From kanani at cshl.edu Wed May 5 11:14:57 2004 From: kanani at cshl.edu (Ardavan Kanani) Date: Wed May 5 11:32:48 2004 Subject: [MOBY-dev] need help with register service :) Message-ID: Hello all, I am trying to register service called getIndvsOnPanel() that takes a panel lsid and returns a collection of simple objects with their id set to the individual's lsid on that panel. Here is how I am registering the service: sub register_getIndvsOnPanel_service { my ($C, $description) = @_; my $reg = $C->registerService( serviceName => "getIndvsOnPanel", authURI => $authURI, contactEmail => $email, description => $description, URL => $url, input => ['panelLSID', ["Object" => []] ], output => ['indvLSID', [["Object" => []]] ], category => "moby", serviceType => "Retrieval", ); die "Bad return value from registerService for getIndvsOnPanel service.\n" unless $reg; if ($reg->success == 1){ print "Registration successful for getIndvsOnPanel service.\n"; } else { print "Registration failed for getIndvsOnPanel service: ", $reg->message, "\n"; } } I get the following error message: Can't use string ("indvLSID") as an ARRAY ref while "strict refs" in use at /usr/local/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line 710. What am I doing wrong? Thanks, Ardavan Kanani From markw at illuminae.com Wed May 5 10:21:31 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed May 5 11:37:47 2004 Subject: [MOBY] [MOBY-dev] need help with register service :) In-Reply-To: References: Message-ID: <1083766890.1634.28.camel@myhost.mydomain> Hi Ardavan! You are missing one layer of brackets. Yes, I know it is arcane :-) I'm going to add a bit of documentation to the POD showing why it has to be this way, and how each layer of brackets should be interpreted. I posted a message of explanation to the list a couple of weeks ago in response to a similar question from Catherine's group, but I notice that you are not subscribed to this mailing list, so you wouldn't have read it... The correct signature for registerService inputs/outputs is detailed in the pod docs, but it requires one more layer of array-ref brackets than you have used. So your message: input => ['panelLSID', ["Object" => []] ], output=> ['indvLSID', [["Object" => []]] ], should be: input => [ ['panelLSID', ["Object" => []] ] ], output=> [ ['indvLSID', [["Object" => []]] ] ], cheers! M On Wed, 2004-05-05 at 08:14, Ardavan Kanani wrote: > Hello all, > > I am trying to register service called getIndvsOnPanel() that takes a > panel lsid and returns a collection of simple objects with their id set > to the individual's lsid on that panel. Here is how I am registering > the service: > > > sub register_getIndvsOnPanel_service { > my ($C, $description) = @_; > my $reg = $C->registerService( > serviceName => "getIndvsOnPanel", > authURI => $authURI, > contactEmail => $email, > description => $description, > URL => $url, > input => ['panelLSID', ["Object" > => []] ], > output => ['indvLSID', [["Object" > => []]] ], > category => "moby", > serviceType => "Retrieval", > ); > die "Bad return value from registerService for getIndvsOnPanel > service.\n" unless $reg; > if ($reg->success == 1){ > print "Registration successful for getIndvsOnPanel service.\n"; > } > else { > print "Registration failed for getIndvsOnPanel service: ", > $reg->message, "\n"; > } > } > > > I get the following error message: > > Can't use string ("indvLSID") as an ARRAY ref while "strict refs" in > use at /usr/local/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line > 710. > > > > What am I doing wrong? > > > > Thanks, Ardavan Kanani > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed May 5 10:30:39 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed May 5 11:46:52 2004 Subject: [MOBY] [MOBY-dev] need help with register service :) In-Reply-To: <1083766890.1634.28.camel@myhost.mydomain> References: <1083766890.1634.28.camel@myhost.mydomain> Message-ID: <1083767439.1634.39.camel@myhost.mydomain> On Wed, 2004-05-05 at 07:21, Mark Wilkinson wrote: > input => ['panelLSID', ["Object" => []] ], > output=> ['indvLSID', [["Object" => []]] ], > > should be: > > input => [ > ['panelLSID', ["Object" => []] ] > ], > output=> [ > ['indvLSID', [["Object" => []]] ] > ], This is because there may be multiple inputs to, or outputs from, a service, with multiple names and/or object types; therefore the inputs and outputs from a service are a list of lists. M -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From kanani at cshl.edu Thu May 13 15:14:11 2004 From: kanani at cshl.edu (Ardavan Kanani) Date: Thu May 13 15:18:00 2004 Subject: [MOBY-dev] xml dump of MOBY objects Message-ID: Hello, Is there a tool, already written, that would dump out the MOBY objects in their XML format? From senger at ebi.ac.uk Thu May 13 15:38:32 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu May 13 15:42:20 2004 Subject: [MOBY-dev] xml dump of MOBY objects In-Reply-To: Message-ID: > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > Well, almost everything you get back from both Moby Central (registry) and from Moby-native services are XML-based objects. So, for example, if you want to get all service instances, you can use a Java client (but the same is available in Perl) like this: 1) create a file (e.g. tmp/moby.txt) with this contents: moby 1 1 0 2) call Java command-line client: ./run-cmdline-client -call findService tmp/moby.xml And you get all service instances in XML. Was this what you were asking for? Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Thu May 13 15:38:32 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu May 13 15:42:23 2004 Subject: [MOBY-dev] xml dump of MOBY objects In-Reply-To: Message-ID: > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > Well, almost everything you get back from both Moby Central (registry) and from Moby-native services are XML-based objects. So, for example, if you want to get all service instances, you can use a Java client (but the same is available in Perl) like this: 1) create a file (e.g. tmp/moby.txt) with this contents: moby 1 1 0 2) call Java command-line client: ./run-cmdline-client -call findService tmp/moby.xml And you get all service instances in XML. Was this what you were asking for? Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Thu May 13 17:21:21 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri May 14 18:25:34 2004 Subject: [MOBY] [MOBY-dev] xml dump of MOBY objects In-Reply-To: References: Message-ID: <1084483281.9647.7.camel@myhost.mydomain> Under "cool tools" link on the moby homepage there is a link to Ken Steube's fantastic service encyclopedia. From there you can click-into the object structures. You can also link directly to them using the following GET string: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=FOO where FOO is the object you wish to see the structure of. I have just taken on a co-op student whose primary task will be creating GUI interfaces to assist with object browsing, new object creation/registration, service type and namespace browsing and registration, as well as service instance registration. Things should start getting easier SOON! M On Thu, 2004-05-13 at 12:14, Ardavan Kanani wrote: > Hello, > > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Thu May 13 17:21:21 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri May 14 18:25:37 2004 Subject: [MOBY] [MOBY-dev] xml dump of MOBY objects In-Reply-To: References: Message-ID: <1084483281.9647.7.camel@myhost.mydomain> Under "cool tools" link on the moby homepage there is a link to Ken Steube's fantastic service encyclopedia. From there you can click-into the object structures. You can also link directly to them using the following GET string: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=FOO where FOO is the object you wish to see the structure of. I have just taken on a co-op student whose primary task will be creating GUI interfaces to assist with object browsing, new object creation/registration, service type and namespace browsing and registration, as well as service instance registration. Things should start getting easier SOON! M On Thu, 2004-05-13 at 12:14, Ardavan Kanani wrote: > Hello, > > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From letondal at pasteur.fr Mon May 17 08:03:24 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Mon May 17 08:07:30 2004 Subject: [MOBY-dev] Fwd: Google of Web services / donating CPU cycles through Web services Message-ID: <200405171203.i4HC3OA0348681@electre.pasteur.fr> Hi, There was a discussion about this idea last week in the [bioclusters] mailing list that reminds me a lot the discussion at CSHL (the discussion was about having a moby service provider publishing "somewhere" its service - not in a repository like moby central but in a place where Google could find it - and having a client find it as a Web (visible) document with a proper URI). ------- Forwarded Message From: Dan Bolser To: bioclusters@bioinformatics.org Subject: [Bioclusters] Question about grid List-Archive: Date: Thu, 13 May 2004 14:01:49 +0100 (BST) Hello, I had an idea to do with grid computing, but it may be total garbage. I heard about some clever people who started to 'steal' computation from unsuspecting web sites by hijacking the normal function of the site and co-opting its computations into a different program. If these stories are true, surly we could do this with a bit more civility, and set up a bunch of generic 'calculators' through the web which could then be used for grid computing. The way I imagine the system is this... Program starts by searching the web for calculators, the code is compiled for the 'web-engine' so every single instruction is encoded as an HTTP / CGI / XML request, and all instructions are performed over the web on a shifting number of calculators. Actually, I found something similar hear... http://ausweb.scu.edu.au/aw02/papers/refereed/kelly/paper.html I wanted to ask about the feasibility of such an idea. For example if one machine sent all its instructions to another over a gigabit intra net, how much slower would this be than local computation? Is a gigabit LAN 1/2/3/10/100/1000 orders of magnitude slower than internal CPU communication channels? The power of an open source system like this would be if someone like Apache would take the idea on board and release it as part of its standard distribution. However, even if every web server on the web were running such a calculator (why not be ambitious), could the system be fast enough? Naturally there are a lot of issues regarding distribution / allocation / scheduling etc. but before we get into nasty details, is the idea remotely worth consideration? How difficult would it be to make a Java compiler accommodate such a web-engine? Thanks very much for any feedback, Dan. _______________________________________________ Bioclusters maillist - Bioclusters@bioinformatics.org https://bioinformatics.org/mailman/listinfo/bioclusters ------- End of Forwarded Message From senger at ebi.ac.uk Tue May 18 06:13:32 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Tue May 18 06:17:13 2004 Subject: [MOBY-dev] a bug in expandXXX tags? In-Reply-To: <1083278395.1662.17.camel@myhost.mydomain> Message-ID: Hi Mark, Working on findService method (in Java's MobyCmdLineClient) I found that there might be perhaps a bug when using expandXXX tags: 1) This query object: Service moby 1 1 0 did not find any services. I thought that serviceType 'Service' is parent of all service types, and because I put 'expandService@ to 1, I expect to find all services. The API says "this flag will cause MOBY Central to traverse the Service ontology and discover services that are child types (more specific) than the Service-type you requested." 