCW conference - generally, bioinformatics is considered as a "very specific" area, and since the differences between "generial" applications such as e-commerce and e-science are very well explained in your paper, I'm curious to know whether the audience reacted). I still have a question about the comparison to OWL-S. In section 7 of your paper (Service provision and Service interfaces), you explain that OWL-S defines a grounding ontology, and that the 3 approaches (moby-s, s-moby and myGrid) have chosen a simpler approach. I understand that the problem that is addressed here is to have a high description not only of domain concepts, but also on their relations, and that this is not required in the 3 approaches, for different reasons. But I don't understand your explanations: How is the S-Moby interface defined by its "upper" ontology? I have carefully read the S-moby design document (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html), what do you call an upper ontology there - the set of RDF graphs submitted by providers? You also mention that moby-s interfaces are not heterogeneous (and thus does not need an ontology to interconnect concepts). What is not heterogeneous and why? Thanks for any reference or additional explananation, -- Catherine Letondal -- Institut Pasteur From gss at ncgr.org Fri Nov 12 12:26:54 2004 From: gss at ncgr.org (Gary Schiltz) Date: Fri Nov 12 12:29:09 2004 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Message-ID: <4194F25E.90904@ncgr.org> Catherine Letondal wrote: > > How is the S-Moby interface defined by its "upper" ontology? I have > carefully read the S-moby design document > (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html), > what do you call an upper ontology there - the set of RDF graphs > submitted by providers? Phil, since you're the ontology guy, feel free to chip in. If I understand the term "upper ontology" correctly, it refers to concepts and relationships (i.e. an ontology) that are somewhat generic, and thus applicable to multiple domains. As such, what is referred to in Semantic MOBY as the "canonical graph structure" (Figure 2 in the design document that you referenced) is the upper ontology. // Gary Schiltz, NCGR From gss at ncgr.org Fri Nov 12 16:57:05 2004 From: gss at ncgr.org (Gary Schiltz) Date: Fri Nov 12 16:59:12 2004 Subject: [MOBY-dev] MOBY Meeting: Reminder & Updates In-Reply-To: <4191470F.9010001@ncgr.org> References: <4191470F.9010001@ncgr.org> Message-ID: <419531B1.20208@ncgr.org> This is another reminder that the MOBY autumn 2004 meeting is quickly approaching (8 days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register. The meeting pages on semanticmoby.org have been updated. I look forward to seeing you there! ---- Gary Schiltz Principal Software Engineer National Center for Genome Resources Santa Fe, New Mexico USA From p.lord at cs.man.ac.uk Sun Nov 14 09:23:37 2004 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: Mon Nov 15 10:48:59 2004 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: <4194F25E.90904@ncgr.org> References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> <4194F25E.90904@ncgr.org> Message-ID: >>>>> "Gary" == Gary Schiltz writes: Gary> Catherine Letondal wrote: >> How is the S-Moby interface defined by its "upper" ontology? I >> have carefully read the S-moby design document >> (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html), >> what do you call an upper ontology there - the set of RDF graphs >> submitted by providers? Gary> Phil, since you're the ontology guy Having just been to the semantic web conference, I've realised that really, I'm a yeast biologist! Gary> feel free to chip in. If I understand the term "upper Gary> ontology" correctly, it refers to concepts and relationships Gary> (i.e. an ontology) that are somewhat generic, and thus Gary> applicable to multiple domains. This is generally correct. "Upper Ontology" is often used to describe an ontology of highly abstract concepts (1) that is meant to be shared among many ontologies. Some times, upper ontology just means the top half of an ontology. OWL-S has been described as an upper ontology, which is why I used terminology. Gary> As such, what is referred to in Semantic MOBY as the Gary> "canonical graph structure" (Figure 2 in the design document Gary> that you referenced) is the upper ontology. That's the thing I meant. Or, at least the vocabulary used to define this structure. "input", "output", "mapsto" and so on. Oh dear. I seem to be explaining the contents of a paper which I partly authored. This is like a comedian or cartoonist having to explain their jokes. Cheers Phil (1) The most notorious of which are "perjurant" and "endurant"; names which are nearly as self-explanatory as "ortholog" and "paralog". From gss at ncgr.org Tue Nov 16 12:39:01 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue Nov 16 12:41:06 2004 Subject: [MOBY-dev] MOBY Meeting: LAST CALL In-Reply-To: <419531B1.20208@ncgr.org> References: <4191470F.9010001@ncgr.org> <419531B1.20208@ncgr.org> Message-ID: <419A3B35.4020400@ncgr.org> This is a final reminder that the MOBY autumn 2004 meeting is next Saturday and Sunday, November 20 & 21 at NCGR in Santa Fe, New Mexico (four days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register. If you plan to attend, please register as soon as possible. The list of people I have recorded as registering are the following; please let me know if you are planning to attend and your name is not on the list: Andrew Farmer (NCGR) Bill Beavis (NCGR) Damian Gessler (NCGR) Dirk Haase (MIPS) Fernando Rojas (CIAT) Gary Schiltz (NCGR) Guy Davenport (CIMMYT) Manuel Ruiz (CIRAD) Mark Wilkinson (UBC) Martin Senger (EBI) Milko Skofic (IPGRI) Rex Nelson (USDA-ARS CICGR) Richard Bruskiewich (IRRI) Thomas Hazekamp (IPGRI) ---- Gary Schiltz Principal Software Engineer National Center for Genome Resources Santa Fe, New Mexico USA From gss at ncgr.org Tue Nov 16 17:37:36 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue Nov 16 17:39:38 2004 Subject: [MOBY-dev] [Fwd: an application for MOBY developers to consider] Message-ID: <419A8130.6010103@ncgr.org> Bill Beavis of NCGR asked that I pass this along to the list. Since I seem to remember the Listsrv software sometimes not liking attachments, I have put the attachments from Bill's email at www.semanticmoby.org/meeting/vpn instead of leaving them attached. The white paper Bill refers to is the file An_app_for_MOBY.pdf // Gary -------- Original Message -------- Subject: an application for MOBY developers to consider Date: Tue, 16 Nov 2004 14:55:23 -0700 From: Bill Beavis Greetings from Santa Fe, As many of you are aware, we'd like to visit about an application for the BioMOBY projects during our meeting this weekend. Because many of us work with Plant Information Resources we'd like to discuss the potential of using BioMOBY for development of a Virtual Plant Network (we may have to name it something else so that the acronym is not confused with another VPN). After visiting with