From david.baux at cirad.fr Wed May 18 09:07:40 2005 From: david.baux at cirad.fr (David Baux) Date: Wed May 18 08:57:22 2005 Subject: [MOBY-l] RDF file problem Message-ID: <428B3E1C.8040100@cirad.fr> hello, i'd like to use the biomoby tool "Applet to retrieve the RDF Signature of your service" to generate the RDF file of my service. But when I fill in the form with the right Domain and URL, the browser prints: Unable to update your information Make sure that you specify a valid signature url! This field looks like the following: http://myAuthority.domain/path/to/rdf/for/service. Also make sure that you have specified the right case-sensitive service name, if applicable. while the url is: http://tropgenedb.cirad.fr/cgi-bin/biomoby Does somebody know what to do? thanks for your answers -- Baux david Equipe G?nomique et Bioinformatique CIRAD, UMR PIA, TA40/03 Avenue Agropolis 34398 Montpellier Cedex 5 France Tel : (33) 4 67 61 65 29 david.baux@cirad.fr From markw at illuminae.com Wed May 18 11:05:45 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed May 18 10:58:17 2005 Subject: [MOBY-l] RDF file problem In-Reply-To: <428B3E1C.8040100@cirad.fr> References: <428B3E1C.8040100@cirad.fr> Message-ID: <1116428745.25744.17.camel@mobycentral.mrl.ubc.ca> try now. Sorry about that M On Wed, 2005-05-18 at 15:07 +0200, David Baux wrote: > hello, > i'd like to use the biomoby tool "Applet to retrieve the RDF Signature > of your service" to generate the RDF file of my service. But when I fill > in the form with the right Domain and URL, the browser prints: > > > Unable to update your information > > > Make sure that you specify a valid signature url! This field looks > like the following: > http://myAuthority.domain/path/to/rdf/for/service. Also make sure > that you have specified the right case-sensitive service name, if > applicable. > > while the url is: http://tropgenedb.cirad.fr/cgi-bin/biomoby > > Does somebody know what to do? > > thanks for your answers > From markw at illuminae.com Wed May 18 11:30:30 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed May 18 11:25:29 2005 Subject: [MOBY-l] receipts for the MOBY meeting registration Message-ID: <1116430230.25744.44.camel@mobycentral.mrl.ubc.ca> Hi all, If you need receipts for your registration fees please send your mailing address to Shemim smanji@mrl.ubc.ca Cheers! M From Pieter.Neerincx at wur.nl Thu May 19 10:38:02 2005 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu May 19 10:31:04 2005 Subject: [MOBY-l] Perl API: complexResponse() in CommonSubs.pm ? Message-ID: Dear all, I'm working on a service that takes simple & secondary articles as input and has simple & secondary articles as output. In CommonSubs.pm I did find: genericServiceInputParser (doesn't handle collections nor secondaries) complexServiceInputParser (does handle collections and secondaries) simpleResponse (doesn't handle collections nor secondaries) collectionResponse (does handle collections but not secondaries) But I couldn't find a sub that handles secondary output articles. Based on some of the subs mentioned above and MOBY::Client::Service::execute() I compiled (copy & paste) the code below and added it to my CommonSubs.pm. Works fine for me :). Would this be something for the main CVS tree as well or did I miss something? Cheers, Pieter Wageningen University and Research Centre Laboratory of Bioinformatics Transitorium (Building 312) room 1038 Dreijenlaan 3 6703 HA Wageningen The Netherlands Phone: +31 (0)317-484 706 Fax: +31 (0)317-483 584 ####### Start section added by Pieter @ WUR ####### =head2 complexResponse ?name???? : complexResponse ?function : wraps articles in the appropriate (mobyData) structure ?usage??? : $resp .= &complexResponse(\@data, $queryID); ?args???? : (in order) ??????????? \@data??? - (optional) a listref of arrays containing MOBY articleNames and raw XML. ??????????????????????? each element of @data is itself a listref of [articleName, $XML] ??????????? $queryID? - (optional, but strongly recommended) the queryID value for the ??????????????????????? mobyData block to which you are responding ?notes??? : as required by the API you must return a response for every input. ??????????? If one of the inputs was invalid, you return a valid (empty) MOBY ??????????? response by calling &complexResponse(undef, $queryID) with no arguments. =cut sub complexResponse { ??????? my ( $data, $qID ) = @_; ??????? #return 'ERROR:? expected listref [element1, element2, ...] for data' unless ( ref( $data ) =~ /array/i ); ??????? return "\n" unless ( ref( $data ) =~ /array/i ); ??????? $qID = &_getQueryID( $qID ) ??????? ? if ref( $qID ) =~ /XML::LibXML/;??? # in case they send the DOM instead of the ID ??????? my @inputs = @{$data}; ??????? my $output; ??????? foreach ( @inputs ) { ??????? ??????? #return 'ERROR:? expected listref [articleName, XML] for data element' unless ( ref( $_ ) =~ /array/i ); ??????? ??????? return "\n" unless ( ref( $_ ) =~ /array/i ); ??????? ??????? $output .= ""; ??????? ??????? while ( my ( $articleName, $XML ) = splice( @{$_}, 0, 2 ) ) { ??????? ??????? ??????? if ( !( ref( $XML ) =~ /array/i ) ) { ??????? ??????? ??????? ??????? $articleName ||= ""; ??????? ??????? ??????? ??????? $XML???????? ||= ""; ??????? ??????? ??????? ??????? if ( ( $XML =~ /\/ ) || ( $XML =~ /\/ ) ) ??????? ??????? ??????? ??????? { ??????? ??????? ??????? ??????? ??????? $output .= "$XML"; ??????? ??????? ??????? ??????? } else { ??????? ??????? ??????? ??????? ??????? $output .= "\n$XML\n\n"; ??????? ??????? ??????? ??????? } ??????? ??????? ??????? ??????? # need to do this for collections also!!!!!! ??????? ??????? ??????? } elsif ( ref( $XML ) =~ /array/i ) { ??????? ??????? ??????? ??????? my @objs = @{$XML}; ??????? ??????? ??????? ??????? $output .= "\n"; ??????? ??????? ??????? ??????? foreach ( @objs ) { ??????? ??????? ??????? ??????? ??????? $output .= "$_\n"; ??????? ??????? ??????? ??????? } ??????? ??????? ??????? ??????? $output .= "\n"; ??????? ??????? ??????? } ??????? ??????? } ??????? ??????? $output .= "\n"; ??????? } ??????? return $output; } ####### End section added by Pieter @ WUR ####### From fgibbons at hms.harvard.edu Sun May 22 18:31:23 2005 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Sun May 22 18:22:02 2005 Subject: [MOBY-l] Test MOBY Central still down.... Message-ID: <5.2.1.1.2.20050522182823.010f6780@email.med.harvard.edu> Hi MOBYers, I'm hereby re-reporting that the Test MOBY Central appears to have been down. Or at least, it's not accepting connections from me! I reported this problem yesterday, having noticed it since Friday afternoon, but my email bounced from the mailing list. Not sure why, but I sent it from home, and perhaps I got the address wrong. Anyhoo, it'd be nice to know what's happening there. Thanks, -Frank Gibbons 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 markw at illuminae.com Sun May 22 18:31:56 2005 From: markw at illuminae.com (mark wilkinson) Date: Sun May 22 18:25:00 2005 Subject: [MOBY-l] Test MOBY Central still down.... Message-ID: <363423851-1116801151-cardhu_blackberry.rim.net-22929-@engine13-cell01> Hiya, There is no test Central anymore. It