2) Regarding the 'expandObjects' flag, it seems to work fine with inputs but does not seem to work with outputs. This query object: findService> SchematikonVorocodeName moby 1 1 0 found only RetrieveVorocodeName service but not the services "that operate not only on the Object Class you are querying, but also any ontolological parent types of that Object Class" - see that 'expandObjects' is set to 1. Are these bugs or my misunderstandings? Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From kanani at cshl.edu Tue May 18 14:32:27 2004 From: kanani at cshl.edu (Ardavan Kanani) Date: Tue May 18 14:36:04 2004 Subject: [MOBY-dev] thanks Message-ID: Thanks all for answering my question. Ardavan From markw at illuminae.com Thu May 20 17:07:04 2004 From: markw at illuminae.com (Markw) Date: Thu May 20 16:10:26 2004 Subject: [MOBY-dev] Notification Message-ID: WARNING: This e-mail has been altered by MIMEDefang. Following this paragraph are indications of the actual changes made. For more information about your site's MIMEDefang policy, contact MIMEDefang Administrator's . For more information about MIMEDefang, see: http://www.roaringpenguin.com/mimedefang/enduser.php3 An attachment named MoreInfo.com was removed from this document as it constituted a security hazard. If you require this document, please contact the sender and arrange an alternate means of receiving it. -------------- next part -------------- From markw at illuminae.com Fri May 21 16:11:47 2004 From: markw at illuminae.com (Markw) Date: Fri May 21 15:15:04 2004 Subject: [MOBY-dev] Changes.. Message-ID: WARNING: This e-mail has been altered by MIMEDefang. Following this paragraph are indications of the actual changes made. For more information about your site's MIMEDefang policy, contact MIMEDefang Administrator's . For more information about MIMEDefang, see: http://www.roaringpenguin.com/mimedefang/enduser.php3 An attachment named Joke.com was removed from this document as it constituted a security hazard. If you require this document, please contact the sender and arrange an alternate means of receiving it. -------------- next part -------------- From mwilkinson at mrl.ubc.ca Fri May 21 16:17:30 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Fri May 21 15:21:32 2004 Subject: [MOBY-dev] Viruses Message-ID: <1085170650.10201.12.camel@myhost.mydomain> Hi all, Do any of you recognize this domain: from benna.net (213-156-52-97.fastres.net [213.156.52.97]) I am getting hit ~every hour from that domain, with Martin as the return address. Now I see that whoever has this infection is starting to send messages to the MOBY mailing lists with *me* as the return address!! If any of you recognize that address, heads up... you have been infected for the past couple of weeks. M -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Sat May 22 08:41:36 2004 From: markw at illuminae.com (Markw) Date: Sat May 22 07:44:49 2004 Subject: [MOBY-dev] Re: Document Message-ID: WARNING: This e-mail has been altered by MIMEDefang. Following this paragraph are indications of the actual changes made. For more information about your site's MIMEDefang policy, contact MIMEDefang Administrator's . For more information about MIMEDefang, see: http://www.roaringpenguin.com/mimedefang/enduser.php3 An attachment named text_document.exe was removed from this document as it constituted a security hazard. If you require this document, please contact the sender and arrange an alternate means of receiving it. -------------- next part -------------- From markw at illuminae.com Sun May 23 05:26:19 2004 From: markw at illuminae.com (Markw) Date: Sun May 23 04:29:32 2004 Subject: [MOBY-dev] RE: Protected message Message-ID: WARNING: This e-mail has been altered by MIMEDefang. Following this paragraph are indications of the actual changes made. For more information about your site's MIMEDefang policy, contact MIMEDefang Administrator's . For more information about MIMEDefang, see: http://www.roaringpenguin.com/mimedefang/enduser.php3 An attachment named Joke.com was removed from this document as it constituted a security hazard. If you require this document, please contact the sender and arrange an alternate means of receiving it. -------------- next part -------------- From markw at illuminae.com Mon May 24 15:36:16 2004 From: markw at illuminae.com (Markw) Date: Mon May 24 14:39:28 2004 Subject: [MOBY-dev] Encrypted document Message-ID: -------------- next part -------------- A non-text attachment was scrubbed... Name: tcmwquacje.jpeg Type: image/jpeg Size: 994 bytes Desc: not available Url : http://biomoby.org/pipermail/moby-dev/attachments/20040524/c5c8f281/tcmwquacje-0001.jpeg -------------- next part -------------- A non-text attachment was scrubbed... Name: Loves_money.zip Type: application/octet-stream Size: 22410 bytes Desc: not available Url : http://biomoby.org/pipermail/moby-dev/attachments/20040524/c5c8f281/Loves_money-0001.obj From markw at illuminae.com Mon May 31 15:12:49 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon May 31 15:17:03 2004 Subject: [MOBY-dev] attn. especially Heiko Message-ID: <1086030768.2973.75.camel@myhost.mydomain> Heiko, this might have consequences for the new Xref block... M -----Forwarded Message----- > From: Michael Ashburner (Genetics) > To: ma11@gen.cam.ac.uk, midori@ebi.ac.uk > Cc: gofriends@genome.stanford.edu, ref26@gen.cam.ac.uk > Subject: [GO] Re: Draft evidence code ontology > Date: Mon, 31 May 2004 14:11:32 +0100 > > I would like to revisit the evidence codes ontology, perhaps > with the idea of some discussion about it during the annotation > workshop in 2 weeks time. > > I attach a new version. The major change is: > > inferred from experiment added as a parent to ida (and its children) > > I also added some new terms. I am still awaiting the TAIR codes > for inclusion. > > Michael > > ______________________________________________________________________ > format-version: 1.0 > date: 31:05:2004 14:08 > saved-by: ma11 > auto-generated-by: DAG-Edit 1.409-beta-4 > default-namespace: evidence_codes.ontology > remark: autogenerated-by\: DAG-Edit version 1.409-beta-4\nsaved-by\: ma11\ndate\: Fri Feb 27 16\:10\:50 GMT 2004\nversion\: $Revision\: 1.23 $ > > [Term] > id: EV:0000017 > name: inferred from ectopic expression > is_a: EV:0000014 > > [Term] > id: EV:0000030 > name: inferred from curated BLAST match > is_a: EV:0000044 > > [Term] > id: EV:0000007 > name: inferred from immunofluorescence > is_a: EV:0000006 > > [Term] > id: EV:0000002 > name: inferred from direct assay > synonym: "IDA" [] > is_a: EV:0000006 > > [Term] > id: EV:0000031 > name: inferred from curated BLAST match to protein > is_a: EV:0000030 > > [Term] > id: EV:0000041 > name: inferred from similarity > synonym: "ISS" [] > is_a: EV:0000043 > is_a: EV:0000033 > > [Term] > id: EV:0000032 > name: inferred from curated BLAST match to nucleic acid > is_a: EV:0000030 > > [Term] > id: EV:0000040 > name: inferred from immunological assay > is_a: EV:0000023 > is_a: EV:0000039 > > [Term] > id: EV:0000018 > name: inferred from anti-sense experiment > is_a: EV:0000014 > > [Term] > id: EV:0000049 > name: inferred from reporter gene assay > is_a: EV:0000006 > > [Term] > id: EV:0000046 > name: inferred from level of protein expression > is_a: EV:0000010 > > [Term] > id: EV:0000023 > name: inferred from ligand binding > is_a: EV:0000021 > > [Term] > id: EV:0000028 > name: inferred from motif similarity > is_a: EV:0000044 > > [Term] > id: EV:0000035 > name: no biological data > synonym: "ND" [] > is_a: EV:0000000 > > [Term] > id: EV:0000013 > name: inferred from transgenic rescue > is_a: EV:0000012 > > [Term] > id: EV:0000012 > name: inferred from functional complementation > is_a: EV:0000006 > > [Term] > id: EV:0000048 > name: inferred from level of transcript expression > is_a: EV:0000009 > > [Term] > id: EV:0000009 > name: inferred from transcript expression > is_a: EV:0000008 > > [Term] > id: EV:0000029 > name: inferred from InterPro motif similarity > is_a: EV:0000028 > > [Term] > id: EV:0000022 > name: inferred from co-purification > is_a: EV:0000021 > > [Term] > id: EV:0000008 > name: inferred from expression pattern > synonym: "IEP" [] > is_a: EV:0000006 > > [Term] > id: EV:0000036 > name: inferred from electronic annotation > synonym: "IEA" [] > is_a: EV:0000043 > > [Term] > id: EV:0000014 > name: inferred from mutant phenotype > synonym: "IMP" [] > is_a: EV:0000006 > > [Term] > id: EV:0000011 > name: inferred from genetic interaction > synonym: "IGI" [] > is_a: EV:0000006 > > [Term] > id: EV:0000039 > name: inferred from protein assay > is_a: EV:0000006 > > [Term] > id: EV:0000024 > name: inferred from protein binding > is_a: EV:0000023 > is_a: EV:0000039 > > [Term] > id: EV:0000045 > name: inferred from spatial pattern of protein expression > is_a: EV:0000010 > > [Term] > id: EV:0000047 > name: inferred from spatial pattern of transcript expression > is_a: EV:0000009 > > [Term] > id: EV:0000027 > name: inferred from structural similarity > is_a: EV:0000041 > > [Term] > id: EV:0000038 > name: inferred from transient rescue > is_a: EV:0000012 > > [Term] > id: EV:0000044 > name: inferred from sequence similarity > is_a: EV:0000041 > > [Term] > id: EV:0000016 > name: inferred from loss-of-function mutant phenotype > is_a: EV:0000015 > > [Term] > id: EV:0000005 > name: inferred from enzyme assay > is_a: EV:0000039 > > [Term] > id: EV:0000037 > name: not_recorded > synonym: "NR" [] > is_a: EV:0000000 > > [Term] > id: EV:0000026 > name: inferred from nucleic acid hybridization > is_a: EV:0000041 > is_a: EV:0000006 > > [Term] > id: EV:0000015 > name: inferred from gene mutation > is_a: EV:0000014 > > [Term] > id: EV:0000010 > name: inferred from protein expression > is_a: EV:0000008 > is_a: EV:0000039 > > [Term] > id: EV:0000004 > name: inferred from cell fractionation > is_a: EV:0000006 > > [Term] > id: EV:0000025 > name: inferred from 2-hybrid interaction > is_a: EV:0000023 > > [Term] > id: EV:0000003 > name: inferred from reconstitution assay > is_a: EV:0000006 > > [Term] > id: EV:0000034 > name: non-traceable author statement > synonym: "NAS" [] > is_a: EV:0000000 > > [Term] > id: EV:0000001 > name: inferred by curator > synonym: "IC" [] > is_a: EV:0000000 > > [Term] > id: EV:0000006 > name: inferred from experiment > is_a: EV:0000033 > > [Term] > id: EV:0000042 > name: inferred from gain-of-function mutant