From bneron at pasteur.fr  Mon May  3 04:22:52 2004
From: bneron at pasteur.fr (Bertrand Neron)
Date: Mon May  3 04:36:59 2004
Subject: [MOBY-l] how to call a service with secondaries?
Message-ID: <20040503082252.GA20511@caroline.sis.pasteur.fr>


I'd like to implement a bioMoby service with a Simple (a dnaSequence) and severals secondaries
but I have some problems.

to parse the XML input, I use the sub MOBY::CommonSubs::complexServiceInputParser($message)
 and XML::DOM . I see on the API (http://biomoby.org/moby-live/Perl/MOBY/CommonSubs.html#complexserviceinputparser) that the xml input should have this structure

<queryInput queryID = '1'>
   <Simple articleName='name1'>
       <Object namespace=blah id=blah/>
   </Simple>
   <Parameter articleName='cutoff'>
       <datatype>Float</datatype>
       <default>10</default>
   </Parameter>
</queryInput>
 

but the xml which my service recieve when I invoke it with the execute method had this structure


<?xml version='1.0' encoding='UTF-8'?>
        <moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>
            <moby:Query>
                <moby:queryInput queryID='1'>
                   <moby:Simple moby:articleName=''>
                     <dnaSequence namespace="" id=""    articleName="sequence">
                          <Integer namespace="" id="" articleName="Length">19<\In
teger>
                          <String namespace="" id="" articleName="SequenceString"
>ACGGTAGCTAGGTACCCAT<\String>
                     </dnaSequence>
                   </moby:Simple>
                   <moby:Simple moby:articleName=''>
                   <Parameter namespace="" id="" articleName="hybridation_type">
                             <Value>dnadna</Value>
                   <\Parameter>
                   </moby:Simple>
                   <moby:Simple moby:articleName=''>
                       <Parameter namespace="" id="" articleName="nucacid_concentration">
                            <Value>0.005</Value>
                       <\Parameter>
                   </moby:Simple>
                   <moby:Simple moby:articleName=''>
                         <Parameter namespace="" id="" articleName="salt_concentratio">
                            <Value>1.5</Value>
                         <\Parameter>
                    </moby:Simple>
                    </moby:queryInput>

              </moby:Query>
        </moby:MOBY>


each Parameter is embeded in a moby:Simple and the Parameter end Markups have an \  instead of / ??

How can I invoke a service with a Simple and several secondaries?
what kind of xml I should expected?

thanks.

bertrand

ps.

this the code I used to register the service and to call the service.


#########################################################################
# Register the service
#########################################################################
sub register_service {
  my $C = shift;
  my $reg = $C->registerService(
				serviceName  => 'Melting',
				serviceType  => "Analysis",
				authURI      => $authURI,
				contactEmail => $email,

				description  => "Melting: enthalpie, entropy and melting temperature (N. Le Novere)",
				category => "moby",
				URL          => $url,
				input        => [ ["sequence",['dnaSequence' => [] ] ]],
		   
				output       => [ ['', ["text-plain" => []]], ],
				secondary => {
					      "hybridation_type" => {'dataType' => 'String' ,
								    'enum' => ['dnadna','dnarna','rnarna']},
					      "nnfile" => {'dataType'=> 'String' ,
							   'default' =>'default' ,
							   'enum' => ['default','all97a.nn','bre86a.nn','fre86a.nn','san96a.nn','sug95a.nn','sug96a.nn','xia98a.nn']},
					      "complement_string" =>{'dataType' => 'String' },
					      "salt_concentratio" =>{'data_type' => 'Float' ,
								    'min' => 0.0 ,
								   ' max' => 10.0 },
					      "nucaid_concentration" => {'data_type' => 'Float',
									min => 0.0 ,
									max => 1.0 },
					      "correction_factor" => {'data_type' => 'Float' },
					      "salt_correction" => {'data_type' => 'String', 
								    'enum' => ['wet91a','san96a','san98a']},
					      "approx" => {'data_type' => 'Integer',
							   'default' => 0,
							  'enum' => [ 0 , 1]},
					      "dandling_ends" => {'data_type' => 'Integer',
								  'default' => 0,
								 'enum' => [ 0 , 1 ]},
					      "mismatches" => {'da













From o023163 at ncgr.ncgr.org  Mon May  3 11:29:10 2004
From: o023163 at ncgr.ncgr.org (o023163@ncgr.ncgr.org)
Date: Mon May 10 16:51:53 2004
Subject: [MOBY-l] Re: Re: Thanks!
Message-ID: <200405031536.i43Fa06B032000@portal.open-bio.org>

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MIMEDefang Administrator's <dag@sonsorol.org>.  For more information about MIMEDefang, see:

            http://www.roaringpenguin.com/mimedefang/enduser.php3

An attachment named document.pif 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 --------------
Please read the attached file.
From icho at svsu.edu  Wed May  5 13:59:03 2004
From: icho at svsu.edu (Il-Hyung Cho)
Date: Mon May 10 16:51:53 2004
Subject: [MOBY-l] Java implemenation on Axis
Message-ID: <s098f337.011@gw.svsu.edu>

Hello,
 
I am new to this group.
Hope this message is relevant to this group.
I am trying to implement web services on Apache Axis platform. I wonder
whether there is any tutorial or simple examples that I can follow to
make a small application up and running.
Could anyone help?
 
Many thanks,
 
 
 
Il-Hyung Cho
Ph.D. Computer Science
Saginaw Valley State Univ
From viji at gsf.de  Tue May 11 03:32:38 2004
From: viji at gsf.de (Viji)
Date: Tue May 11 03:37:54 2004
Subject: [MOBY-l] Java implemenation on Axis
In-Reply-To: <s098f337.011@gw.svsu.edu>
References: <s098f337.011@gw.svsu.edu>
Message-ID: <40A08196.9090607@gsf.de>

Hi Il-Hyung Cho,

I would suggest you to read the User guide of Axis first which(is very 
important) will be in "http://ws.apache.org/axis/java/user-guide.html"

Then, after understanding the concepts, if you still need some examples, 
scroll to the end of the page "http://ammai.com" and you will find three 
tutorials which will help you write Axis web services.

Then, you can register those web services as Moby services in BioMoby. 
Until then, this (list) will be inappropriate for your queries.

I hope I answered your questions.

All the Best.

Regards
Viji

Il-Hyung Cho wrote:

>Hello,
> 
>I am new to this group.
>Hope this message is relevant to this group.
>I am trying to implement web services on Apache Axis platform. I wonder
>whether there is any tutorial or simple examples that I can follow to
>make a small application up and running.
>Could anyone help?
> 
>Many thanks,
> 
> 
> 
>Il-Hyung Cho
>Ph.D. Computer Science
>Saginaw Valley State Univ
>_______________________________________________
>moby-l mailing list
>moby-l@biomoby.org
>http://biomoby.org/mailman/listinfo/moby-l
>
>
>  
>


From barbara.re at studenti.unicam.it  Tue May 11 05:27:56 2004
From: barbara.re at studenti.unicam.it (RE BARBARA)
Date: Tue May 11 05:31:53 2004
Subject: [MOBY-l] Request information about MOBY
Message-ID: <1084267676.40a09c9cce3c6@mail.studenti.unicam.it>



Hi!

I'am a problem about MOBY CENTRAL.
I have download and install it, now I work with Perl and API to interact with it.
How do we do to insert the varius services in our local MOBY?
Can we already unload those existing from some part without manually rewriting? 
Our databases is empty!
How can we question the system from the Client? (SOAP, JAVA, PERL)
Where can we find a precise documentation to use the unloaded MOBY CENTRAL?

Thanks you very match!

BACHI

From senger at ebi.ac.uk  Tue May 11 05:40:19 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue May 11 05:44:14 2004
Subject: [MOBY-l] Request information about MOBY
In-Reply-To: <1084267676.40a09c9cce3c6@mail.studenti.unicam.it>
Message-ID: <Pine.LNX.4.44.0405111037220.24372-100000@bagheera.ebi.ac.uk>

Hi,

> I'am a problem about MOBY CENTRAL.
>
   Don't worry, surely you *are* not a problem. But perhaps you *have* a
problem :-)

   Now, seriously: with Java, you can get everything typing this command:

   cd <your-biomoby-cvs-copy>/Java
   ./run-cmdline-client -call DUMP > moby.sql

   It will download everything as SQL statements into file moby.sql. You 
can then open your mysql client and 'source moby.sql'.

   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 dag at sonsorol.org  Tue May 11 10:01:20 2004
From: dag at sonsorol.org (Chris Dagdigian)
Date: Tue May 11 10:05:19 2004
Subject: [MOBY-l] testing a new Open-Bio website and mail list archive search
Message-ID: <40A0DCB0.1050207@sonsorol.org>

Hello Everyone,

A fantastic volunteer (Kyle Jensen) has been steathily working on a 
problem for us that has long been a major issue for us -- website 
searching and indexing.

We've tried various solutions and ht://dig implementations in the past 
and nothing really worked well.

Kyle has been setting up a search indexing system based on the code from 
www.swish-e.org and so far it looks very very promising.

We have 2 main indexed search sites:

This page is a search index for all of the open-bio hosted websites:
http://search.open-bio.org/cgi-bin/obf-search.cgi

This page is just for searching mailing list archives:
http://search.open-bio.org/cgi-bin/mail-search.cgi


Please give the pages a whirl and let me know what you think.

Thanks again Kyle!

-Chris
open-bio.org admin team


From fgibbons at hms.harvard.edu  Tue May 11 11:49:09 2004
From: fgibbons at hms.harvard.edu (Frank Gibbons)
Date: Tue May 11 11:48:44 2004
Subject: [MOBY-l] empty responses: Collection or Simple? How to match
 responses to queries?
Message-ID: <5.2.1.1.2.20040511113738.01a291e0@email.med.harvard.edu>

MOBYers,

I'm working on some services, trying to figure out how to provide robust 
responses, and then parse them robustly. In particular, there may be a lot 
of valid queries, for which there an empty response. In theory (according 
to the API), I should return a response for every query, even if it's 
empty. The API will not allow me to return an empty collectionResponse, it 
requires me to use simpleResponse. My problem then is, how do I match the 
queries with the responses? If all the responses are of the same type, I 
can assume the array order corresponds to the ordering using queryID (is 
this correct?), and match them up like that. If they're of different types, 
I can pull out the collections and simples using getResponseArticles, which 
is fine as far as it goes. But how do I match the queries to their 
respective responses, given that the queryIDs live in the mobyData tags, 
which have already been stripped out by the time I get the 
Collections/Simples?

On a personal level, the easiest thing for me to do would be to use MOBY to 
handle communication, but just parse the XML response completely on my own 
(using XML::DOM, but none of MOBY::Client::CommonSubs). I know what it 
looks like, I know what I need to know in order to parse the response, and 
I know what problems to look out for. But the strength of an API lies in 
the use of a common way of doing things, so I'd like to go with that if I 
can. It's just not obvious to me how I should do that. Anyone have ideas?

Thanks,

-Frank

PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
617-432-3557       http://llama.med.harvard.edu/~fgibbons 

From bmg at sfu.ca  Wed May 12 22:04:39 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Wed May 12 22:27:24 2004
Subject: [MOBY-l] moby keyword services?
In-Reply-To: <5.2.1.1.2.20040511113738.01a291e0@email.med.harvard.edu>
References: <5.2.1.1.2.20040511113738.01a291e0@email.med.harvard.edu>
Message-ID: <40A2D7B7.2090701@sfu.ca>

 Dear MOBY people,

 I am working on a moby client to be used in a demo two weeks from now. 
 If possible, I would like to use a service like 
"RetrieveGOfromKeywords" to take a keyword query and return a list of 
interesting things.  So far, the only service that I have found that 
both accepts a keyword query and seems to be working is "SearchPubMed" 
from prometheus.brc.mcw.edu .  SearchPubMed works from the Moby Browser, 
but I get an access denied message when I try to hit from my client 
(which works fine on other services).

 Does anyone have a service that accepts a keyword query, is working, 
and will allow me access to it?

thanks,
Ben

PS. This summer I'll be working on utilizing MOBY to integrate data 
sources for the International Rice Research Institute info system 
http://www.iris.irri.org/ .  I will undoubtedly have many questions for 
you, hopefully I'll eventually be able to answer some of yours!





From mwilkinson at mobile.rogers.com  Wed May 12 22:35:23 2004
From: mwilkinson at mobile.rogers.com (mwilkinson)
Date: Wed May 12 22:40:46 2004
Subject: [MOBY-l] moby keyword services?
Message-ID: <200405130240.i4D2eh6B024046@portal.open-bio.org>

Hey Ben,

I'll check what's wrong with my GO service tomorrow AM when I get to work.  I left my computer there this evening so I can't check right now.  It is likely that the GO database has moved and that my script is unable to connect to it now.

In any case, I'll fix it first thing tomorrow.

M

-----Original Message-----
From: Benjamin Good <bmg@sfu.ca>
Date: Thu, 13 May 2004 10:04:39 
To:moby-l@biomoby.org
Subject: [MOBY-l] moby keyword services?

 Dear MOBY people,

 I am working on a moby client to be used in a demo two weeks from now. 
 If possible, I would like to use a service like 
"RetrieveGOfromKeywords" to take a keyword query and return a list of 
interesting things.  So far, the only service that I have found that 
both accepts a keyword query and seems to be working is "SearchPubMed" 
from prometheus.brc.mcw.edu .  SearchPubMed works from the Moby Browser, 
but I get an access denied message when I try to hit from my client 
(which works fine on other services).