used to run as a separate instance of Apache on the same machine but that was a nightmare. Until some generous person donates a server we likely won't have one... I suppose we could run test central from my lab's server in Vancouver. Let me look into that - we do a lot of experimentation on that server so it might not be particularluy stable. M -----Original Message----- From: Frank Gibbons Date: Sun, 22 May 2005 18:31:23 To:moby-l@biomoby.org Subject: [MOBY-l] Test MOBY Central still down.... Hi MOBYers, I'm hereby re-reporting that the Test MOBY Central appears to have been down. Or at least, it's not accepting connections from me! I reported this problem yesterday, having noticed it since Friday afternoon, but my email bounced from the mailing list. Not sure why, but I sent it from home, and perhaps I got the address wrong. Anyhoo, it'd be nice to know what's happening there. Thanks, -Frank Gibbons 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 -- Mark Wilkinson ...on the road! From dag at sonsorol.org Sun May 22 19:49:35 2005 From: dag at sonsorol.org (Chris Dagdigian) Date: Sun May 22 19:41:57 2005 Subject: [MOBY-l] Test MOBY Central still down.... In-Reply-To: <363423851-1116801151-cardhu_blackberry.rim.net-22929-@engine13-cell01> References: <363423851-1116801151-cardhu_blackberry.rim.net-22929-@engine13-cell01> Message-ID: <7AC44FB2-EAC1-4EAD-B04E-CF11C6E9A842@sonsorol.org> I might have colocated server hardware and bandwidth to donate in a few weeks. What sort of admin burden would I be picking up if I offered to host a test moby central? Regards, Chris On May 22, 2005, at 6:31 PM, mark wilkinson wrote: > Hiya, > > There is no test Central anymore. It used to run as a separate > instance of Apache on the same machine but that was a nightmare. > Until some generous person donates a server we likely won't have > one... > > I suppose we could run test central from my lab's server in > Vancouver. Let me look into that - we do a lot of experimentation > on that server so it might not be particularluy stable. > > M > > -----Original Message----- > From: Frank Gibbons > Date: Sun, 22 May 2005 18:31:23 > To:moby-l@biomoby.org > Subject: [MOBY-l] Test MOBY Central still down.... > > Hi MOBYers, > > I'm hereby re-reporting that the Test MOBY Central appears to have > been > down. Or at least, it's not accepting connections from me! > > I reported this problem yesterday, having noticed it since Friday > afternoon, but my email bounced from the mailing list. Not sure > why, but I > sent it from home, and perhaps I got the address wrong. Anyhoo, > it'd be > nice to know what's happening there. > > Thanks, > > -Frank Gibbons > > 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 > > -- > Mark Wilkinson > ...on the road! > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From p.lord at cs.man.ac.uk Mon May 23 12:28:11 2005 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: Mon May 23 12:20:38 2005 Subject: [MOBY-l] Eighth Bio-Ontologies Meeting: Programme Now Available Message-ID: The Eighth Annual Bio-Ontologies Meeting ======================================== Key Information =============== Organisers: Robert Stevens(1), Phillip Lord(1), Robin McEntire(2), and James.A.Butler(2) (1) School of Computer Science, University of Manchester (2) GlaxoSmithKline Website: http://bio-ontologies.man.ac.uk Location: Detroit, Michigan Submission Deadline: 29th April Main Conference: http://www.iscb.org/ismb2005 Programme ========= This year has seen an unprecedented rise in the number of submissions, which has resulted in a particularly excellent programme. Highlights include: Keynote Address by Mark Musen A Panel Session with Mark Musen Larry Hunter Judith Blake Eric Neumann As a result of the increase in number of submissions this years, as well as 12 podium presentations, there will be 11 posters. Full details are available at http://bio-ontologies.man.ac.uk http://bio-ontologies.man.ac.uk/talks_programme.html http://bio-ontologies.man.ac.uk/poster_programme.html General Information =================== The Bio-Ontologies workshop has been a satellite meeting to the annual ISMB conference since 1998, and is now operated as a Special Interest Group at the ISMB Conference. Bio-Ontologies is well established as one of the key meetings for dissemination of latest information and research on ontologies in the life sciences and has drawn the key researchers in the field. Ontologies provide a mechanism for organising, sharing and reconciling data. Within recent years there has been a great deal of interest in the use of ontologies within bioinformatics, particularly in providing computationally accessible annotation, or standard data models for complex data for microarray or pathway information. Meetings such as last years workshop and SOFG have made it clear that there are many important uses of ontologies and a clear realisation of the importance of implementing mechanisms for integrating source ontologies rather than duplicating effort or causing confusion by extending a given ontology to include everything. However, with the increase in scope and use of ontologies within bioinformatics, issues of scalability, expressivity and best practices for modelling are becoming more important. We are particularly interested, therefore, in work involving multiple source ontologies, and which cut across the different levels of granularity implicit within biological systems. BioOntologies is an informal workshop. Submissions will be reviewed by the programme committee. A number of talks will be invited for ***full publication*** as papers in Comparative and Functional Genomics (see http://www3.interscience.wiley.com/cgi-bin/jissue/109860809 for last years papers) From paolo.romano at istge.it Tue May 24 10:59:13 2005 From: paolo.romano at istge.it (Paolo Romano) Date: Tue May 24 10:52:01 2005 Subject: [MOBY-l] CFP: NETTAB 2005 Workflows management in bioinformatics, 5-7 October, 2005, Naples, Italy Message-ID: <6.2.0.14.0.20050524164918.0357ad60@10.1.0.4> NETTAB 2005 Workflows management: new abilities for the biological information overflow 5-7 October, 2005, Second University of Naples, Naples, Italy Web page : http://www.nettab.org/2005 Call for Papers: http://www.nettab.org/2005/call.html A call for position papers, posters and oral presentations is open. TOPICS Submitted contributions should address one or more of the following topics: Technologies and technological platforms of interest to the field, with emphasis on: - Web Services (SOAP, WSDL, WSFL, UDDI, ....) - Web Services Choreography and Orchestration - Semantic Web (RDF, LSID, OWL, ...) - comparison of available technologies, limitations, pros and cons - Knowledge representation - Biological data and knowledge modeling tools - Ontologies, Databases and Applications of Semantics in Bioinformatics Workflow management systems in bioinformatics: - implementations of web services - implementations of registries - reuse and versioning of web services and workflows - workflow management systems - web interfaces for accessing and executing workflows - interactive systems to support work flows Applications of workflow management