phenotype > is_a: EV:0000015 > > [Term] > id: EV:0000020 > name: inferred from specific protein inhibition > is_a: EV:0000039 > > [Term] > id: EV:0000019 > name: inferred from RNAi experiment > is_a: EV:0000014 > > [Term] > id: EV:0000021 > name: inferred from physical interaction > synonym: "IPI" [] > is_a: EV:0000006 > > [Term] > id: EV:0000033 > name: traceable author statement > synonym: "TAS" [] > is_a: EV:0000000 > > [Term] > id: EV:0000000 > name: Evidence_Codes_Ontology > > [Term] > id: EV:0000043 > name: inferred from in-silico analysis > is_a: EV:0000000 > > [Term] > id: EV:0000051 > name: inferred from gain of function mutant phenotype > is_obsolete: true > > [Term] > id: EV:0000050 > name: inferred from loss of function mutant phenotype > is_obsolete: true > > > ______________________________________________________________________ > !autogenerated-by: DAG-Edit version 1.409-beta-4 > !saved-by: ma11 > !date: Mon May 31 14:07:42 BST 2004 > !version: $Revision: 1.23 $ > !type: @is_a@ is_a is a > $Evidence_Codes_Ontology ; EV:0000000 > @is_a@inferred by curator ; EV:0000001 ; synonym:IC > @is_a@inferred from in-silico analysis ; EV:0000043 > @is_a@inferred from electronic annotation ; EV:0000036 ; synonym:IEA > @is_a@inferred from similarity ; EV:0000041 ; synonym:ISS @is_a@ traceable author statement ; EV:0000033 > @is_a@inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from experiment ; EV:0000006 > @is_a@inferred from sequence similarity ; EV:0000044 > @is_a@inferred from curated BLAST match ; EV:0000030 > @is_a@inferred from curated BLAST match to nucleic acid ; EV:0000032 > @is_a@inferred from curated BLAST match to protein ; EV:0000031 > @is_a@inferred from motif similarity ; EV:0000028 > @is_a@inferred from InterPro motif similarity ; EV:0000029 > @is_a@inferred from structural similarity ; EV:0000027 > @is_a@no biological data ; EV:0000035 ; synonym:ND > @is_a@non-traceable author statement ; EV:0000034 ; synonym:NAS > @is_a@not_recorded ; EV:0000037 ; synonym:NR > @is_a@traceable author statement ; EV:0000033 ; synonym:TAS > @is_a@inferred from experiment ; EV:0000006 > @is_a@inferred from cell fractionation ; EV:0000004 > @is_a@inferred from direct assay ; EV:0000002 ; synonym:IDA > @is_a@inferred from expression pattern ; EV:0000008 ; synonym:IEP > @is_a@inferred from protein expression ; EV:0000010 @is_a@ inferred from protein assay ; EV:0000039 > @is_a@inferred from level of protein expression ; EV:0000046 > @is_a@inferred from spatial pattern of protein expression ; EV:0000045 > @is_a@inferred from transcript expression ; EV:0000009 > @is_a@inferred from level of transcript expression ; EV:0000048 > @is_a@inferred from spatial pattern of transcript expression ; EV:0000047 > @is_a@inferred from functional complementation ; EV:0000012 > @is_a@inferred from transgenic rescue ; EV:0000013 > @is_a@inferred from transient rescue ; EV:0000038 > @is_a@inferred from genetic interaction ; EV:0000011 ; synonym:IGI > @is_a@inferred from immunofluorescence ; EV:0000007 > @is_a@inferred from mutant phenotype ; EV:0000014 ; synonym:IMP > @is_a@inferred from anti-sense experiment ; EV:0000018 > @is_a@inferred from ectopic expression ; EV:0000017 > @is_a@inferred from gene mutation ; EV:0000015 > @is_a@inferred from gain-of-function mutant phenotype ; EV:0000042 > @is_a@inferred from loss-of-function mutant phenotype ; EV:0000016 > @is_a@inferred from RNAi experiment ; EV:0000019 > @is_a@inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from similarity ; EV:0000041 > @is_a@inferred from physical interaction ; EV:0000021 ; synonym:IPI > @is_a@inferred from co-purification ; EV:0000022 > @is_a@inferred from ligand binding ; EV:0000023 > @is_a@inferred from 2-hybrid interaction ; EV:0000025 > @is_a@inferred from immunological assay ; EV:0000040 @is_a@ inferred from protein assay ; EV:0000039 > @is_a@inferred from protein binding ; EV:0000024 @is_a@ inferred from protein assay ; EV:0000039 > @is_a@inferred from protein assay ; EV:0000039 > @is_a@inferred from enzyme assay ; EV:0000005 > @is_a@inferred from immunological assay ; EV:0000040 @is_a@ inferred from ligand binding ; EV:0000023 > @is_a@inferred from protein binding ; EV:0000024 @is_a@ inferred from ligand binding ; EV:0000023 > @is_a@inferred from protein expression ; EV:0000010 @is_a@ inferred from expression pattern ; EV:0000008 > @is_a@inferred from level of protein expression ; EV:0000046 > @is_a@inferred from spatial pattern of protein expression ; EV:0000045 > @is_a@inferred from specific protein inhibition ; EV:0000020 > @is_a@inferred from reconstitution assay ; EV:0000003 > @is_a@inferred from reporter gene assay ; EV:0000049 > @is_a@inferred from similarity ; EV:0000041 ; synonym:ISS @is_a@ inferred from in-silico analysis ; EV:0000043 > @is_a@inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from experiment ; EV:0000006 > @is_a@inferred from sequence similarity ; EV:0000044 > @is_a@inferred from curated BLAST match ; EV:0000030 > @is_a@inferred from curated BLAST match to nucleic acid ; EV:0000032 > @is_a@inferred from curated BLAST match to protein ; EV:0000031 > @is_a@inferred from motif similarity ; EV:0000028 > @is_a@inferred from InterPro motif similarity ; EV:0000029 > @is_a@inferred from structural similarity ; EV:0000027 -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From bioboy at uga.edu Mon May 10 03:09:51 2004 From: bioboy at uga.edu (Xian) Date: Thu Jun 3 10:52:53 2004 Subject: [MOBY-dev] optimal integration of primer3 into biopython and others using swig and biomoby In-Reply-To: <70D7B115-A117-11D8-A663-000A956845CE@stanfordalumni.org> References: <409CB249.2090900@uga.edu> <70D7B115-A117-11D8-A663-000A956845CE@stanfordalumni.org> Message-ID: <409F29D0.7010708@uga.edu> optimal integration of primer3 into biopython and others using swig and biomoby Abstract: Primer3 is the de facto open source C program for automated PCR primer selection; it is used by emboss and biopython, among others. There is no active development [last release 0.9 9/98]. I have used primer3 and python to study Arabidopsis genome function. I aim to integrate primer3 into biopython. Specifically, my goal is to develop primer3 into a set of C modules or libraries to provide: a) standardized access via python, perl, etc b) impetus to further primer3 development. I propose here an optimal development path that maximizes target audience while minimizing code rewriting. Discussion: TTBOMK, Biopython and bioperl each have a primer3 i/o parser. These multiple, unstandardized dependencies may hinder future primer3 development [such as the addition of R. Griffais's K-tuple frequency method, Nucl. Acids. Res. 1991 19: 3887-3891 ]. My aim is to develop primer3 into a maintainable and easily extendable set of C modules or libraries that are natively accessible by perl and python. Swig is a "C compiler" that provide this functionality; e.g. primer3's Tm analysis module [oligotm.h and oligotm.c] can be compiled and imported as a python module whose methods are native C functions. Once this is done adding new language support is trivial. Well-defined, standard i/o structures for these libraries will facilitate their use by the bioinformatics community from within perl or python, and should be considered in development. Biomoby is an XML-based data ontology which represents data as heirarchical objects in the ontology, e.g. the hypothetical object "PrimerPair" contains two instances of "DNASequence" along with any other data such as Tm, self-hybridization, etc. Designing a biomoby object for primer3 data i/o has the additional benefit of easing information-sharing with existing databases and other biomoby-aware services. Please reply if you are interested in using, testing, designing, or developing this project. Likewise, feel free to forward this to such people. If there is sufficient interest, I will spawn a mailing group or possibly a sourceforge project. Thanks for your time, xian References/Links: Primer3[down at time of writing]: http://www-genome.wi.mit.edu/genome_software/other/primer3.html Emboss's eprimer3 [primer3 wrapper]: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Apps/eprimer3.html SWIG, Simplified Wrapper and Interface Generator: http://www.swig.org/ biomoby: http://www.biomoby.org/overview.html biomoby, bioperl, and much more: http://open-bio.org/ From kanani at cshl.edu Wed May 5 11:14:57 2004 From: kanani at cshl.edu (Ardavan Kanani) Date: Wed, 5 May 2004 11:14:57 -0400 Subject: [MOBY-dev] need help with register service :) Message-ID: Hello all, I am trying to register service called getIndvsOnPanel() that takes a panel lsid and returns a collection of simple objects with their id set to the individual's lsid on that panel. Here is how I am registering the service: sub register_getIndvsOnPanel_service { my ($C, $description) = @_; my $reg = $C->registerService( serviceName => "getIndvsOnPanel", authURI => $authURI, contactEmail => $email, description => $description, URL => $url, input => ['panelLSID', ["Object" => []] ], output => ['indvLSID', [["Object" => []]] ], category => "moby", serviceType => "Retrieval", ); die "Bad return value from registerService for getIndvsOnPanel service.\n" unless $reg; if ($reg->success == 1){ print "Registration successful for getIndvsOnPanel service.\n"; } else { print "Registration failed for getIndvsOnPanel service: ", $reg->message, "\n"; } } I get the following error message: Can't use string ("indvLSID") as an ARRAY ref while "strict refs" in use at /usr/local/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line 710. What am I doing wrong? Thanks, Ardavan Kanani From markw at illuminae.com Wed May 5 10:21:31 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 05 May 2004 07:21:31 -0700 Subject: [MOBY] [MOBY-dev] need help with register service :) In-Reply-To: References: Message-ID: <1083766890.1634.28.camel@myhost.mydomain> Hi Ardavan! You are missing one layer of brackets. Yes, I know it is arcane :-) I'm going to add a bit of documentation to the POD showing why it has to be this way, and how each layer of brackets should be interpreted. I posted a message of explanation to the list a couple of weeks ago in response to a similar question from Catherine's group, but I notice that you are not subscribed to this mailing list, so you wouldn't have read it... The correct signature for registerService inputs/outputs is detailed in the pod docs, but it requires one more layer of array-ref brackets than you have used. So your message: input => ['panelLSID', ["Object" => []] ], output=> ['indvLSID', [["Object" => []]] ], should be: input => [ ['panelLSID', ["Object" => []] ] ], output=> [ ['indvLSID', [["Object" => []]] ] ], cheers! M On Wed, 2004-05-05 at 08:14, Ardavan Kanani wrote: > Hello all, > > I am trying to register service called getIndvsOnPanel() that takes a > panel lsid and returns a collection of simple objects with their id set > to the individual's lsid on that panel. Here is how I am registering > the service: > > > sub register_getIndvsOnPanel_service { > my ($C, $description) = @_; > my $reg = $C->registerService( > serviceName => "getIndvsOnPanel", > authURI => $authURI, > contactEmail => $email, > description => $description, > URL => $url, > input => ['panelLSID', ["Object" > => []] ], > output => ['indvLSID', [["Object" > => []]] ], > category => "moby", > serviceType => "Retrieval", > ); > die "Bad return value from registerService for getIndvsOnPanel > service.