From michael at acutrans.net Tue Aug 3 09:48:26 2004 From: michael at acutrans.net (Michael Jensen) Date: Tue Aug 3 09:49:48 2004 Subject: [MOBY-l] new MobyXMLObject.pm? Message-ID: I am about to use MobyXMLObject.pm for a new service, but was wondering if there was an updated version or if what I have (from mid-late 2003) is still the current working version. Is there some form of distribution for this that I am missing? -Michael Jensen michael@inblosam.com From steube at sdsc.edu Tue Aug 3 12:46:01 2004 From: steube at sdsc.edu (Ken Steube) Date: Tue Aug 3 12:47:16 2004 Subject: [MOBY-l] new MobyXMLObject.pm? In-Reply-To: Message-ID: That's the latest version, and it doesn't give you the IDs of the input/output parameters as specified in the API. I have a new MOBY project starting in the next few days and will update it to meet the API at that time. Until then it should still give you the proper answers as long as you don't require the IDs. Ken On Tue, 3 Aug 2004, Michael Jensen wrote: > I am about to use MobyXMLObject.pm for a new service, but was wondering > if there was an updated version or if what I have (from mid-late 2003) > is still the current working version. Is there some form of > distribution for this that I am missing? > > -Michael Jensen > michael@inblosam.com > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > -- -- -- Ken Steube San Diego Supercomputer Center University of California, San Diego, MC 0505 9500 Gilman Drive San Diego, California, 92093-0505 USA FAX (858) 822-3610 From letondal at pasteur.fr Mon Aug 9 07:01:29 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Mon Aug 9 07:02:35 2004 Subject: [MOBY-l] W3C Workshop on Semantic Web for Life Sciences Message-ID: <200408091101.i79B1Tfw286590@electre.pasteur.fr> Hi, Does someone from biomoby or s-moby go to this workshop? http://www.w3.org/2004/07/swls-cfp.html BTW, has someone heard of REWERSE in bioinformatics? http://rewerse.net/A2/ (Adding Semantics to the Bioinformatics Web) -- Catherine Letondal -- Pasteur Institute Computing Center From fgibbons at hms.harvard.edu Mon Aug 9 10:49:04 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Mon Aug 9 10:47:54 2004 Subject: [MOBY-l] W3C Workshop on Semantic Web for Life Sciences In-Reply-To: <200408091101.i79B1Tfw286590@electre.pasteur.fr> Message-ID: <5.2.1.1.2.20040809102432.019ccbf8@email.med.harvard.edu> Hi Catherine, My presentations at the BOSC & BioPathways conferences went over fairly well (providers of centralized databases didn't like it so much though... ;) Interestingly, though they didn't really advertise the fact, more and more protein/pathway databases are starting to provide web-service-based access. There's really a lot of excitement out there for applying semantic-web technologies to biology, and perhaps it's even reaching critical mass. Unfortunately, none of them was using MOBY (as far as I could tell), though awareness of MOBY as the canonical web-service-for-bioinformatics-framework seemed high. So I heard about this workshop (W3C on semantic web for life sciences) at BioPathways, and I'm certainly interested in going, if I can convince my boss that that's a direction our lab should go. The fact that there's no travel involved on my part should make it easier to convince him.... BTW, I just joined the BioGraphNet project up to sourceforge two weeks ago (biographnet.sourceforge.net). Today is my first day back in the lab, so I'm going to try and get code up for those who are interested in taking a look. -F At 07:01 AM 8/9/2004, Catherine Letondal wrote: >Hi, > >Does someone from biomoby or s-moby go to this workshop? >http://www.w3.org/2004/07/swls-cfp.html > >BTW, has someone heard of REWERSE in bioinformatics? >http://rewerse.net/A2/ >(Adding Semantics to the Bioinformatics Web) > >-- >Catherine Letondal -- Pasteur Institute Computing Center >_______________________________________________ >moby-l mailing list >moby-l@biomoby.org >http://biomoby.org/mailman/listinfo/moby-l PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From mwilkinson at mrl.ubc.ca Mon Aug 9 11:28:53 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon Aug 9 11:29:59 2004 Subject: [MISC] [MOBY-l] W3C Workshop on Semantic Web for Life Sciences In-Reply-To: <200408091101.i79B1Tfw286590@electre.pasteur.fr> References: <200408091101.i79B1Tfw286590@electre.pasteur.fr> Message-ID: <1092065333.1974.21.camel@myhost.mydomain> On Mon, 2004-08-09 at 04:01, Catherine Letondal wrote: > BTW, has someone heard of REWERSE in bioinformatics? > http://rewerse.net/A2/ > (Adding Semantics to the Bioinformatics Web) That looks really interesting! I wonder if it is possible for N.American participants to join freely, or if they must be invited? M -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From steube at sdsc.edu Sat Aug 14 19:03:55 2004 From: steube at sdsc.edu (Ken Steube) Date: Sat Aug 14 19:04:51 2004 Subject: [MOBY-l] base64 In-Reply-To: Message-ID: Hi all, if I use base64 as recommened in Mark's tutorial with this: return SOAP::Data->type('base64' => (responseHeader("www.sdsc.edu") . $MOBY_RESPONSE . responseFooter)); how do I undo the encoding? The return value of my service is an object but I want the string of XML. Ken From mwilkinson at mobile.rogers.com Sat Aug 14 19:01:21 2004 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Sat Aug 14 19:07:59 2004 Subject: [MOBY-l] base64 Message-ID: <200408142307.i7EN7sKr022785@portal.open-bio.org> If you are using SOAP::Lite it will happen automatically on the server side. If you are using Moby::Client::Service it also handles everything for you. M -----Original Message----- From: Ken Steube Date: Sat, 14 Aug 2004 16:03:55 To: Subject: [MOBY-l] base64 Hi all, if I use base64 as recommened in Mark's tutorial with this: return SOAP::Data->type('base64' => (responseHeader("www.sdsc.edu") . $MOBY_RESPONSE . responseFooter)); how do I undo the encoding? The return value of my service is an object but I want the string of XML. Ken _______________________________________________ moby-l mailing list moby-l@biomoby.org http://biomoby.org/mailman/listinfo/moby-l !!!!!!!!!!!!!!!! 