systems in bioinformatics - Methodologies for life sciences analysis: gene expression, genome annotation, mass spec peptide fragment identification, etc... - Encoding of the above in workflows - Case studies - Scenarios and use cases SUBMISSION OF CONTRIBUTIONS Abstracts can be submitted now through the NETTAB 2005 Paper Review System availble at the workshop web site. Authors are invited to submit: ORAL PRESENTATIONS: submit an extended abstract (4-5 A4 pages, size 12pt, MS Word format). Abstracts will be reviewed and acceptance or rejection will be communicated to authors. All submissions for oral presentation which are not selected will automatically be considered for posters presentation. POSTERS: submit an extended abstract (2-3 A4 pages, size 12pt, MS Word format). Abstracts will be reviewed by relevance and acceptance or rejection will be communicated to authors. POSITION PAPERS: submit a short abstract (max 1 A4 pages in length, size 12pt, MS Word format) specifying research interests and issues to be debated during the workshop. Authors submitting position papers do not engage themselves to present a poster. Instead, they will be invited to introduce the issues they arose before open discussion sessions. Contributions will be reviewed by the scientific committee for relevance, clarity and novelty of results. Accepted oral presentations, posters and position papers will be published in the conference proceedings. Authors of a selection of best papers will be asked to submit an extended version of their paper in view of a joint submission to a peer-reviewed international journal. DEADLINES - Oral presentations due: June 17, 2005. - Notification to authors: July 29, 2005. - Posters and position papers due: August 26, 2005. Registration: - Early registration: August 26, 2005 For further information ask to the Secretariat by email to info@nettab.org . Looking forward to seeing you in Naples. Best regards. Paolo Romano (on behalf of the Organizing Committee) Paolo Romano (paolo.romano@istge.it) Bioinformatics and Structural Proteomics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From markw at illuminae.com Wed May 25 10:45:45 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed May 25 10:38:00 2005 Subject: [MOBY-l] From the mouth of Tim Berners Lee Message-ID: <1117032345.25071.45.camel@mobycentral.mrl.ubc.ca> http://www.bio-itworld.com/news/051905_report8434.html?action=print The ball is ours to drop :-) M From markw at illuminae.com Fri May 27 15:57:02 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri May 27 15:49:13 2005 Subject: [MOBY-l] weeding out the "dead" services Message-ID: <1117223822.30771.66.camel@mobycentral.mrl.ubc.ca> Hi all, so, it's about time we finally switch this RDF Agent on... again... :-) As we did last time, can I request that you visit the RDF Signature Generator (http://mobycentral.cbr.nrc.ca:8090/servlets/forms/getSignatureForm) retrieve your Service Signatures, then make them available at whatever signatureURL you indicate on that web form. Running the RDF Signature Generator more than once will simply over- write your signature URL with whatever new signature URL you enter, so it is perfectly safe to do this. Thanks! M From simont at mcw.edu Fri May 27 16:23:41 2005 From: simont at mcw.edu (Twigger Simon) Date: Fri May 27 16:18:11 2005 Subject: [MOBY-l] weeding out the "dead" services In-Reply-To: <1117223822.30771.66.camel@mobycentral.mrl.ubc.ca> References: <1117223822.30771.66.camel@mobycentral.mrl.ubc.ca> Message-ID: Hi Mark, Just so I understand how this should work: I can go to the form, select my domain, leave the instance name field blank so I get every service, fill in a signature URL (should this point to a directory or to a file?) and click Submit. Back comes the RDF which I move to the location specified in the signature URL and then I can throw away all the old signature files with a clean conscience? I was hoping I could leave the service instance blank, specify one file name in the signature URL and then that would give me back one RDF document for all services so I can just throw that one file on the server and ditch the old files. Is this correct? Simon. On May 27, 2005, at 2:57 PM, Mark Wilkinson wrote: > Hi all, > > so, it's about time we finally switch this RDF Agent on... > again... :-) > > As we did last time, can I request that you visit the RDF Signature > Generator > (http://mobycentral.cbr.nrc.ca:8090/servlets/forms/getSignatureForm) > retrieve your Service Signatures, then make them available at whatever > signatureURL you indicate on that web form. > > Running the RDF Signature Generator more than once will simply over- > write your signature URL with whatever new signature URL you enter, so > it is perfectly safe to do this. > > Thanks! > > M > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From bmg at sfu.ca Fri May 27 16:42:14 2005 From: bmg at sfu.ca (Benjamin Good) Date: Fri May 27 16:34:34 2005 Subject: [MOBY-l] 2 ontologies Message-ID: <319d32e74261b6c9a729acd780bd53db@sfu.ca> From Yan: "There is another solution instead which I think is more elegant: Associate biological objects with computer data types. For Example: a DNA Sequence is the biological object but FASTA, EMBL and all the fancy bioinformatic formats are its computer representation? ." -Ben -> I agree with this thinking and in fact that was what I was trying to suggest. However, I think that you have things reversed in the following statement. Yan: "So as I see things, we have two ontologies representing two logics: -The biologocial logic represented by the bioMoby ontology -A data type logic which should be represented by a separated ontology with of course our "primitives String/Float/Bytes etc.." -> Ben As I understand it, the BioMOBY object ontology is meant to describe data-types, not biological logic. It does a nice job of the former but I would say not the latter. My suggestion is to introduce a separate ontology that does describe the biology of the things represented by the data-types (that would NOT include things like "FASTA formatted sequence"!). I think this may happen by default when moby-central merges with Grimoire/Feta, but this list needs to pay attention! I think that it is very important to rectify this confusion between syntax and semantics as soon as we can. What happens when the tools are written that create bioMoby services automatically from websites get going? I think you will quickly see that the moby object ontology loses any notion of "biological logic" as it rapidly becomes populated by perfectly syntactically valid machine produced Objects - and this is GOOD. We WANT thousands of services in there and they may require thousands of new objects! Its important to keep in mind the underlying goals of these things. The Object ontology exists to ensure interoperability - not integration. To me, that means that I can easily consume any service that uses objects from this ontology and it ensures (only helps actually) that the data types produced by service providers are sensible. These SYNTACTIC problems are solved quite nicely by the Object ontology - regardless of the specific serialization