the cognizant program officers, Stinger Guala and Manfred Zorn, I believe that we would have a reasonably good chance of obtaining support from the NSF-BDI for such a proposal. In order to stimulate discussion of the idea, please find attached a white paper utlining the concept and specific aims that might be included in such a proposal. Note that yellow highlights indicate areas that need clarification. Also, please find attached a couple of references that are germane to the discussion. For those of you who have been interested in utilizing MOBY for the CGIAR - Grand Challenge Program, there is a mechanism to obtain supplemental funding in this proposal for development of international collaborations. Thus, for those of you from non-US institutions, participation in this proposal could bring in some funding to support your efforts to utilize MOBY. For those of you who are not able to attend the MOBY meeting, you can join the discussion, which will begin at 1:00 pm MST, through a teleconference. Instructions for joining us: Date : Saturday, Nov. 20, 2004 Time : 1 pm Mountain Standard Time Discussion : Integrating Semantic MOBY and MOBY Services in a real world, distributed application: The Virtual Plant Network. Instructions to join: 1 - Dial the toll-free On-Demand Plus Number: 1-888-387-8686 (For international users, dial the international dial-out plus the country code (1) followed by 303-928-3281) 2 - Enter the Room number: 4139056, and press # 3 - You will be placed directly into the meeting if the moderator has already joined. If the moderator hasn't joined, you will be placed on hold for up to 10 minutes. Best regards, Bill Beavis From mwilkinson at mrl.ubc.ca Thu Nov 18 12:50:11 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu Nov 18 12:26:47 2004 Subject: [MOBY-dev] CVS tagged today Message-ID: <1100800211.21729.30.camel@mobycentral.icapture.ubc.ca> Hi all, Eddie is about to make some fairly significant commits in which the underlying XML parser for all of the Perl libraries is swapped out in favour of an XML namespace aware parser (XML::LibXML in place of XML::DOM) I have just tagged the repository November18_2004 so that we can rollback if that becomes necessary, and also to allow people to check-out what we know is a functional version if things go wrong. Anyone who is running a production shop using the Perl code SHOULD NOT update their code until we know that everything is working. It seems to pass all tests, but I want to give it a bit more time to reveal any oopsies :-) Cheers all! Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mark.fiers at wur.nl Fri Nov 26 09:57:35 2004 From: mark.fiers at wur.nl (Mark Fiers) Date: Fri Nov 26 09:55:53 2004 Subject: [MOBY-dev] question about the bioMoby python API In-Reply-To: <1097760189.14174.7.camel@prot1.rpbs.jussieu.fr> References: <1097760189.14174.7.camel@prot1.rpbs.jussieu.fr> Message-ID: <41A7445F.3000403@wur.nl> Hi We've succeeded in using the biomoby python module to create an in house biomoby service. Now we have registered this service and all of the sudden it doesn't work anymore. Has anybody successfully done this? As far as I can tell, ZSI does not parse the incoming xml correctly and does not execute the service. Upon parsing the xml (oh,I'm using http://mobycentral.cbr.nrc.ca/cgi-bin/gbrowse_moby): ################################################## ]]> ################################################## I I try a local script calling this function I get : ################################################## <moby:Object moby:namespace="PO_acc" moby:id="9054" moby:articleName="PO_query"/> ################################################## Which works fine. As far as I can see ZSI does not like the "" tag in the upper xml. It barfs and tells me : "Any cannot parse untyped element" Does anybod have a clue why this is going wrong? Cheers Mark Fiers Plant Research International Wageningen The Netherlands >I am modifying the API in order to deal with the RDF files and solving >some bugs: > >-Bug in the Dispatcher corrected (troubles with handling multiple >queries simultaneously) >added signatureURL and RDF for Registration process (in Service, >ServiceList) >-debug option when executing a service (trace of HTTP calls) in Central >and Service Class > (allows you to have the dump of all your SOAP transaction with the >webservice) > >if you want to trace a SOAP call while executing a service just put: > service.execute(mobyqueries, debug=True) >and you'll have the complete trace of the execution > >when you deal with the Moby Central Server: > client=Client(debug=True) >to trace execution of your moby Query > >As Errare Humanum Est, feel free to notify me errors I missed :) > >I expect to release a corrected version in the end of next week. >_______________________________________________ >MOBY-dev mailing list >MOBY-dev@biomoby.org >http://www.biomoby.org/mailman/listinfo/moby-dev > > > From wong.yan at netcourrier.com Sat Nov 27 17:01:51 2004 From: wong.yan at netcourrier.com (wong.yan@netcourrier.com) Date: Sat Nov 27 10:59:30 2004 Subject: [MOBY-dev] question about the bioMoby python API Message-ID: I am studying the problem, actually it comes from the fact that "body" is not a type and that the method dispatch.AsCGI() deserializes the SOAP content into a Python object (and as object body doesn't exist, it fails to do anything else). I'll change the ZSI package in order to treat bioMoby XML directly. I'll post a patch ASAP (expect it during the week). If people got a better work around... ------------------------------------------------------------- NetCourrier, votre bureau virtuel sur Internet : Mail, Agenda, Clubs, Toolbar... Web/Wap : www.netcourrier.com T?l?phone/Fax : 08 92 69 00 21 (0,34 ? TTC/min) Minitel: 3615 NETCOURRIER (0,16 ? TTC/min) From mwilkinson at mobile.rogers.com Tue Nov 30 16:10:06 2004 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Tue Nov 30 16:09:19 2004 Subject: [MOBY-dev] Message to Eddie Message-ID: <200411302109.iAUL8wKr010844@portal.open-bio.org> Sorry everyone, I don't have Eddie's email on my blackberry... Eddie, I have your new code running on the test server. All tests pass in both perl and java (good job!!) but the perl tests do complain about a concatenated blank string. That may indicate an insidious error, or may be trivial. Can you look into that? Otherwise, I'm thrilled!! That's the easiest major code shift we've ever done :-) Greetings from Montreal Dorval, underway to Halifax... M !!!!!!!!!!!!!!!! To respond to this message you MUST send your response to (note new address!) markw_mobile2 at illuminae dot com Responses to the reply-to address go directly to trash! !!!!!!!!!!!!!!!!!!!!!!!!!!!! From aw3 at ebgm.jussieu.fr Thu Nov 4 09:09:23 2004 From: aw3 at ebgm.jussieu.fr (Apache) Date: Thu, 4 Nov 2004 15:09:23 +0100 Subject: [MOBY-dev] RDF ? Message-ID: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> Hi, Newbie in the concepts of biomoby, can someone explain me how the RDF is supposed to work exactly ? After