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 steube at sdsc.edu Mon Aug 23 18:41:34 2004 From: steube at sdsc.edu (Ken Steube) Date: Mon Aug 23 18:42:13 2004 Subject: [MOBY-l] What type of collection? In-Reply-To: Message-ID: Say, how do I query Moby-Central to figure out what a collection input needs to look like for a service? Our WSDL doesn't give the full story. I just changed one of my services to take a collection as input and now as far as I know nobody can figure out how to run it without asking me. Ken From markw at illuminae.com Mon Aug 23 20:50:24 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon Aug 23 22:16:17 2004 Subject: [MISC] [MOBY-l] What type of collection? In-Reply-To: References: Message-ID: <1093308624.11536.56.camel@myhost.mydomain> It's part of the service signature that is passed back to you in the XML message (or parsed into the MOBY::Client::ServiceInstance object) when you make a findService call to MOBY Central. There is currently no client that is capable of hitting services that consume collections, however (AFAIK... it may be that Taverna can do it??) so that might be causing the headaches for your users. M On Mon, 2004-08-23 at 15:41, Ken Steube wrote: > Say, how do I query Moby-Central to figure out what a collection input > needs to look like for a service? Our WSDL doesn't give the full story. > > I just changed one of my services to take a collection as input and now as > far as I know nobody can figure out how to run it without asking me. > > Ken > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From gordonp at cbr.nrc.ca Tue Aug 24 13:45:36 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Tue Aug 24 13:46:15 2004 Subject: [MOBY-l] findServices problem Message-ID: <412B7EC0.4010009@cbr.nrc.ca> Hey folks, If I submit a LSID type request to MOBY central's findServices, like so urn:lsid:biomoby.org:objectclass:DNASequence I get every service back! Does MOBY central not recognize the LSID format? If it doesn't recognize a format, should it return every service? The LSID style is the data type of ID returned by Java MOBY objects. I wasn't running into this problem with base Objects because I was writing those data types myself. From steube at sdsc.edu Tue Aug 24 15:18:20 2004 From: steube at sdsc.edu (Ken Steube) Date: Tue Aug 24 15:19:07 2004 Subject: [MOBY-l] services list CGI updated In-Reply-To: <1093308624.11536.56.camel@myhost.mydomain> Message-ID: Hiya, I updated my service list CGI to show email contact a link to view contents of collection inputs/outputs/parameters The CGI is still at http://plantsp.sdsc.edu/plantsp/cgi-bin/MOBY/list.services.cgi Ken -- -- -- Ken Steube San Diego Supercomputer Center University of California, San Diego, MC 0505 9500 Gilman Drive San Diego, California, 92093-0505 USA FAX (858) 822-3610 From fgibbons at hms.harvard.edu Tue Aug 24 16:35:05 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Tue Aug 24 16:35:57 2004 Subject: [MOBY-l] Problems searching with semantic moby dot org Message-ID: <5.2.1.1.2.20040824162140.019fbf40@email.med.harvard.edu> From mwilkinson at mrl.ubc.ca Tue Aug 24 16:47:07 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Aug 24 16:47:45 2004 Subject: [SPAM] [MOBY-l] findServices problem In-Reply-To: <412B7EC0.4010009@cbr.nrc.ca> References: <412B7EC0.4010009@cbr.nrc.ca> Message-ID: <1093380427.3646.178.camel@myhost.mydomain> I am unable to duplicate this error - when I run it, I get only three services back. Can you please send me your full message so that I can check the structure? I have noticed that, if there is an uncaught error in the message structure, it will by default return everything. This is because it auto-substitutes "moby" for the service type if that parameter isn't included in the search request, and in the absence of any other parameters (since the message had an invalid structure) it will find everything. I don't know how badly it would hurt anyone to switch off this default behaviour...?? M On Tue, 2004-08-24 at 10:45, Paul Gordon wrote: > Hey folks, > > If I submit a LSID type request to MOBY central's findServices, like so > > > urn:lsid:biomoby.org:objectclass:DNASequence > > > > I get every service back! Does MOBY central not recognize the LSID format? > If it doesn't recognize a format, should it return every service? The > LSID style is the data type of ID returned by Java MOBY objects. I > wasn't running into this problem with base Objects because I was writing > those data types myself. > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From fgibbons at hms.harvard.edu Tue Aug 24 17:41:18 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Tue Aug 24 17:39:16 2004 Subject: [MOBY-l] Fwd: Problems searching with semantic moby dot org Message-ID: <5.2.1.1.2.20040824173935.01aa3ef8@email.med.harvard.edu> Mark, For some reason, the entire body of my recent posting was stripped. I also had a message telling me that the message would be subject to moderator approval (perhaps because of the included HTML?). I'm re-sending in plain text. -Frank >Date: Tue, 24 Aug 2004 16:35:05 -0400 >To: moby-l@biomoby.org >From: Frank Gibbons >Subject: Problems searching with semantic moby dot org > >Hi, > >I've tried using semanticmoby.org to see what's out there in the S-MOBY >world. I know it just went up a few weeks ago, so it's bound to have some >hiccups. Several things struck me immediately, and I thought you'd like to >hear about them: > >1. How do I compose a query? There is a link to 'Help on Searching', but >it seems curiously generic ('HELLO means the same thing as hello as does >HeLlo"), not at all specific to the semantic task at hand. Also, it >appears that the page works by allowing the user to specify a provider, >subject and object of interest, but isn't the real thing supposed to query >using an RDF graph of subject-predicate-object? How far off is that? > >2. A couple of examples would help a lot, both for the current >(provider-subject-object) incarnation, and especially when the full RDF >capabilities are added. I believe this is true even if the services that >are 'discovered' don't do much that's practical yet. > >3. When I click the 'search' button, this message appears: > > > >Not Found > > > >The requested URL /keyword-search was not found on this server. > >---------- >Apache/2.0.49 (Unix) DAV/2 Resin/3.0.8 Server at semanticmoby.org Port 80 > >Just my 2 cents. > >-Frank > >PhD, Computational Biologist, >Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. >Tel: 617-432-3555 Fax: >617-432-3557 http://llama.med.harvard.edu/~fgibbons PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From gss at ncgr.org Tue Aug 24 19:25:27 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue Aug 24 19:29:38 2004 Subject: [MOBY-l] Fwd: Problems searching with semantic moby dot org In-Reply-To: <5.2.1.1.2.20040824173935.01aa3ef8@email.med.harvard.edu> References: <5.2.1.1.2.20040824173935.01aa3ef8@email.med.harvard.edu> Message-ID: <412BCE67.5090801@ncgr.org> Frank, Sorry, but the semanticmoby.org web site is still pretty rough, hence the "Under Construction" banner needs to be taken quite literally for the time being. I have about three weeks worth of work on Semantic MOBY, running locally, that has not yet been released to semanticmoby.org; things should be in a much better state by the end of the week. That said, here is