you end up choosing and regardless of the name you give to your objects. The SEMANTIC problems associated with INTEGRATION are different, large and growing and will need different solutions. rant over. -Ben http://bioinfo.icapture.ubc.ca/bgood From markw at illuminae.com Fri May 27 17:03:00 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri May 27 16:55:09 2005 Subject: [moby] Re: [MOBY-l] weeding out the "dead" services In-Reply-To: References: <1117223822.30771.66.camel@mobycentral.mrl.ubc.ca> Message-ID: <1117227780.30771.71.camel@mobycentral.mrl.ubc.ca> On Fri, 2005-05-27 at 15:23 -0500, Twigger Simon wrote: > RDF document for all services so I can just throw that one file on > the server and ditch the old files. > > Is this correct? That is correct (if Eddie has done his job properly ;-) ) M From r.bruskiewich at cgiar.org Sun May 29 20:00:23 2005 From: r.bruskiewich at cgiar.org (Bruskiewich, Richard (IRRI)) Date: Sun May 29 19:52:50 2005 Subject: [MOBY-l] 2 ontologies Message-ID: <2A491C94FFBC5843A212A69CBEA5CEC7021FBC9F@IRRIMAIL.IRRI.CGIARAD.ORG> If by "biological logic" you mean *real* semantics, then I would hazard to say that the domain modeling activity of the Generation Challenge Programme is going in that direction, at least, for crop/plant science (though some of the semantics is generic to all biology, of necessity). It is interesting to note that human beings construct domain models, not machines. Domain models cannot be autogenerated. Real semantics is what sets human beings apart from (practically) the rest of the animal kingdom, let alone, the stupid (but ultra fast) machines that we've created in this era. Richard "Daisy, daaaissy, ...." -----Original Message----- From: Benjamin Good [mailto:bmg@sfu.ca] Sent: Saturday, 2005 May 28 4:42 AM To: mobydev; mobyl Subject: [MOBY-l] 2 ontologies From Yan: "There is another solution instead which I think is more elegant: Associate biological objects with computer data types. For Example: a DNA Sequence is the biological object but FASTA, EMBL and all the fancy bioinformatic formats are its computer representation? ." -Ben -> I agree with this thinking and in fact that was what I was trying to suggest. However, I think that you have things reversed in the following statement. Yan: "So as I see things, we have two ontologies representing two logics: -The biologocial logic represented by the bioMoby ontology -A data type logic which should be represented by a separated ontology with of course our "primitives String/Float/Bytes etc.." -> Ben As I understand it, the BioMOBY object ontology is meant to describe data-types, not biological logic. It does a nice job of the former but I would say not the latter. My suggestion is to introduce a separate ontology that does describe the biology of the things represented by the data-types (that would NOT include things like "FASTA formatted sequence"!). I think this may happen by default when moby-central merges with Grimoire/Feta, but this list needs to pay attention! I think that it is very important to rectify this confusion between syntax and semantics as soon as we can. What happens when the tools are written that create bioMoby services automatically from websites get going? I think you will quickly see that the moby object ontology loses any notion of "biological logic" as it rapidly becomes populated by perfectly syntactically valid machine produced Objects - and this is GOOD. We WANT thousands of services in there and they may require thousands of new objects! Its important to keep in mind the underlying goals of these things. The Object ontology exists to ensure interoperability - not integration. To me, that means that I can easily consume any service that uses objects from this ontology and it ensures (only helps actually) that the data types produced by service providers are sensible. These SYNTACTIC problems are solved quite nicely by the Object ontology - regardless of the specific serialization you end up choosing and regardless of the name you give to your objects. The SEMANTIC problems associated with INTEGRATION are different, large and growing and will need different solutions. rant over. -Ben http://bioinfo.icapture.ubc.ca/bgood _______________________________________________ moby-l mailing list moby-l@biomoby.org http://biomoby.org/mailman/listinfo/moby-l From jmfernandez at cnb.uam.es Mon May 30 16:20:31 2005 From: jmfernandez at cnb.uam.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Mon May 30 16:14:56 2005 Subject: [MOBY-l] RDF file problem In-Reply-To: <1116428745.25744.17.camel@mobycentral.mrl.ubc.ca> References: <428B3E1C.8040100@cirad.fr> <1116428745.25744.17.camel@mobycentral.mrl.ubc.ca> Message-ID: <429B758F.5020903@cnb.uam.es> Hi everybody, I have a different problem. CNB machines are behind a firewall which doesn't allow a connection to 'strange' ports like 8090 (we have a very restrictive security policy). I can solve it talking to CNB's sysadmins (and signing a liability sheet), but it could be an annoyance if we had to do it for many addresses and/or ports. With this annoyance, I'm concerned by those services which live on a different port from HTTP and HTTPS ones. Those BioMOBY users behind a firewall (like us) won't be able to use those services, and so they could think the services are not working. I think we should include some sort of warning about this potencial problem, and also we should recommend MOBY service creators to use standard HTTP/HTTPS ports for their services. Best regards, Jos? Mar?a Mark Wilkinson wrote: > try now. > > Sorry about that > > M > > > On Wed, 2005-05-18 at 15:07 +0200, David Baux wrote: > >>hello, >>i'd like to use the biomoby tool "Applet to retrieve the RDF Signature >>of your service" to generate the RDF file of my service. But when I fill >>in the form with the right Domain and URL, the browser prints: >> >> >> Unable to update your information >> >> >> Make sure that you specify a valid signature url! This field looks >> like the following: >> http://myAuthority.domain/path/to/rdf/for/service. Also make sure >> that you have specified the right case-sensitive service name, if >> applicable. >> >>while the url is: http://tropgenedb.cirad.fr/cgi-bin/biomoby >> >>Does somebody know what to do? >> >>thanks for your answers >> > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > -- Jos? Mar?a Fern?ndez Gonz?lez e-mail: jmfernandez@cnb.uam.es Tlfn: (+34) 91 585 54 50 Fax: (+34) 91 585 45 06 Grupo de Dise?o de Proteinas Protein Design Group Centro Nacional de Biotecnolog?a National Center of Biotechnology C.P.: 28049 Zip Code: 28049 C/. Darwin n? 3 (Campus Cantoblanco, U. Aut?noma), Madrid (Spain) From francis_gibbons at hms.harvard.edu Sat May 21 14:58:47 2005 From: francis_gibbons at hms.harvard.edu (Gibbons, Francis ) Date: Mon Aug 15 11:29:01 2005 Subject: [MOBY-l] MOBY Central OK? Message-ID: <16C1B7E52D13C54D9297F8102407AC800D4BFC@MAILSERVER02.MED.HARVARD.EDU> I noticed that MOBY Central was down yesterday (I got the "ERROR ERROR ERROR" message), and appears to still be down today. Anyone know what's going on? -Frank From david.baux at cirad.fr Wed May 18 09:07:40 2005 From: david.baux at cirad.fr (David Baux) Date: Wed, 18 May 2005 15:07:40 +0200 Subject: [MOBY-l] RDF file problem Message-ID: <428B3E1C.8040100@cirad.fr> hello, i'd like to use the biomoby tool "Applet to retrieve the RDF Signature of your service" to generate the RDF file of my service. But when I fill in the form with the right Domain and URL, the browser prints: Unable to update your information Make sure that you specify a valid signature url! This field looks like the following: http://myAuthority.domain/path/to/rdf/for/service. Also make sure that you have specified the right case-sensitive service name, if applicable. while the url is: http://tropgenedb.cirad.fr/cgi-bin/biomoby Does somebody know what to do? thanks for your answers -- Baux david Equipe G?nomique et Bioinformatique CIRAD, UMR PIA, TA40/03 Avenue Agropolis 34398 Montpellier Cedex 5 France Tel : (33) 4 67 61 65 29 david.baux at cirad.fr From markw at illuminae.com Wed May 18 11:05:45 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 18 May 2005 08:05:45 -0700 Subject: [MOBY-l] RDF file problem In-Reply-To: <428B3E1C.8040100@cirad.fr> References: <428B3E1C.8040100@cirad.fr> Message-ID: <1116428745.25744.17.camel@mobycentral.mrl.ubc.ca> try now. Sorry about that M On Wed, 2005-05-18 at 15:07 +0200, David Baux wrote: > hello, > i'd like to use the biomoby tool "Applet to retrieve the RDF Signature > of your service" to generate the RDF file of my service. But when I fill > in the form with the right Domain and URL, the browser prints: > > > Unable to update your information > > > Make sure that you specify a valid signature url! This field looks > like the following: > http://myAuthority.domain/path/to/rdf/for/service. Also make sure > that you have specified the right case-sensitive service name, if > applicable. > > while the url is: http://tropgenedb.cirad.fr/cgi-bin/biomoby > > Does somebody know what to do? > > thanks for your answers > From markw at illuminae.com Wed May 18 11:30:30 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 18 May 2005 08:30:30 -0700 Subject: [MOBY-l] receipts for the MOBY meeting registration Message-ID: <1116430230.25744.44.camel@mobycentral.mrl.ubc.ca> Hi all, If you need receipts for your registration fees please send your mailing address to Shemim smanji at mrl.ubc.ca Cheers! M From Pieter.Neerincx at wur.nl Thu May 19 10:38:02 2005 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 19 May 2005 16:38:02 +0200 Subject: [MOBY-l] Perl API: complexResponse() in CommonSubs.pm ? Message-ID: Dear all, I'm working on a service that takes simple & secondary articles as input and has simple & secondary articles as output. In CommonSubs.pm I did find: genericServiceInputParser (doesn't handle collections nor secondaries) complexServiceInputParser (does handle collections and secondaries) simpleResponse (doesn't handle collections nor secondaries) collectionResponse (does handle collections but not secondaries) But I couldn't find a sub that handles secondary output articles. Based on some of the subs mentioned above and MOBY::Client::Service::execute() I compiled (copy & paste) the code below and added it to my CommonSubs.pm. Works fine for me :). Would this be something for the main CVS tree as well or did I miss something? Cheers, Pieter Wageningen University and Research Centre Laboratory of Bioinformatics Transitorium (Building 312) room 1038 Dreijenlaan 3 6703 HA Wageningen The Netherlands Phone: +31 (0)317-484 706 Fax: +31 (0)317-483 584 ####### Start section added by Pieter @ WUR ####### =head2 complexResponse ?name???? : complexResponse ?function : wraps articles in the appropriate (mobyData) structure ?usage??? : $resp .= &complexResponse(\@data, $queryID); ?args???? : (in order) ??????????? \@data??? - (optional) a listref of arrays containing MOBY articleNames and raw XML. ??????????????????????? each element of @data is itself a listref of [articleName, $XML] ??????????? $queryID? - (optional, but strongly recommended) the queryID value for the ??????????????????????? mobyData block to which you are responding ?notes??? : as required by the API you must return a response for every input. ??????????? If one of the inputs was invalid, you return a valid (empty) MOBY ??????????? response by calling &complexResponse(undef, $queryID) with no arguments. =cut sub complexResponse { ??????? my ( $data, $qID ) = @_; ??????? #return 'ERROR:? expected listref [element1, element2, ...] for data' unless ( ref( $data ) =~ /array/i ); ??????? return "\n" unless ( ref( $data ) =~ /array/i ); ??????? $qID = &_getQueryID( $qID ) ??????? ? if ref( $qID ) =~ /XML::LibXML/;??? # in case they send the DOM instead of the ID ??????? my @inputs = @{$data}; ??????? my $output; ??????? foreach ( @inputs ) { ??????? ??????? #return 'ERROR:? expected listref [articleName, XML] for data element' unless ( ref( $_ ) =~ /array/i ); ??????? ??????? return "\n" unless ( ref( $_ ) =~ /array/i ); ??????? ??????? $output .= ""; ??????? ??????? while ( my ( $articleName, $XML ) = splice( @{$_}, 0, 2 ) ) { ??????? ??????? ??????? if ( !( ref( $XML ) =~ /array/i ) ) { ??????? ??????? ??????? ??????? $articleName ||= ""; ??????? ??????? ??????? ??????? $XML???????? ||= ""; ??????? ??????? ??????? ??????? if ( ( $XML =~ /\/ ) || ( $XML =~ /\/ ) ) ??????? ??????? ??????? ??????? { ??????? ??????? ??????? ??????? ??????? $output .= "$XML"; ??????? ??????? ??????? ??????? } else { ??????? ??????? ??????? ??????? ??????? $output .= "\n$XML\n\n"; ??????? ??????? ??????? ??????? } ??????? ??????? ??????? ??????? # need to do this for collections also!!!!!! ??????? ??????? ??????? } elsif ( ref( $XML ) =~ /array/i ) { ??????? ??????? ??????? ??????? my @objs = @{$XML}; ??????? ??????? ??????? ??????? $output .= "\n"; ??????? ??????? ??????? ??????? foreach ( @objs ) { ??????? ??????? ??????? ??????? ??????? $output .= "$_\n"; ??????? ??????? ??????? ??????? } ??????? ??????? ??????? ??????? $output .= "\n"; ??????? ??????? ??????? } ??????? ??????? } ??????? ??????? $output .= "\n"; ??????? } ??????? return $output; } ####### End section added by Pieter @ WUR ####### From fgibbons at hms.harvard.edu Sun May 22 18:31:23 2005 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Sun, 22 May 2005 18:31:23 -0400 Subject: [MOBY-l] Test MOBY Central still down.... Message-ID: <5.2.1.1.2.20050522182823.010f6780@email.med.harvard.edu> Hi MOBYers, I'm hereby re-reporting that the Test MOBY Central appears to have been down. Or at least, it's not accepting connections from me! I reported this problem yesterday, having noticed it since Friday afternoon, but my email bounced from the mailing list. Not sure why, but I sent it from home, and perhaps I got the address wrong. Anyhoo, it'd be nice to know what's happening there. Thanks, -Frank Gibbons 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 markw at illuminae.com Sun May 22 18:31:56 2005 From: markw at illuminae.com (mark wilkinson) Date: Sun, 22 May 2005 22:31:56 +0000 GMT Subject: [MOBY-l] Test MOBY Central still down.... Message-ID: <363423851-1116801151-cardhu_blackberry.rim.net-22929-@engine13-cell01> Hiya, There is no test Central anymore. It used to run as a