having registered a service, how to unregister ? Is it sufficient to edit the local copy of the RDF ? Or is (will) it (be) necessary to re-post it ? Or is the RDF layer not fully functional yet ? Idem for modifying the service specification. Thanks by advance ! Pierre From mwilkinson at mrl.ubc.ca Thu Nov 4 17:49:44 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 04 Nov 2004 14:49:44 -0800 Subject: [spam] [MOBY-dev] RDF ? In-Reply-To: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> References: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> Message-ID: <1099608583.29632.45.camel@mobycentral.icapture.ubc.ca> On Thu, 2004-11-04 at 06:09, Apache wrote: > Newbie in the concepts of biomoby, can someone explain me how the > RDF is supposed to work exactly ? Don't worry about being a newbie - this is new to everyone... > After having registered a service, how to unregister ? Is it sufficient > to edit the local copy of the RDF ? Or is (will) it (be) necessary to > re-post it ? Or is the RDF layer not fully functional yet ? the RDF layer is not fully functional *yet*, but we will be switching it on soon. There have been problems with different versions of the Java libraries between the different developers, and that caused compilation problems and such. Apparently, that might be fixed now, so we should soon be able to switch on the agent "for real". Nina is just running some last-minute tests on it now to make sure that it is registering/deregistering services correctly. It will be sufficient to edit the RDF to change a service. It will also be sufficient to delete that sub-graph of the RDF document in order to delete your service. You can also do the same thing via the MOBY Central API as previously. I'll be sending out a message once the agent is running to let everyone know that they should keep an eye on their services just in case something goes wrong. I will do a complete backup of the database just beforehand in case there is an error. Cheers, M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Thu Nov 4 17:49:44 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 04 Nov 2004 14:49:44 -0800 Subject: [spam] [MOBY-dev] RDF ? In-Reply-To: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> References: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> Message-ID: <1099608583.29632.45.camel@mobycentral.icapture.ubc.ca> On Thu, 2004-11-04 at 06:09, Apache wrote: > Newbie in the concepts of biomoby, can someone explain me how the > RDF is supposed to work exactly ? Don't worry about being a newbie - this is new to everyone... > After having registered a service, how to unregister ? Is it sufficient > to edit the local copy of the RDF ? Or is (will) it (be) necessary to > re-post it ? Or is the RDF layer not fully functional yet ? the RDF layer is not fully functional *yet*, but we will be switching it on soon. There have been problems with different versions of the Java libraries between the different developers, and that caused compilation problems and such. Apparently, that might be fixed now, so we should soon be able to switch on the agent "for real". Nina is just running some last-minute tests on it now to make sure that it is registering/deregistering services correctly. It will be sufficient to edit the RDF to change a service. It will also be sufficient to delete that sub-graph of the RDF document in order to delete your service. You can also do the same thing via the MOBY Central API as previously. I'll be sending out a message once the agent is running to let everyone know that they should keep an eye on their services just in case something goes wrong. I will do a complete backup of the database just beforehand in case there is an error. Cheers, M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gss at ncgr.org Tue Nov 9 17:39:11 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 09 Nov 2004 15:39:11 -0700 Subject: [MOBY-dev] MOBY Meeting: Reminder & Details Message-ID: <4191470F.9010001@ncgr.org> This is a reminder that the MOBY autumn 2004 meeting is approaching quickly (11 days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register: Date : November 20-21 (Saturday & Sunday) Location : Santa Fe, New Mexico USA Venue : National Center for Genome Resources (www.ncgr.org) Fee : $50 USD/person (covers lunch and transportation between hotels and NCGR) The tentative agenda is as follows; please post any suggestions to the moby-l or moby-dev lists: Saturday, November 20, 2004: 8:30 am Bagels and coffee 9:00 am Semantic MOBY (Damian Gessler) 10:00 am Taverna (Martin Senger) 10:45 am Break 11:00 am MOBY Services (Mark Wilkinson) 12:00 pm Lunch provided 1:00 pm: Virtual Plant Network (Bill Beavis, discussion leader) 2:00 pm: Conceptual ways to merge S-MOBY, MOBY-S, and MyGrid in a real-world application (joined by Phil Lord via telecon [Manchester is seven hours ahead of Santa Fe]) 6:00pm Dinner Sunday, November 21, 2004 9:00 am Bagels and coffee 9:30 am Technical challenges to merging S-MOBY, MOBY-S, and MyGrid 11:30 am Next steps From letondal at pasteur.fr Wed Nov 10 11:47:01 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Wed, 10 Nov 2004 17:47:01 +0100 Subject: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? Message-ID: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Hi, I would have a question: how is the Moby-S branch of Biomoby connected to other efforts that seek to integrate Web services and Semantic Web? I mean groups, systems or forums such as: http://www.w3.org/2002/ws/swsig/ http://www.wsmo.org (Web service modelling Ontology) http://www.wsmo.org/wsml (Web Service Modeling Language) http://www.daml.org/services/owl-s (OWL-based Web service ontology) ...? BTW, I have just heard of this book: Developing Semantic Web Services (A. K. Peters) : http://www.akpeters.com/product.asp?ProdCode=2124 -- Catherine Letondal -- Institut Pasteur From letondal at pasteur.fr Fri Nov 12 04:48:21 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Fri, 12 Nov 2004 10:48:21 +0100 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Message-ID: On Nov 11, 2004, at 1:28 AM, Phillip Lord wrote: > > OWL-S/WSMO are trying to do a different thing to moby-s. The main aim > for these technologies is to use highly expressive logics to enable > automated composition and choreography of web services. This is a nice > idea, but, my own suspicion is that most biologists, or bioinformatics > service providers are not going to go to the effort to describe their > services logically. > > Moby-s on the other hand takes a more constrained view of > semantics. It's trying to produce semantic descriptions which are good > enough to reduce the problem for the biologist to selecting from one > or a short list, rather than then 500. > I meant S-Moby in fact, not Moby-S, sorry for this mistake. > There is a paper in this years ISWC (currently going on now!), which > you can get from here... > > http://www.cs.man.ac.uk/~phillord/download/publications/biomoby- > comparison-iswc2004.pdf > Thanks a lot for this