some (long-winded) clarification - I need to add similar explanation to the site itself. Semantic MOBY does indeed use an RDF-based discovery and engagement paradigm (post the RDF/XML serialization of a query graph to the discovery server and get back a set of matching graphs as RDF/XML; post an RDF/XML ("input") graph to a Semantic MOBY provider and get the RDF/XML graph back (as "output"), where the graph has been augmented by having blank nodes filled in). This really is the heart of Semantic MOBY, and it needs to be (will be as soon as I can get to it) documented and made accessible. However, RDF/XML is very unwieldy for non-geek users. Hence, one of the goals of Semantic MOBY was to have a "Google-like" interface for discovery and engagement Semantic MOBY service providers. That is what you see at the www.semanticmoby.org home page. In a sense, it's the Semantic equivalent of the MOBY Central 'gbrowse' front end (http://mobycentral.cbr.nrc.ca/cgi-bin/gbrowse_moby) and the very immature beginning of a "Semantic Google". In a nutshell, here is how this works: when the Semantic MOBY discovery server decides to add a provider graph to its repository of known services, it looks at all the nodes in the graph that are of type moby:Provider, moby:Subject, and moby:Object. For each of these nodes, it looks for other statements asserting the node to be of other types (RDF nodes can have multiple rdf:type statements made about them). For each of these additional types (i.e. the objects of the rdf:type statements), the discovery server retrieves the class definition (to be a good MOBY player requires that all classes are retrieveable by HTTP GET - see, for example, the Semantic MOBY core definitions at www.semanticmoby.org/ontologies/core), and looks for moby:keyword property statements in these class definition. For each such keyword, the discovery server remembers that the provider node (or subject node or object node) in the provider graph is associated with that keyword. When you do a search from the www.semanticmoby.org page, the discovery server looks in its stored keyword/provider associations in order to find providers that match "by keyword" and displays links to them in Google-like fashion. That gets us to the provider engagement side of the equation, which would take at least as long to describe as the description that I just gave about discovery, so I'm going to skip it for now, other than to say that the links are to another Semantic MOBY service which tries to invoke and display the results of invoking the provider. This "keyword based" search is completely separate from the Semantic, RDF-graph based search, which is also there (but again, not yet documented). We (Damian and I) decided that the most conspicuous, hence first thing you see on the site, version of Semantic MOBY search should be up front; the RDF-graph based search, though in a sense more what Semantic MOBY is all about, will be less conspicuous, to be dug up by the "real geeks" such as readers of this list :-) Regarding the "Not Found" error you got, I believe that the Servlet container had failed to restart when the server got rebooted the other day - sorry. It is up now, but again, a lot of the functionality that I described is still under construction, and should be there by the end of the week... // Gary Frank Gibbons wrote: > Mark, > > For some reason, the entire body of my recent posting was stripped. I > also had a message telling me that the message would be subject to > moderator approval (perhaps because of the included HTML?). I'm > re-sending in plain text. > > -Frank > >> Date: Tue, 24 Aug 2004 16:35:05 -0400 >> To: moby-l@biomoby.org >> From: Frank Gibbons >> Subject: Problems searching with semantic moby dot org >> >> Hi, >> >> I've tried using semanticmoby.org to see what's out there in the >> S-MOBY world. I know it just went up a few weeks ago, so it's bound to >> have some hiccups. Several things struck me immediately, and I thought >> you'd like to hear about them: >> >> 1. How do I compose a query? There is a link to 'Help on Searching', >> but it seems curiously generic ('HELLO means the same thing as hello >> as does HeLlo"), not at all specific to the semantic task at hand. >> Also, it appears that the page works by allowing the user to specify a >> provider, subject and object of interest, but isn't the real thing >> supposed to query using an RDF graph of subject-predicate-object? How >> far off is that? >> >> 2. A couple of examples would help a lot, both for the current >> (provider-subject-object) incarnation, and especially when the full >> RDF capabilities are added. I believe this is true even if the >> services that are 'discovered' don't do much that's practical yet. >> >> 3. When I click the 'search' button, this message appears: >> >> >> >> Not Found >> >> >> >> The requested URL /keyword-search was not found on this server. >> >> ---------- >> Apache/2.0.49 (Unix) DAV/2 Resin/3.0.8 Server at semanticmoby.org Port 80 >> >> Just my 2 cents. >> >> -Frank >> >> PhD, Computational Biologist, >> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA >> 02115, USA. >> Tel: 617-432-3555 Fax: 617-432-3557 >> http://llama.med.harvard.edu/~fgibbons > > > PhD, Computational Biologist, > Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, > USA. > Tel: 617-432-3555 Fax: 617-432-3557 > http://llama.med.harvard.edu/~fgibbons > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > From fgibbons at hms.harvard.edu Wed Aug 25 11:56:39 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Wed Aug 25 11:54:32 2004 Subject: [MOBY-l] Fwd: Problems searching with semantic moby In-Reply-To: <412BCE67.5090801@ncgr.org> References: <5.2.1.1.2.20040824173935.01aa3ef8@email.med.harvard.edu> <5.2.1.1.2.20040824173935.01aa3ef8@email.med.harvard.edu> Message-ID: <5.2.1.1.2.20040825114659.019cd8c8@email.med.harvard.edu> Gary, At 07:25 PM 8/24/2004, you wrote: >However, RDF/XML is very unwieldy for non-geek users. Hence, one of the >goals of Semantic MOBY was to have a "Google-like" interface for discovery >and engagement Semantic MOBY service providers. That is what you see at >the www.semanticmoby.org home page. In a sense, it's the Semantic >equivalent of the MOBY Central 'gbrowse' front end >(http://mobycentral.cbr.nrc.ca/cgi-bin/gbrowse_moby) and the very immature >beginning of a "Semantic Google". Thanks for that detailed response. Query composition seems like the biggest hurdle to using 'smoogle' (Semantic-Moby Google), and your provider/subject/object interface certainly seems like a sensible first step towards simplifying it. On a broader level, what do you know about how other semantic web groups are approaching this problem? Another question/suggestion: are there any toy