separate instance of Apache on the same machine but that was a nightmare. Until some generous person donates a server we likely won't have one... I suppose we could run test central from my lab's server in Vancouver. Let me look into that - we do a lot of experimentation on that server so it might not be particularluy stable. M -----Original Message----- From: Frank Gibbons Date: Sun, 22 May 2005 18:31:23 To:moby-l at biomoby.org Subject: [MOBY-l] Test MOBY Central still down.... Hi MOBYers, I'm hereby re-reporting that the Test MOBY Central appears to have been down. Or at least, it's not accepting connections from me! I reported this problem yesterday, having noticed it since Friday afternoon, but my email bounced from the mailing list. Not sure why, but I sent it from home, and perhaps I got the address wrong. Anyhoo, it'd be nice to know what's happening there. Thanks, -Frank Gibbons 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 -- Mark Wilkinson ...on the road! From dag at sonsorol.org Sun May 22 19:49:35 2005 From: dag at sonsorol.org (Chris Dagdigian) Date: Sun, 22 May 2005 19:49:35 -0400 Subject: [MOBY-l] Test MOBY Central still down.... In-Reply-To: <363423851-1116801151-cardhu_blackberry.rim.net-22929-@engine13-cell01> References: <363423851-1116801151-cardhu_blackberry.rim.net-22929-@engine13-cell01> Message-ID: <7AC44FB2-EAC1-4EAD-B04E-CF11C6E9A842@sonsorol.org> I might have colocated server hardware and bandwidth to donate in a few weeks. What sort of admin burden would I be picking up if I offered to host a test moby central? Regards, Chris On May 22, 2005, at 6:31 PM, mark wilkinson wrote: > Hiya, > > There is no test Central anymore. It used to run as a separate > instance of Apache on the same machine but that was a nightmare. > Until some generous person donates a server we likely won't have > one... > > I suppose we could run test central from my lab's server in > Vancouver. Let me look into that - we do a lot of experimentation > on that server so it might not be particularluy stable. > > M > > -----Original Message----- > From: Frank Gibbons > Date: Sun, 22 May 2005 18:31:23 > To:moby-l at biomoby.org > Subject: [MOBY-l] Test MOBY Central still down.... > > Hi MOBYers, > > I'm hereby re-reporting that the Test MOBY Central appears to have > been > down. Or at least, it's not accepting connections from me! > > I reported this problem yesterday, having noticed it since Friday > afternoon, but my email bounced from the mailing list. Not sure > why, but I > sent it from home, and perhaps I got the address wrong. Anyhoo, > it'd be > nice to know what's happening there. > > Thanks, > > -Frank Gibbons > > 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 > > -- > Mark Wilkinson > ...on the road! > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From p.lord at cs.man.ac.uk Mon May 23 12:28:11 2005 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: 23 May 2005 17:28:11 +0100 Subject: [MOBY-l] Eighth Bio-Ontologies Meeting: Programme Now Available Message-ID: The Eighth Annual Bio-Ontologies Meeting ======================================== Key Information =============== Organisers: Robert Stevens(1), Phillip Lord(1), Robin McEntire(2), and James.A.Butler(2) (1) School of Computer Science, University of Manchester (2) GlaxoSmithKline Website: http://bio-ontologies.man.ac.uk Location: Detroit, Michigan Submission Deadline: 29th April Main Conference: http://www.iscb.org/ismb2005 Programme ========= This year has seen an unprecedented rise in the number of submissions, which has resulted in a particularly excellent programme. Highlights include: Keynote Address by Mark Musen A Panel Session with Mark Musen Larry Hunter Judith Blake Eric Neumann As a result of the increase in number of submissions this years, as well as 12 podium presentations, there will be 11 posters. Full details are available at http://bio-ontologies.man.ac.uk http://bio-ontologies.man.ac.uk/talks_programme.html http://bio-ontologies.man.ac.uk/poster_programme.html General Information =================== The Bio-Ontologies workshop has been a satellite meeting to the annual ISMB conference since 1998, and is now operated as a Special Interest Group at the ISMB Conference. Bio-Ontologies is well established as one of the key meetings for dissemination of latest information and research on ontologies in the life sciences and has drawn the key researchers in the field. Ontologies provide a mechanism for organising, sharing and reconciling data. Within recent years there has been a great deal of interest in the use of ontologies within bioinformatics, particularly in providing computationally accessible annotation, or standard data models for complex data for microarray or pathway information. Meetings such as last years workshop and SOFG have made it clear that there are many important uses of ontologies and a clear realisation of the importance of implementing mechanisms for integrating source ontologies rather than duplicating effort or causing confusion by extending a given ontology to include everything. However, with the increase in scope and use of ontologies within bioinformatics, issues of scalability, expressivity and best practices for modelling are becoming more important. We are particularly interested, therefore, in work involving multiple source ontologies, and which cut across the different levels of granularity implicit within biological systems. BioOntologies is an informal workshop. Submissions will be reviewed by the programme committee. A number of talks will be invited for ***full publication*** as papers in Comparative and Functional Genomics (see http://www3.interscience.wiley.com/cgi-bin/jissue/109860809 for last years papers) From paolo.romano at istge.it Tue May 24 10:59:13 2005 From: paolo.romano at istge.it (Paolo Romano) Date: Tue, 24 May 2005 16:59:13 +0200 Subject: [MOBY-l] CFP: NETTAB 2005 Workflows management in bioinformatics, 5-7 October, 2005, Naples, Italy Message-ID: <6.2.0.14.0.20050524164918.0357ad60@10.1.0.4> NETTAB 2005 Workflows management: new abilities for the biological information overflow 5-7 October, 2005, Second University of Naples, Naples, Italy Web page : http://www.nettab.org/2005 Call for Papers: http://www.nettab.org/2005/call.html A call for position papers, posters and oral presentations is open. TOPICS Submitted contributions should address one or more of the following topics: Technologies and technological platforms of interest to the field, with emphasis on: - Web Services (SOAP, WSDL, WSFL, UDDI, ....) - Web Services Choreography and Orchestration - Semantic Web (RDF, LSID, OWL, ...) - comparison of available technologies, limitations, pros and cons - Knowledge representation - Biological data and knowledge modeling tools - Ontologies, Databases and Applications of Semantics in Bioinformatics Workflow management systems in bioinformatics: - implementations of web services - implementations of registries - reuse and versioning of web services and workflows - workflow management systems - web interfaces for accessing and executing workflows - interactive systems to support work flows Applications of workflow