 Does anyone have a service that accepts a keyword query, is working, 
and will allow me access to it?

thanks,
Ben

PS. This summer I'll be working on utilizing MOBY to integrate data 
sources for the International Rice Research Institute info system 
http://www.iris.irri.org/ .  I will undoubtedly have many questions for 
you, hopefully I'll eventually be able to answer some of yours!





_______________________________________________
moby-l mailing list
moby-l@biomoby.org
http://biomoby.org/mailman/listinfo/moby-l

!!!!!!!!!!!!!!!!
To respond to this message you MUST send your response to (note new address!)

markw_mobile2 at illuminae dot com

Responses to the reply-to address go directly to trash!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!
From barbara.re at studenti.unicam.it  Tue May 11 04:43:18 2004
From: barbara.re at studenti.unicam.it (RE BARBARA)
Date: Thu May 13 18:43:41 2004
Subject: [MOBY-l] Request information about MOBY
Message-ID: <1084264998.40a092261a199@mail.studenti.unicam.it>


Hi!
We are two students of university of Camerino (ITALY).
We are download and instal MOBY CENTRAL.
Now we study about perl and the different API but in the database of MOBY
CENTRAL there isn't any services.
How we do to insert the various services in our local MOBY?
And where do we find them?

Thanks you very match!

Barbara 
Chiara 

From icho at svsu.edu  Thu May 13 16:47:52 2004
From: icho at svsu.edu (Il-Hyung Cho)
Date: Thu May 13 18:44:17 2004
Subject: [MOBY-l] Java implemenation on
	Axis&In-Reply-To=s098f337.011@gw.svsu.edu
Message-ID: <s0a3a6da.022@gw.svsu.edu>

Hello Viji,
 
Here's what I have done successfully:
1. Installed Tomcat, Axis, jdk, mysql, ...
2. Ran over Axis user guide and successfully followed their examples
(in sample.userguide.example1~6).
3. Went over the Axis tutorial provided in www.ammal.com.
4. Implemeted a simple mysql access example by
    - setting up a simple database (not bioinformatics data) using
mysql 
    - providing a simple query server on axis
    - running a client sending a query to the server and receiving the
result
 
So, I think I basically went over most features needed in web services,
but what I am still not sure about is how to register my service to moby
so that clients can send inquiry to moby central and get the link to my
service.
Do my service have to be bioinformatics application? I am not a
bioinformatist, but just tring to see how biomoby works. Once I get my
simple service running on Moby, I can help my fellow bioinfomatist setup
their applications on Moby.
 
So far, I haven't been able to find a step by step procedure/tutorial
to register a service in Java to BioMoby.
 
Many thanks,
 
Il-Hyung Cho
From senger at ebi.ac.uk  Thu May 13 19:01:55 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Thu May 13 19:05:51 2004
Subject: [MOBY-l] Java implemenation on
	Axis&In-Reply-To=s098f337.011@gw.svsu.edu
In-Reply-To: <s0a3a6da.022@gw.svsu.edu>
Message-ID: <Pine.OSF.4.10.10405132356330.613946-100000@ice.ebi.ac.uk>

> So far, I haven't been able to find a step by step procedure/tutorial
> to register a service in Java to BioMoby.
>
   There is no step-by-step- procedure for java. Sorry for that...
   Here is what you *can* do:

1) Make sure that you know enought about *your* service (name, type,
input/output data etc.)

2) Try: ./run-cmdline-client -h
It gives you following help:

 To register a service:

   -rs-name  <service-name>
   -rs-type  <service-type-name>
   -rs-categ <service-category>
   -rs-desc  <service-description>
   -rs-auth  <service-authority>
   -rs-email <service-contact>
   -rs-url   <service-URL>
   -rs-main  <service-authoritative>  use: 1 or 0

   -rs-in    <inputs>
      <inputs> are comma-delimited names of inputs;
      each of them is a pair of an input type and a namespace
      separated by an equal sign... sorry

   -rs-ifile <files-with-inputs>
      <files-with-inputs> are a comma-separated list of
      file names defining input data; the files should
      have format of Java properties, e.g...

   One can combine both methods: -rs-in and -rs-ifile.

   -rs-out   <outputs>
      <outputs> are comma-delimited names of output types

   -rs-ofile <files-with-outputs>
      <files-with-outputs> are a comma-separated list of
      file names defining output data; the files should
      have format of Java properties, e.g...

   One can combine both methods: -rs-out and -rs-ofile.

3) You can start ./run-cmdline-client with some of the mentioned
parameters to register your service. But...

4) You need to register *first* the pieces that the service consists of -
like service type, and input/output data typs, and namespaces. The
command-line clinent run-cmdline-client can register all of them.

If these instructions are too abstract try to send here/me info about your
service and I will try to be more concrete.

   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 mwilkinson at mobile.rogers.com  Thu May 13 21:07:59 2004
From: mwilkinson at mobile.rogers.com (mwilkinson)
Date: Thu May 13 21:15:41 2004
Subject: [MOBY-l] Request information about MOBY
Message-ID: <200405140115.i4E1Fd6B021945@portal.open-bio.org>

Hi Barbara and Chiara

You don't need to download and install the database unless you intend to set up a specialized registry just for yourselves.  Generally speaking you should be able to accomplish most of what you need by using the client-side libraries.

Have a look at the documentation for MOBY::Client::Cental, and Catherine has some excellent tutorials (follow the tutorials link on the website) for using Moby through the client libraries.

If you have more specific questions, or if I didn't answer your question adequately, please go ahead and ask!

Cheers!

Mark

-----Original Message-----
From: RE BARBARA <barbara.re@studenti.unicam.it>
Date: Tue, 11 May 2004 10:43:18 
To:moby-l@biomoby.org
Subject: [MOBY-l] Request information about MOBY


Hi!
We are two students of university of Camerino (ITALY).
We are download and instal MOBY CENTRAL.
Now we study about perl and the different API but in the database of MOBY
CENTRAL there isn't any services.
How we do to insert the various services in our local MOBY?
And where do we find them?

Thanks you very match!

Barbara 
Chiara 

_______________________________________________
moby-l mailing list
moby-l@biomoby.org
http://biomoby.org/mailman/listinfo/moby-l


!!!!!!!!!!!!!!!!
To respond to this message you MUST send your response to (note new address!)

markw_mobile2 at illuminae dot com

Responses to the reply-to address go directly to trash!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!
From bmg at sfu.ca  Mon May 17 05:38:08 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Mon May 17 06:01:12 2004
Subject: [MOBY-l] java client question
Message-ID: <40A88800.1090105@sfu.ca>

Dear Moby java developers,

 I am working on a java client and am having problems making it ask the 
question "what services exist that accept this kind of input"?   I see 
the example in the MobyCmdLineClient class, but can't seem to get it to 
work properly.  It seems that a couple lines that may once have caused 
the correct behavior have been commented out such that the service 
request actually ignores information pertaining to inputs.  It seems 
that perhaps this code is in the midst of a change???

Is there a newer version in progress somewhere?  

Here is what appears to be the pertinent code from MobyCmdLineClient:

                if ((param = cmd.getParam ("-fs-in")) != null ) {
                    String[] inputs = StringUtils.split (param, ",");
                       for (int i = 0; i < inputs.length; i++) {
                        String[] parts = StringUtils.split (inputs[i], "=");
                        if (parts.length >= 2) {
//                             pattern.addInput (parts[0], parts[1]);
                        } else {
//                             pattern.addInput (parts[0], "");
                        }
                    }

thanks
-Ben

From senger at ebi.ac.uk  Mon May 17 06:13:19 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Mon May 17 06:17:17 2004
Subject: [MOBY-l] java client question
In-Reply-To: <40A88800.1090105@sfu.ca>
Message-ID: <Pine.LNX.4.44.0405171112040.7061-100000@bagheera.ebi.ac.uk>

Good point made.
I simply do not remember why the lines are commented out. Perhaps it was 
never finished - which is sad and blame me.
I will look at it this evening...

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 bmg at sfu.ca  Tue May 18 03:08:46 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Tue May 18 03:31:45 2004
Subject: [MOBY-l] MobyRequest or CentralImpl ?
Message-ID: <40A9B67E.9080001@sfu.ca>

Hello,

 When I want to execute a moby service from my java client, it seems 
that there are two choices present in cvs,  the invokeService() method 
from the MobyRequest class and the doCall method from the CentralImpl class.

  Any opinions about which one I should be using ?

thanks
-Ben

From senger at ebi.ac.uk  Tue May 18 04:04:03 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue May 18 04:08:02 2004
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40A9B67E.9080001@sfu.ca>
Message-ID: <Pine.LNX.4.44.0405180853170.8181-100000@bagheera.ebi.ac.uk>

>   Any opinions about which one I should be using ?
>
   Actually, the third one - which does not exist yet :-)
   More seriously:

   1) The doCall of CentralImpl is there as a "side-effect". It was never 
meant to be used regularly but the life proved differently. The whole 
CentralImpl was meant to be used to access Moby registries, not the Moby 
services, but the method doCall was there so people started to use it. And 
it will still be there, so you are safe to use it.

   2) Then Paul started with MobyRequest. I have not used it myself so I 
cannot compare it - but I know that MobyRequest was meant to provide not 
only a simple call to a service (such as doCall in CentralImpl) but also 
to help with building the input XML query object and possibly to decode 
the returned result XML object.

   So, if you are looking just how to call a service, both methods will do 
it for you (but as I said I may be mistaken because I have not used 
MobyRequest myself).

   3) So, why did I start this reply with the third option? Because I 
still hope to write a code that will help service providers hopefully 
more that any of the two methods you mentioned. But it does not exist 
yet...

   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  Tue May 18 06:02:38 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue May 18 06:06:48 2004
Subject: [MOBY-l] java client question
In-Reply-To: <40A88800.1090105@sfu.ca>
Message-ID: <Pine.OSF.4.10.10405181057210.716676-100000@ice.ebi.ac.uk>

>  I am working on a java client and am having problems making it ask the 
> question "what services exist that accept this kind of input"?
>
   I fixed that (actually I have added it, it was never finished :-)).
Try it please if it does what is expected.
   Using this opportunity I also add few new options to the 'find
services' in MobyCmdLineClient:
   -nc ... do not include in the search result services that are child
           types (more specific) than the service type you requested
   -np ... do not include in the search result services operating on
           the parent types of the data types you requested
   -on ... print only names of the fou8nd services

   With 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 gordonp at cbr.nrc.ca  Tue May 18 09:33:12 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Tue May 18 09:36:52 2004
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40A9B67E.9080001@sfu.ca>
References: <40A9B67E.9080001@sfu.ca>
Message-ID: <40AA1098.7060205@cbr.nrc.ca>

Benjamin Good wrote:

> Hello,
>
> When I want to execute a moby service from my java client, it seems 
> that there are two choices present in cvs,  the invokeService() method 
> from the MobyRequest class and the doCall method from the CentralImpl 
> class.
>
>  Any opinions about which one I should be using ?

MobyRequest is designed specifically for this purpose.  If you look at 
the ChangeLog, there is an example:

    // Assumes you already have a service (mobyService) and data 
(mobyInputData) around
    mobyRequest = new MobyRequest(new CentralImpl());
    mobyRequest.setDebugMode(true);
    mobyRequest.setService(mobyService);
    mobyRequest.setInput((MobyDataInstance[]) mobyInputData);
    try{
        mobyRequest.invokeService();
    } catch(MobyException mobye){
        System.err.println("Failure in MOBY protocol: " + mobye);
    } catch(SOAPException soape){
        System.err.println("Failure in SOAP transaction: " + soape);
    } catch(NOSuccessException nse){
        System.err.println("Failure in MOBY logic (input was not 
acceptable " +
                           "for this service)" + nse);
    }


You can reuse the MobyRequest object as many times as you like...

>
> thanks
> -Ben
>
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>


From bmg at sfu.ca  Wed May 19 23:56:49 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Thu May 20 00:00:12 2004
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AA1098.7060205@cbr.nrc.ca>
References: <40A9B67E.9080001@sfu.ca> <40AA1098.7060205@cbr.nrc.ca>
Message-ID: <40AC2C81.6090108@sfu.ca>


 Hi Paul,

 I'm trying to get your method running but am having some trouble 
creating the mobyInputData for my request.  Running with Martin's method 
I built the query object directly as a string of xml as shown below. 
 I've been trying to create a MobyData instance, but am getting a bit 
lost.    What is the best procedure for creating a useful MobyData object ?