\n" unless $reg; > if ($reg->success == 1){ > print "Registration successful for getIndvsOnPanel service.\n"; > } > else { > print "Registration failed for getIndvsOnPanel service: ", > $reg->message, "\n"; > } > } > > > I get the following error message: > > Can't use string ("indvLSID") as an ARRAY ref while "strict refs" in > use at /usr/local/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line > 710. > > > > What am I doing wrong? > > > > Thanks, Ardavan Kanani > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed May 5 10:30:39 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 05 May 2004 07:30:39 -0700 Subject: [MOBY] [MOBY-dev] need help with register service :) In-Reply-To: <1083766890.1634.28.camel@myhost.mydomain> References: <1083766890.1634.28.camel@myhost.mydomain> Message-ID: <1083767439.1634.39.camel@myhost.mydomain> On Wed, 2004-05-05 at 07:21, Mark Wilkinson wrote: > input => ['panelLSID', ["Object" => []] ], > output=> ['indvLSID', [["Object" => []]] ], > > should be: > > input => [ > ['panelLSID', ["Object" => []] ] > ], > output=> [ > ['indvLSID', [["Object" => []]] ] > ], This is because there may be multiple inputs to, or outputs from, a service, with multiple names and/or object types; therefore the inputs and outputs from a service are a list of lists. M -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From kanani at cshl.edu Thu May 13 15:14:11 2004 From: kanani at cshl.edu (Ardavan Kanani) Date: Thu, 13 May 2004 15:14:11 -0400 Subject: [MOBY-dev] xml dump of MOBY objects Message-ID: Hello, Is there a tool, already written, that would dump out the MOBY objects in their XML format? From senger at ebi.ac.uk Thu May 13 15:38:32 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 13 May 2004 20:38:32 +0100 (BST) Subject: [MOBY-dev] xml dump of MOBY objects In-Reply-To: Message-ID: > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > Well, almost everything you get back from both Moby Central (registry) and from Moby-native services are XML-based objects. So, for example, if you want to get all service instances, you can use a Java client (but the same is available in Perl) like this: 1) create a file (e.g. tmp/moby.txt) with this contents: moby 1 1 0 2) call Java command-line client: ./run-cmdline-client -call findService tmp/moby.xml And you get all service instances in XML. Was this what you were asking for? Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Thu May 13 15:38:32 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 13 May 2004 20:38:32 +0100 (BST) Subject: [MOBY-dev] xml dump of MOBY objects In-Reply-To: Message-ID: > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > Well, almost everything you get back from both Moby Central (registry) and from Moby-native services are XML-based objects. So, for example, if you want to get all service instances, you can use a Java client (but the same is available in Perl) like this: 1) create a file (e.g. tmp/moby.txt) with this contents: moby 1 1 0 2) call Java command-line client: ./run-cmdline-client -call findService tmp/moby.xml And you get all service instances in XML. Was this what you were asking for? Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Thu May 13 17:21:21 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 13 May 2004 14:21:21 -0700 Subject: [MOBY] [MOBY-dev] xml dump of MOBY objects In-Reply-To: References: Message-ID: <1084483281.9647.7.camel@myhost.mydomain> Under "cool tools" link on the moby homepage there is a link to Ken Steube's fantastic service encyclopedia. From there you can click-into the object structures. You can also link directly to them using the following GET string: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=FOO where FOO is the object you wish to see the structure of. I have just taken on a co-op student whose primary task will be creating GUI interfaces to assist with object browsing, new object creation/registration, service type and namespace browsing and registration, as well as service instance registration. Things should start getting easier SOON! M On Thu, 2004-05-13 at 12:14, Ardavan Kanani wrote: > Hello, > > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Thu May 13 17:21:21 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 13 May 2004 14:21:21 -0700 Subject: [MOBY] [MOBY-dev] xml dump of MOBY objects In-Reply-To: References: Message-ID: <1084483281.9647.7.camel@myhost.mydomain> Under "cool tools" link on the moby homepage there is a link to Ken Steube's fantastic service encyclopedia. From there you can click-into the object structures. You can also link directly to them using the following GET string: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=FOO where FOO is the object you wish to see the structure of. I have just taken on a co-op student whose primary task will be creating GUI interfaces to assist with object browsing, new object creation/registration, service type and namespace browsing and registration, as well as service instance registration. Things should start getting easier SOON! M On Thu, 2004-05-13 at 12:14, Ardavan Kanani wrote: > Hello, > > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From letondal at pasteur.fr Mon May 17 08:03:24 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Mon, 17 May 2004 14:03:24 +0200 Subject: [MOBY-dev] Fwd: Google of Web services / donating CPU cycles through Web services Message-ID: <200405171203.i4HC3OA0348681@electre.pasteur.fr> Hi, There was a discussion about this idea last week in the [bioclusters] mailing list that reminds me a lot the discussion at CSHL (the discussion was about having a moby service provider publishing "somewhere" its service - not in a repository like moby central but in a place where Google could find it - and having a client find it as a Web (visible) document with a proper URI). ------- Forwarded Message From: Dan Bolser To: bioclusters at bioinformatics.org Subject: [Bioclusters] Question about grid List-Archive: Date: Thu, 13 May 2004 14:01:49 +0100 (BST) Hello, I had an idea to do with grid computing, but it may be total garbage. I heard about some clever people who started to 'steal' computation from unsuspecting web sites by hijacking the normal function of the site and co-opting its computations into a different program. If these stories are true, surly we could do this with a bit more civility, and set up a bunch of generic 'calculators' through the web which could then be used for grid computing. The way I imagine the system is this... Program starts by searching the web for calculators, the code is compiled for the 'web-engine' so every single instruction is encoded as an HTTP / CGI / XML request, and all instructions are performed over the web on a shifting number of calculators. Actually, I found something similar hear... http://ausweb.scu.edu.au/aw02/papers/refereed/kelly/paper.html I wanted to ask about the feasibility of such an idea. For example if one machine sent all its instructions to another over a gigabit intra net, how much slower would this be than local computation? Is a gigabit LAN 1/2/3/10/100/1000 orders of magnitude slower than internal CPU communication channels? The power of an open source system like this would be if someone like Apache would take the idea on board and release it as part of its standard distribution. However, even if every web server on the web were running such a calculator (why not be ambitious), could the system be fast enough? Naturally there are a lot of issues regarding distribution / allocation / scheduling etc. but before we get into nasty details, is the idea remotely worth consideration? How difficult would it be to make a Java compiler accommodate such a web-engine? Thanks very much for any feedback, Dan. _______________________________________________ Bioclusters maillist - Bioclusters at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bioclusters ------- End of Forwarded Message From senger at ebi.ac.uk Tue May 18 06:13:32 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 18 May 2004 11:13:32 +0100 (BST) Subject: [MOBY-dev] a bug in expandXXX tags? In-Reply-To: <1083278395.1662.17.camel@myhost.mydomain> Message-ID: Hi Mark, Working on findService method (in Java's MobyCmdLineClient) I found that there might be perhaps a bug when using expandXXX tags: 1) This query object: Service moby 1 1 0 did not find any services. I thought that serviceType 'Service' is parent of all service types, and because I put 'expandService@ to 1, I expect to find all services. The API says "this flag will cause MOBY Central to traverse the Service ontology and discover services that are child types (more specific) than the Service-type you requested." 2) Regarding the 'expandObjects' flag, it seems to work fine with inputs but does not seem to work with outputs. This query object: findService> SchematikonVorocodeName moby 1 1 0 found only RetrieveVorocodeName service but not the services "that operate not only on the Object Class you are querying, but also any ontolological parent types of that Object Class" - see that 'expandObjects' is set to 1. Are these bugs or my misunderstandings? Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From kanani at cshl.edu Tue May 18 14:32:27 2004 From: kanani at cshl.edu (Ardavan Kanani) Date: Tue, 18 May 2004 14:32:27 -0400 Subject: [MOBY-dev] thanks Message-ID: Thanks all for answering my question. Ardavan From markw at illuminae.com Thu May 20 17:07:04 2004 From: markw at illuminae.com (Markw) Date: Thu, 20 May 2004 22:07:04 +0100 Subject: [MOBY-dev] Notification Message-ID: An embedded and charset-unspecified text was scrubbed... Name: warning1.txt Url: http://www.biomoby.org/pipermail/moby-dev/attachments/20040520/cc18ccf3/warning1.txt -------------- next part -------------- From markw at illuminae.com Fri May 21 16:11:47 2004 From: markw at illuminae.com (Markw) Date: Fri, 21 May 2004 21:11:47 +0100 Subject: [MOBY-dev] Changes.. Message-ID: An embedded and charset-unspecified text was scrubbed... Name: warning1.txt Url: http://www.biomoby.org/pipermail/moby-dev/attachments/20040521/620ebc8b/warning1.txt -------------- next part -------------- From mwilkinson at mrl.ubc.ca Fri May 21 16:17:30 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Fri, 21 May 2004 13:17:30 -0700 Subject: [MOBY-dev] Viruses Message-ID: <1085170650.10201.12.camel@myhost.mydomain> Hi all, Do any of you recognize this domain: from benna.net (213-156-52-97.fastres.net [213.156.52.97]) I am getting hit ~every hour from that domain, with Martin as the return address. Now I see that whoever has this infection is starting to send messages to the MOBY mailing lists with *me* as the return address!! If any of you recognize that address, heads up... you have been infected for the past couple of weeks. M -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Sat May 22 08:41:36 2004 From: markw at illuminae.com (Markw) Date: Sat, 22 May 2004 13:41:36 +0100 Subject: [MOBY-dev] Re: Document Message-ID: An embedded and charset-unspecified text was scrubbed... Name: warning1.txt Url: http://www.biomoby.org/pipermail/moby-dev/attachments/20040522/43214f20/warning1.txt -------------- next part -------------- From markw at illuminae.com Sun May 23 05:26:19 2004 From: markw at illuminae.com (Markw) Date: Sun, 23 May 2004 10:26:19 +0100 Subject: [MOBY-dev] RE: Protected message Message-ID: An embedded and charset-unspecified text was scrubbed... Name: warning1.txt Url: http://www.biomoby.org/pipermail/moby-dev/attachments/20040523/c50fe996/warning1.txt -------------- next part -------------- From markw at illuminae.com Mon May 24 15:36:16 2004 From: markw at illuminae.com (Markw) Date: Mon, 24 May 2004 20:36:16 +0100 Subject: [MOBY-dev] Encrypted document Message-ID: -------------- next part -------------- A non-text attachment was scrubbed... Name: tcmwquacje.jpeg Type: image/jpeg Size: 994 bytes Desc: not available Url : http://www.biomoby.org/pipermail/moby-dev/attachments/20040524/c5c8f281/tcmwquacje-0002.jpeg -------------- next part -------------- A non-text attachment was scrubbed... Name: Loves_money.zip Type: application/octet-stream Size: 22410 bytes Desc: not available Url : http://www.biomoby.org/pipermail/moby-dev/attachments/20040524/c5c8f281/Loves_money-0002.obj From markw at illuminae.com Mon May 31 15:12:49 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 31 May 2004 12:12:49 -0700 Subject: [MOBY-dev] attn. especially Heiko Message-ID: <1086030768.2973.75.camel@myhost.mydomain> Heiko, this might have consequences for the new Xref block... M -----Forwarded Message----- > From: Michael Ashburner (Genetics) > To: ma11 at gen.cam.ac.uk, midori at ebi.ac.uk > Cc: gofriends at genome.stanford.edu, ref26 at gen.cam.ac.uk > Subject: [GO] Re: Draft evidence code ontology > Date: Mon, 31 May 2004 14:11:32 +0100 > > I would like to revisit the evidence codes ontology, perhaps > with the idea of some discussion about it during the annotation > workshop in 2 weeks time. > > I attach a new version. The major change is: > > inferred from experiment added as a parent to ida (and its children) > > I also added some new terms. I am still awaiting the TAIR codes > for inclusion. > > Michael > > ______________________________________________________________________ > format-version: 1.0 > date: 31:05:2004 14:08 > saved-by: ma11 > auto-generated-by: DAG-Edit 1.409-beta-4 > default-namespace: evidence_codes.ontology > remark: autogenerated-by\: DAG-Edit version 1.409-beta-4\nsaved-by\: ma11\ndate\: Fri Feb 27 16\:10\:50 GMT 2004\nversion\: $Revision\: 1.23 $ > > [Term] > id: EV:0000017 > name: inferred from ectopic expression > is_a: EV:0000014 > > [Term] > id: EV:0000030 > name: inferred from curated BLAST match > is_a: EV:0000044 > > [Term] > id: EV:0000007 > name: inferred from immunofluorescence > is_a: EV:0000006 > > [Term] > id: EV:0000002 > name: inferred from direct assay > synonym: "IDA" [] > is_a: EV:0000006 > > [Term] > id: EV:0000031 > name: inferred from curated BLAST match to protein > is_a: EV:0000030 > > [Term] > id: EV:0000041 > name: inferred from similarity > synonym: "ISS" [] > is_a: EV:0000043 > is_a: EV:0000033 > > [Term] > id: EV:0000032 > name: inferred from curated BLAST match to nucleic acid > is_a: EV:0000030 > > [Term] > id: EV:0000040 > name: inferred from immunological assay > is_a: EV:0000023 > is_a: EV:0000039 > > [Term] > id: EV:0000018 > name: inferred from anti-sense experiment > is_a: EV:0000014 > > [Term] > id: EV:0000049 > name: inferred from reporter gene assay > is_a: EV:0000006 > > [Term] > id: EV:0000046 > name: inferred from level of protein expression > is_a: EV:0000010 > > [Term] > id: EV:0000023 > name: inferred from ligand binding > is_a: EV:0000021 > > [Term] > id: EV:0000028 > name: inferred from motif similarity > is_a: EV:0000044 > > [Term] > id: EV:0000035 > name: no biological data > synonym: "ND" [] > is_a: EV:0000000 > > [Term] > id: EV:0000013 > name: inferred from transgenic rescue > is_a: EV:0000012 > > [Term] > id: EV:0000012 > name: inferred from functional complementation > is_a: EV:0000006 > > [Term] > id: EV:0000048 > name: inferred from level of transcript expression > is_a: EV:0000009 > > [Term] > id: EV:0000009 > name: inferred from transcript expression > is_a: EV:0000008 > > [Term] > id: EV:0000029 > name: inferred from InterPro motif similarity > is_a: EV:0000028 > > [Term] > id: EV:0000022 > name: inferred from co-purification > is_a: EV:0000021 > > [Term] > id: EV:0000008 > name: inferred from expression pattern > synonym: "IEP" [] > is_a: EV:0000006 > > [Term] > id: EV:0000036 > name: inferred from electronic annotation > synonym: "IEA" [] > is_a: EV:0000043 > > [Term] > id: EV:0000014 > name: inferred from mutant phenotype > synonym: "IMP" [] > is_a: EV:0000006 > > [Term] > id: EV:0000011 > name: inferred from genetic interaction > synonym: "IGI" [] > is_a: EV:0000006 > > [Term] > id: EV:0000039 > name: inferred from protein assay > is_a: EV:0000006 > > [Term] > id: EV:0000024 > name: inferred from protein binding > is_a: EV:0000023 > is_a: EV:0000039 > > [Term] > id: EV:0000045 > name: inferred from spatial pattern of protein expression > is_a: EV:0000010 > > [Term] > id: EV:0000047 > name: inferred from spatial pattern of transcript expression > is_a: EV:0000009 > > [Term] > id: EV:0000027 > name: inferred from structural similarity > is_a: EV:0000041 > > [Term] > id: EV:0000038 > name: inferred from transient rescue > is_a: EV:0000012 > > [Term] > id: EV:0000044 > name: inferred from sequence similarity > is_a: EV:0000041 > > [Term] > id: EV:0000016 > name: inferred from loss-of-function mutant phenotype > is_a: EV:0000015 > > [Term] > id: EV:0000005 > name: inferred from enzyme assay > is_a: EV:0000039 > > [Term] > id: EV:0000037 > name: not_recorded > synonym: "NR" [] > is_a: EV:0000000 > > [Term] > id: EV:0000026 > name: inferred from nucleic acid hybridization > is_a: EV:0000041 > is_a: EV:0000006 > > [Term] > id: EV:0000015 > name: inferred from gene mutation > is_a: EV:0000014 > > [Term] > id: EV:0000010 > name: inferred from protein expression > is_a: EV:0000008 > is_a: EV:0000039 > > [Term] > id: EV:0000004 > name: inferred from cell fractionation > is_a: EV:0000006 > > [Term] > id: EV:0000025 > name: inferred from 2-hybrid interaction > is_a: EV:0000023 > > [Term] > id: EV:0000003 > name: inferred from reconstitution assay > is_a: EV:0000006 > > [Term] > id: EV:0000034 > name: non-traceable author statement > synonym: "NAS" [] > is_a: EV:0000000 > > [Term] > id: EV:0000001 > name: inferred by curator > synonym: "IC" [] > is_a: EV:0000000 > > [Term] > id: EV:0000006 > name: inferred from experiment > is_a: EV:0000033 > > [Term] > id: EV:0000042 > name: inferred from gain-of-function mutant phenotype > is_a: EV:0000015 > > [Term] > id: EV:0000020 > name: inferred from specific protein inhibition > is_a: EV:0000039 > > [Term] > id: EV:0000019 > name: inferred from RNAi experiment > is_a: EV:0000014 > > [Term] > id: EV:0000021 > name: inferred from physical interaction > synonym: "IPI" [] > is_a: EV:0000006 > > [Term] > id: EV:0000033 > name: traceable author statement > synonym: "TAS" [] > is_a: EV:0000000 > > [Term] > id: EV:0000000 > name: Evidence_Codes_Ontology > > [Term] > id: EV:0000043 > name: inferred from in-silico analysis > is_a: EV:0000000 > > [Term] > id: EV:0000051 > name: inferred from gain of function mutant phenotype > is_obsolete: true > > [Term] > id: EV:0000050 > name: inferred from loss of function mutant phenotype > is_obsolete: true > > > ______________________________________________________________________ > !autogenerated-by: DAG-Edit version 1.409-beta-4 > !saved-by: ma11 > !date: Mon May 31 14:07:42 BST 2004 > !version: $Revision: 1.23 $ > !type: @is_a@ is_a is a > $Evidence_Codes_Ontology ; EV:0000000 > @is_a at inferred by curator ; EV:0000001 ; synonym:IC > @is_a at inferred from in-silico analysis ; EV:0000043 > @is_a at inferred from electronic annotation ; EV:0000036 ; synonym:IEA > @is_a at inferred from similarity ; EV:0000041 ; synonym:ISS @is_a@ traceable author statement ; EV:0000033 > @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from experiment ; EV:0000006 > @is_a at inferred from sequence similarity ; EV:0000044 > @is_a at inferred from curated BLAST match ; EV:0000030 > @is_a at inferred from curated BLAST match to nucleic acid ; EV:0000032 > @is_a at inferred from curated BLAST match to protein ; EV:0000031 > @is_a at inferred from motif similarity ; EV:0000028 > @is_a at inferred from InterPro motif similarity ; EV:0000029 > @is_a at inferred from structural similarity ; EV:0000027 > @is_a at no biological data ; EV:0000035 ; synonym:ND > @is_a at non-traceable author statement ; EV:0000034 ; synonym:NAS > @is_a at not_recorded ; EV:0000037 ; synonym:NR > @is_a at traceable author statement ; EV:0000033 ; synonym:TAS > @is_a at inferred from experiment ; EV:0000006 > @is_a at inferred from cell fractionation ; EV:0000004 > @is_a at inferred from direct assay ; EV:0000002 ; synonym:IDA > @is_a at inferred from expression pattern ; EV:0000008 ; synonym:IEP > @is_a at inferred from protein expression ; EV:0000010 @is_a@ inferred from protein assay ; EV:0000039 > @is_a at inferred from level of protein expression ; EV:0000046 > @is_a at inferred from spatial pattern of protein expression ; EV:0000045 > @is_a at inferred from transcript expression ; EV:0000009 > @is_a at inferred from level of transcript expression ; EV:0000048 > @is_a at inferred from spatial pattern of transcript expression ; EV:0000047 > @is_a at inferred from functional complementation ; EV:0000012 > @is_a at inferred from transgenic rescue ; EV:0000013 > @is_a at inferred from transient rescue ; EV:0000038 > @is_a at inferred from genetic interaction ; EV:0000011 ; synonym:IGI > @is_a at inferred from immunofluorescence ; EV:0000007 > @is_a at inferred from mutant phenotype ; EV:0000014 ; synonym:IMP > @is_a at inferred from anti-sense experiment ; EV:0000018 > @is_a at inferred from ectopic expression ; EV:0000017 > @is_a at inferred from gene mutation ; EV:0000015 > @is_a at inferred from gain-of-function mutant phenotype ; EV:0000042 > @is_a at inferred from loss-of-function mutant phenotype ; EV:0000016 > @is_a at inferred from RNAi experiment ; EV:0000019 > @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from similarity ; EV:0000041 > @is_a at inferred from physical interaction ; EV:0000021 ; synonym:IPI > @is_a at inferred from co-purification ; EV:0000022 > @is_a at inferred from ligand binding ; EV:0000023 > @is_a at inferred from 2-hybrid interaction ; EV:0000025 > @is_a at inferred from immunological assay ; EV:0000040 @is_a@ inferred from protein assay ; EV:0000039 > @is_a at inferred from protein