management systems in bioinformatics - Methodologies for life sciences analysis: gene expression, genome annotation, mass spec peptide fragment identification, etc... - Encoding of the above in workflows - Case studies - Scenarios and use cases SUBMISSION OF CONTRIBUTIONS Abstracts can be submitted now through the NETTAB 2005 Paper Review System availble at the workshop web site. Authors are invited to submit: ORAL PRESENTATIONS: submit an extended abstract (4-5 A4 pages, size 12pt, MS Word format). Abstracts will be reviewed and acceptance or rejection will be communicated to authors. All submissions for oral presentation which are not selected will automatically be considered for posters presentation. POSTERS: submit an extended abstract (2-3 A4 pages, size 12pt, MS Word format). Abstracts will be reviewed by relevance and acceptance or rejection will be communicated to authors. POSITION PAPERS: submit a short abstract (max 1 A4 pages in length, size 12pt, MS Word format) specifying research interests and issues to be debated during the workshop. Authors submitting position papers do not engage themselves to present a poster. Instead, they will be invited to introduce the issues they arose before open discussion sessions. Contributions will be reviewed by the scientific committee for relevance, clarity and novelty of results. Accepted oral presentations, posters and position papers will be published in the conference proceedings. Authors of a selection of best papers will be asked to submit an extended version of their paper in view of a joint submission to a peer-reviewed international journal. DEADLINES - Oral presentations due: June 17, 2005. - Notification to authors: July 29, 2005. - Posters and position papers due: August 26, 2005. Registration: - Early registration: August 26, 2005 For further information ask to the Secretariat by email to info at nettab.org . Looking forward to seeing you in Naples. Best regards. Paolo Romano (on behalf of the Organizing Committee) Paolo Romano (paolo.romano at istge.it) Bioinformatics and Structural Proteomics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From markw at illuminae.com Wed May 25 10:45:45 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 25 May 2005 07:45:45 -0700 Subject: [MOBY-l] From the mouth of Tim Berners Lee Message-ID: <1117032345.25071.45.camel@mobycentral.mrl.ubc.ca> http://www.bio-itworld.com/news/051905_report8434.html?action=print The ball is ours to drop :-) M From markw at illuminae.com Fri May 27 15:57:02 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 27 May 2005 12:57:02 -0700 Subject: [MOBY-l] weeding out the "dead" services Message-ID: <1117223822.30771.66.camel@mobycentral.mrl.ubc.ca> Hi all, so, it's about time we finally switch this RDF Agent on... again... :-) As we did last time, can I request that you visit the RDF Signature Generator (http://mobycentral.cbr.nrc.ca:8090/servlets/forms/getSignatureForm) retrieve your Service Signatures, then make them available at whatever signatureURL you indicate on that web form. Running the RDF Signature Generator more than once will simply over- write your signature URL with whatever new signature URL you enter, so it is perfectly safe to do this. Thanks! M From simont at mcw.edu Fri May 27 16:23:41 2005 From: simont at mcw.edu (Twigger Simon) Date: Fri, 27 May 2005 15:23:41 -0500 Subject: [MOBY-l] weeding out the "dead" services In-Reply-To: <1117223822.30771.66.camel@mobycentral.mrl.ubc.ca> References: <1117223822.30771.66.camel@mobycentral.mrl.ubc.ca> Message-ID: Hi Mark, Just so I understand how this should work: I can go to the form, select my domain, leave the instance name field blank so I get every service, fill in a signature URL (should this point to a directory or to a file?) and click Submit. Back comes the RDF which I move to the location specified in the signature URL and then I can throw away all the old signature files with a clean conscience? I was hoping I could leave the service instance blank, specify one file name in the signature URL and then that would give me back one RDF document for all services so I can just throw that one file on the server and ditch the old files. Is this correct? Simon. On May 27, 2005, at 2:57 PM, Mark Wilkinson wrote: > Hi all, > > so, it's about time we finally switch this RDF Agent on... > again... :-) > > As we did last time, can I request that you visit the RDF Signature > Generator > (http://mobycentral.cbr.nrc.ca:8090/servlets/forms/getSignatureForm) > retrieve your Service Signatures, then make them available at whatever > signatureURL you indicate on that web form. > > Running the RDF Signature Generator more than once will simply over- > write your signature URL with whatever new signature URL you enter, so > it is perfectly safe to do this. > > Thanks! > > M > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From bmg at sfu.ca Fri May 27 16:42:14 2005 From: bmg at sfu.ca (Benjamin Good) Date: Fri, 27 May 2005 16:42:14 -0400 Subject: [MOBY-l] 2 ontologies Message-ID: <319d32e74261b6c9a729acd780bd53db@sfu.ca> From Yan: "There is another solution instead which I think is more elegant: Associate biological objects with computer data types. For Example: a DNA Sequence is the biological object but FASTA, EMBL and all the fancy bioinformatic formats are its computer representation? ." -Ben -> I agree with this thinking and in fact that was what I was trying to suggest. However, I think that you have things reversed in the following statement. Yan: "So as I see things, we have two ontologies representing two logics: -The biologocial logic represented by the bioMoby ontology -A data type logic which should be represented by a separated ontology with of course our "primitives String/Float/Bytes etc.." -> Ben As I understand it, the BioMOBY object ontology is meant to describe data-types, not biological logic. It does a nice job of the former but I would say not the latter. My suggestion is to introduce a separate ontology that does describe the biology of the things represented by the data-types (that would NOT include things like "FASTA formatted sequence"!). I think this may happen by default when moby-central merges with Grimoire/Feta, but this list needs to pay attention! I think that it is very important to rectify this confusion between syntax and semantics as soon as we can. What happens when the tools are written that create bioMoby services automatically from websites get going? I think you will quickly see that the moby object ontology loses any notion of "biological logic" as it rapidly becomes populated by perfectly syntactically valid machine produced Objects - and this is GOOD. We WANT thousands of services in there and they may require thousands of new objects! Its important to keep in mind the underlying goals of these things. The Object ontology exists to ensure interoperability - not integration. To me, that means that I can easily consume any service that uses objects from this ontology and it ensures (only helps actually) that the data types produced by service providers are sensible. These SYNTACTIC problems are solved quite nicely by the Object ontology - regardless