Sorry for being a little slow on the uptake here, but I'm sure a 
complete example would also be helpful for others in the future.

cheers
-Ben

    private String mobyQuery(String ns, String query){
        return "<?xml version='1.0' encoding='UTF-8'?> "+
        "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>" +
              "<moby:Query>" +
                  "<moby:queryInput moby:articleName=''>"+
                        "<moby:Simple>"+
                            "<Object namespace='"+ns+"' id=\""+query+"\"/>"+
                        "</moby:Simple>"+
                    "</moby:queryInput>"+
               "</moby:Query>"+
        "</moby:MOBY>";
    }



Paul Gordon wrote:

> Benjamin Good wrote:
>
>> Hello,
>>
>> When I want to execute a moby service from my java client, it seems 
>> that there are two choices present in cvs,  the invokeService() 
>> method from the MobyRequest class and the doCall method from the 
>> CentralImpl class.
>>
>>  Any opinions about which one I should be using ?
>
>
> MobyRequest is designed specifically for this purpose.  If you look at 
> the ChangeLog, there is an example:
>
>    // Assumes you already have a service (mobyService) and data 
> (mobyInputData) around
>    mobyRequest = new MobyRequest(new CentralImpl());
>    mobyRequest.setDebugMode(true);
>    mobyRequest.setService(mobyService);
>    mobyRequest.setInput((MobyDataInstance[]) mobyInputData);
>    try{
>        mobyRequest.invokeService();
>    } catch(MobyException mobye){
>        System.err.println("Failure in MOBY protocol: " + mobye);
>    } catch(SOAPException soape){
>        System.err.println("Failure in SOAP transaction: " + soape);
>    } catch(NOSuccessException nse){
>        System.err.println("Failure in MOBY logic (input was not 
> acceptable " +
>                           "for this service)" + nse);
>    }
>
>
> You can reuse the MobyRequest object as many times as you like...
>
>>
>> thanks
>> -Ben
>>
>> _______________________________________________
>> moby-l mailing list
>> moby-l@biomoby.org
>> http://biomoby.org/mailman/listinfo/moby-l
>>
>
>
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>


From p.lord at russet.org.uk  Thu May 20 06:06:09 2004
From: p.lord at russet.org.uk (Phillip Lord)
Date: Thu May 20 06:13:20 2004
Subject: [MOBY-l] CFP: The Seventh Annual Bio-ontologies Meeting
Message-ID: <vfhdubmmzy.fsf@rpc71.cs.man.ac.uk>







Apologies for those of you who get this more than once. 

The deadline for submissions is now approaching. 









The Seventh Annual Bio-ontologies Meeting Call For Submissions
==============================================================

Key Information
===============      


Organisers: Robert Stevens(1), Robin McEntire(2),
      Phillip Lord(1), and James.A.Butler(2)

(1) Dept of Computer Science, University of Manchester
(2) GlaxoSmithKline

Submission Deadline: 31st May 2004      
Contact:  bio-ontologies@lists.man.ac.uk    
Website:  http://bio-ontologies.man.ac.uk
Location: Glasgow, Scotland.
Date: 30th July
Main Conference: http://www.iscb.org/ismbeccb2004/
Registration: http://www.iscb.org/ismbeccb2004/reg.html
Registration Costs:  80 Academic, 110 Corporate, 60 Student
   (Prices in UK Pounds. 17.5% VAT will be added. Coffee and lunch included)



General Information
===================
      
The Bio-Ontologies workshop has been in existence since 1998, and now
operates as a Special Interest Group at the ISMB Conference.
Bio-Ontologies is well established as one of the key meetings for
dissemination of the latest information and research on ontologies in the
life sciences and has drawn the key researchers in the field.

After last year's highly successful theme of "Ontologies and Text
Analysis", we will follow with the timely theme of "Ontologies and
Bio-Images". Work is currently being done in the area of ontologies of
images, especially in the domain of developmental biology and
medicine. A prime example of this work is the Bio-Image databank,
which makes extensive use of ontologies.

Our guest speaker for this year's topic will be Dr. David Shotton, who
will talk about the use of ontologies within the BioImage database.


New this year
=============

This year, Comparative and Functional Genomics will publish selected
presentations from the Seventh Annual Bio-Ontologies
Workshop. Previously we have published Conference Reviews in CFG. We are
very pleased that last year's Workshop had enough substantial,
high-quality work to enable such a special issue this year. We do, however,
believe that a level of informality is critical to the success of this
Workshop, and so we hope the meeting offers a venue for news and
views, perhaps less developed, but up to the minute work. All are
welcome!

      
Submissions
===========
We invite the submission of two A4 page abstracts for presentation along
this theme. Suitable topics include, but are not restricted to:

The content of bio-images;
The technical origins  of images
Support for image analysis (e.g., change in shape, colour,
texture, etc.)

We wish, however, not to restrict the topics presented to the theme
alone. So, we are also interested in:

Shared experiences in using ontology tools, development methodologies, 
comparing ontologies, and reusing other people's ontologies; 

Current research in ontology languages and ontology exchange
languages;

Updates on ontologies in development by members of the life
sciences community, including genomics, proteomics and
metabolomics;

Practical uses of ontologies in research and drug discovery
especially pre-competitive ontologies for the industry.


Submission details at http://bio-ontologies.man.ac.uk
-- 
Phillip Lord,				Phone: +44 (0) 161 275 6139
PostDoctoral Research Associate,        Email: p.lord@russet.org.uk
Department of Computer Science          http://www.russet.org.uk  
Kilburn Building                        http://www.cs.man.ac.uk/~phillord
University of Manchester                
Oxford Road
Manchester
M13 9PL
From markw at illuminae.com  Thu May 20 11:24:50 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu May 20 10:28:51 2004
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AC2C81.6090108@sfu.ca>
References: <40A9B67E.9080001@sfu.ca> <40AA1098.7060205@cbr.nrc.ca>
	<40AC2C81.6090108@sfu.ca>
Message-ID: <1085066689.7946.5.camel@myhost.mydomain>

Hi Ben, 

heads up that the Query and queryInput tags are deprecated.  Please see
the API documentation.

M


On Wed, 2004-05-19 at 20:56, Benjamin Good wrote:
>  Hi Paul,
> 
>  I'm trying to get your method running but am having some trouble 
> creating the mobyInputData for my request.  Running with Martin's method 
> I built the query object directly as a string of xml as shown below. 
>  I've been trying to create a MobyData instance, but am getting a bit 
> lost.    What is the best procedure for creating a useful MobyData object ?
> 
> Sorry for being a little slow on the uptake here, but I'm sure a 
> complete example would also be helpful for others in the future.
> 
> cheers
> -Ben
> 
>     private String mobyQuery(String ns, String query){
>         return "<?xml version='1.0' encoding='UTF-8'?> "+
>         "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>" +
>               "<moby:Query>" +
>                   "<moby:queryInput moby:articleName=''>"+
>                         "<moby:Simple>"+
>                             "<Object namespace='"+ns+"' id=\""+query+"\"/>"+
>                         "</moby:Simple>"+
>                     "</moby:queryInput>"+
>                "</moby:Query>"+
>         "</moby:MOBY>";
>     }
> 
> 
> 
> Paul Gordon wrote:
> 
> > Benjamin Good wrote:
> >
> >> Hello,
> >>
> >> When I want to execute a moby service from my java client, it seems 
> >> that there are two choices present in cvs,  the invokeService() 
> >> method from the MobyRequest class and the doCall method from the 
> >> CentralImpl class.
> >>
> >>  Any opinions about which one I should be using ?
> >
> >
> > MobyRequest is designed specifically for this purpose.  If you look at 
> > the ChangeLog, there is an example:
> >
> >    // Assumes you already have a service (mobyService) and data 
> > (mobyInputData) around
> >    mobyRequest = new MobyRequest(new CentralImpl());
> >    mobyRequest.setDebugMode(true);
> >    mobyRequest.setService(mobyService);
> >    mobyRequest.setInput((MobyDataInstance[]) mobyInputData);
> >    try{
> >        mobyRequest.invokeService();
> >    } catch(MobyException mobye){
> >        System.err.println("Failure in MOBY protocol: " + mobye);
> >    } catch(SOAPException soape){
> >        System.err.println("Failure in SOAP transaction: " + soape);
> >    } catch(NOSuccessException nse){
> >        System.err.println("Failure in MOBY logic (input was not 
> > acceptable " +
> >                           "for this service)" + nse);
> >    }
> >
> >
> > You can reuse the MobyRequest object as many times as you like...
> >
> >>
> >> thanks
> >> -Ben
> >>
> >> _______________________________________________
> >> moby-l mailing list
> >> moby-l@biomoby.org
> >> http://biomoby.org/mailman/listinfo/moby-l
> >>
> >
> >
> > _______________________________________________
> > moby-l mailing list
> > moby-l@biomoby.org
> > http://biomoby.org/mailman/listinfo/moby-l
> >
> >
> 
> 
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 
Mark Wilkinson (mwilkinson@mrl.ubc.ca)
University of British Columbia iCAPTURE Centre
From gordonp at cbr.nrc.ca  Thu May 20 11:10:51 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Thu May 20 11:14:26 2004
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <1085066689.7946.5.camel@myhost.mydomain>
References: <40A9B67E.9080001@sfu.ca> <40AA1098.7060205@cbr.nrc.ca>	
	<40AC2C81.6090108@sfu.ca> <1085066689.7946.5.camel@myhost.mydomain>
Message-ID: <40ACCA7B.2090907@cbr.nrc.ca>

Mark Wilkinson wrote:

>Hi Ben, 
>
>heads up that the Query and queryInput tags are deprecated.  Please see
>the API documentation.
>  
>
Actually, with the Java client, you don't need to put any of that in 
your code anyway :-)  I'm creating a Wiki document with a complete 
example right now, will send the URL as soon as I'm done...

From fgibbons at hms.harvard.edu  Thu May 20 11:23:57 2004
From: fgibbons at hms.harvard.edu (Frank Gibbons)
Date: Thu May 20 11:24:16 2004
Subject: [MOBY-l] New MOBY application: "BioGraphNet: a distributed forum for
 heterogeneous biological networks"
Message-ID: <5.2.1.1.2.20040520110235.01a0a610@email.med.harvard.edu>

Hey fellow MOBYers,

Below is an abstract I've submitted for BOSC (Bioinformatics Open Source 
Conference) and BioPathways, satellite conferences of ISMC/ECCB in Glasgow, 
Scotland this year. BioGraphNet is our 'sandbox' within the BioMOBY 
'playground', in which we're looking at ways to share and view biological 
networks.

At this point, Gabriel Berriz and I have a working prototype: a registered 
object for describing fairly generic pairwise interactions, half a dozen 
working services, and an application that runs in a web-browser to allow 
end-users to play with the interaction data. A key element of this is that 
anyone can make their data available at any time, and it will be discovered 
and included in the webpage displayed to users (bench biologists). There's 
no installation, no updating of databases. I'd appreciate your giving it a 
try (http://llama.med.harvard.edu/cgi/BioTrawler) and letting us know what 
you think. We're looking for feedback on a number of levels:

* Does the overall idea, (being able to view an interactive graphical 
display of your chosen data sources for your favorite genes), seem useful 
to you? What pitfalls do you see in the near or distant future?
* So far we've got correlated expression, synthetic lethality, homology, 
transcription-factor/target (known and predicted), as well as experimental 
protein-protein interaction results. What kinds of data would make it more 
useful?
* Do you have some data you'd like to share? We've developed tools to 
facilitate making data available as a MOBY service: drop a text file in the 
right place, enter the textual description of your service - BOOM, it's 
registered and available to the world. One goal of this project is to make 
it easy for people with data to put it out there.
* Anything else that strikes you....

We're really keen to get input on this, just reply to me: 
mailto:fgibbons@hms.harvard.edu

I'm looking forward to seeing some of you again in Glasgow!

-Frank Gibbons

--------------------------------------- ABSTRACT 
---------------------------------------

TITLE: BioGraphNet, a distributed forum for heterogeneous biological networks.
AUTHORS: Francis D. Gibbons, Gabriel F. Berriz, and Frederick P. Roth
Dept. of Biological Chemistry and Molecular Pharmacology, 250 Longwood 
Ave., Harvard Medical School, Boston MA 02115, USA

ABSTRACT:
Biological network information is increasingly abundant.  The combination 
of biological networks may be viewed as a multicolor graph, with each color 
representing a different gene-gene or protein-protein relationship, e.g., 
protein interaction, sequence homology, correlated expression, 
transcriptional regulation, genetic interaction (sensu synthetic 
lethality), or metabolic relationship.  Relationship types may be further 
stratified by type of evidence supporting the relationship, by 
directionality or by confidence measure.  Furthermore, each organism has 
its own collection of networks.  Although this information's complexity 
argues for its maintenance by distributed groups, much of its value is 
derived through network integration.

BioMOBY has established a 'playground' for distributed services.  We have 
developed a 'sandbox' within BioMOBY called BioGraphNet.  BioGraphNet is a 
common standard and collection of services for sharing distributed network 
information.  We now serve several network data types, and encourage others 
to participate, using the common standard objects we have registered in 
BioMOBY's ontology.

As an example application illustrating the use of BioGraphNet, we provide 
BioTrawler, a web-based biological network browser that dynamically 
discovers suitable distributed data sources within BioGraphNet, integrates 
those selected by the end-user 'just in time', and visualizes the graph 
neighboring a user-defined set of genes. Graph layout is handled by the 
open-source GraphViz package (modified to handle multiple edges between a 
pair of nodes). BioTrawler also exports graph representations in several 
commonly used formats (GIF by default, but also Pajek, Cytoscape, and PDF).

The combination of BioMOBY and BioGraphNet represents a distributed network 
annotation system analogous to the Distributed Annotation System (DAS) for 
sharing genome annotation.

LICENSING:
The object descriptions and service interfaces are already available to all 
BioMOBY users. We plan to release BioTrawler under the Artistic License.

URL: http://llama.med.harvard.edu/cgi/BioTrawler


PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
617-432-3557       http://llama.med.harvard.edu/~fgibbons 

From simont at mcw.edu  Thu May 20 12:00:54 2004
From: simont at mcw.edu (Simon Twigger)
Date: Thu May 20 12:04:39 2004
Subject: [MOBY-l] New MOBY application: "BioGraphNet: a distributed forum
	for heterogeneous biological networks"
In-Reply-To: <5.2.1.1.2.20040520110235.01a0a610@email.med.harvard.edu>
References: <5.2.1.1.2.20040520110235.01a0a610@email.med.harvard.edu>
Message-ID: <DF90F624-AA76-11D8-812A-000A959D1D82@mcw.edu>

Hi Frank,

This looks very nice - is it possible to view the graph data into 
something like a java graph-viewing applet so people could zoom in and 
select things, etc? The image that comes back is nice but too small to 
see anything. Im cc'ing this to Vijay Narayanasamy in my group as he 
has built tools like this that display interaction data using this type 
of applet and he might be able to offer some suggestions and show you 
what he has done previously so you can see if it would be of use.