services out there, that I could play with? What are some of the providers? I'm thinking back to the first days of Mosaic, before there were any search engines. You'd fire up Mosaic, and it would load a page from NCSA listing all the new websites for that day, with a little textual description. (It's astonishing to think that this was ever possible!) I guess Ken Steube's scripts do something similar, albeit dynamically, providing a list of all available MOBY-S services. Given the world's general unfamiliarity with semantic web concepts, I wonder if it wouldn't help to list a few of the available S-MOBY services, just to get people playing. Right now, I don't know where to look for services. One last thing: I tried using the search interface again, I'm still getting the error about '/keyword-search not found'. This is exciting stuff, I'm looking forward to seeing the updated page you're working on now! -F PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From gordonp at cbr.nrc.ca Thu Aug 26 11:59:23 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu Aug 26 11:59:56 2004 Subject: [MOBY-l] findServices problem In-Reply-To: <1093533386.1979.3.camel@myhost.mydomain> References: <412B7EC0.4010009@cbr.nrc.ca> <1093380427.3646.178.camel@myhost.mydomain> <412DF427.1000507@cbr.nrc.ca> <1093533386.1979.3.camel@myhost.mydomain> Message-ID: <412E08DB.1010704@cbr.nrc.ca> Hmm. This search retrieves things that work on Object, VirtualSequence, GenericSequence, NucleotideSequence, or DNASequence. The DNASequence doesn't have a namespace, so none is provided as input to findService. The behaviour of MOBY Central is to return services that match any namespace for these objects, which will produce services that can't use the template input. e.g. PDBtoMotifID comes up as a service, since it works on an Object, but the fact that it requires a PDB namspace object makes a non-namespaced DNASequence invalid input. How can we run findServices MOBY Central to distinguish between any namespace and no namespace? Is it not a misinterpretation to consider a blank namespace as a wildcard (since namespaces are not a hierarchy)? Mark Wilkinson wrote: >It's because you have "expand objects" switched on. You aren't finding >"all", but you are finding "many" > >M > > >>Hey Mark, >> >> Here's the message... >> >>Mark Wilkinson wrote: >> >> >>>I am unable to duplicate this error - when I run it, I get only three >>>services back. >>> >>>Can you please send me your full message so that I can check the >>>structure? >>> >>> >> >> >> >>urn:lsid:biomoby.org:objectclass:DNASequence >> >> >> >> >> >> >> >> >>moby >> >>1 >>1 >>0 >> >> >> >> >> >> From mwilkinson at mrl.ubc.ca Thu Aug 26 12:08:05 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu Aug 26 12:08:57 2004 Subject: [SPAM] Re:[MOBY-l] findServices problem In-Reply-To: <412E08DB.1010704@cbr.nrc.ca> References: <412B7EC0.4010009@cbr.nrc.ca> <1093380427.3646.178.camel@myhost.mydomain> <412DF427.1000507@cbr.nrc.ca> <1093533386.1979.3.camel@myhost.mydomain> <412E08DB.1010704@cbr.nrc.ca> Message-ID: <1093536485.2025.27.camel@myhost.mydomain> On Thu, 2004-08-26 at 08:59, Paul Gordon wrote: > e.g. PDBtoMotifID comes up as a service, since it > works on an Object, but the fact that it requires a PDB namspace object > makes a non-namespaced DNASequence invalid input. Aha... I agree, that is a bug. I'll work on that later this week. M -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From midori at ebi.ac.uk Thu Aug 26 13:58:01 2004 From: midori at ebi.ac.uk (Midori Harris) Date: Thu Aug 26 13:58:35 2004 Subject: [MOBY-l] Standards and Ontologies for Functional Genomics Conference (fwd) Message-ID: Dear Colleague, This message is posted to several lists and we apologize if you receive multiple copies that become annoying. However, please forward it to your colleagues who might be interested in attending this conference and may not have heard about the event. Registration Is Open for the 2nd Standards and Ontologies for Functional Genomics Meeting to be held at the University of Pennsylvania, Philadelphia, PA October 23-26, 2004 The 2nd Standards and Ontologies for Functional Genomics (SOFG) Meeting will be held on October 23-26, 2004 in Philadelphia, PA USA. Information about the SOFG meeting can be found at the SOFG site http://www.sofg.org/ or at http://www.jax.org/courses/events/coursedetails.do?id=44 . Registrations and abstracts will be accepted until Sept. 23, 2004 or until the event has filled. Student support to attend is available. Downloadable pdf registration form URL: http://www.jax.org/courses/2004/sfog_reg.pdf Abstracts submitted by Sept. 10 will be considered for oral presentation by Organizers and Session Chairs. Abstracts submitted after Sept 10 will be considered for poster session only. Abstract submissions will be reproduced and included with the conference notebook material. If you wish to submit, please follow the http://www.jax.org/courses/2004/functional_genomics_abstract_guidelines.html . The conference will focus on advances in the development of standards and ontologies to facilitate the exchange of biological information by computers and computation analysis applications. A particular emphasis will be on developments in ontological annotation systems for the genomics and bioinformatics communities. Toward this end, students and established investigators from different areas of computer science, experimental biology, and bioinformatics will have an opportunity to share new ideas, demonstrate new tools and applications, and identify potential collaborations. Topics include: * Ontological Systems: Theory and Development * Ontologies for Biology Systems * Ontology Systems Development: Electronic Demonstrations * Thesauri, Nomenclatures and the Biomedical Literature * Standards and Protocols * Functional Genomics Applications * From Resource to Application Plenary Speaker Carole Goble, University of Manchester Conference Organizers and Session Chairs: Judith Blake, The Jackson Laboratory Midori Harris, EBI-Hinxton Win Hide, SANBI Lynette Hirschman, MITRE Suzanna Lewis, UC Berkeley Helen Parkinson, EBI-Hinxton Martin Ringwald, The Jackson Laboratory Susanan-Assunta Sansone, EBI-Hinxton Chris Stoeckert, UPenn Please contact me with any questions about this meeting. Judi Alexander Medlin Lead Coordinator, Courses and Conferences The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6326 Fax: 207-288-6080 Please check out our web site http://www.jax.org/courses/events/current.do for the current listing of courses and conferences at The Jackson Laboratory. -- Helen Parkinson, PhD Curation Coordinator Microarray Informatics Team EBI From michael at acutrans.net Tue Aug 3 09:48:26 2004 From: michael at acutrans.net (Michael