of the specific serialization you end up choosing and regardless of the name you give to your objects. The SEMANTIC problems associated with INTEGRATION are different, large and growing and will need different solutions. rant over. -Ben http://bioinfo.icapture.ubc.ca/bgood From markw at illuminae.com Fri May 27 17:03:00 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 27 May 2005 14:03:00 -0700 Subject: [moby] Re: [MOBY-l] weeding out the "dead" services In-Reply-To: References: <1117223822.30771.66.camel@mobycentral.mrl.ubc.ca> Message-ID: <1117227780.30771.71.camel@mobycentral.mrl.ubc.ca> On Fri, 2005-05-27 at 15:23 -0500, Twigger Simon wrote: > RDF document for all services so I can just throw that one file on > the server and ditch the old files. > > Is this correct? That is correct (if Eddie has done his job properly ;-) ) M From r.bruskiewich at cgiar.org Sun May 29 20:00:23 2005 From: r.bruskiewich at cgiar.org (Bruskiewich, Richard (IRRI)) Date: Sun, 29 May 2005 17:00:23 -0700 Subject: [MOBY-l] 2 ontologies Message-ID: <2A491C94FFBC5843A212A69CBEA5CEC7021FBC9F@IRRIMAIL.IRRI.CGIARAD.ORG> If by "biological logic" you mean *real* semantics, then I would hazard to say that the domain modeling activity of the Generation Challenge Programme is going in that direction, at least, for crop/plant science (though some of the semantics is generic to all biology, of necessity). It is interesting to note that human beings construct domain models, not machines. Domain models cannot be autogenerated. Real semantics is what sets human beings apart from (practically) the rest of the animal kingdom, let alone, the stupid (but ultra fast) machines that we've created in this era. Richard "Daisy, daaaissy, ...." -----Original Message----- From: Benjamin Good [mailto:bmg at sfu.ca] Sent: Saturday, 2005 May 28 4:42 AM To: mobydev; mobyl Subject: [MOBY-l] 2 ontologies From Yan: "There is another solution instead which I think is more elegant: Associate biological objects with computer data types. For Example: a DNA Sequence is the biological object but FASTA, EMBL and all the fancy bioinformatic formats are its computer representation? ." -Ben -> I agree with this thinking and in fact that was what I was trying to suggest. However, I think that you have things reversed in the following statement. Yan: "So as I see things, we have two ontologies representing two logics: -The biologocial logic represented by the bioMoby ontology -A data type logic which should be represented by a separated ontology with of course our "primitives String/Float/Bytes etc.." -> Ben As I understand it, the BioMOBY object ontology is meant to describe data-types, not biological logic. It does a nice job of the former but I would say not the latter. My suggestion is to introduce a separate ontology that does describe the biology of the things represented by the data-types (that would NOT include things like "FASTA formatted sequence"!). I think this may happen by default when moby-central merges with Grimoire/Feta, but this list needs to pay attention! I think that it is very important to rectify this confusion between syntax and semantics as soon as we can. What happens when the tools are written that create bioMoby services automatically from websites get going? I think you will quickly see that the moby object ontology loses any notion of "biological logic" as it rapidly becomes populated by perfectly syntactically valid machine produced Objects - and this is GOOD. We WANT thousands of services in there and they may require thousands of new objects! Its important to keep in mind the underlying goals of these things. The Object ontology exists to ensure interoperability - not integration. To me, that means that I can easily consume any service that uses objects from this ontology and it ensures (only helps actually) that the data types produced by service providers are sensible. These SYNTACTIC problems are solved quite nicely by the Object ontology - regardless of the specific serialization you end up choosing and regardless of the name you give to your objects. The SEMANTIC problems associated with INTEGRATION are different, large and growing and will need different solutions. rant over. -Ben http://bioinfo.icapture.ubc.ca/bgood _______________________________________________ moby-l mailing list moby-l at biomoby.org http://biomoby.org/mailman/listinfo/moby-l From jmfernandez at cnb.uam.es Mon May 30 16:20:31 2005 From: jmfernandez at cnb.uam.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Mon, 30 May 2005 22:20:31 +0200 Subject: [MOBY-l] RDF file problem In-Reply-To: <1116428745.25744.17.camel@mobycentral.mrl.ubc.ca> References: <428B3E1C.8040100@cirad.fr> <1116428745.25744.17.camel@mobycentral.mrl.ubc.ca> Message-ID: <429B758F.5020903@cnb.uam.es> Hi everybody, I have a different problem. CNB machines are behind a firewall which doesn't allow a connection to 'strange' ports like 8090 (we have a very restrictive security policy). I can solve it talking to CNB's sysadmins (and signing a liability sheet), but it could be an annoyance if we had to do it for many addresses and/or ports. With this annoyance, I'm concerned by those services which live on a different port from HTTP and HTTPS ones. Those BioMOBY users behind a firewall (like us) won't be able to use those services, and so they could think the services are not working. I think we should include some sort of warning about this potencial problem, and also we should recommend MOBY service creators to use standard HTTP/HTTPS ports for their services. Best regards, Jos? Mar?a Mark Wilkinson wrote: > try now. > > Sorry about that > > M > > > On Wed, 2005-05-18 at 15:07 +0200, David Baux wrote: > >>hello, >>i'd like to use the biomoby tool "Applet to retrieve the RDF Signature >>of your service" to generate the RDF file of my service. But when I fill >>in the form with the right Domain and URL, the browser prints: >> >> >> Unable to update your information >> >> >> Make sure that you specify a valid signature url! This field looks >> like the following: >> http://myAuthority.domain/path/to/rdf/for/service. Also make sure >> that you have specified the right case-sensitive service name, if >> applicable. >> >>while the url is: http://tropgenedb.cirad.fr/cgi-bin/biomoby >> >>Does somebody know what to do? >> >>thanks for your answers >> > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > -- Jos? Mar?a Fern?ndez Gonz?lez e-mail: jmfernandez at cnb.uam.es Tlfn: (+34) 91 585 54 50 Fax: (+34) 91 585 45 06 Grupo de Dise?o de Proteinas Protein Design Group Centro Nacional de Biotecnolog?a National Center of Biotechnology C.P.: 28049 Zip Code: 28049 C/. Darwin n? 3 (Campus Cantoblanco, U. Aut?noma), Madrid (Spain) From francis_gibbons at hms.harvard.edu Sat May 21 14:58:47 2005 From: francis_gibbons at hms.harvard.edu (Gibbons, Francis ) Date: Sat, 21 May 2005 18:58:47 -0000 Subject: [MOBY-l] MOBY Central OK? Message-ID: <16C1B7E52D13C54D9297F8102407AC800D4BFC@MAILSERVER02.MED.HARVARD.EDU> I noticed that MOBY Central was down yesterday (I got the "ERROR ERROR ERROR" message), and appears to still be down today. Anyone know what's going on? -Frank