I wonder if it would be worth coloring the genes (grey elipses) as well 
as the lines connecting the genes? It might give a better overview of 
the types of interacting partners if they were colored light green, 
light pink, etc. rather than all being grey.

I'd be interested in getting you some rat data, we're working on some 
rat services here so perhaps we can chat more about that and see what 
makes sense. I'd love to see the tools you have for making text files 
available - I've done similar stuff myself but its not very generic, if 
you have something like that we can certainly make use of it.

I have to run to a meeting but will probably write some more later on.

Cheers,

	Simon.


On May 20, 2004, at 10:23 AM, Frank Gibbons wrote:

> Hey fellow MOBYers,
>
> Below is an abstract I've submitted for BOSC (Bioinformatics Open 
> Source Conference) and BioPathways, satellite conferences of ISMC/ECCB 
> in Glasgow, Scotland this year. BioGraphNet is our 'sandbox' within 
> the BioMOBY 'playground', in which we're looking at ways to share and 
> view biological networks.
>
> At this point, Gabriel Berriz and I have a working prototype: a 
> registered object for describing fairly generic pairwise interactions, 
> half a dozen working services, and an application that runs in a 
> web-browser to allow end-users to play with the interaction data. A 
> key element of this is that anyone can make their data available at 
> any time, and it will be discovered and included in the webpage 
> displayed to users (bench biologists). There's no installation, no 
> updating of databases. I'd appreciate your giving it a try 
> (http://llama.med.harvard.edu/cgi/BioTrawler) and letting us know what 
> you think. We're looking for feedback on a number of levels:
>
> * Does the overall idea, (being able to view an interactive graphical 
> display of your chosen data sources for your favorite genes), seem 
> useful to you? What pitfalls do you see in the near or distant future?
> * So far we've got correlated expression, synthetic lethality, 
> homology, transcription-factor/target (known and predicted), as well 
> as experimental protein-protein interaction results. What kinds of 
> data would make it more useful?
> * Do you have some data you'd like to share? We've developed tools to 
> facilitate making data available as a MOBY service: drop a text file 
> in the right place, enter the textual description of your service - 
> BOOM, it's registered and available to the world. One goal of this 
> project is to make it easy for people with data to put it out there.
> * Anything else that strikes you....
>
> We're really keen to get input on this, just reply to me: 
> mailto:fgibbons@hms.harvard.edu
>
> I'm looking forward to seeing some of you again in Glasgow!
>
> -Frank Gibbons
>
> --------------------------------------- ABSTRACT 
> ---------------------------------------
>
> TITLE: BioGraphNet, a distributed forum for heterogeneous biological 
> networks.
> AUTHORS: Francis D. Gibbons, Gabriel F. Berriz, and Frederick P. Roth
> Dept. of Biological Chemistry and Molecular Pharmacology, 250 Longwood 
> Ave., Harvard Medical School, Boston MA 02115, USA
>
> ABSTRACT:
> Biological network information is increasingly abundant.  The 
> combination of biological networks may be viewed as a multicolor 
> graph, with each color representing a different gene-gene or 
> protein-protein relationship, e.g., protein interaction, sequence 
> homology, correlated expression, transcriptional regulation, genetic 
> interaction (sensu synthetic lethality), or metabolic relationship.  
> Relationship types may be further stratified by type of evidence 
> supporting the relationship, by directionality or by confidence 
> measure.  Furthermore, each organism has its own collection of 
> networks.  Although this information's complexity argues for its 
> maintenance by distributed groups, much of its value is derived 
> through network integration.
>
> BioMOBY has established a 'playground' for distributed services.  We 
> have developed a 'sandbox' within BioMOBY called BioGraphNet.  
> BioGraphNet is a common standard and collection of services for 
> sharing distributed network information.  We now serve several network 
> data types, and encourage others to participate, using the common 
> standard objects we have registered in BioMOBY's ontology.
>
> As an example application illustrating the use of BioGraphNet, we 
> provide BioTrawler, a web-based biological network browser that 
> dynamically discovers suitable distributed data sources within 
> BioGraphNet, integrates those selected by the end-user 'just in time', 
> and visualizes the graph neighboring a user-defined set of genes. 
> Graph layout is handled by the open-source GraphViz package (modified 
> to handle multiple edges between a pair of nodes). BioTrawler also 
> exports graph representations in several commonly used formats (GIF by 
> default, but also Pajek, Cytoscape, and PDF).
>
> The combination of BioMOBY and BioGraphNet represents a distributed 
> network annotation system analogous to the Distributed Annotation 
> System (DAS) for sharing genome annotation.
>
> LICENSING:
> The object descriptions and service interfaces are already available 
> to all BioMOBY users. We plan to release BioTrawler under the Artistic 
> License.
>
> URL: http://llama.med.harvard.edu/cgi/BioTrawler
>
>
> PhD, Computational Biologist,
> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 
> 02115, USA.
> Tel: 617-432-3555       Fax: 617-432-3557       
> http://llama.med.harvard.edu/~fgibbons
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>
--

Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw

From gordonp at cbr.nrc.ca  Thu May 20 12:19:08 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Thu May 20 12:22:43 2004
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AC2C81.6090108@sfu.ca>
References: <40A9B67E.9080001@sfu.ca> <40AA1098.7060205@cbr.nrc.ca>
	<40AC2C81.6090108@sfu.ca>
Message-ID: <40ACDA7C.7000000@cbr.nrc.ca>

I've created two TWiki documents to explain the usage and interaction of 
the jMOBY classes:

http://www.biomoby.org/twiki/bin//view/General/MOBYJavaClient

and

http://www.biomoby.org/twiki/bin//view/General/ServiceInvocationjMOBY

Hopefully this will help!

>
> I'm trying to get your method running but am having some trouble 
> creating the mobyInputData for my request.  Running with Martin's 
> method I built the query object directly as a string of xml as shown 
> below. I've been trying to create a MobyData instance, but am getting 
> a bit lost.    What is the best procedure for creating a useful 
> MobyData object ?



From willy_valdivia at orionbiosciences.com  Thu May 20 12:22:47 2004
From: willy_valdivia at orionbiosciences.com (Willy Valdivia-Granda)
Date: Thu May 20 13:02:21 2004
Subject: [MOBY-l] New MOBY application: "BioGraphNet: a distributed forum
	for heterogeneous biological networks"
Message-ID: <20040520162247.16792.qmail@webmail07.mesa1.secureserver.net>

From bmg at sfu.ca  Fri May 21 00:06:06 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Fri May 21 00:09:35 2004
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40ACDA7C.7000000@cbr.nrc.ca>
References: <40A9B67E.9080001@sfu.ca>
	<40AA1098.7060205@cbr.nrc.ca>	<40AC2C81.6090108@sfu.ca>
	<40ACDA7C.7000000@cbr.nrc.ca>
Message-ID: <40AD802E.1090502@sfu.ca>

Thanks, your example was very helpful.  I have two questions now,

1)  Why do I keep getting this message and is there a way to stop it?
- No returnType was specified to the Call object!  You must call 
setReturnType() if you have called addParameter().
2) How do I specify a query object for a Moby object such as 
genericSequence?
For example,
<moby:Simple moby:articleName=''>
         <moby:GenericSequence namespace='' id=''>
                    <moby:String namespace='' id='' 
articleName='SequenceString'>ATATATATATATATATA</moby:String>
         </moby:GenericSequence>
 </moby:Simple>

I've tried to start building it like this

        MobyDataType the_type = new MobyDataType("");
        the_type = central.getDataType("GenericSequence");
        System.out.println(the_type.toString());       
        MobyDataSimpleInstance mobySimpleInstance = new 
MobyDataSimpleInstance(the_type,"","");

but it is not working as I would expect.  I would think at this point I 
would have an empty genericSequence object, but when I get he XML at 
this point it doesn't know anything about being a Sequence.

<Simple xmlns="http://www.biomoby.org/moby" 
xmlns:moby="http://www.biomoby.org/moby" moby:articleName=""><Object 
namespace="" id=""/></Simple>

Is it necessary to create a DOM object for the instantiation?  (What is 
the best way to do that :) ?)

thanks
-Ben

ps.  I'm trying to a build a nice clean implementation because its going 
to form the guts of a bunch of applications..



Paul Gordon wrote:

> I've created two TWiki documents to explain the usage and interaction 
> of the jMOBY classes:
>
> http://www.biomoby.org/twiki/bin//view/General/MOBYJavaClient
>
> and
>
> http://www.biomoby.org/twiki/bin//view/General/ServiceInvocationjMOBY
>
> Hopefully this will help!
>
>>
>> I'm trying to get your method running but am having some trouble 
>> creating the mobyInputData for my request.  Running with Martin's 
>> method I built the query object directly as a string of xml as shown 
>> below. I've been trying to create a MobyData instance, but am getting 
>> a bit lost.    What is the best procedure for creating a useful 
>> MobyData object ?
>
>
>
>
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>


From bmg at sfu.ca  Fri May 21 04:11:18 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Fri May 21 04:14:44 2004
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AD802E.1090502@sfu.ca>
References: <40A9B67E.9080001@sfu.ca>	<40AA1098.7060205@cbr.nrc.ca>	<40AC2C81.6090108@sfu.ca>	<40ACDA7C.7000000@cbr.nrc.ca>
	<40AD802E.1090502@sfu.ca>
Message-ID: <40ADB9A6.9080803@sfu.ca>

In response to my own question regarding building a GenericSequence 
query object, the following bit of code does the job but I feel like I'm 
missing something.  

        MobyDataType the_type = new MobyDataType("");
        the_type = central.getDataType("GenericSequence");
        String seq_object =    "<moby:GenericSequence namespace='' id=''>"+
            "<moby:String namespace='' id='' 
articleName='SequenceString'>"+query+"</moby:String>"+
            "</moby:GenericSequence>";
        MobyDataSimpleInstance mobySimpleInstance = new 
MobyDataSimpleInstance(the_type,"","");
        mobySimpleInstance.setValue(seq_object);       

It looks like the only alternative is to build the object as a DOM, but 
not being familiar with DOM building this seems like more trouble than 
its worth.  Please, show me the path to enlightenment and intelligent 
creation of moby objects in Java.

-Ben




Benjamin Good wrote:

> Thanks, your example was very helpful.  I have two questions now,
>
> 1)  Why do I keep getting this message and is there a way to stop it?
> - No returnType was specified to the Call object!  You must call 
> setReturnType() if you have called addParameter().
> 2) How do I specify a query object for a Moby object such as 
> genericSequence?
> For example,
> <moby:Simple moby:articleName=''>
>         <moby:GenericSequence namespace='' id=''>
>                    <moby:String namespace='' id='' 
> articleName='SequenceString'>ATATATATATATATATA</moby:String>
>         </moby:GenericSequence>
> </moby:Simple>
>
> I've tried to start building it like this
>
>        MobyDataType the_type = new MobyDataType("");
>        the_type = central.getDataType("GenericSequence");
>        System.out.println(the_type.toString());              
> MobyDataSimpleInstance mobySimpleInstance = new 
> MobyDataSimpleInstance(the_type,"","");
>
> but it is not working as I would expect.  I would think at this point 
> I would have an empty genericSequence object, but when I get he XML at 
> this point it doesn't know anything about being a Sequence.
>
> <Simple xmlns="http://www.biomoby.org/moby" 
> xmlns:moby="http://www.biomoby.org/moby" moby:articleName=""><Object 
> namespace="" id=""/></Simple>
>
> Is it necessary to create a DOM object for the instantiation?  (What 
> is the best way to do that :) ?)
>
> thanks
> -Ben
>
> ps.  I'm trying to a build a nice clean implementation because its 
> going to form the guts of a bunch of applications..
>
>
>
> Paul Gordon wrote:
>
>> I've created two TWiki documents to explain the usage and interaction 
>> of the jMOBY classes:
>>
>> http://www.biomoby.org/twiki/bin//view/General/MOBYJavaClient
>>
>> and
>>
>> http://www.biomoby.org/twiki/bin//view/General/ServiceInvocationjMOBY
>>
>> Hopefully this will help!
>>
>>>
>>> I'm trying to get your method running but am having some trouble 
>>> creating the mobyInputData for my request.  Running with Martin's 
>>> method I built the query object directly as a string of xml as shown 
>>> below. I've been trying to create a MobyData instance, but am 
>>> getting a bit lost.    What is the best procedure for creating a 
>>> useful MobyData object ?
>>
>>
>>
>>
>>
>> _______________________________________________
>> moby-l mailing list
>> moby-l@biomoby.org
>> http://biomoby.org/mailman/listinfo/moby-l
>>
>>
>
>
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>


From gordonp at cbr.nrc.ca  Fri May 21 10:12:48 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Fri May 21 10:16:22 2004
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40ADB9A6.9080803@sfu.ca>
References: <40A9B67E.9080001@sfu.ca>	<40AA1098.7060205@cbr.nrc.ca>	<40AC2C81.6090108@sfu.ca>	<40ACDA7C.7000000@cbr.nrc.ca>
	<40AD802E.1090502@sfu.ca> <40ADB9A6.9080803@sfu.ca>
Message-ID: <40AE0E60.5030605@cbr.nrc.ca>


> In response to my own question regarding building a GenericSequence 
> query object, the following bit of code does the job but I feel like 
> I'm missing something. 
>        MobyDataType the_type = new MobyDataType("");
>        the_type = central.getDataType("GenericSequence");
>        String seq_object =    "<moby:GenericSequence namespace='' 
> id=''>"+
>            "<moby:String namespace='' id='' 
> articleName='SequenceString'>"+query+"</moby:String>"+
>            "</moby:GenericSequence>";
>        MobyDataSimpleInstance mobySimpleInstance = new 
> MobyDataSimpleInstance(the_type,"","");
>        mobySimpleInstance.setValue(seq_object);      
> It looks like the only alternative is to build the object as a DOM, 
> but not being familiar with DOM building this seems like more trouble 
> than its worth.  Please, show me the path to enlightenment and 
> intelligent creation of moby objects in Java.