information. I have read the paper, which indeed helped a lot to understand your underlying choices (BTW, I would be interested to know about the feedback it had at the ISCW conference - generally, bioinformatics is considered as a "very specific" area, and since the differences between "generial" applications such as e-commerce and e-science are very well explained in your paper, I'm curious to know whether the audience reacted). I still have a question about the comparison to OWL-S. In section 7 of your paper (Service provision and Service interfaces), you explain that OWL-S defines a grounding ontology, and that the 3 approaches (moby-s, s-moby and myGrid) have chosen a simpler approach. I understand that the problem that is addressed here is to have a high description not only of domain concepts, but also on their relations, and that this is not required in the 3 approaches, for different reasons. But I don't understand your explanations: How is the S-Moby interface defined by its "upper" ontology? I have carefully read the S-moby design document (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html), what do you call an upper ontology there - the set of RDF graphs submitted by providers? You also mention that moby-s interfaces are not heterogeneous (and thus does not need an ontology to interconnect concepts). What is not heterogeneous and why? Thanks for any reference or additional explananation, -- Catherine Letondal -- Institut Pasteur From gss at ncgr.org Fri Nov 12 12:26:54 2004 From: gss at ncgr.org (Gary Schiltz) Date: Fri, 12 Nov 2004 10:26:54 -0700 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Message-ID: <4194F25E.90904@ncgr.org> Catherine Letondal wrote: > > How is the S-Moby interface defined by its "upper" ontology? I have > carefully read the S-moby design document > (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html), > what do you call an upper ontology there - the set of RDF graphs > submitted by providers? Phil, since you're the ontology guy, feel free to chip in. If I understand the term "upper ontology" correctly, it refers to concepts and relationships (i.e. an ontology) that are somewhat generic, and thus applicable to multiple domains. As such, what is referred to in Semantic MOBY as the "canonical graph structure" (Figure 2 in the design document that you referenced) is the upper ontology. // Gary Schiltz, NCGR From gss at ncgr.org Fri Nov 12 16:57:05 2004 From: gss at ncgr.org (Gary Schiltz) Date: Fri, 12 Nov 2004 14:57:05 -0700 Subject: [MOBY-dev] MOBY Meeting: Reminder & Updates In-Reply-To: <4191470F.9010001@ncgr.org> References: <4191470F.9010001@ncgr.org> Message-ID: <419531B1.20208@ncgr.org> This is another reminder that the MOBY autumn 2004 meeting is quickly approaching (8 days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register. The meeting pages on semanticmoby.org have been updated. I look forward to seeing you there! ---- Gary Schiltz Principal Software Engineer National Center for Genome Resources Santa Fe, New Mexico USA From p.lord at cs.man.ac.uk Sun Nov 14 09:23:37 2004 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: 14 Nov 2004 14:23:37 +0000 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: <4194F25E.90904@ncgr.org> References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> <4194F25E.90904@ncgr.org> Message-ID: >>>>> "Gary" == Gary Schiltz writes: Gary> Catherine Letondal wrote: >> How is the S-Moby interface defined by its "upper" ontology? I >> have carefully read the S-moby design document >> (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html), >> what do you call an upper ontology there - the set of RDF graphs >> submitted by providers? Gary> Phil, since you're the ontology guy Having just been to the semantic web conference, I've realised that really, I'm a yeast biologist! Gary> feel free to chip in. If I understand the term "upper Gary> ontology" correctly, it refers to concepts and relationships Gary> (i.e. an ontology) that are somewhat generic, and thus Gary> applicable to multiple domains. This is generally correct. "Upper Ontology" is often used to describe an ontology of highly abstract concepts (1) that is meant to be shared among many ontologies. Some times, upper ontology just means the top half of an ontology. OWL-S has been described as an upper ontology, which is why I used terminology. Gary> As such, what is referred to in Semantic MOBY as the Gary> "canonical graph structure" (Figure 2 in the design document Gary> that you referenced) is the upper ontology. That's the thing I meant. Or, at least the vocabulary used to define this structure. "input", "output", "mapsto" and so on. Oh dear. I seem to be explaining the contents of a paper which I partly authored. This is like a comedian or cartoonist having to explain their jokes. Cheers Phil (1) The most notorious of which are "perjurant" and "endurant"; names which are nearly as self-explanatory as "ortholog" and "paralog". From gss at ncgr.org Tue Nov 16 12:39:01 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 16 Nov 2004 10:39:01 -0700 Subject: [MOBY-dev] MOBY Meeting: LAST CALL In-Reply-To: <419531B1.20208@ncgr.org> References: <4191470F.9010001@ncgr.org> <419531B1.20208@ncgr.org> Message-ID: <419A3B35.4020400@ncgr.org> This is a final reminder that the MOBY autumn 2004 meeting is next Saturday and Sunday, November 20 & 21 at NCGR in Santa Fe, New Mexico (four days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register. If you plan to attend, please register as soon as possible. The list of people I have recorded as registering are the following; please let me know if you are planning to attend and your name is not on the list: Andrew Farmer (NCGR) Bill Beavis (NCGR) Damian Gessler (NCGR) Dirk Haase (MIPS) Fernando Rojas (CIAT) Gary Schiltz (NCGR) Guy Davenport (CIMMYT) Manuel Ruiz (CIRAD) Mark Wilkinson (UBC) Martin Senger (EBI) Milko Skofic (IPGRI) Rex Nelson (USDA-ARS CICGR) Richard Bruskiewich (IRRI) Thomas Hazekamp (IPGRI) ---- Gary Schiltz Principal Software Engineer National Center for Genome Resources Santa Fe, New Mexico USA From gss at ncgr.org Tue Nov 16 17:37:36 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 16 Nov 2004 15:37:36 -0700 Subject: [MOBY-dev] [Fwd: an application for MOBY developers to consider] Message-ID: <419A8130.6010103@ncgr.org> Bill Beavis of NCGR asked that I pass this along to the list. Since I seem to remember the Listsrv software sometimes not liking attachments, I have put the attachments from Bill's email at www.semanticmoby.org/meeting/vpn instead of leaving them attached. The white paper Bill refers to is the file An_app_for_MOBY.pdf // Gary -------- Original Message -------- Subject: an application for MOBY developers to consider Date: Tue, 16 Nov 2004 14:55:23 -0700 From: Bill Beavis Greetings from Santa Fe, As many of you are aware, we'd like to visit about an application for the BioMOBY projects during our meeting this weekend. Because many of us work with Plant Information Resources we'd like to discuss