Jensen) Date: Tue, 3 Aug 2004 09:48:26 -0400 Subject: [MOBY-l] new MobyXMLObject.pm? Message-ID: I am about to use MobyXMLObject.pm for a new service, but was wondering if there was an updated version or if what I have (from mid-late 2003) is still the current working version. Is there some form of distribution for this that I am missing? -Michael Jensen michael at inblosam.com From steube at sdsc.edu Tue Aug 3 12:46:01 2004 From: steube at sdsc.edu (Ken Steube) Date: Tue, 3 Aug 2004 09:46:01 -0700 (PDT) Subject: [MOBY-l] new MobyXMLObject.pm? In-Reply-To: Message-ID: That's the latest version, and it doesn't give you the IDs of the input/output parameters as specified in the API. I have a new MOBY project starting in the next few days and will update it to meet the API at that time. Until then it should still give you the proper answers as long as you don't require the IDs. Ken On Tue, 3 Aug 2004, Michael Jensen wrote: > I am about to use MobyXMLObject.pm for a new service, but was wondering > if there was an updated version or if what I have (from mid-late 2003) > is still the current working version. Is there some form of > distribution for this that I am missing? > > -Michael Jensen > michael at inblosam.com > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > -- -- -- Ken Steube San Diego Supercomputer Center University of California, San Diego, MC 0505 9500 Gilman Drive San Diego, California, 92093-0505 USA FAX (858) 822-3610 From letondal at pasteur.fr Mon Aug 9 07:01:29 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Mon, 09 Aug 2004 13:01:29 +0200 Subject: [MOBY-l] W3C Workshop on Semantic Web for Life Sciences Message-ID: <200408091101.i79B1Tfw286590@electre.pasteur.fr> Hi, Does someone from biomoby or s-moby go to this workshop? http://www.w3.org/2004/07/swls-cfp.html BTW, has someone heard of REWERSE in bioinformatics? http://rewerse.net/A2/ (Adding Semantics to the Bioinformatics Web) -- Catherine Letondal -- Pasteur Institute Computing Center From fgibbons at hms.harvard.edu Mon Aug 9 10:49:04 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Mon, 09 Aug 2004 10:49:04 -0400 Subject: [MOBY-l] W3C Workshop on Semantic Web for Life Sciences In-Reply-To: <200408091101.i79B1Tfw286590@electre.pasteur.fr> Message-ID: <5.2.1.1.2.20040809102432.019ccbf8@email.med.harvard.edu> Hi Catherine, My presentations at the BOSC & BioPathways conferences went over fairly well (providers of centralized databases didn't like it so much though... ;) Interestingly, though they didn't really advertise the fact, more and more protein/pathway databases are starting to provide web-service-based access. There's really a lot of excitement out there for applying semantic-web technologies to biology, and perhaps it's even reaching critical mass. Unfortunately, none of them was using MOBY (as far as I could tell), though awareness of MOBY as the canonical web-service-for-bioinformatics-framework seemed high. So I heard about this workshop (W3C on semantic web for life sciences) at BioPathways, and I'm certainly interested in going, if I can convince my boss that that's a direction our lab should go. The fact that there's no travel involved on my part should make it easier to convince him.... BTW, I just joined the BioGraphNet project up to sourceforge two weeks ago (biographnet.sourceforge.net). Today is my first day back in the lab, so I'm going to try and get code up for those who are interested in taking a look. -F At 07:01 AM 8/9/2004, Catherine Letondal wrote: >Hi, > >Does someone from biomoby or s-moby go to this workshop? >http://www.w3.org/2004/07/swls-cfp.html > >BTW, has someone heard of REWERSE in bioinformatics? >http://rewerse.net/A2/ >(Adding Semantics to the Bioinformatics Web) > >-- >Catherine Letondal -- Pasteur Institute Computing Center >_______________________________________________ >moby-l mailing list >moby-l at biomoby.org >http://biomoby.org/mailman/listinfo/moby-l PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From mwilkinson at mrl.ubc.ca Mon Aug 9 11:28:53 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon, 09 Aug 2004 08:28:53 -0700 Subject: [MISC] [MOBY-l] W3C Workshop on Semantic Web for Life Sciences In-Reply-To: <200408091101.i79B1Tfw286590@electre.pasteur.fr> References: <200408091101.i79B1Tfw286590@electre.pasteur.fr> Message-ID: <1092065333.1974.21.camel@myhost.mydomain> On Mon, 2004-08-09 at 04:01, Catherine Letondal wrote: > BTW, has someone heard of REWERSE in bioinformatics? > http://rewerse.net/A2/ > (Adding Semantics to the Bioinformatics Web) That looks really interesting! I wonder if it is possible for N.American participants to join freely, or if they must be invited? M -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From steube at sdsc.edu Sat Aug 14 19:03:55 2004 From: steube at sdsc.edu (Ken Steube) Date: Sat, 14 Aug 2004 16:03:55 -0700 (PDT) Subject: [MOBY-l] base64 In-Reply-To: Message-ID: Hi all, if I use base64 as recommened in Mark's tutorial with this: return SOAP::Data->type('base64' => (responseHeader("www.sdsc.edu") . $MOBY_RESPONSE . responseFooter)); how do I undo the encoding? The return value of my service is an object but I want the string of XML. Ken From mwilkinson at mobile.rogers.com Sat Aug 14 19:01:21 2004 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Sat, 14 Aug 2004 19:01:21 -0400 Subject: [MOBY-l] base64 Message-ID: <200408142307.i7EN7sKr022785@portal.open-bio.org> If you are using SOAP::Lite it will happen automatically on the server side. If you are using Moby::Client::Service it also handles everything for you. M -----Original Message----- From: Ken Steube Date: Sat, 14 Aug 2004 16:03:55 To: Subject: [MOBY-l] base64 Hi all, if I use base64 as recommened in Mark's tutorial with this: return SOAP::Data->type('base64' => (responseHeader("www.sdsc.edu") . $MOBY_RESPONSE . responseFooter)); how do I undo the encoding? The return value of my service is an object but I want the string of XML. Ken _______________________________________________ moby-l mailing list moby-l at biomoby.org http://biomoby.org/mailman/listinfo/moby-l !!!!!!!!!!!!!!!! 