This is indeed the way to build the object, as per the comments in my 
example class. I was hoping that by making direct string XML input 
inconvenient, people would pay more attention to making sure the 
declared data type and XML corresponded, and were correct.  The fact 
that you can't build an instance directly from a string is explicitly 
stated in the javadocs, you have to call setValue().  But if you really 
want to add a constructor with an extra argument you can, it's open 
source.  Even better, someone could make setValue() parse the XML string 
and check it against the Moby Object ontology for validity :-)

There is a error in your XML: according to 
http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects , GenericSequence is 
a subclass of VirtualSequence, which hasa Integer(Length).  So you 
should also have in the encapsulating GenericSequence a tag like

<moby:Integer moby:namespace="" moby:id="" ></moby:Integer>

This brings up a new issue though that requires a policy formulation on 
the part of the community:  Suppose VirtualSequence had two Integer 
members, how would these be distinguished in the XML (i..e the Length 
field vs. the foo field)?  There are no examples in the 0.7 API 
distinguishing object members by name.  Should we not make articleName a 
required attribute when there is more than one component to an object?

Once we've resolved this, I'll make the automatic creation of XML for 
primitives part of the MobyDataSimpleInstance (like base Object creation 
is now), so creating more complicated objects is just a question of 
collating other instance of the same class.  This should avoid a lot of 
the query formulation issues, as you'll never be inputting XML directly 
(unless of course your object is a subclass of the text-xml object).



From senger at ebi.ac.uk  Fri May 21 10:24:03 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Fri May 21 10:27:46 2004
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AE0E60.5030605@cbr.nrc.ca>
Message-ID: <Pine.LNX.4.44.0405211520500.3173-100000@bagheera.ebi.ac.uk>

> This brings up a new issue though that requires a policy formulation on 
> the part of the community:  Suppose VirtualSequence had two Integer 
> members, how would these be distinguished in the XML (i..e the Length 
> field vs. the foo field)?
>
   Articles can be named. The API says: "Articles are, optionally, named 
using the articleName attribute. This might be used if, for example, the 
service requires named inputs. The order of non-named articles in a single 
Input or Output set MUST not be meaningful.".
   Mark, is this correct answer? I am still not sure about calling 
services :-(

   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  Fri May 21 11:38:41 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri May 21 10:42:43 2004
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <Pine.LNX.4.44.0405211520500.3173-100000@bagheera.ebi.ac.uk>
References: <Pine.LNX.4.44.0405211520500.3173-100000@bagheera.ebi.ac.uk>
Message-ID: <1085153921.9874.7.camel@myhost.mydomain>

Martin is 100% correct.  In fact, the articleName attributes of
sub-objects really defines an ontology of their own, with the
articleName being the "relationship predicate" linking the sub-object to
its parent object.

M


On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
> > This brings up a new issue though that requires a policy formulation on 
> > the part of the community:  Suppose VirtualSequence had two Integer 
> > members, how would these be distinguished in the XML (i..e the Length 
> > field vs. the foo field)?
> >
>    Articles can be named. The API says: "Articles are, optionally, named 
> using the articleName attribute. This might be used if, for example, the 
> service requires named inputs. The order of non-named articles in a single 
> Input or Output set MUST not be meaningful.".
>    Mark, is this correct answer? I am still not sure about calling 
> services :-(
> 
>    Martin
-- 
Mark Wilkinson (mwilkinson@mrl.ubc.ca)
University of British Columbia iCAPTURE Centre
From gordonp at cbr.nrc.ca  Fri May 21 12:20:15 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Fri May 21 12:23:50 2004
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <1085153921.9874.7.camel@myhost.mydomain>
References: <Pine.LNX.4.44.0405211520500.3173-100000@bagheera.ebi.ac.uk>
	<1085153921.9874.7.camel@myhost.mydomain>
Message-ID: <40AE2C3F.6000007@cbr.nrc.ca>

Then perhaps we should have some examples of that in the API (i.e. data 
*instances* with articleName attributes)?  Under the MOBY Data Class 
Ontology section, none of the examples have articleNames, even though 
the GO objects contain several sibling String elements... or am I 
missing something?


Mark Wilkinson wrote:

>Martin is 100% correct.  In fact, the articleName attributes of
>sub-objects really defines an ontology of their own, with the
>articleName being the "relationship predicate" linking the sub-object to
>its parent object.
>
>M
>
>
>On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
>  
>
>>>This brings up a new issue though that requires a policy formulation on 
>>>the part of the community:  Suppose VirtualSequence had two Integer 
>>>members, how would these be distinguished in the XML (i..e the Length 
>>>field vs. the foo field)?
>>>
>>>      
>>>
>>   Articles can be named. The API says: "Articles are, optionally, named 
>>using the articleName attribute. This might be used if, for example, the 
>>service requires named inputs. The order of non-named articles in a single 
>>Input or Output set MUST not be meaningful.".
>>   Mark, is this correct answer? I am still not sure about calling 
>>services :-(
>>
>>   Martin
>>    
>>


From mwilkinson at mobile.rogers.com  Fri May 21 12:20:26 2004
From: mwilkinson at mobile.rogers.com (mwilkinson)
Date: Fri May 21 12:26:57 2004
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
Message-ID: <200405211626.i4LGQsKr015549@portal.open-bio.org>

Point me to what you are looking at.
-----Original Message-----
From: Paul Gordon <gordonp@cbr.nrc.ca>
Date: Fri, 21 May 2004 10:20:15 
To:mobyl <moby-l@biomoby.org>
Subject: Re: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?

Then perhaps we should have some examples of that in the API (i.e. data 
*instances* with articleName attributes)?  Under the MOBY Data Class 
Ontology section, none of the examples have articleNames, even though 
the GO objects contain several sibling String elements... or am I 
missing something?


Mark Wilkinson wrote:

>Martin is 100% correct.  In fact, the articleName attributes of
>sub-objects really defines an ontology of their own, with the
>articleName being the "relationship predicate" linking the sub-object to
>its parent object.
>
>M
>
>
>On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
>  
>
>>>This brings up a new issue though that requires a policy formulation on 
>>>the part of the community:  Suppose VirtualSequence had two Integer 
>>>members, how would these be distinguished in the XML (i..e the Length 
>>>field vs. the foo field)?
>>>
>>>      
>>>
>>   Articles can be named. The API says: "Articles are, optionally, named 
>>using the articleName attribute. This might be used if, for example, the 
>>service requires named inputs. The order of non-named articles in a single 
>>Input or Output set MUST not be meaningful.".
>>   Mark, is this correct answer? I am still not sure about calling 
>>services :-(
>>
>>   Martin
>>    
>>


_______________________________________________
moby-l mailing list
moby-l@biomoby.org
http://biomoby.org/mailman/listinfo/moby-l

!!!!!!!!!!!!!!!!
To respond to this message you MUST send your response to (note new address!)

markw_mobile2 at illuminae dot com

Responses to the reply-to address go directly to trash!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!
From gordonp at cbr.nrc.ca  Fri May 21 12:39:40 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Fri May 21 12:43:13 2004
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <200405211623.i4LGNN62007555@furry.cbr.nrc.ca>
References: <200405211623.i4LGNN62007555@furry.cbr.nrc.ca>
Message-ID: <40AE30CC.5040701@cbr.nrc.ca>

mwilkinson wrote:

>Point me to what you are looking at.
>
The GO_Term example looks like:

<GO_Term namespace="GO/Acc" id="GO:0005575">
  <String namespace="" id="">cellular component</String>
  <String namespace="" id=""> That fraction of cells, prepared by 
disruptive biochemical
      methods, that includes the plasma and other membranes.</String>
</GO_Term>

Should probably look something like:

<GO_Term namespace="GO/Acc" id="GO:0005575">
  <String namespace="" id="" articleName="Term">cellular component</String>
  <String namespace="" id="" articleName="Definition"> That fraction of 
cells, prepared by disruptive biochemical
      methods, that includes the plasma and other membranes.</String>
</GO_Term>

My CDN $0.02 :-)

>-----Original Message-----
>From: Paul Gordon <gordonp@cbr.nrc.ca>
>Date: Fri, 21 May 2004 10:20:15 
>To:mobyl <moby-l@biomoby.org>
>Subject: Re: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
>
>Then perhaps we should have some examples of that in the API (i.e. data 
>*instances* with articleName attributes)?  Under the MOBY Data Class 
>Ontology section, none of the examples have articleNames, even though 
>the GO objects contain several sibling String elements... or am I 
>missing something?
>
>
>Mark Wilkinson wrote:
>
>  
>
>>Martin is 100% correct.  In fact, the articleName attributes of
>>sub-objects really defines an ontology of their own, with the
>>articleName being the "relationship predicate" linking the sub-object to
>>its parent object.
>>
>>M
>>
>>
>>On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
>> 
>>
>>    
>>
>>>>This brings up a new issue though that requires a policy formulation on 
>>>>the part of the community:  Suppose VirtualSequence had two Integer 
>>>>members, how would these be distinguished in the XML (i..e the Length 
>>>>field vs. the foo field)?
>>>>
>>>>     
>>>>
>>>>        
>>>>
>>>  Articles can be named. The API says: "Articles are, optionally, named 
>>>using the articleName attribute. This might be used if, for example, the 
>>>service requires named inputs. The order of non-named articles in a single 
>>>Input or Output set MUST not be meaningful.".
>>>  Mark, is this correct answer? I am still not sure about calling 
>>>services :-(
>>>
>>>  Martin
>>>   
>>>
>>>      
>>>
>
>
>_______________________________________________
>moby-l mailing list
>moby-l@biomoby.org
>http://biomoby.org/mailman/listinfo/moby-l
>
>!!!!!!!!!!!!!!!!
>To respond to this message you MUST send your response to (note new address!)
>
>markw_mobile2 at illuminae dot com
>
>Responses to the reply-to address go directly to trash!
>!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>
>  
>


From markw at illuminae.com  Fri May 21 13:47:49 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri May 21 12:51:52 2004
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AE30CC.5040701@cbr.nrc.ca>
References: <200405211623.i4LGNN62007555@furry.cbr.nrc.ca>
	<40AE30CC.5040701@cbr.nrc.ca>
Message-ID: <1085161668.10201.6.camel@myhost.mydomain>

Well would you believe it - nobody has ever noticed that before (or at
least, never mentioned it)!

I'll fix that as soon as I can!  It should be exactly as you say.

my bad...

M



On Fri, 2004-05-21 at 09:39, Paul Gordon wrote:
> mwilkinson wrote:
> 
> >Point me to what you are looking at.
> >
> The GO_Term example looks like:
> 
> <GO_Term namespace="GO/Acc" id="GO:0005575">
>   <String namespace="" id="">cellular component</String>
>   <String namespace="" id=""> That fraction of cells, prepared by 
> disruptive biochemical
>       methods, that includes the plasma and other membranes.</String>
> </GO_Term>
> 
> Should probably look something like:
> 
> <GO_Term namespace="GO/Acc" id="GO:0005575">
>   <String namespace="" id="" articleName="Term">cellular component</String>
>   <String namespace="" id="" articleName="Definition"> That fraction of 
> cells, prepared by disruptive biochemical
>       methods, that includes the plasma and other membranes.</String>
> </GO_Term>
> 
> My CDN $0.02 :-)
> 
> >-----Original Message-----
> >From: Paul Gordon <gordonp@cbr.nrc.ca>
> >Date: Fri, 21 May 2004 10:20:15 
> >To:mobyl <moby-l@biomoby.org>
> >Subject: Re: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
> >
> >Then perhaps we should have some examples of that in the API (i.e. data 
> >*instances* with articleName attributes)?  Under the MOBY Data Class 
> >Ontology section, none of the examples have articleNames, even though 
> >the GO objects contain several sibling String elements... or am I 
> >missing something?
> >
> >
> >Mark Wilkinson wrote:
> >
> >  
> >
> >>Martin is 100% correct.  In fact, the articleName attributes of
> >>sub-objects really defines an ontology of their own, with the
> >>articleName being the "relationship predicate" linking the sub-object to
> >>its parent object.
> >>
> >>M
> >>
> >>
> >>On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
> >> 
> >>
> >>    
> >>
> >>>>This brings up a new issue though that requires a policy formulation on 
> >>>>the part of the community:  Suppose VirtualSequence had two Integer 
> >>>>members, how would these be distinguished in the XML (i..e the Length 
> >>>>field vs. the foo field)?
> >>>>
> >>>>     
> >>>>
> >>>>        
> >>>>
> >>>  Articles can be named. The API says: "Articles are, optionally, named 
> >>>using the articleName attribute. This might be used if, for example, the 
> >>>service requires named inputs. The order of non-named articles in a single 
> >>>Input or Output set MUST not be meaningful.".
> >>>  Mark, is this correct answer? I am still not sure about calling 
> >>>services :-(
> >>>
> >>>  Martin
> >>>   
> >>>
> >>>      
> >>>
> >
> >
> >_______________________________________________
> >moby-l mailing list
> >moby-l@biomoby.org
> >http://biomoby.org/mailman/listinfo/moby-l
> >
> >!!!!!!!!!!!!!!!!
> >To respond to this message you MUST send your response to (note new address!)
> >
> >markw_mobile2 at illuminae dot com
> >
> >Responses to the reply-to address go directly to trash!
> >!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> >
> >  
> >
> 
> 
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 
Mark Wilkinson (mwilkinson@mrl.ubc.ca)
University of British Columbia iCAPTURE Centre
From VNarayan at mail.brc.mcw.edu  Fri May 21 12:58:18 2004
From: VNarayan at mail.brc.mcw.edu (Vijay Narayanasamy)
Date: Fri May 21 13:07:06 2004
Subject: [MOBY-l] New MOBY application: "BioGraphNet: a distributed fo
	rum for heterogeneous biological networks"
Message-ID: <295CC5EB4257D411B34D00D0B7748F4432E02F@baldar.brc.mcw.edu>

Hi Frank,

If you are interested in Java Graphlayout Applet look at the following links
http://java.sun.com/applets/jdk/1.0/demo/GraphLayout/

Several groups have modified this program to suit their needs.