the potential of using BioMOBY for development of a Virtual Plant Network (we may have to name it something else so that the acronym is not confused with another VPN). After visiting with the cognizant program officers, Stinger Guala and Manfred Zorn, I believe that we would have a reasonably good chance of obtaining support from the NSF-BDI for such a proposal. In order to stimulate discussion of the idea, please find attached a white paper utlining the concept and specific aims that might be included in such a proposal. Note that yellow highlights indicate areas that need clarification. Also, please find attached a couple of references that are germane to the discussion. For those of you who have been interested in utilizing MOBY for the CGIAR - Grand Challenge Program, there is a mechanism to obtain supplemental funding in this proposal for development of international collaborations. Thus, for those of you from non-US institutions, participation in this proposal could bring in some funding to support your efforts to utilize MOBY. For those of you who are not able to attend the MOBY meeting, you can join the discussion, which will begin at 1:00 pm MST, through a teleconference. Instructions for joining us: Date : Saturday, Nov. 20, 2004 Time : 1 pm Mountain Standard Time Discussion : Integrating Semantic MOBY and MOBY Services in a real world, distributed application: The Virtual Plant Network. Instructions to join: 1 - Dial the toll-free On-Demand Plus Number: 1-888-387-8686 (For international users, dial the international dial-out plus the country code (1) followed by 303-928-3281) 2 - Enter the Room number: 4139056, and press # 3 - You will be placed directly into the meeting if the moderator has already joined. If the moderator hasn't joined, you will be placed on hold for up to 10 minutes. Best regards, Bill Beavis From mwilkinson at mrl.ubc.ca Thu Nov 18 12:50:11 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 18 Nov 2004 09:50:11 -0800 Subject: [MOBY-dev] CVS tagged today Message-ID: <1100800211.21729.30.camel@mobycentral.icapture.ubc.ca> Hi all, Eddie is about to make some fairly significant commits in which the underlying XML parser for all of the Perl libraries is swapped out in favour of an XML namespace aware parser (XML::LibXML in place of XML::DOM) I have just tagged the repository November18_2004 so that we can rollback if that becomes necessary, and also to allow people to check-out what we know is a functional version if things go wrong. Anyone who is running a production shop using the Perl code SHOULD NOT update their code until we know that everything is working. It seems to pass all tests, but I want to give it a bit more time to reveal any oopsies :-) Cheers all! Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mark.fiers at wur.nl Fri Nov 26 09:57:35 2004 From: mark.fiers at wur.nl (Mark Fiers) Date: Fri, 26 Nov 2004 15:57:35 +0100 Subject: [MOBY-dev] question about the bioMoby python API In-Reply-To: <1097760189.14174.7.camel@prot1.rpbs.jussieu.fr> References: <1097760189.14174.7.camel@prot1.rpbs.jussieu.fr> Message-ID: <41A7445F.3000403@wur.nl> Hi We've succeeded in using the biomoby python module to create an in house biomoby service. Now we have registered this service and all of the sudden it doesn't work anymore. Has anybody successfully done this? As far as I can tell, ZSI does not parse the incoming xml correctly and does not execute the service. Upon parsing the xml (oh,I'm using http://mobycentral.cbr.nrc.ca/cgi-bin/gbrowse_moby): ################################################## ]]> ################################################## I I try a local script calling this function I get : ################################################## <moby:Object moby:namespace="PO_acc" moby:id="9054" moby:articleName="PO_query"/> ################################################## Which works fine. As far as I can see ZSI does not like the "" tag in the upper xml. It barfs and tells me : "Any cannot parse untyped element" Does anybod have a clue why this is going wrong? Cheers Mark Fiers Plant Research International Wageningen The Netherlands >I am modifying the API in order to deal with the RDF files and solving >some bugs: > >-Bug in the Dispatcher corrected (troubles with handling multiple >queries simultaneously) >added signatureURL and RDF for Registration process (in Service, >ServiceList) >-debug option when executing a service (trace of HTTP calls) in Central >and Service Class > (allows you to have the dump of all your SOAP transaction with the >webservice) > >if you want to trace a SOAP call while executing a service just put: > service.execute(mobyqueries, debug=True) >and you'll have the complete trace of the execution > >when you deal with the Moby Central Server: > client=Client(debug=True) >to trace execution of your moby Query > >As Errare Humanum Est, feel free to notify me errors I missed :) > >I expect to release a corrected version in the end of next week. >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://www.biomoby.org/mailman/listinfo/moby-dev > > > From wong.yan at netcourrier.com Sat Nov 27 17:01:51 2004 From: wong.yan at netcourrier.com (wong.yan@netcourrier.com) Date: Sat, 27 Nov 2004 17:01:51 CET Subject: [MOBY-dev] question about the bioMoby python API Message-ID: I am studying the problem, actually it comes from the fact that "body" is not a type and that the method dispatch.AsCGI() deserializes the SOAP content into a Python object (and as object body doesn't exist, it fails to do anything else). I'll change the ZSI package in order to treat bioMoby XML directly. I'll post a patch ASAP (expect it during the week). If people got a better work around... ------------------------------------------------------------- NetCourrier, votre bureau virtuel sur Internet : Mail, Agenda, Clubs, Toolbar... Web/Wap : www.netcourrier.com T?l?phone/Fax : 08 92 69 00 21 (0,34 ? TTC/min) Minitel: 3615 NETCOURRIER (0,16 ? TTC/min) From mwilkinson at mobile.rogers.com Tue Nov 30 16:10:06 2004 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Tue, 30 Nov 2004 16:10:06 -0500 Subject: [MOBY-dev] Message to Eddie Message-ID: <200411302109.iAUL8wKr010844@portal.open-bio.org> Sorry everyone, I don't have Eddie's email on my blackberry... Eddie, I have your new code running on the test server. All tests pass in both perl and java (good job!!) but the perl tests do complain about a concatenated blank string. That may indicate an insidious error, or may be trivial. Can you look into that? Otherwise, I'm thrilled!! That's the easiest major code shift we've ever done :-) Greetings from Montreal Dorval, underway to Halifax... M !!!!!!!!!!!!!!!! To respond to this message you MUST send your response to (note new address!) markw_mobile2 at illuminae dot com Responses to the reply-to address go directly to trash! !!!!!!!!!!!!!!!!!!!!!!!!!!!! From aw3 at ebgm.jussieu.fr Thu Nov 4 14:09:23 2004 From: aw3 at ebgm.jussieu.fr (Apache) Date: Thu, 4 Nov 2004 15:09:23 +0100 Subject: [MOBY-dev] RDF ? Message-ID: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> Hi, Newbie in the concepts of biomoby, can someone explain me how the RDF is supposed to work exactly ? After having registered a service, how to unregister ? Is it sufficient to edit the local copy of the RDF ? Or is (will) it (be) necessary to re-post it ? Or is the RDF layer not fully functional yet ? Idem for modifying the service specification. Thanks by advance ! Pierre From mwilkinson at mrl.ubc.ca Thu Nov 4 22:49:44 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 04 Nov 2004 14:49:44 -0800 Subject: [spam] [MOBY-dev] RDF ? In-Reply-To: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> References: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> Message-ID: <1099608583.29632.45.camel@mobycentral.icapture.ubc.ca> On Thu, 2004-11-04 at 06:09, Apache wrote: > Newbie in the concepts of biomoby, can someone explain me how the > RDF is supposed to work exactly ? Don't worry about being a newbie - this is new to everyone... > After having registered a service, how to unregister ? Is it sufficient > to edit the local copy of the RDF ? Or is (will) it (be) necessary to > re-post it ? Or is the RDF layer not fully functional yet ? the RDF layer is not fully functional *yet*, but we will be switching it on soon. There have been problems with different versions of the Java libraries between the different developers, and that caused compilation problems and such. Apparently, that might be fixed now, so we should soon be able to switch on the agent "for real". Nina is just running some last-minute tests on it now to make sure that it is registering/deregistering services correctly. It will be sufficient to edit the RDF to change a service. It will also be sufficient to delete that sub-graph of the RDF document in order to delete your service. You can also do the same thing via the MOBY Central API as previously. I'll be sending out a message once the agent is running to let everyone know that they should keep an eye on their services just in case something goes wrong. I will do a complete backup of the database just beforehand in case there is an error. Cheers, M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Thu Nov 4 22:49:44 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 04 Nov 2004 14:49:44 -0800 Subject: [spam] [MOBY-dev] RDF ? In-Reply-To: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> References: <20041104140923.GA3871@bioserv.rpbs.jussieu.fr> Message-ID: <1099608583.29632.45.camel@mobycentral.icapture.ubc.ca> On Thu, 2004-11-04 at 06:09, Apache wrote: > Newbie in the concepts of biomoby, can someone explain me how the > RDF is supposed to work exactly ? Don't worry about being a newbie - this is new to everyone... > After having registered a service, how to unregister ? Is it sufficient > to edit the local copy of the RDF ? Or is (will) it (be) necessary to > re-post it ? Or is the RDF layer not fully functional yet ? the RDF layer is not fully functional *yet*, but we will be switching it on soon. There have been problems with different versions of the Java libraries between the different developers, and that caused compilation problems and such. Apparently, that might be fixed now, so we should soon be able to switch on the agent "for real". Nina is just running some last-minute tests on it now to make sure that it is registering/deregistering services correctly. It will be sufficient to edit the RDF to change a service. It will also be sufficient to delete that sub-graph of the RDF document in order to delete your service. You can also do the same thing via the MOBY Central API as previously. I'll be sending out a message once the agent is running to let everyone know that they should keep an eye on their services just in case something goes wrong. I will do a complete backup of the database just beforehand in case there is an error. Cheers, M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gss at ncgr.org Tue Nov 9 22:39:11 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 09 Nov 2004 15:39:11 -0700 Subject: [MOBY-dev] MOBY Meeting: Reminder & Details Message-ID: <4191470F.9010001@ncgr.org> This is a reminder that the MOBY autumn 2004 meeting is approaching quickly (11 days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register: Date : November 20-21 (Saturday & Sunday) Location : Santa Fe, New Mexico USA Venue : National Center for Genome Resources (www.ncgr.org) Fee : $50 USD/person (covers lunch and transportation between hotels and NCGR) The tentative agenda is as follows; please post any suggestions to the moby-l or moby-dev lists: Saturday, November 20, 2004: 8:30 am Bagels and coffee 9:00 am Semantic MOBY (Damian Gessler) 10:00 am Taverna (Martin Senger) 10:45 am Break 11:00 am MOBY Services (Mark Wilkinson) 12:00 pm Lunch provided 1:00 pm: Virtual Plant Network (Bill Beavis, discussion leader) 2:00 pm: Conceptual ways to merge S-MOBY, MOBY-S, and MyGrid in a real-world application (joined by Phil Lord via telecon [Manchester is seven hours ahead of Santa Fe]) 6:00pm Dinner Sunday, November 21, 2004 9:00 am Bagels and coffee 9:30 am Technical challenges to merging S-MOBY, MOBY-S, and MyGrid 11:30 am Next steps From letondal at pasteur.fr Wed Nov 10 16:47:01 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Wed, 10 Nov 2004 17:47:01 +0100 Subject: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? Message-ID: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Hi, I would have a question: how is the Moby-S branch of Biomoby connected to other efforts that seek to integrate Web services and Semantic Web? I mean groups, systems or forums such as: http://www.w3.org/2002/ws/swsig/ http://www.wsmo.org (Web service modelling Ontology) http://www.wsmo.org/wsml (Web Service Modeling Language) http://www.daml.org/services/owl-s (OWL-based Web service ontology) ...? BTW, I have just heard of this book: Developing Semantic Web Services (A. K. Peters) : http://www.akpeters.com/product.asp?ProdCode=2124 -- Catherine Letondal -- Institut Pasteur From letondal at pasteur.fr Fri Nov 12 09:48:21 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Fri, 12 Nov 2004 10:48:21 +0100 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Message-ID: On Nov 11, 2004, at 1:28 AM, Phillip Lord wrote: > > OWL-S/WSMO are trying to do a different thing to moby-s. The main aim > for these technologies is to use highly expressive logics to enable > automated composition and choreography of web services. This is a nice > idea, but, my own suspicion is that most biologists, or bioinformatics > service providers are not going to go to the effort to describe their > services logically. > > Moby-s on the other hand takes a more constrained view of > semantics. It's trying to produce semantic descriptions which are good > enough to reduce the problem for the biologist to selecting from one > or a short list, rather than then 500. > I meant S-Moby in fact, not Moby-S, sorry for this mistake. > There is a paper in this years ISWC (currently going on