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 steube at sdsc.edu Mon Aug 23 18:41:34 2004 From: steube at sdsc.edu (Ken Steube) Date: Mon, 23 Aug 2004 15:41:34 -0700 (PDT) Subject: [MOBY-l] What type of collection? In-Reply-To: Message-ID: Say, how do I query Moby-Central to figure out what a collection input needs to look like for a service? Our WSDL doesn't give the full story. I just changed one of my services to take a collection as input and now as far as I know nobody can figure out how to run it without asking me. Ken From markw at illuminae.com Mon Aug 23 20:50:24 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 23 Aug 2004 17:50:24 -0700 Subject: [MISC] [MOBY-l] What type of collection? In-Reply-To: References: Message-ID: <1093308624.11536.56.camel@myhost.mydomain> It's part of the service signature that is passed back to you in the XML message (or parsed into the MOBY::Client::ServiceInstance object) when you make a findService call to MOBY Central. There is currently no client that is capable of hitting services that consume collections, however (AFAIK... it may be that Taverna can do it??) so that might be causing the headaches for your users. M On Mon, 2004-08-23 at 15:41, Ken Steube wrote: > Say, how do I query Moby-Central to figure out what a collection input > needs to look like for a service? Our WSDL doesn't give the full story. > > I just changed one of my services to take a collection as input and now as > far as I know nobody can figure out how to run it without asking me. > > Ken > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From gordonp at cbr.nrc.ca Tue Aug 24 13:45:36 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Tue, 24 Aug 2004 11:45:36 -0600 Subject: [MOBY-l] findServices problem Message-ID: <412B7EC0.4010009@cbr.nrc.ca> Hey folks, If I submit a LSID type request to MOBY central's findServices, like so urn:lsid:biomoby.org:objectclass:DNASequence I get every service back! Does MOBY central not recognize the LSID format? If it doesn't recognize a format, should it return every service? The LSID style is the data type of ID returned by Java MOBY objects. I wasn't running into this problem with base Objects because I was writing those data types myself. From steube at sdsc.edu Tue Aug 24 15:18:20 2004 From: steube at sdsc.edu (Ken Steube) Date: Tue, 24 Aug 2004 12:18:20 -0700 (PDT) Subject: [MOBY-l] services list CGI updated In-Reply-To: <1093308624.11536.56.camel@myhost.mydomain> Message-ID: Hiya, I updated my service list CGI to show email contact a link to view contents of collection inputs/outputs/parameters The CGI is still at http://plantsp.sdsc.edu/plantsp/cgi-bin/MOBY/list.services.cgi Ken -- -- -- Ken Steube San Diego Supercomputer Center University of California, San Diego, MC 0505 9500 Gilman Drive San Diego, California, 92093-0505 USA FAX (858) 822-3610 From fgibbons at hms.harvard.edu Tue Aug 24 16:35:05 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Tue, 24 Aug 2004 16:35:05 -0400 Subject: [MOBY-l] Problems searching with semantic moby dot org Message-ID: <5.2.1.1.2.20040824162140.019fbf40@email.med.harvard.edu> From mwilkinson at mrl.ubc.ca Tue Aug 24 16:47:07 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 24 Aug 2004 13:47:07 -0700 Subject: [SPAM] [MOBY-l] findServices problem In-Reply-To: <412B7EC0.4010009@cbr.nrc.ca> References: <412B7EC0.4010009@cbr.nrc.ca> Message-ID: <1093380427.3646.178.camel@myhost.mydomain> I am unable to duplicate this error - when I run it, I get only three services back. Can you please send me your full message so that I can check the structure? I have noticed that, if there is an uncaught error in the message structure, it will by default return everything. This is because it auto-substitutes "moby" for the service type if that parameter isn't included in the search request, and in the absence of any other parameters (since the message had an invalid structure) it will find everything. I don't know how badly it would hurt anyone to switch off this default behaviour...?? M On Tue, 2004-08-24 at 10:45, Paul Gordon wrote: > Hey folks, > > If I submit a LSID type request to MOBY central's findServices, like so > > > urn:lsid:biomoby.org:objectclass:DNASequence > > > > I get every service back! Does MOBY central not recognize the LSID format? > If it doesn't recognize a format, should it return every service? The > LSID style is the data type of ID returned by Java MOBY objects. I > wasn't running into this problem with base Objects because I was writing > those data types myself. > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From fgibbons at hms.harvard.edu Tue Aug 24 17:41:18 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Tue, 24 Aug 2004 17:41:18 -0400 Subject: [MOBY-l] Fwd: Problems searching with semantic moby dot org Message-ID: <5.2.1.1.2.20040824173935.01aa3ef8@email.med.harvard.edu> Mark, For some reason, the entire body of my recent posting was stripped. I also had a message telling me that the message would be subject to moderator approval (perhaps because of the included HTML?). I'm re-sending in plain text. -Frank >Date: Tue, 24 Aug 2004 16:35:05 -0400 >To: moby-l at biomoby.org >From: Frank Gibbons >Subject: Problems searching with semantic moby dot org > >Hi, > >I've tried using semanticmoby.org to see what's out there in the S-MOBY >world. I know it just went up a few weeks ago, so it's bound to have some >hiccups. Several things struck me immediately, and I thought you'd like to >hear about them: > >1. How do I compose a query? There is a link to 'Help on Searching', but >it seems curiously generic ('HELLO means the same thing as hello as does >HeLlo"), not at all specific to the semantic task at hand. Also, it >appears that the page works by allowing the user to specify a provider, >subject and object of interest, but isn't the real thing supposed to query >using an RDF graph of subject-predicate-object? How far off is that? > >2. A couple of examples would help a lot, both for the current >(provider-subject-object) incarnation, and especially when the full RDF >capabilities are added. I believe this is true even if the services that >are 'discovered' don't do much that's practical yet. > >3. When I click the 'search' button, this message appears: > > > >Not Found > > > >The requested URL /keyword-search was not found on this server. > >---------- >Apache/2.0.49 (Unix) DAV/2 Resin/3.0.8 Server at semanticmoby.org Port 80 > >Just my 2 cents. > >-Frank > >PhD, Computational Biologist, >Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. >Tel: 617-432-3555 Fax: >617-432-3557 http://llama.med.harvard.edu/~fgibbons PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From gss at ncgr.org Tue Aug 24 19:25:27 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 24 Aug 2004 17:25:27 -0600 Subject: [MOBY-l] Fwd: Problems searching with semantic moby dot org In-Reply-To: <5.2.1.1.2.20040824173935.01aa3ef8@email.med.harvard.edu> References: <5.2.1.1.2.20040824173935.01aa3ef8@email.med.harvard.edu> Message-ID: <412BCE67.5090801@ncgr.org> Frank, Sorry, but the semanticmoby.org web site is still pretty rough, hence the "Under Construction" banner needs to be taken quite literally for the time being. I have about three weeks worth of work on Semantic MOBY, running locally, that has not yet been released to semanticmoby.org; things should be in a much better