A modified version for my application TransMiner
(http://www.bisti.nih.gov/2003meeting/Abstracts/III45.pdf) can be found at

http://sifter.cs.iupui.edu/~sifter/transMiner/BCTrans1.html 

Let me know if you are interested in this Graphlayout applet.

Cheers,

Vijay


-----Original Message-----
From: Simon Twigger [mailto:simont@mcw.edu] 
Sent: Thursday, May 20, 2004 11:01 AM
To: Frank Gibbons
Cc: 'moby-l@biomoby.org'; vnarayan@mcw.edu
Subject: Re: [MOBY-l] New MOBY application: "BioGraphNet: a distributed
forum for heterogeneous biological networks"

Hi Frank,

This looks very nice - is it possible to view the graph data into 
something like a java graph-viewing applet so people could zoom in and 
select things, etc? The image that comes back is nice but too small to 
see anything. Im cc'ing this to Vijay Narayanasamy in my group as he 
has built tools like this that display interaction data using this type 
of applet and he might be able to offer some suggestions and show you 
what he has done previously so you can see if it would be of use.

I wonder if it would be worth coloring the genes (grey elipses) as well 
as the lines connecting the genes? It might give a better overview of 
the types of interacting partners if they were colored light green, 
light pink, etc. rather than all being grey.

I'd be interested in getting you some rat data, we're working on some 
rat services here so perhaps we can chat more about that and see what 
makes sense. I'd love to see the tools you have for making text files 
available - I've done similar stuff myself but its not very generic, if 
you have something like that we can certainly make use of it.

I have to run to a meeting but will probably write some more later on.

Cheers,

	Simon.


On May 20, 2004, at 10:23 AM, Frank Gibbons wrote:

> Hey fellow MOBYers,
>
> Below is an abstract I've submitted for BOSC (Bioinformatics Open 
> Source Conference) and BioPathways, satellite conferences of ISMC/ECCB 
> in Glasgow, Scotland this year. BioGraphNet is our 'sandbox' within 
> the BioMOBY 'playground', in which we're looking at ways to share and 
> view biological networks.
>
> At this point, Gabriel Berriz and I have a working prototype: a 
> registered object for describing fairly generic pairwise interactions, 
> half a dozen working services, and an application that runs in a 
> web-browser to allow end-users to play with the interaction data. A 
> key element of this is that anyone can make their data available at 
> any time, and it will be discovered and included in the webpage 
> displayed to users (bench biologists). There's no installation, no 
> updating of databases. I'd appreciate your giving it a try 
> (http://llama.med.harvard.edu/cgi/BioTrawler) and letting us know what 
> you think. We're looking for feedback on a number of levels:
>
> * Does the overall idea, (being able to view an interactive graphical 
> display of your chosen data sources for your favorite genes), seem 
> useful to you? What pitfalls do you see in the near or distant future?
> * So far we've got correlated expression, synthetic lethality, 
> homology, transcription-factor/target (known and predicted), as well 
> as experimental protein-protein interaction results. What kinds of 
> data would make it more useful?
> * Do you have some data you'd like to share? We've developed tools to 
> facilitate making data available as a MOBY service: drop a text file 
> in the right place, enter the textual description of your service - 
> BOOM, it's registered and available to the world. One goal of this 
> project is to make it easy for people with data to put it out there.
> * Anything else that strikes you....
>
> We're really keen to get input on this, just reply to me: 
> mailto:fgibbons@hms.harvard.edu
>
> I'm looking forward to seeing some of you again in Glasgow!
>
> -Frank Gibbons
>
> --------------------------------------- ABSTRACT 
> ---------------------------------------
>
> TITLE: BioGraphNet, a distributed forum for heterogeneous biological 
> networks.
> AUTHORS: Francis D. Gibbons, Gabriel F. Berriz, and Frederick P. Roth
> Dept. of Biological Chemistry and Molecular Pharmacology, 250 Longwood 
> Ave., Harvard Medical School, Boston MA 02115, USA
>
> ABSTRACT:
> Biological network information is increasingly abundant.  The 
> combination of biological networks may be viewed as a multicolor 
> graph, with each color representing a different gene-gene or 
> protein-protein relationship, e.g., protein interaction, sequence 
> homology, correlated expression, transcriptional regulation, genetic 
> interaction (sensu synthetic lethality), or metabolic relationship.  
> Relationship types may be further stratified by type of evidence 
> supporting the relationship, by directionality or by confidence 
> measure.  Furthermore, each organism has its own collection of 
> networks.  Although this information's complexity argues for its 
> maintenance by distributed groups, much of its value is derived 
> through network integration.
>
> BioMOBY has established a 'playground' for distributed services.  We 
> have developed a 'sandbox' within BioMOBY called BioGraphNet.  
> BioGraphNet is a common standard and collection of services for 
> sharing distributed network information.  We now serve several network 
> data types, and encourage others to participate, using the common 
> standard objects we have registered in BioMOBY's ontology.
>
> As an example application illustrating the use of BioGraphNet, we 
> provide BioTrawler, a web-based biological network browser that 
> dynamically discovers suitable distributed data sources within 
> BioGraphNet, integrates those selected by the end-user 'just in time', 
> and visualizes the graph neighboring a user-defined set of genes. 
> Graph layout is handled by the open-source GraphViz package (modified 
> to handle multiple edges between a pair of nodes). BioTrawler also 
> exports graph representations in several commonly used formats (GIF by 
> default, but also Pajek, Cytoscape, and PDF).
>
> The combination of BioMOBY and BioGraphNet represents a distributed 
> network annotation system analogous to the Distributed Annotation 
> System (DAS) for sharing genome annotation.
>
> LICENSING:
> The object descriptions and service interfaces are already available 
> to all BioMOBY users. We plan to release BioTrawler under the Artistic 
> License.
>
> URL: http://llama.med.harvard.edu/cgi/BioTrawler
>
>
> PhD, Computational Biologist,
> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 
> 02115, USA.
> Tel: 617-432-3555       Fax: 617-432-3557       
> http://llama.med.harvard.edu/~fgibbons
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>
--

Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw
From mwilkinson at mrl.ubc.ca  Fri May 21 16:17:30 2004
From: mwilkinson at mrl.ubc.ca (Mark Wilkinson)
Date: Fri May 21 15:21:31 2004
Subject: [MOBY-l] 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  Fri May 21 18:10:08 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri May 21 17:14:14 2004
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AE30CC.5040701@cbr.nrc.ca>
References: <200405211623.i4LGNN62007555@furry.cbr.nrc.ca>
	<40AE30CC.5040701@cbr.nrc.ca>
Message-ID: <1085177408.10201.21.camel@myhost.mydomain>

Fixed.

On Fri, 2004-05-21 at 09:39, Paul Gordon wrote:
> mwilkinson wrote:
> 
> >Point me to what you are looking at.
> >
> The GO_Term example looks like:
> 
> <GO_Term namespace="GO/Acc" id="GO:0005575">
>   <String namespace="" id="">cellular component</String>
>   <String namespace="" id=""> That fraction of cells, prepared by 
> disruptive biochemical
>       methods, that includes the plasma and other membranes.</String>
> </GO_Term>
> 
> Should probably look something like:
> 
> <GO_Term namespace="GO/Acc" id="GO:0005575">
>   <String namespace="" id="" articleName="Term">cellular component</String>
>   <String namespace="" id="" articleName="Definition"> That fraction of 
> cells, prepared by disruptive biochemical
>       methods, that includes the plasma and other membranes.</String>
> </GO_Term>
> 
> My CDN $0.02 :-)
> 
> >-----Original Message-----
> >From: Paul Gordon <gordonp@cbr.nrc.ca>
> >Date: Fri, 21 May 2004 10:20:15 
> >To:mobyl <moby-l@biomoby.org>
> >Subject: Re: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
> >
> >Then perhaps we should have some examples of that in the API (i.e. data 
> >*instances* with articleName attributes)?  Under the MOBY Data Class 
> >Ontology section, none of the examples have articleNames, even though 
> >the GO objects contain several sibling String elements... or am I 
> >missing something?
> >
> >
> >Mark Wilkinson wrote:
> >
> >  
> >
> >>Martin is 100% correct.  In fact, the articleName attributes of
> >>sub-objects really defines an ontology of their own, with the
> >>articleName being the "relationship predicate" linking the sub-object to
> >>its parent object.
> >>
> >>M
> >>
> >>
> >>On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
> >> 
> >>
> >>    
> >>
> >>>>This brings up a new issue though that requires a policy formulation on 
> >>>>the part of the community:  Suppose VirtualSequence had two Integer 
> >>>>members, how would these be distinguished in the XML (i..e the Length 
> >>>>field vs. the foo field)?
> >>>>
> >>>>     
> >>>>
> >>>>        
> >>>>
> >>>  Articles can be named. The API says: "Articles are, optionally, named 
> >>>using the articleName attribute. This might be used if, for example, the 
> >>>service requires named inputs. The order of non-named articles in a single 
> >>>Input or Output set MUST not be meaningful.".
> >>>  Mark, is this correct answer? I am still not sure about calling 
> >>>services :-(
> >>>
> >>>  Martin
> >>>   
> >>>
> >>>      
> >>>
> >
> >
> >_______________________________________________
> >moby-l mailing list
> >moby-l@biomoby.org
> >http://biomoby.org/mailman/listinfo/moby-l
> >
> >!!!!!!!!!!!!!!!!
> >To respond to this message you MUST send your response to (note new address!)
> >
> >markw_mobile2 at illuminae dot com
> >
> >Responses to the reply-to address go directly to trash!
> >!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> >
> >  
> >
> 
> 
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 
Mark Wilkinson (mwilkinson@mrl.ubc.ca)
University of British Columbia iCAPTURE Centre
From barbara.re at studenti.unicam.it  Mon May 24 13:07:07 2004
From: barbara.re at studenti.unicam.it (RE BARBARA)
Date: Mon May 24 13:10:37 2004
Subject: [MOBY-l] Request about ontologi
Message-ID: <1085418427.40b22bbbcb942@mail.studenti.unicam.it>



Hi!

we have installed in local the moby central and after some interrogations in 
perl I esteem there interesting in the ontological part. 
 
We have read the whole material found in the directory /moby-live/docs but we 
have not understood as biomoby it interacts with these ontologies. 
 
Do you have some information in respect? 

Do you know how to interact with the ontologies? 

Do you have some documentation in respect? 

thanks very much!

BACHI

From bmg at sfu.ca  Tue May 25 06:55:46 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Tue May 25 06:59:19 2004
Subject: [MOBY-l] java xml parsing
Message-ID: <40B32632.2060908@sfu.ca>

Say I have a Query response like this

"<?xml version='1.0' encoding='UTF-8'?>"+
        "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' 
xmlns='http://www.biomoby.org/moby'>"+
        "<moby:mobyContent 
moby:authority='illuminae.com'><moby:serviceNotes>This is provided by 
SeqHound</moby:serviceNotes>"+
                "<moby:mobyData moby:queryID='1'>"+
                    "<moby:Simple moby:articleName=''>" +
                    "<genbank-flatfile namespace='NCBI_gi' 
id='111076'><![CDATA[LOCUS D31461 32 aa linear   ROD 30-MAY-1997"+
        "DEFINITION  T-cell receptor delta chain BDN7, thymus - mouse 
(fragment)."+
        "ACCESSION   D31461"+
        "PID         g111076"+
        "ORIGIN"+
         "       1 atyfcalmer vsrrgapdkl vfgqgtqvtv ep"+
        "//]]></genbank-flatfile></moby:Simple>"+
                "</moby:mobyData>"+
                "</moby:mobyContent></moby:MOBY>";       

Any suggestions regarding the best way to extract the gi id or the CDATA 
?  It seems there are many options, just wondering if the Java group has 
already settled on an approach.

thanks
-Ben

From gordonp at cbr.nrc.ca  Tue May 25 10:45:41 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Tue May 25 10:49:08 2004
Subject: [MOBY-l] java xml parsing
In-Reply-To: <40B32632.2060908@sfu.ca>
References: <40B32632.2060908@sfu.ca>
Message-ID: <40B35C15.8080006@cbr.nrc.ca>

If you are using MobyRequest, the getOutput will return a Vector with 
one element (corresponding to the one response).  This element is a 
MobySimpleDataInstance array of length one.  The MobySimpleDataInstance 
will just contain the genbank-flatfile tag and its nested contents.  
Unfortunately, for now this is as far as the autoparsing goes.  
Hopefully soon
MobySimpleDataInstance will soon give you its constituent members as 
other MobySimpleDataInstances, down to the primitives of the ontology. 