binding ; EV:0000024 @is_a@ inferred from protein assay ; EV:0000039 > @is_a at inferred from protein assay ; EV:0000039 > @is_a at inferred from enzyme assay ; EV:0000005 > @is_a at inferred from immunological assay ; EV:0000040 @is_a@ inferred from ligand binding ; EV:0000023 > @is_a at inferred from protein binding ; EV:0000024 @is_a@ inferred from ligand binding ; EV:0000023 > @is_a at inferred from protein expression ; EV:0000010 @is_a@ inferred from expression pattern ; EV:0000008 > @is_a at inferred from level of protein expression ; EV:0000046 > @is_a at inferred from spatial pattern of protein expression ; EV:0000045 > @is_a at inferred from specific protein inhibition ; EV:0000020 > @is_a at inferred from reconstitution assay ; EV:0000003 > @is_a at inferred from reporter gene assay ; EV:0000049 > @is_a at inferred from similarity ; EV:0000041 ; synonym:ISS @is_a@ inferred from in-silico analysis ; EV:0000043 > @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from experiment ; EV:0000006 > @is_a at inferred from sequence similarity ; EV:0000044 > @is_a at inferred from curated BLAST match ; EV:0000030 > @is_a at inferred from curated BLAST match to nucleic acid ; EV:0000032 > @is_a at inferred from curated BLAST match to protein ; EV:0000031 > @is_a at inferred from motif similarity ; EV:0000028 > @is_a at inferred from InterPro motif similarity ; EV:0000029 > @is_a at inferred from structural similarity ; EV:0000027 -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From bioboy at uga.edu Mon May 10 03:09:51 2004 From: bioboy at uga.edu (Xian) Date: Mon, 10 May 2004 07:09:51 -0000 Subject: [MOBY-dev] optimal integration of primer3 into biopython and others using swig and biomoby In-Reply-To: <70D7B115-A117-11D8-A663-000A956845CE@stanfordalumni.org> References: <409CB249.2090900@uga.edu> <70D7B115-A117-11D8-A663-000A956845CE@stanfordalumni.org> Message-ID: <409F29D0.7010708@uga.edu> optimal integration of primer3 into biopython and others using swig and biomoby Abstract: Primer3 is the de facto open source C program for automated PCR primer selection; it is used by emboss and biopython, among others. There is no active development [last release 0.9 9/98]. I have used primer3 and python to study Arabidopsis genome function. I aim to integrate primer3 into biopython. Specifically, my goal is to develop primer3 into a set of C modules or libraries to provide: a) standardized access via python, perl, etc b) impetus to further primer3 development. I propose here an optimal development path that maximizes target audience while minimizing code rewriting. Discussion: TTBOMK, Biopython and bioperl each have a primer3 i/o parser. These multiple, unstandardized dependencies may hinder future primer3 development [such as the addition of R. Griffais's K-tuple frequency method, Nucl. Acids. Res. 1991 19: 3887-3891 ]. My aim is to develop primer3 into a maintainable and easily extendable set of C modules or libraries that are natively accessible by perl and python. Swig is a "C compiler" that provide this functionality; e.g. primer3's Tm analysis module [oligotm.h and oligotm.c] can be compiled and imported as a python module whose methods are native C functions. Once this is done adding new language support is trivial. Well-defined, standard i/o structures for these libraries will facilitate their use by the bioinformatics community from within perl or python, and should be considered in development. Biomoby is an XML-based data ontology which represents data as heirarchical objects in the ontology, e.g. the hypothetical object "PrimerPair" contains two instances of "DNASequence" along with any other data such as Tm, self-hybridization, etc. Designing a biomoby object for primer3 data i/o has the additional benefit of easing information-sharing with existing databases and other biomoby-aware services. Please reply if you are interested in using, testing, designing, or developing this project. Likewise, feel free to forward this to such people. If there is sufficient interest, I will spawn a mailing group or possibly a sourceforge project. Thanks for your time, xian References/Links: Primer3[down at time of writing]: http://www-genome.wi.mit.edu/genome_software/other/primer3.html Emboss's eprimer3 [primer3 wrapper]: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Apps/eprimer3.html SWIG, Simplified Wrapper and Interface Generator: http://www.swig.org/ biomoby: http://www.biomoby.org/overview.html biomoby, bioperl, and much more: http://open-bio.org/ From kanani at cshl.edu Wed May 5 15:14:57 2004 From: kanani at cshl.edu (Ardavan Kanani) Date: Wed, 5 May 2004 11:14:57 -0400 Subject: [MOBY-dev] need help with register service :) Message-ID: Hello all, I am trying to register service called getIndvsOnPanel() that takes a panel lsid and returns a collection of simple objects with their id set to the individual's lsid on that panel. Here is how I am registering the service: sub register_getIndvsOnPanel_service { my ($C, $description) = @_; my $reg = $C->registerService( serviceName => "getIndvsOnPanel", authURI => $authURI, contactEmail => $email, description => $description, URL => $url, input => ['panelLSID', ["Object" => []] ], output => ['indvLSID', [["Object" => []]] ], category => "moby", serviceType => "Retrieval", ); die "Bad return value from registerService for getIndvsOnPanel service.\n" unless $reg; if ($reg->success == 1){ print "Registration successful for getIndvsOnPanel service.\n"; } else { print "Registration failed for getIndvsOnPanel service: ", $reg->message, "\n"; } } I get the following error message: Can't use string ("indvLSID") as an ARRAY ref while "strict refs" in use at /usr/local/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line 710. What am I doing wrong? Thanks, Ardavan Kanani From markw at illuminae.com Wed May 5 14:21:31 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 05 May 2004 07:21:31 -0700 Subject: [MOBY] [MOBY-dev] need help with register service :) In-Reply-To: References: Message-ID: <1083766890.1634.28.camel@myhost.mydomain> Hi Ardavan! You are missing one layer of brackets. Yes, I know it is arcane :-) I'm going to add a bit of documentation to the POD showing why it has to be this way, and how each layer of brackets should be interpreted. I posted a message of explanation to the list a couple of weeks ago in response to a similar question from Catherine's group, but I notice that you are not subscribed to this mailing list, so you wouldn't have read it... The correct signature for registerService inputs/outputs is detailed in the pod docs, but it requires one more layer of array-ref brackets than you have used. So your message: input => ['panelLSID', ["Object" => []] ], output=> ['indvLSID', [["Object" => []]] ], should be: input => [ ['panelLSID', ["Object" => []] ] ], output=> [ ['indvLSID', [["Object" => []]] ] ], cheers! M On Wed, 2004-05-05 at 08:14, Ardavan Kanani wrote: > Hello all, > > I am trying to register service called getIndvsOnPanel() that takes a > panel lsid and returns a collection of simple objects with their id set > to the individual's lsid on that panel. Here is how I am registering > the service: > > > sub register_getIndvsOnPanel_service { > my ($C, $description) = @_; > my $reg = $C->registerService( > serviceName => "getIndvsOnPanel", > authURI => $authURI, > contactEmail => $email, > description => $description, > URL => $url, > input => ['panelLSID', ["Object" > => []] ], > output => ['indvLSID', [["Object" > => []]] ], > category => "moby", > serviceType => "Retrieval", > ); > die "Bad return value from registerService for getIndvsOnPanel > service.\n" unless $reg; > if ($reg->success == 1){ > print "Registration successful for getIndvsOnPanel service.\n"; > } > else { > print "Registration failed for getIndvsOnPanel service: ", > $reg->message, "\n"; > } > } > > > I get the following error message: > > Can't use string ("indvLSID") as an ARRAY ref while "strict refs" in > use at /usr/local/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line > 710. > > > > What am I doing wrong? > > > > Thanks, Ardavan Kanani > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed May 5 14:30:39 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 05 May 2004 07:30:39 -0700 Subject: [MOBY] [MOBY-dev] need help with register service :) In-Reply-To: <1083766890.1634.28.camel@myhost.mydomain> References: <1083766890.1634.28.camel@myhost.mydomain> Message-ID: <1083767439.1634.39.camel@myhost.mydomain> On Wed, 2004-05-05 at 07:21, Mark Wilkinson wrote: > input => ['panelLSID', ["Object" => []] ], > output=> ['indvLSID', [["Object" => []]] ], > > should be: > > input => [ > ['panelLSID', ["Object" => []] ] > ], > output=> [ > ['indvLSID', [["Object" => []]] ] > ], This is because there may be multiple inputs to, or outputs from, a service, with multiple names and/or object types; therefore the inputs and outputs from a service are a list of lists. M -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From kanani at cshl.edu Thu May 13 19:14:11 2004 From: kanani at cshl.edu (Ardavan Kanani) Date: Thu, 13 May 2004 15:14:11 -0400 Subject: [MOBY-dev] xml dump of MOBY objects Message-ID: Hello, Is there a tool, already written, that would dump out the MOBY objects in their XML format? From senger at ebi.ac.uk Thu May 13 19:38:32 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 13 May 2004 20:38:32 +0100 (BST) Subject: [MOBY-dev] xml dump of MOBY objects In-Reply-To: Message-ID: > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > Well, almost everything you get back from both Moby Central (registry) and from Moby-native services are XML-based objects. So, for example, if you want to get all service instances, you can use a Java client (but the same is available in Perl) like this: 1) create a file (e.g. tmp/moby.txt) with this contents: moby 1 1 0 2) call Java command-line client: ./run-cmdline-client -call findService tmp/moby.xml And you get all service instances in XML. Was this what you were asking for? Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Thu May 13 19:38:32 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 13 May 2004 20:38:32 +0100 (BST) Subject: [MOBY-dev] xml dump of MOBY objects In-Reply-To: Message-ID: > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > Well, almost everything you get back from both Moby Central (registry) and from Moby-native services are XML-based objects. So, for example, if you want to get all service instances, you can use a Java client (but the same is available in Perl) like this: 1) create a file (e.g. tmp/moby.txt) with this contents: moby 1 1 0 2) call Java command-line client: ./run-cmdline-client -call findService tmp/moby.xml And you get all service instances in XML. Was this what you were asking for? Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Thu May 13 21:21:21 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 13 May 2004 14:21:21 -0700 Subject: [MOBY] [MOBY-dev] xml dump of MOBY objects In-Reply-To: References: Message-ID: <1084483281.9647.7.camel@myhost.mydomain> Under "cool tools" link on the moby homepage there is a link to Ken Steube's fantastic service encyclopedia. From there you can click-into the object structures. You can also link directly to them using the following GET string: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=FOO where FOO is the object you wish to see the structure of. I have just taken on a co-op student whose primary task will be creating GUI interfaces to assist with object browsing, new object creation/registration, service type and namespace browsing and registration, as well as service instance registration. Things should start getting easier SOON! M On Thu, 2004-05-13 at 12:14, Ardavan Kanani wrote: > Hello, > > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Thu May 13 21:21:21 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 13 May 2004 14:21:21 -0700 Subject: [MOBY] [MOBY-dev] xml dump of MOBY objects In-Reply-To: References: Message-ID: <1084483281.9647.7.camel@myhost.mydomain> Under "cool tools" link on the moby homepage there is a link to Ken Steube's fantastic service encyclopedia. From there you can click-into the object structures. You can also link directly to them using the following GET string: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=FOO where FOO is the object you wish to see the structure of. I have just taken on a co-op student whose primary task will be creating GUI interfaces to assist with object browsing, new object creation/registration, service type and namespace browsing and registration, as well as service instance registration. Things should start getting easier SOON! M On Thu, 2004-05-13 at 12:14, Ardavan Kanani wrote: > Hello, > > Is there a tool, already written, that would dump out the MOBY objects > in their XML format? > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From letondal at pasteur.fr Mon May 17 12:03:24 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Mon, 17 May 2004 14:03:24 +0200 Subject: [MOBY-dev] Fwd: Google of Web services / donating CPU cycles through Web services Message-ID: <200405171203.i4HC3OA0348681@electre.pasteur.fr> Hi, There was a discussion about this idea last week in the [bioclusters] mailing list that reminds me a lot the discussion at CSHL (the discussion was about having a moby service provider publishing "somewhere" its service - not in a repository like moby central but in a place where Google could find it - and having a client find it as a Web (visible) document with a proper URI). ------- Forwarded Message From: Dan Bolser To: bioclusters at bioinformatics.org Subject: [Bioclusters] Question about grid List-Archive: Date: Thu, 13 May 2004 14:01:49 +0100 (BST) Hello, I had an idea to do with grid computing, but it may be total garbage. I heard about some clever people who started to 'steal' computation from unsuspecting web sites by hijacking the normal function of the site and co-opting its computations into a different program. If these stories are true, surly we could do this with a bit more civility, and set up a bunch of generic 'calculators' through the web which could then be used for grid computing. The way I imagine the system is this... Program starts by searching the web for calculators, the code is compiled for the 'web-engine' so every single instruction is encoded as an HTTP / CGI / XML request, and all instructions are performed over the web on a shifting number of calculators. Actually, I found something similar hear... http://ausweb.scu.edu.au/aw02/papers/refereed/kelly/paper.html I wanted to ask about the feasibility of such an idea. For example if one machine sent all its instructions to another over a gigabit intra net, how much slower would this be than local computation? Is a gigabit LAN 1/2/3/10/100/1000 orders of magnitude slower than internal CPU communication channels? The power of an open source system like this would be if someone like Apache would take the idea on board and release it as part of its standard distribution. However, even if every web server on the web were running such a calculator (why not be ambitious), could the system be fast enough? Naturally there are a lot of issues regarding distribution / allocation / scheduling etc. but before we get into nasty details, is the idea remotely worth consideration? How difficult would it be to make a Java compiler accommodate such a web-engine? Thanks very much for any feedback, Dan. _______________________________________________ Bioclusters maillist - Bioclusters at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bioclusters ------- End of Forwarded Message From senger at ebi.ac.uk Tue May 18 10:13:32 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 18 May 2004 11:13:32 +0100 (BST) Subject: [MOBY-dev] a bug in expandXXX tags? In-Reply-To: <1083278395.1662.17.camel@myhost.mydomain> Message-ID: Hi Mark, Working on findService method (in Java's MobyCmdLineClient) I found that there might be perhaps a bug when using expandXXX tags: 1) This query object: Service moby 1 1 0 did not find any services. I thought that serviceType 'Service' is parent of all service types, and because I put 'expandService@ to 1, I expect to find all services. The API says "this flag will cause MOBY Central to traverse the Service ontology and discover services that are child types (more specific) than the Service-type you requested." 2) Regarding the 'expandObjects' flag, it seems to work fine with inputs but does not seem to work with outputs. This query object: findService> SchematikonVorocodeName moby 1 1 0 found only RetrieveVorocodeName service but not the services "that operate not only on the Object Class you are querying, but also any ontolological parent types of that Object Class" - see that 'expandObjects' is set to 1. Are these bugs or my misunderstandings? Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From kanani at cshl.edu Tue May 18 18:32:27 2004 From: kanani at cshl.edu (Ardavan Kanani) Date: Tue, 18 May 2004 14:32:27 -0400 Subject: [MOBY-dev] thanks Message-ID: Thanks all for answering my question. Ardavan From markw at illuminae.com Thu May 20 21:07:04 2004 From: markw at illuminae.com (Markw) Date: Thu, 20 May 2004 22:07:04 +0100 Subject: [MOBY-dev] Notification Message-ID: An embedded and charset-unspecified text was scrubbed... Name: warning1.txt URL: From markw at illuminae.com Fri May 21 20:11:47 2004 From: markw at illuminae.com (Markw) Date: Fri, 21 May 2004 21:11:47 +0100 Subject: [MOBY-dev] Changes.. Message-ID: An embedded and charset-unspecified text was scrubbed... Name: warning1.txt URL: From mwilkinson at mrl.ubc.ca Fri May 21 20:17:30 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Fri, 21 May 2004 13:17:30 -0700 Subject: [MOBY-dev] Viruses Message-ID: <1085170650.10201.12.camel@myhost.mydomain> Hi all, Do any of you recognize this domain: from benna.net (213-156-52-97.fastres.net [213.156.52.97]) I am getting hit ~every hour from that domain, with Martin as the return address. Now I see that whoever has this infection is starting to send messages to the MOBY mailing lists with *me* as the return address!! If any of you recognize that address, heads up... you have been infected for the past couple of weeks. M -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Sat May 22 12:41:36 2004 From: markw at illuminae.com (Markw) Date: Sat, 22 May 2004 13:41:36 +0100 Subject: [MOBY-dev] Re: Document Message-ID: An embedded and charset-unspecified text was scrubbed... Name: warning1.txt URL: From markw at illuminae.com Sun May 23 09:26:19 2004 From: markw at illuminae.com (Markw) Date: Sun, 23 May 2004 10:26:19 +0100 Subject: [MOBY-dev] RE: Protected message Message-ID: An embedded and charset-unspecified text was scrubbed... Name: warning1.txt URL: From markw at illuminae.com Mon May 24 19:36:16 2004 From: markw at illuminae.com (Markw) Date: Mon, 24 May 2004 20:36:16 +0100 Subject: [MOBY-dev] Encrypted document Message-ID: A non-text attachment was scrubbed... Name: tcmwquacje.jpeg Type: image/jpeg Size: 994 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Loves_money.zip Type: application/octet-stream Size: 22410 bytes Desc: not available URL: From markw at illuminae.com Mon May 31 19:12:49 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 31 May 2004 12:12:49 -0700 Subject: [MOBY-dev] attn. especially Heiko Message-ID: <1086030768.2973.75.camel@myhost.mydomain> Heiko, this might have consequences for the new Xref block... M -----Forwarded Message----- > From: Michael Ashburner (Genetics) > To: ma11 at gen.cam.ac.uk, midori at ebi.ac.uk > Cc: gofriends at genome.stanford.edu, ref26 at gen.cam.ac.uk > Subject: [GO] Re: Draft evidence code ontology > Date: Mon, 31 May 2004 14:11:32 +0100 > > I would like to revisit the evidence codes ontology, perhaps > with the idea of some discussion about it during the annotation > workshop in 2 weeks time. > > I attach a new version. The major change is: > > inferred from experiment added as a parent to ida (and its children) > > I also added some new terms. I am still awaiting the TAIR codes > for inclusion. > > Michael > > ______________________________________________________________________ > format-version: 1.0 > date: 31:05:2004 14:08 > saved-by: ma11 > auto-generated-by: DAG-Edit 1.409-beta-4 > default-namespace: evidence_codes.ontology > remark: autogenerated-by\: DAG-Edit version 1.409-beta-4\nsaved-by\: ma11\ndate\: Fri Feb 27 16\:10\:50 GMT 2004\nversion\: $Revision\: 1.23 $ > > [Term] > id: EV:0000017 > name: inferred from ectopic expression > is_a: EV:0000014 > > [Term] > id: EV:0000030 > name: inferred from curated BLAST match > is_a: EV:0000044 > > [Term] > id: EV:0000007 > name: inferred from immunofluorescence > is_a: EV:0000006 > > [Term] > id: EV:0000002 > name: inferred from direct assay > synonym: "IDA" [] > is_a: EV:0000006 > > [Term] > id: EV:0000031 > name: inferred from curated BLAST match to protein > is_a: EV:0000030 > > [Term] > id: EV:0000041 > name: inferred from similarity > synonym: "ISS" [] > is_a: EV:0000043 > is_a: EV:0000033 > > [Term] > id: EV:0000032 > name: inferred from curated BLAST match to nucleic acid > is_a: EV:0000030 > > [Term] > id: EV:0000040 > name: inferred from immunological assay > is_a: EV:0000023 > is_a: EV:0000039 > > [Term] > id: EV:0000018 > name: inferred from anti-sense experiment > is_a: EV:0000014 > > [Term] > id: EV:0000049 > name: inferred from reporter gene assay > is_a: EV:0000006 > > [Term] > id: EV:0000046 > name: inferred from level of protein expression > is_a: EV:0000010 > > [Term] > id: EV:0000023 > name: inferred from ligand binding > is_a: EV:0000021 > > [Term] > id: EV:0000028 > name: inferred from motif similarity > is_a: EV:0000044 > > [Term] > id: EV:0000035 > name: no biological data > synonym: "ND" [] > is_a: EV:0000000 > > [Term] > id: EV:0000013 > name: inferred from transgenic rescue > is_a: EV:0000012 > > [Term] > id: EV:0000012 > name: inferred from functional complementation > is_a: EV:0000006 > > [Term] > id: EV:0000048 > name: inferred from level of transcript expression > is_a: EV:0000009 > > [Term] > id: EV:0000009 > name: inferred from transcript expression > is_a: EV:0000008 > > [Term] > id: EV:0000029 > name: inferred from InterPro motif similarity > is_a: EV:0000028 > > [Term] > id: EV:0000022 > name: inferred from co-purification > is_a: EV:0000021 > > [Term] > id: EV:0000008 > name: inferred from expression pattern > synonym: "IEP" [] > is_a: EV:0000006 > > [Term] > id: EV:0000036 > name: inferred from electronic annotation > synonym: "IEA" [] > is_a: EV:0000043 > > [Term] > id: EV:0000014 > name: inferred from mutant phenotype > synonym: "IMP" [] > is_a: EV:0000006 > > [Term] > id: EV:0000011 > name: inferred from genetic interaction > synonym: "IGI" [] > is_a: EV:0000006 > > [Term] > id: EV:0000039 > name: inferred from protein assay > is_a: EV:0000006 > > [Term] > id: EV:0000024 > name: inferred from protein binding > is_a: EV:0000023 > is_a: EV:0000039 > > [Term] > id: EV:0000045 > name: inferred from spatial pattern of protein expression > is_a: EV:0000010 > > [Term] > id: EV:0000047 > name: inferred from spatial pattern of transcript expression > is_a: EV:0000009 > > [Term] > id: EV:0000027 > name: inferred from structural similarity > is_a: EV:0000041 > > [Term] > id: EV:0000038 > name: inferred from transient rescue > is_a: EV:0000012 > > [Term] > id: EV:0000044 > name: inferred from sequence similarity > is_a: EV:0000041 > > [Term] > id: EV:0000016 > name: inferred from loss-of-function mutant phenotype > is_a: EV:0000015 > > [Term] > id: EV:0000005 > name: inferred from enzyme assay > is_a: EV:0000039 > > [Term] > id: EV:0000037 > name: not_recorded > synonym: "NR" [] > is_a: EV:0000000 > > [Term] > id: EV:0000026 > name: inferred from nucleic acid hybridization > is_a: EV:0000041 > is_a: EV:0000006 > > [Term] > id: EV:0000015 > name: inferred from gene mutation > is_a: EV:0000014 > > [Term] > id: EV:0000010 > name: inferred from protein expression > is_a: EV:0000008 > is_a: EV:0000039 > > [Term] > id: EV:0000004 > name: inferred from cell fractionation > is_a: EV:0000006 > > [Term] > id: EV:0000025 > name: inferred from 2-hybrid interaction > is_a: EV:0000023 > > [Term] > id: EV:0000003 > name: inferred from reconstitution assay > is_a: EV:0000006 > > [Term] > id: EV:0000034 > name: non-traceable author statement > synonym: "NAS" [] > is_a: EV:0000000 > > [Term] > id: EV:0000001 > name: inferred by curator > synonym: "IC" [] > is_a: EV:0000000 > > [Term] > id: EV:0000006 > name: inferred from experiment > is_a: EV:0000033 > > [Term] > id: EV:0000042 > name: inferred from gain-of-function mutant phenotype > is_a: EV:0000015 > > [Term] > id: EV:0000020 > name: inferred from specific protein inhibition > is_a: EV:0000039 > > [Term] > id: EV:0000019 > name: inferred from RNAi experiment > is_a: EV:0000014 > > [Term] > id: EV:0000021 > name: inferred from physical interaction > synonym: "IPI" [] > is_a: EV:0000006 > > [Term] > id: EV:0000033 > name: traceable author statement > synonym: "TAS" [] > is_a: EV:0000000 > > [Term] > id: EV:0000000 > name: Evidence_Codes_Ontology > > [Term] > id: EV:0000043 > name: inferred from in-silico analysis > is_a: EV:0000000 > > [Term] > id: EV:0000051 > name: inferred from gain of function mutant phenotype > is_obsolete: true > > [Term] > id: EV:0000050 > name: inferred from loss of function mutant phenotype > is_obsolete: true > > > ______________________________________________________________________ > !autogenerated-by: DAG-Edit version 1.409-beta-4 > !saved-by: ma11 > !date: Mon May 31 14:07:42 BST 2004 > !version: $Revision: 1.23 $ > !type: @is_a@ is_a is a > $Evidence_Codes_Ontology ; EV:0000000 > @is_a at inferred by curator ; EV:0000001 ; synonym:IC > @is_a at inferred from in-silico analysis ; EV:0000043 > @is_a at inferred from electronic annotation ; EV:0000036 ; synonym:IEA > @is_a at inferred from similarity ; EV:0000041 ; synonym:ISS @is_a@ traceable author statement ; EV:0000033 > @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from experiment ; EV:0000006 > @is_a at inferred from sequence similarity ; EV:0000044 > @is_a at inferred from curated BLAST match ; EV:0000030 > @is_a at inferred from curated BLAST match to nucleic acid ; EV:0000032 > @is_a at inferred from curated BLAST match to protein ; EV:0000031 > @is_a at inferred from motif similarity ; EV:0000028 > @is_a at inferred from InterPro motif similarity ; EV:0000029 > @is_a at inferred from structural similarity ; EV:0000027 > @is_a at no biological data ; EV:0000035 ; synonym:ND > @is_a at non-traceable author statement ; EV:0000034 ; synonym:NAS > @is_a at not_recorded ; EV:0000037 ; synonym:NR > @is_a at traceable author statement ; EV:0000033 ; synonym:TAS > @is_a at inferred from experiment ; EV:0000006 > @is_a at inferred from cell fractionation ; EV:0000004 > @is_a at inferred from direct assay ; EV:0000002 ; synonym:IDA > @is_a at inferred from expression pattern ; EV:0000008 ; synonym:IEP > @is_a at inferred from protein expression ; EV:0000010 @is_a@ inferred from protein assay ; EV:0000039 > @is_a at inferred from level of protein expression ; EV:0000046 > @is_a at inferred from spatial pattern of protein expression ; EV:0000045 > @is_a at inferred from transcript expression ; EV:0000009 > @is_a at inferred from level of transcript expression ; EV:0000048 > @is_a at inferred from spatial pattern of transcript expression ; EV:0000047 > @is_a at inferred from functional complementation ; EV:0000012 > @is_a at inferred from transgenic rescue ; EV:0000013 > @is_a at inferred from transient rescue ; EV:0000038 > @is_a at inferred from genetic interaction ; EV:0000011 ; synonym:IGI > @is_a at inferred from immunofluorescence ; EV:0000007 > @is_a at inferred from mutant phenotype ; EV:0000014 ; synonym:IMP > @is_a at inferred from anti-sense experiment ; EV:0000018 > @is_a at inferred from ectopic expression ; EV:0000017 > @is_a at inferred from gene mutation ; EV:0000015 > @is_a at inferred from gain-of-function mutant phenotype ; EV:0000042 > @is_a at inferred from loss-of-function mutant phenotype ; EV:0000016 > @is_a at inferred from RNAi experiment ; EV:0000019 > @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from similarity ; EV:0000041 > @is_a at inferred from physical interaction ; EV:0000021 ; synonym:IPI > @is_a at inferred from co-purification ; EV:0000022 > @is_a at inferred from ligand binding ; EV:0000023 > @is_a at inferred from 2-hybrid interaction ; EV:0000025 > @is_a at inferred from immunological assay ; EV:0000040 @is_a@ inferred from protein assay ; EV:0000039 > @is_a at inferred from protein binding ; EV:0000024 @is_a@ inferred from protein assay ; EV:0000039 > @is_a at inferred from protein assay ; EV:0000039 > @is_a at inferred from enzyme assay ; EV:0000005 > @is_a at inferred from immunological assay ; EV:0000040 @is_a@ inferred from ligand binding ; EV:0000023 > @is_a at inferred from protein binding ; EV:0000024 @is_a@ inferred from ligand binding ; EV:0000023 > @is_a at inferred from protein expression ; EV:0000010 @is_a@ inferred from expression pattern ; EV:0000008 > @is_a at inferred from level of protein expression ; EV:0000046 > @is_a at inferred from spatial pattern of protein expression ; EV:0000045 > @is_a at inferred from specific protein inhibition ; EV:0000020 > @is_a at inferred from reconstitution assay ; EV:0000003 > @is_a at inferred from reporter gene assay ; EV:0000049 > @is_a at inferred from similarity ; EV:0000041 ; synonym:ISS @is_a@ inferred from in-silico analysis ; EV:0000043 > @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from experiment ; EV:0000006 > @is_a at inferred from sequence similarity ; EV:0000044 > @is_a at inferred from curated BLAST match ; EV:0000030 > @is_a at inferred from curated BLAST match to nucleic acid ; EV:0000032 > @is_a at inferred from curated BLAST match to protein ; EV:0000031 > @is_a at inferred from motif similarity ; EV:0000028 > @is_a at inferred from InterPro motif similarity ; EV:0000029 > @is_a at inferred from structural similarity ; EV:0000027 -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From bioboy at uga.edu Mon May 10 07:09:51 2004 From: bioboy at uga.edu (Xian) Date: Mon, 10 May 2004 07:09:51 -0000 Subject: [MOBY-dev] optimal integration of primer3 into biopython and others using swig and biomoby In-Reply-To: <70D7B115-A117-11D8-A663-000A956845CE@stanfordalumni.org> References: <409CB249.2090900@uga.edu> <70D7B115-A117-11D8-A663-000A956845CE@stanfordalumni.org> Message-ID: <409F29D0.7010708@uga.edu> optimal integration of primer3 into biopython and others using swig and biomoby Abstract: Primer3 is the de facto open source C program for automated PCR primer selection; it is used by emboss and biopython, among others. There is no active development [last release 0.9 9/98]. I have used primer3 and python to study Arabidopsis genome function. I aim to integrate primer3 into biopython. Specifically, my goal is to develop primer3 into a set of C modules or libraries to provide: a) standardized access via python, perl, etc b) impetus to further primer3 development. I propose here an optimal development path that maximizes target audience while minimizing code rewriting. Discussion: TTBOMK, Biopython and bioperl each have a primer3 i/o parser. These multiple, unstandardized dependencies may hinder future primer3 development [such as the addition of R. Griffais's K-tuple frequency method, Nucl. Acids. Res. 1991 19: 3887-3891 ]. My aim is to develop primer3 into a maintainable and easily extendable set of C modules or libraries that are natively accessible by perl and python. Swig is a "C compiler" that provide this functionality; e.g. primer3's Tm analysis module [oligotm.h and oligotm.c] can be compiled and imported as a python module whose methods are native C functions. Once this is done adding new language support is trivial. Well-defined, standard i/o structures for these libraries will facilitate their use by the bioinformatics community from within perl or python, and should be considered in development. Biomoby is an XML-based data ontology which represents data as heirarchical objects in the ontology, e.g. the hypothetical object "PrimerPair" contains two instances of "DNASequence" along with any other data such as Tm, self-hybridization, etc. Designing a biomoby object for primer3 data i/o has the additional benefit of easing information-sharing with existing databases and other biomoby-aware services. Please reply if you are interested in using, testing, designing, or developing this project. Likewise, feel free to forward this to such people. If there is sufficient interest, I will spawn a mailing group or possibly a sourceforge project. Thanks for your time, xian References/Links: Primer3[down at time of writing]: http://www-genome.wi.mit.edu/genome_software/other/primer3.html Emboss's eprimer3 [primer3 wrapper]: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Apps/eprimer3.html SWIG, Simplified Wrapper and Interface Generator: http://www.swig.org/ biomoby: http://www.biomoby.org/overview.html biomoby, bioperl, and much more: http://open-bio.org/