state by the end of the week. That said, here is some (long-winded) clarification - I need to add similar explanation to the site itself. Semantic MOBY does indeed use an RDF-based discovery and engagement paradigm (post the RDF/XML serialization of a query graph to the discovery server and get back a set of matching graphs as RDF/XML; post an RDF/XML ("input") graph to a Semantic MOBY provider and get the RDF/XML graph back (as "output"), where the graph has been augmented by having blank nodes filled in). This really is the heart of Semantic MOBY, and it needs to be (will be as soon as I can get to it) documented and made accessible. However, RDF/XML is very unwieldy for non-geek users. Hence, one of the goals of Semantic MOBY was to have a "Google-like" interface for discovery and engagement Semantic MOBY service providers. That is what you see at the www.semanticmoby.org home page. In a sense, it's the Semantic equivalent of the MOBY Central 'gbrowse' front end (http://mobycentral.cbr.nrc.ca/cgi-bin/gbrowse_moby) and the very immature beginning of a "Semantic Google". In a nutshell, here is how this works: when the Semantic MOBY discovery server decides to add a provider graph to its repository of known services, it looks at all the nodes in the graph that are of type moby:Provider, moby:Subject, and moby:Object. For each of these nodes, it looks for other statements asserting the node to be of other types (RDF nodes can have multiple rdf:type statements made about them). For each of these additional types (i.e. the objects of the rdf:type statements), the discovery server retrieves the class definition (to be a good MOBY player requires that all classes are retrieveable by HTTP GET - see, for example, the Semantic MOBY core definitions at www.semanticmoby.org/ontologies/core), and looks for moby:keyword property statements in these class definition. For each such keyword, the discovery server remembers that the provider node (or subject node or object node) in the provider graph is associated with that keyword. When you do a search from the www.semanticmoby.org page, the discovery server looks in its stored keyword/provider associations in order to find providers that match "by keyword" and displays links to them in Google-like fashion. That gets us to the provider engagement side of the equation, which would take at least as long to describe as the description that I just gave about discovery, so I'm going to skip it for now, other than to say that the links are to another Semantic MOBY service which tries to invoke and display the results of invoking the provider. This "keyword based" search is completely separate from the Semantic, RDF-graph based search, which is also there (but again, not yet documented). We (Damian and I) decided that the most conspicuous, hence first thing you see on the site, version of Semantic MOBY search should be up front; the RDF-graph based search, though in a sense more what Semantic MOBY is all about, will be less conspicuous, to be dug up by the "real geeks" such as readers of this list :-) Regarding the "Not Found" error you got, I believe that the Servlet container had failed to restart when the server got rebooted the other day - sorry. It is up now, but again, a lot of the functionality that I described is still under construction, and should be there by the end of the week... // Gary Frank Gibbons wrote: > Mark, > > For some reason, the entire body of my recent posting was stripped. I > also had a message telling me that the message would be subject to > moderator approval (perhaps because of the included HTML?). I'm > re-sending in plain text. > > -Frank > >> Date: Tue, 24 Aug 2004 16:35:05 -0400 >> To: moby-l at biomoby.org >> From: Frank Gibbons >> Subject: Problems searching with semantic moby dot org >> >> Hi, >> >> I've tried using semanticmoby.org to see what's out there in the >> S-MOBY world. I know it just went up a few weeks ago, so it's bound to >> have some hiccups. Several things struck me immediately, and I thought >> you'd like to hear about them: >> >> 1. How do I compose a query? There is a link to 'Help on Searching', >> but it seems curiously generic ('HELLO means the same thing as hello >> as does HeLlo"), not at all specific to the semantic task at hand. >> Also, it appears that the page works by allowing the user to specify a >> provider, subject and object of interest, but isn't the real thing >> supposed to query using an RDF graph of subject-predicate-object? How >> far off is that? >> >> 2. A couple of examples would help a lot, both for the current >> (provider-subject-object) incarnation, and especially when the full >> RDF capabilities are added. I believe this is true even if the >> services that are 'discovered' don't do much that's practical yet. >> >> 3. When I click the 'search' button, this message appears: >> >> >> >> Not Found >> >> >> >> The requested URL /keyword-search was not found on this server. >> >> ---------- >> Apache/2.0.49 (Unix) DAV/2 Resin/3.0.8 Server at semanticmoby.org Port 80 >> >> Just my 2 cents. >> >> -Frank >> >> PhD, Computational Biologist, >> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA >> 02115, USA. >> Tel: 617-432-3555 Fax: 617-432-3557 >> http://llama.med.harvard.edu/~fgibbons > > > PhD, Computational Biologist, > Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, > USA. > Tel: 617-432-3555 Fax: 617-432-3557 > http://llama.med.harvard.edu/~fgibbons > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > From fgibbons at hms.harvard.edu Wed Aug 25 11:56:39 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Wed, 25 Aug 2004 11:56:39 -0400 Subject: [MOBY-l] Fwd: Problems searching with semantic moby In-Reply-To: <412BCE67.5090801@ncgr.org> References: <5.2.1.1.2.20040824173935.01aa3ef8@email.med.harvard.edu> <5.2.1.1.2.20040824173935.01aa3ef8@email.med.harvard.edu> Message-ID: <5.2.1.1.2.20040825114659.019cd8c8@email.med.harvard.edu> Gary, At 07:25 PM 8/24/2004, you wrote: >However, RDF/XML is very unwieldy for non-geek users. Hence, one of the >goals of Semantic MOBY was to have a "Google-like" interface for discovery >and engagement Semantic MOBY service providers. That is what you see at >the www.semanticmoby.org home page. In a sense, it's the Semantic >equivalent of the MOBY Central 'gbrowse' front end >(http://mobycentral.cbr.nrc.ca/cgi-bin/gbrowse_moby) and the very immature >beginning of a "Semantic Google". Thanks for that detailed response. Query composition seems like the biggest hurdle to using 'smoogle' (Semantic-Moby Google), and your provider/subject/object interface certainly seems like a sensible first step towards simplifying it. On a broader level, what do you know about how other semantic web groups are approaching