But for now, you can parse the XML response in an XML parser (determined 
by Java using the runtime libraries available) and run an XPath.  I 
haven't tried to compile the following code, but it should give you an 
idea of how to parse robustly (given that your XML object 
genbank-flatfile is not attributed to the MOBY namespace):

import javax.xml.parsers.*;
import org.w3c.dom.*;
import org.apache.xpath.XPathAPI; // xpath statement execution env

try{
  // Insert your code to get the XML string

  // Get a parser and parse the document
 DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
 DocumentBuilder docBuilder = dbf.newDocumentBuilder();
 Document document=docBuilder.parse(new 
java.io.StringBufferInputStream(xmlString));
 Element mobyPayload = document.getDocumentElement();

  // Now run the XPath statement that will be used fetch data from the 
server response   
  Node idAttr = XPathAPI.selectSingleNode(mobyPayload, 
"//genbank-flatfile/@id");
  if(idAttr != null){
        System.out.println("Output of XPath was " + idAttr.getNodeValue());
  }
}
catch(TransformerException te){
  // Insert your favourite death scene here
}
catch(ParserConfigurationException){
  // Ditto
}
catch(org.xml.sax.SAXException saxe){
  // Ditto
}
catch(java.io.IOException ioe){
  //Ditto
}


Benjamin Good wrote:

> Say I have a Query response like this
>
> "<?xml version='1.0' encoding='UTF-8'?>"+
>        "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' 
> xmlns='http://www.biomoby.org/moby'>"+
>        "<moby:mobyContent 
> moby:authority='illuminae.com'><moby:serviceNotes>This is provided by 
> SeqHound</moby:serviceNotes>"+
>                "<moby:mobyData moby:queryID='1'>"+
>                    "<moby:Simple moby:articleName=''>" +
>                    "<genbank-flatfile namespace='NCBI_gi' 
> id='111076'><![CDATA[LOCUS D31461 32 aa linear   ROD 30-MAY-1997"+
>        "DEFINITION  T-cell receptor delta chain BDN7, thymus - mouse 
> (fragment)."+
>        "ACCESSION   D31461"+
>        "PID         g111076"+
>        "ORIGIN"+
>         "       1 atyfcalmer vsrrgapdkl vfgqgtqvtv ep"+
>        "//]]></genbank-flatfile></moby:Simple>"+
>                "</moby:mobyData>"+
>                "</moby:mobyContent></moby:MOBY>";      
> Any suggestions regarding the best way to extract the gi id or the 
> CDATA ?  It seems there are many options, just wondering if the Java 
> group has already settled on an approach.
>
> thanks
> -Ben
>
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>


From markw at illuminae.com  Wed May 26 12:18:56 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed May 26 11:22:54 2004
Subject: [MOBY-l] [Fwd: [MISC] [bioped-l] Help me! (fwd)]
Message-ID: <1085588336.7304.11.camel@myhost.mydomain>

-----Forwarded Message-----
> From: Jason Stajich <jason@cgt.duhs.duke.edu>
> To: Mark Wilkinson <markw@illuminae.com>
> Subject: [MISC] [bioped-l] Help me! (fwd)
> Date: Wed, 26 May 2004 09:37:55 -0400
> 
> this went to the wrong list I guess.
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
> ---------- Forwarded message ----------
> Date: Wed, 26 May 2004 15:32:24 +0200
> From: ERCOLI CHIARA <chiara.ercoli@studenti.unicam.it>
> To: bioped-l@open-bio.org
> Subject: [bioped-l] Help me!
> 
> 
> 
> Hi,
> I'm BACHI, I have installed biomoby and I have developed some interrogations
> in perl.
> Besides I have noticed the presence of ontologie in the directory /moby-
> live/Docs but I have not understood their role.
> 
> Do you know how to tell me where and does as biomoby use the ontologies?
> 
> If it uses her, where are they considered?
> 
> Thanks you.
> 
> BACHI
> 
> _______________________________________________
> bioped-l mailing list
> bioped-l@open-bio.org
> http://open-bio.org/mailman/listinfo/bioped-l
-- 
Mark Wilkinson (mwilkinson@mrl.ubc.ca)
University of British Columbia iCAPTURE Centre
From gberriz at hms.harvard.edu  Wed May 26 09:50:24 2004
From: gberriz at hms.harvard.edu (Gabriel Berriz)
Date: Wed May 26 12:12:12 2004
Subject: [MOBY-l] Namespaces
Message-ID: <5.2.1.1.2.20040526094806.02897fd0@email.med.harvard.edu>

Hi, all.

What's the official list of valid BioMOBY namespaces?

Provisionally I have been referring to 
http://www.geneontology.org/doc/GO.xrf_abbs , but I'm not sure if this is 
actually/exactly what BioMOBY goes by.

Thanks,

Gabriel

From markw at illuminae.com  Wed May 26 13:49:18 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed May 26 12:53:21 2004
Subject: [MOBY] [MOBY-l] Namespaces
In-Reply-To: <5.2.1.1.2.20040526094806.02897fd0@email.med.harvard.edu>
References: <5.2.1.1.2.20040526094806.02897fd0@email.med.harvard.edu>
Message-ID: <1085593758.7304.16.camel@myhost.mydomain>

Hi Gabriel, 

You can find this by making a call to MOBY::Central->retrieveNamespaces,
or from the following quick-link (ugly... but effective)

http://mobycentral.cbr.nrc.ca/cgi-bin/types/Namespaces

M


On Wed, 2004-05-26 at 06:50, Gabriel Berriz wrote:
> Hi, all.
> 
> What's the official list of valid BioMOBY namespaces?
> 
> Provisionally I have been referring to 
> http://www.geneontology.org/doc/GO.xrf_abbs , but I'm not sure if this is 
> actually/exactly what BioMOBY goes by.
> 
> Thanks,
> 
> Gabriel
> 
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 
Mark Wilkinson (mwilkinson@mrl.ubc.ca)
University of British Columbia iCAPTURE Centre
From senger at ebi.ac.uk  Fri May 28 06:59:04 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Fri May 28 07:02:27 2004
Subject: [MOBY-l] LSAE - Life Sciences Analysis Engine
In-Reply-To: <1083263157.1632.41.camel@myhost.mydomain>
Message-ID: <Pine.LNX.4.44.0405281149391.28763-100000@bagheera.ebi.ac.uk>

Dear Moby users and developers,
   I am sorry to bother you with a topic that is not directly connected to 
BioMoby - but I hope that it is relevant.
   BioMoby defines its own, very interoperable, standard for the
BioMoby-native web services interface. But:
   1) The BioMoby regitry also includes, at least theoretically now, 
possibility to register other web services, and
   2) The service implementation is up to the service providers - it is
hidden from the outside world, but the LSAE topic I am going to talk about
here, can help with the service implementation (I believe).
   So, that was the rationale why to bother you...

   Now, the LSAE (if you are still reading).
   I have put together (with the De Novo Pharmaceutics) a revised
submission of an OMG spec for the LSAE (Life Sciences Analysis Engine).
With few additional features, it actually carves in stone what we already
have in myGrid (Soaplab).
   This revised submission is due to be considered by OMG in August. But I
have put it together already now because I would like to have as many
comments as I can collect from various communities (BioMoby is a 
significant one for me).
   Therefore, if you have time to look into the spec and give me any 
comments and suggestions, it would be marvelous.

   Last but not least: The spec has two submitters - this cannot be
changed now. But any spec is considered stronger if it has other
organizations as "supporters". The role of a supporter is only that the
name of an institute/company is in the spec - it does not give it any
rights (e.g. to vote on the spec), but neither any responsibility. So if
you consider that your institute could appear as a supporter of this spec,
please let me know and I will be very glad to list it in the spec.

   Now, where you can find it: the documents have been posted to the OMG
server today, so they will appear there later today, or on Monday:
   http://www.omg.org/cgi-bin/doc?lifesci/2004-05-01
   http://www.omg.org/cgi-bin/doc?lifesci/2004-05-02
Before they are available there, I have also put them here:

http://industry.ebi.ac.uk/~senger/storage/lsae/LSAE_AccompaniedFiles.zip
http://industry.ebi.ac.uk/~senger/storage/lsae/LSAE_Revised_submission_1_final.doc

   With best 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 mwilkinson at mrl.ubc.ca  Fri May 28 17:57:26 2004
From: mwilkinson at mrl.ubc.ca (Mark Wilkinson)
Date: Fri May 28 18:01:40 2004
Subject: [MOBY-l] new features in the MOBY browser
Message-ID: <1085781445.12321.102.camel@myhost.mydomain>

Hi all, 

Those of you who are using it will notice some new features in the MOBY
browser.  It is now possible to limit service discovery by service type,
service provider, output type, or keyword.  This helps to clean up the
increasing mass of services that are discovered by default... which I
guess is a sign of success, so we shouldn't bemoan it :-)

I have played with it for a couple of hours and haven't noticed any
obvious bugs, but please let me know if you do.  The code is committed
to the Gbrowse project, if you want to get it for yourself.

Cheers all!  Have a great weekend, 

M
-- 
Mark Wilkinson (mwilkinson@mrl.ubc.ca)
University of British Columbia iCAPTURE Centre
From markw at illuminae.com  Mon May 31 13:55:27 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon May 31 13:59:38 2004
Subject: [MOBY-l] Attn. all those interested in the Service Ontology
Message-ID: <1086026127.2973.8.camel@myhost.mydomain>

This gem has been floating around the GO-friends mailing list.  If they
have a bioinformatics tools ontology already, we should be using it and
working with them to extend it.  It seems to be at exactly the level of
resolution that we require for our Service Ontology...

M


-----Forwarded Message-----
> From: Michael Ashburner (Genetics) <ma11@gen.cam.ac.uk>
> To: ma11@gen.cam.ac.uk, midori@ebi.ac.uk
> Cc: gofriends@genome.stanford.edu, ref26@gen.cam.ac.uk
> Subject: [MISC] Re: Draft evidence code ontology
> Date: Mon, 31 May 2004 14:14:07 +0100
> 
> I should also add that I did not take into account this very useful
> email from Steffen Moeller, tho I would like to.
> Michael
> 
> 
> Envelope-to: m.ashburner@gen.cam.ac.uk
> Delivery-date: Mon, 22 Mar 2004 20:48:49 +0000
> Date: Mon, 22 Mar 2004 21:48:38 +0100
> To: m.ashburner@gen.cam.ac.uk
> Subject: Evidence Ontology - Bioinformatics tools suggestion
> Mime-Version: 1.0
> Content-Disposition: inline
> User-Agent: Mutt/1.3.28i
> From: Steffen Moeller <moeller@pzr3.pzr.uni-rostock.de>
> X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/
> X-Cam-AntiVirus: No virus found
> X-Cam-SpamDetails: scanned, SpamAssassin (score=-2.5, USER_AGENT_MUTT -2.49)
> 
> Dear Michael,
> 
> below you find my revised suggestion of an ontology for bioinformatics
> tools. I perceive the world as a combination of known sources of
> information and various methods that may be applied to get to this
> source.
> 
> Difficult are cases when the language does not distinguish between the
> approach and the tool. Taking "Blast" as an example, Blast certainly
> is an algorithm with many flavours (PSI-...). This has
> multiple implementations (NCBI and WU spring to mind). The method is a
> pairwise sequence comparison. The implementation is an application.
> 
> Hope to have helped to some extend. If you consider this usable and you
> want me to fill the gaps then please tell me.
> 
> Many greetings
> 
> Steffen
> 
> * in-silco analysis
>   & source-of-information (part-of)
>     + application (is-a)
>       + sequence-analysis (is-a)
> 	+ sequence-comparison (is-a)
>         + structure-prediction (is-a)
>           + fold-prediction  (is-a)
>   	  + transmembrane-topology prediction (is-a)
> 	    - TMHMM (part-of) is-a hidden markov model
> 	    - HMMTOP (part-of) is-a hidden markov model
> 	    - PHD (part-of) is-a neuronal network
> 	  + contact prediction
>       + structure-comparison (is-a)
>       + interaction-prediction (is-a)
>       + visualisation (is-a)
>     + databases (is-a)
>       + literature (is-a)
>       + sequence database(is-a)
>         + DNA database (is-a)
> 	  + SNP database (is-a)
>         + RNA database (is-a)
>         + protein database (is-a)
>       + databases connecting other databases (is-a)
>         + protein-interaction (is-a)
> 	+ metabolism (is-a)
>         + abstraction (is-a)
>           + Protein Domain database (is-a)
> 	    + PFAM (instance-of)
> 	    + InterPro (instance-of)
> 	    - Prosite (instance-of) is-a Regular expression, is-a Profile
>   & techniques (part-of)
>     + molecular modeling (is-a)
>     + sequence-similarity (is-a)
>       + direct-comparisons (is-a)
>       	+ pairwise (is-a)
> 	  + global
> 	  + local
> 	+ multiple (is-a)
> 	  + global
> 	  + local
>       + abstraction (is-a)
>         + neuronal network (is-a)
>         + hidden markov model (is-a)
> 	+ Profile (is-a)
> 	+ Weight matrix (is-a)
> 	+ Regular expression (is-a)
> 
> 
> --
> This message is from the GOFriends moderated mailing list.  A list of public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: owner-gofriends@geneontology.org
> Subscribing   send   "subscribe"   to   gofriends-request@geneontology.org
> Unsubscribing send   "unsubscribe"  to  gofriends-request@geneontology.org
> Web:          http://www.geneontology.org/
-- 
Mark Wilkinson (mwilkinson@mrl.ubc.ca)
University of British Columbia iCAPTURE Centre
From bneron at pasteur.fr  Mon May  3 04:22:52 2004
From: bneron at pasteur.fr (Bertrand Neron)
Date: Mon, 3 May 2004 10:22:52 +0200
Subject: [MOBY-l] how to call a service with secondaries?
Message-ID: <20040503082252.GA20511@caroline.sis.pasteur.fr>