now!), which > you can get from here... > > http://www.cs.man.ac.uk/~phillord/download/publications/biomoby- > comparison-iswc2004.pdf > Thanks a lot for this information. I have read the paper, which indeed helped a lot to understand your underlying choices (BTW, I would be interested to know about the feedback it had at the ISCW conference - generally, bioinformatics is considered as a "very specific" area, and since the differences between "generial" applications such as e-commerce and e-science are very well explained in your paper, I'm curious to know whether the audience reacted). I still have a question about the comparison to OWL-S. In section 7 of your paper (Service provision and Service interfaces), you explain that OWL-S defines a grounding ontology, and that the 3 approaches (moby-s, s-moby and myGrid) have chosen a simpler approach. I understand that the problem that is addressed here is to have a high description not only of domain concepts, but also on their relations, and that this is not required in the 3 approaches, for different reasons. But I don't understand your explanations: How is the S-Moby interface defined by its "upper" ontology? I have carefully read the S-moby design document (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html), what do you call an upper ontology there - the set of RDF graphs submitted by providers? You also mention that moby-s interfaces are not heterogeneous (and thus does not need an ontology to interconnect concepts). What is not heterogeneous and why? Thanks for any reference or additional explananation, -- Catherine Letondal -- Institut Pasteur From gss at ncgr.org Fri Nov 12 17:26:54 2004 From: gss at ncgr.org (Gary Schiltz) Date: Fri, 12 Nov 2004 10:26:54 -0700 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Message-ID: <4194F25E.90904@ncgr.org> Catherine Letondal wrote: > > How is the S-Moby interface defined by its "upper" ontology? I have > carefully read the S-moby design document > (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html), > what do you call an upper ontology there - the set of RDF graphs > submitted by providers? Phil, since you're the ontology guy, feel free to chip in. If I understand the term "upper ontology" correctly, it refers to concepts and relationships (i.e. an ontology) that are somewhat generic, and thus applicable to multiple domains. As such, what is referred to in Semantic MOBY as the "canonical graph structure" (Figure 2 in the design document that you referenced) is the upper ontology. // Gary Schiltz, NCGR From gss at ncgr.org Fri Nov 12 21:57:05 2004 From: gss at ncgr.org (Gary Schiltz) Date: Fri, 12 Nov 2004 14:57:05 -0700 Subject: [MOBY-dev] MOBY Meeting: Reminder & Updates In-Reply-To: <4191470F.9010001@ncgr.org> References: <4191470F.9010001@ncgr.org> Message-ID: <419531B1.20208@ncgr.org> This is another reminder that the MOBY autumn 2004 meeting is quickly approaching (8 days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register. The meeting pages on semanticmoby.org have been updated. I look forward to seeing you there! ---- Gary Schiltz Principal Software Engineer National Center for Genome Resources Santa Fe, New Mexico USA From p.lord at cs.man.ac.uk Sun Nov 14 14:23:37 2004 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: 14 Nov 2004 14:23:37 +0000 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: <4194F25E.90904@ncgr.org> References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> <4194F25E.90904@ncgr.org> Message-ID: >>>>> "Gary" == Gary Schiltz writes: Gary> Catherine Letondal wrote: >> How is the S-Moby interface defined by its "upper" ontology? I >> have carefully read the S-moby design document >> (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html), >> what do you call an upper ontology there - the set of RDF graphs >> submitted by providers? Gary> Phil, since you're the ontology guy Having just been to the semantic web conference, I've realised that really, I'm a yeast biologist! Gary> feel free to chip in. If I understand the term "upper Gary> ontology" correctly, it refers to concepts and relationships Gary> (i.e. an ontology) that are somewhat generic, and thus Gary> applicable to multiple domains. This is generally correct. "Upper Ontology" is often used to describe an ontology of highly abstract concepts (1) that is meant to be shared among many ontologies. Some times, upper ontology just means the top half of an ontology. OWL-S has been described as an upper ontology, which is why I used terminology. Gary> As such, what is referred to in Semantic MOBY as the Gary> "canonical graph structure" (Figure 2 in the design document Gary> that you referenced) is the upper ontology. That's the thing I meant. Or, at least the vocabulary used to define this structure. "input", "output", "mapsto" and so on. Oh dear. I seem to be explaining the contents of a paper which I partly authored. This is like a comedian or cartoonist having to explain their jokes. Cheers Phil (1) The most notorious of which are "perjurant" and "endurant"; names which are nearly as self-explanatory as "ortholog" and "paralog". From gss at ncgr.org Tue Nov 16 17:39:01 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 16 Nov 2004 10:39:01 -0700 Subject: [MOBY-dev] MOBY Meeting: LAST CALL In-Reply-To: <419531B1.20208@ncgr.org> References: <4191470F.9010001@ncgr.org> <419531B1.20208@ncgr.org> Message-ID: <419A3B35.4020400@ncgr.org> This is a final reminder that the MOBY autumn 2004 meeting is next Saturday and Sunday, November 20 & 21 at NCGR in Santa Fe, New Mexico (four days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register. If you plan to attend, please register as soon as possible. The list of people I have recorded as registering are the following; please let me know if you are planning to attend and your name is not on the list: Andrew Farmer (NCGR) Bill Beavis (NCGR) Damian Gessler (NCGR) Dirk Haase (MIPS) Fernando Rojas (CIAT) Gary Schiltz (NCGR) Guy Davenport (CIMMYT) Manuel Ruiz (CIRAD) Mark Wilkinson (UBC) Martin Senger (EBI) Milko Skofic (IPGRI) Rex Nelson (USDA-ARS CICGR) Richard Bruskiewich (IRRI) Thomas Hazekamp (IPGRI) ---- Gary Schiltz Principal Software Engineer National Center for Genome Resources Santa Fe, New Mexico USA From gss at ncgr.org Tue Nov 16 22:37:36 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 16 Nov 2004 15:37:36 -0700 Subject: [MOBY-dev] [Fwd: an application for MOBY developers to consider] Message-ID: <419A8130.6010103@ncgr.org> Bill Beavis of NCGR asked that I pass this along to the list. Since I seem to remember the Listsrv software sometimes not liking attachments, I have put the attachments from Bill's email at www.semanticmoby.org/meeting/vpn instead of leaving them attached. The white paper Bill refers to is the file An_app_for_MOBY.pdf // Gary -------- Original Message -------- Subject: an application for MOBY developers to consider Date: Tue, 16 Nov 2004 14:55:23 -0700 From: Bill Beavis Greetings from Santa Fe, As many of you are aware, we'd like to visit