this problem? Another question/suggestion: are there any toy services out there, that I could play with? What are some of the providers? I'm thinking back to the first days of Mosaic, before there were any search engines. You'd fire up Mosaic, and it would load a page from NCSA listing all the new websites for that day, with a little textual description. (It's astonishing to think that this was ever possible!) I guess Ken Steube's scripts do something similar, albeit dynamically, providing a list of all available MOBY-S services. Given the world's general unfamiliarity with semantic web concepts, I wonder if it wouldn't help to list a few of the available S-MOBY services, just to get people playing. Right now, I don't know where to look for services. One last thing: I tried using the search interface again, I'm still getting the error about '/keyword-search not found'. This is exciting stuff, I'm looking forward to seeing the updated page you're working on now! -F PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From gordonp at cbr.nrc.ca Thu Aug 26 11:59:23 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu, 26 Aug 2004 09:59:23 -0600 Subject: [MOBY-l] findServices problem In-Reply-To: <1093533386.1979.3.camel@myhost.mydomain> References: <412B7EC0.4010009@cbr.nrc.ca> <1093380427.3646.178.camel@myhost.mydomain> <412DF427.1000507@cbr.nrc.ca> <1093533386.1979.3.camel@myhost.mydomain> Message-ID: <412E08DB.1010704@cbr.nrc.ca> Hmm. This search retrieves things that work on Object, VirtualSequence, GenericSequence, NucleotideSequence, or DNASequence. The DNASequence doesn't have a namespace, so none is provided as input to findService. The behaviour of MOBY Central is to return services that match any namespace for these objects, which will produce services that can't use the template input. e.g. PDBtoMotifID comes up as a service, since it works on an Object, but the fact that it requires a PDB namspace object makes a non-namespaced DNASequence invalid input. How can we run findServices MOBY Central to distinguish between any namespace and no namespace? Is it not a misinterpretation to consider a blank namespace as a wildcard (since namespaces are not a hierarchy)? Mark Wilkinson wrote: >It's because you have "expand objects" switched on. You aren't finding >"all", but you are finding "many" > >M > > >>Hey Mark, >> >> Here's the message... >> >>Mark Wilkinson wrote: >> >> >>>I am unable to duplicate this error - when I run it, I get only three >>>services back. >>> >>>Can you please send me your full message so that I can check the >>>structure? >>> >>> >> >> >> >>urn:lsid:biomoby.org:objectclass:DNASequence >> >> >> >> >> >> >> >> >>moby >> >>1 >>1 >>0 >> >> >> >> >> >> From mwilkinson at mrl.ubc.ca Thu Aug 26 12:08:05 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 26 Aug 2004 09:08:05 -0700 Subject: [SPAM] Re:[MOBY-l] findServices problem In-Reply-To: <412E08DB.1010704@cbr.nrc.ca> References: <412B7EC0.4010009@cbr.nrc.ca> <1093380427.3646.178.camel@myhost.mydomain> <412DF427.1000507@cbr.nrc.ca> <1093533386.1979.3.camel@myhost.mydomain> <412E08DB.1010704@cbr.nrc.ca> Message-ID: <1093536485.2025.27.camel@myhost.mydomain> On Thu, 2004-08-26 at 08:59, Paul Gordon wrote: > e.g. PDBtoMotifID comes up as a service, since it > works on an Object, but the fact that it requires a PDB namspace object > makes a non-namespaced DNASequence invalid input. Aha... I agree, that is a bug. I'll work on that later this week. M -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From midori at ebi.ac.uk Thu Aug 26 13:58:01 2004 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 26 Aug 2004 18:58:01 +0100 (BST) Subject: [MOBY-l] Standards and Ontologies for Functional Genomics Conference (fwd) Message-ID: Dear Colleague, This message is posted to several lists and we apologize if you receive multiple copies that become annoying. However, please forward it to your colleagues who might be interested in attending this conference and may not have heard about the event. Registration Is Open for the 2nd Standards and Ontologies for Functional Genomics Meeting to be held at the University of Pennsylvania, Philadelphia, PA October 23-26, 2004 The 2nd Standards and Ontologies for Functional Genomics (SOFG) Meeting will be held on October 23-26, 2004 in Philadelphia, PA USA. Information about the SOFG meeting can be found at the SOFG site http://www.sofg.org/ or at http://www.jax.org/courses/events/coursedetails.do?id=44 . Registrations and abstracts will be accepted until Sept. 23, 2004 or until the event has filled. Student support to attend is available. Downloadable pdf registration form URL: http://www.jax.org/courses/2004/sfog_reg.pdf Abstracts submitted by Sept. 10 will be considered for oral presentation by Organizers and Session Chairs. Abstracts submitted after Sept 10 will be considered for poster session only. Abstract submissions will be reproduced and included with the conference notebook material. If you wish to submit, please follow the http://www.jax.org/courses/2004/functional_genomics_abstract_guidelines.html . The conference will focus on advances in the development of standards and ontologies to facilitate the exchange of biological information by computers and computation analysis applications. A particular emphasis will be on developments in ontological annotation systems for the genomics and bioinformatics communities. Toward this end, students and established investigators from different areas of computer science, experimental biology, and bioinformatics will have an opportunity to share new ideas, demonstrate new tools and applications, and identify potential collaborations. Topics include: * Ontological Systems: Theory and Development * Ontologies for Biology Systems * Ontology Systems Development: Electronic Demonstrations * Thesauri, Nomenclatures and the Biomedical Literature * Standards and Protocols * Functional Genomics Applications * From Resource to Application Plenary Speaker Carole Goble, University of Manchester Conference Organizers and Session Chairs: Judith Blake, The Jackson Laboratory Midori Harris, EBI-Hinxton Win Hide, SANBI Lynette Hirschman, MITRE Suzanna Lewis, UC Berkeley Helen Parkinson, EBI-Hinxton Martin Ringwald, The Jackson Laboratory Susanan-Assunta Sansone, EBI-Hinxton Chris Stoeckert, UPenn Please contact me with any questions about this meeting. Judi Alexander Medlin Lead Coordinator, Courses and Conferences The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6326 Fax: 207-288-6080 Please check out our web site http://www.jax.org/courses/events/current.do for the current listing of courses and conferences at The Jackson Laboratory. -- Helen Parkinson, PhD Curation Coordinator Microarray Informatics Team EBI