about an application for the BioMOBY projects during our meeting this weekend. Because many of us work with Plant Information Resources we'd like to discuss the potential of using BioMOBY for development of a Virtual Plant Network (we may have to name it something else so that the acronym is not confused with another VPN). After visiting with the cognizant program officers, Stinger Guala and Manfred Zorn, I believe that we would have a reasonably good chance of obtaining support from the NSF-BDI for such a proposal. In order to stimulate discussion of the idea, please find attached a white paper utlining the concept and specific aims that might be included in such a proposal. Note that yellow highlights indicate areas that need clarification. Also, please find attached a couple of references that are germane to the discussion. For those of you who have been interested in utilizing MOBY for the CGIAR - Grand Challenge Program, there is a mechanism to obtain supplemental funding in this proposal for development of international collaborations. Thus, for those of you from non-US institutions, participation in this proposal could bring in some funding to support your efforts to utilize MOBY. For those of you who are not able to attend the MOBY meeting, you can join the discussion, which will begin at 1:00 pm MST, through a teleconference. Instructions for joining us: Date : Saturday, Nov. 20, 2004 Time : 1 pm Mountain Standard Time Discussion : Integrating Semantic MOBY and MOBY Services in a real world, distributed application: The Virtual Plant Network. Instructions to join: 1 - Dial the toll-free On-Demand Plus Number: 1-888-387-8686 (For international users, dial the international dial-out plus the country code (1) followed by 303-928-3281) 2 - Enter the Room number: 4139056, and press # 3 - You will be placed directly into the meeting if the moderator has already joined. If the moderator hasn't joined, you will be placed on hold for up to 10 minutes. Best regards, Bill Beavis From mwilkinson at mrl.ubc.ca Thu Nov 18 17:50:11 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 18 Nov 2004 09:50:11 -0800 Subject: [MOBY-dev] CVS tagged today Message-ID: <1100800211.21729.30.camel@mobycentral.icapture.ubc.ca> Hi all, Eddie is about to make some fairly significant commits in which the underlying XML parser for all of the Perl libraries is swapped out in favour of an XML namespace aware parser (XML::LibXML in place of XML::DOM) I have just tagged the repository November18_2004 so that we can rollback if that becomes necessary, and also to allow people to check-out what we know is a functional version if things go wrong. Anyone who is running a production shop using the Perl code SHOULD NOT update their code until we know that everything is working. It seems to pass all tests, but I want to give it a bit more time to reveal any oopsies :-) Cheers all! Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mark.fiers at wur.nl Fri Nov 26 14:57:35 2004 From: mark.fiers at wur.nl (Mark Fiers) Date: Fri, 26 Nov 2004 15:57:35 +0100 Subject: [MOBY-dev] question about the bioMoby python API In-Reply-To: <1097760189.14174.7.camel@prot1.rpbs.jussieu.fr> References: <1097760189.14174.7.camel@prot1.rpbs.jussieu.fr> Message-ID: <41A7445F.3000403@wur.nl> Hi We've succeeded in using the biomoby python module to create an in house biomoby service. Now we have registered this service and all of the sudden it doesn't work anymore. Has anybody successfully done this? As far as I can tell, ZSI does not parse the incoming xml correctly and does not execute the service. Upon parsing the xml (oh,I'm using http://mobycentral.cbr.nrc.ca/cgi-bin/gbrowse_moby): ################################################## ]]> ################################################## I I try a local script calling this function I get : ################################################## <moby:Object moby:namespace="PO_acc" moby:id="9054" moby:articleName="PO_query"/> ################################################## Which works fine. As far as I can see ZSI does not like the "" tag in the upper xml. It barfs and tells me : "Any cannot parse untyped element" Does anybod have a clue why this is going wrong? Cheers Mark Fiers Plant Research International Wageningen The Netherlands >I am modifying the API in order to deal with the RDF files and solving >some bugs: > >-Bug in the Dispatcher corrected (troubles with handling multiple >queries simultaneously) >added signatureURL and RDF for Registration process (in Service, >ServiceList) >-debug option when executing a service (trace of HTTP calls) in Central >and Service Class > (allows you to have the dump of all your SOAP transaction with the >webservice) > >if you want to trace a SOAP call while executing a service just put: > service.execute(mobyqueries, debug=True) >and you'll have the complete trace of the execution > >when you deal with the Moby Central Server: > client=Client(debug=True) >to trace execution of your moby Query > >As Errare Humanum Est, feel free to notify me errors I missed :) > >I expect to release a corrected version in the end of next week. >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://www.biomoby.org/mailman/listinfo/moby-dev > > > From wong.yan at netcourrier.com Sat Nov 27 17:01:51 2004 From: wong.yan at netcourrier.com (wong.yan at netcourrier.com) Date: Sat, 27 Nov 2004 17:01:51 CET Subject: [MOBY-dev] question about the bioMoby python API Message-ID: I am studying the problem, actually it comes from the fact that "body" is not a type and that the method dispatch.AsCGI() deserializes the SOAP content into a Python object (and as object body doesn't exist, it fails to do anything else). I'll change the ZSI package in order to treat bioMoby XML directly. I'll post a patch ASAP (expect it during the week). If people got a better work around... ------------------------------------------------------------- NetCourrier, votre bureau virtuel sur Internet : Mail, Agenda, Clubs, Toolbar... Web/Wap : www.netcourrier.com T?l?phone/Fax : 08 92 69 00 21 (0,34 ? TTC/min) Minitel: 3615 NETCOURRIER (0,16 ? TTC/min) From mwilkinson at mobile.rogers.com Tue Nov 30 21:10:06 2004 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Tue, 30 Nov 2004 16:10:06 -0500 Subject: [MOBY-dev] Message to Eddie Message-ID: <200411302109.iAUL8wKr010844@portal.open-bio.org> Sorry everyone, I don't have Eddie's email on my blackberry... Eddie, I have your new code running on the test server. All tests pass in both perl and java (good job!!) but the perl tests do complain about a concatenated blank string. That may indicate an insidious error, or may be trivial. Can you look into that? Otherwise, I'm thrilled!! That's the easiest major code shift we've ever done :-) Greetings from Montreal Dorval, underway to Halifax... M !!!!!!!!!!!!!!!! To respond to this message you MUST send your response to (note new address!) markw_mobile2 at illuminae dot com Responses to the reply-to address go directly to trash! !!!!!!!!!!!!!!!!!!!!!!!!!!!!