I'd like to implement a bioMoby service with a Simple (a dnaSequence) and severals secondaries
but I have some problems.

to parse the XML input, I use the sub MOBY::CommonSubs::complexServiceInputParser($message)
 and XML::DOM . I see on the API (http://biomoby.org/moby-live/Perl/MOBY/CommonSubs.html#complexserviceinputparser) that the xml input should have this structure

<queryInput queryID = '1'>
   <Simple articleName='name1'>
       <Object namespace=blah id=blah/>
   </Simple>
   <Parameter articleName='cutoff'>
       <datatype>Float</datatype>
       <default>10</default>
   </Parameter>
</queryInput>
 

but the xml which my service recieve when I invoke it with the execute method had this structure


<?xml version='1.0' encoding='UTF-8'?>
        <moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>
            <moby:Query>
                <moby:queryInput queryID='1'>
                   <moby:Simple moby:articleName=''>
                     <dnaSequence namespace="" id=""    articleName="sequence">
                          <Integer namespace="" id="" articleName="Length">19<\In
teger>
                          <String namespace="" id="" articleName="SequenceString"
>ACGGTAGCTAGGTACCCAT<\String>
                     </dnaSequence>
                   </moby:Simple>
                   <moby:Simple moby:articleName=''>
                   <Parameter namespace="" id="" articleName="hybridation_type">
                             <Value>dnadna</Value>
                   <\Parameter>
                   </moby:Simple>
                   <moby:Simple moby:articleName=''>
                       <Parameter namespace="" id="" articleName="nucacid_concentration">
                            <Value>0.005</Value>
                       <\Parameter>
                   </moby:Simple>
                   <moby:Simple moby:articleName=''>
                         <Parameter namespace="" id="" articleName="salt_concentratio">
                            <Value>1.5</Value>
                         <\Parameter>
                    </moby:Simple>
                    </moby:queryInput>

              </moby:Query>
        </moby:MOBY>


each Parameter is embeded in a moby:Simple and the Parameter end Markups have an \  instead of / ??

How can I invoke a service with a Simple and several secondaries?
what kind of xml I should expected?

thanks.

bertrand

ps.

this the code I used to register the service and to call the service.


#########################################################################
# Register the service
#########################################################################
sub register_service {
  my $C = shift;
  my $reg = $C->registerService(
				serviceName  => 'Melting',
				serviceType  => "Analysis",
				authURI      => $authURI,
				contactEmail => $email,

				description  => "Melting: enthalpie, entropy and melting temperature (N. Le Novere)",
				category => "moby",
				URL          => $url,
				input        => [ ["sequence",['dnaSequence' => [] ] ]],
		   
				output       => [ ['', ["text-plain" => []]], ],
				secondary => {
					      "hybridation_type" => {'dataType' => 'String' ,
								    'enum' => ['dnadna','dnarna','rnarna']},
					      "nnfile" => {'dataType'=> 'String' ,
							   'default' =>'default' ,
							   'enum' => ['default','all97a.nn','bre86a.nn','fre86a.nn','san96a.nn','sug95a.nn','sug96a.nn','xia98a.nn']},
					      "complement_string" =>{'dataType' => 'String' },
					      "salt_concentratio" =>{'data_type' => 'Float' ,
								    'min' => 0.0 ,
								   ' max' => 10.0 },
					      "nucaid_concentration" => {'data_type' => 'Float',
									min => 0.0 ,
									max => 1.0 },
					      "correction_factor" => {'data_type' => 'Float' },
					      "salt_correction" => {'data_type' => 'String', 
								    'enum' => ['wet91a','san96a','san98a']},
					      "approx" => {'data_type' => 'Integer',
							   'default' => 0,
							  'enum' => [ 0 , 1]},
					      "dandling_ends" => {'data_type' => 'Integer',
								  'default' => 0,
								 'enum' => [ 0 , 1 ]},
					      "mismatches" => {'da















From o023163 at ncgr.ncgr.org  Mon May  3 11:29:10 2004
From: o023163 at ncgr.ncgr.org (o023163@ncgr.ncgr.org)
Date: Mon, 3 May 2004 09:29:10 -0600
Subject: [MOBY-l] Re: Re: Thanks!
Message-ID: <200405031536.i43Fa06B032000@portal.open-bio.org>

An embedded and charset-unspecified text was scrubbed...
Name: warning1.txt
Url: http://biomoby.org/pipermail/moby-l/attachments/20040503/40b43f94/warning1.txt
-------------- next part --------------
Please read the attached file.

From icho at svsu.edu  Wed May  5 13:59:03 2004
From: icho at svsu.edu (Il-Hyung Cho)
Date: Wed, 05 May 2004 13:59:03 -0400
Subject: [MOBY-l] Java implemenation on Axis
Message-ID: <s098f337.011@gw.svsu.edu>

Hello,
 
I am new to this group.
Hope this message is relevant to this group.
I am trying to implement web services on Apache Axis platform. I wonder
whether there is any tutorial or simple examples that I can follow to
make a small application up and running.
Could anyone help?
 
Many thanks,
 
 
 
Il-Hyung Cho
Ph.D. Computer Science
Saginaw Valley State Univ


From viji at gsf.de  Tue May 11 03:32:38 2004
From: viji at gsf.de (Viji)
Date: Tue, 11 May 2004 09:32:38 +0200
Subject: [MOBY-l] Java implemenation on Axis
In-Reply-To: <s098f337.011@gw.svsu.edu>
References: <s098f337.011@gw.svsu.edu>
Message-ID: <40A08196.9090607@gsf.de>

Hi Il-Hyung Cho,

I would suggest you to read the User guide of Axis first which(is very 
important) will be in "http://ws.apache.org/axis/java/user-guide.html"

Then, after understanding the concepts, if you still need some examples, 
scroll to the end of the page "http://ammai.com" and you will find three 
tutorials which will help you write Axis web services.

Then, you can register those web services as Moby services in BioMoby. 
Until then, this (list) will be inappropriate for your queries.

I hope I answered your questions.

All the Best.

Regards
Viji

Il-Hyung Cho wrote:

>Hello,
> 
>I am new to this group.
>Hope this message is relevant to this group.
>I am trying to implement web services on Apache Axis platform. I wonder
>whether there is any tutorial or simple examples that I can follow to
>make a small application up and running.
>Could anyone help?
> 
>Many thanks,
> 
> 
> 
>Il-Hyung Cho
>Ph.D. Computer Science
>Saginaw Valley State Univ
>_______________________________________________
>moby-l mailing list
>moby-l at biomoby.org
>http://biomoby.org/mailman/listinfo/moby-l
>
>
>  
>




From barbara.re at studenti.unicam.it  Tue May 11 05:27:56 2004
From: barbara.re at studenti.unicam.it (RE BARBARA)
Date: Tue, 11 May 2004 11:27:56 +0200
Subject: [MOBY-l] Request information about MOBY
Message-ID: <1084267676.40a09c9cce3c6@mail.studenti.unicam.it>



Hi!

I'am a problem about MOBY CENTRAL.
I have download and install it, now I work with Perl and API to interact with it.
How do we do to insert the varius services in our local MOBY?
Can we already unload those existing from some part without manually rewriting? 
Our databases is empty!
How can we question the system from the Client? (SOAP, JAVA, PERL)
Where can we find a precise documentation to use the unloaded MOBY CENTRAL?

Thanks you very match!

BACHI



From senger at ebi.ac.uk  Tue May 11 05:40:19 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue, 11 May 2004 10:40:19 +0100 (BST)
Subject: [MOBY-l] Request information about MOBY
In-Reply-To: <1084267676.40a09c9cce3c6@mail.studenti.unicam.it>
Message-ID: <Pine.LNX.4.44.0405111037220.24372-100000@bagheera.ebi.ac.uk>

Hi,

> I'am a problem about MOBY CENTRAL.
>
   Don't worry, surely you *are* not a problem. But perhaps you *have* a
problem :-)

   Now, seriously: with Java, you can get everything typing this command:

   cd <your-biomoby-cvs-copy>/Java
   ./run-cmdline-client -call DUMP > moby.sql

   It will download everything as SQL statements into file moby.sql. You 
can then open your mysql client and 'source moby.sql'.

   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 dag at sonsorol.org  Tue May 11 10:01:20 2004
From: dag at sonsorol.org (Chris Dagdigian)
Date: Tue, 11 May 2004 10:01:20 -0400
Subject: [MOBY-l] testing a new Open-Bio website and mail list archive search
Message-ID: <40A0DCB0.1050207@sonsorol.org>

Hello Everyone,

A fantastic volunteer (Kyle Jensen) has been steathily working on a 
problem for us that has long been a major issue for us -- website 
searching and indexing.

We've tried various solutions and ht://dig implementations in the past 
and nothing really worked well.

Kyle has been setting up a search indexing system based on the code from 
www.swish-e.org and so far it looks very very promising.

We have 2 main indexed search sites:

This page is a search index for all of the open-bio hosted websites:
http://search.open-bio.org/cgi-bin/obf-search.cgi

This page is just for searching mailing list archives:
http://search.open-bio.org/cgi-bin/mail-search.cgi


Please give the pages a whirl and let me know what you think.

Thanks again Kyle!

-Chris
open-bio.org admin team




From fgibbons at hms.harvard.edu  Tue May 11 11:49:09 2004
From: fgibbons at hms.harvard.edu (Frank Gibbons)
Date: Tue, 11 May 2004 11:49:09 -0400
Subject: [MOBY-l] empty responses: Collection or Simple? How to match
 responses to queries?
Message-ID: <5.2.1.1.2.20040511113738.01a291e0@email.med.harvard.edu>

MOBYers,

I'm working on some services, trying to figure out how to provide robust 
responses, and then parse them robustly. In particular, there may be a lot 
of valid queries, for which there an empty response. In theory (according 
to the API), I should return a response for every query, even if it's 
empty. The API will not allow me to return an empty collectionResponse, it 
requires me to use simpleResponse. My problem then is, how do I match the 
queries with the responses? If all the responses are of the same type, I 
can assume the array order corresponds to the ordering using queryID (is 
this correct?), and match them up like that. If they're of different types, 
I can pull out the collections and simples using getResponseArticles, which 
is fine as far as it goes. But how do I match the queries to their 
respective responses, given that the queryIDs live in the mobyData tags, 
which have already been stripped out by the time I get the 
Collections/Simples?

On a personal level, the easiest thing for me to do would be to use MOBY to 
handle communication, but just parse the XML response completely on my own 
(using XML::DOM, but none of MOBY::Client::CommonSubs). I know what it 
looks like, I know what I need to know in order to parse the response, and 
I know what problems to look out for. But the strength of an API lies in 
the use of a common way of doing things, so I'd like to go with that if I 
can. It's just not obvious to me how I should do that. Anyone have ideas?

Thanks,

-Frank

PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
617-432-3557       http://llama.med.harvard.edu/~fgibbons 



From bmg at sfu.ca  Wed May 12 22:04:39 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Thu, 13 May 2004 10:04:39 +0800
Subject: [MOBY-l] moby keyword services?
In-Reply-To: <5.2.1.1.2.20040511113738.01a291e0@email.med.harvard.edu>
References: <5.2.1.1.2.20040511113738.01a291e0@email.med.harvard.edu>
Message-ID: <40A2D7B7.2090701@sfu.ca>

 Dear MOBY people,

 I am working on a moby client to be used in a demo two weeks from now. 
 If possible, I would like to use a service like 
"RetrieveGOfromKeywords" to take a keyword query and return a list of 
interesting things.  So far, the only service that I have found that 
both accepts a keyword query and seems to be working is "SearchPubMed" 
from prometheus.brc.mcw.edu .  SearchPubMed works from the Moby Browser, 
but I get an access denied message when I try to hit from my client 
(which works fine on other services).

 Does anyone have a service that accepts a keyword query, is working, 
and will allow me access to it?

thanks,
Ben

PS. This summer I'll be working on utilizing MOBY to integrate data 
sources for the International Rice Research Institute info system 
http://www.iris.irri.org/ .  I will undoubtedly have many questions for 
you, hopefully I'll eventually be able to answer some of yours!







From mwilkinson at mobile.rogers.com  Wed May 12 22:35:23 2004
From: mwilkinson at mobile.rogers.com (mwilkinson)
Date: Wed, 12 May 2004 22:35:23 -0400
Subject: [MOBY-l] moby keyword services?
Message-ID: <200405130240.i4D2eh6B024046@portal.open-bio.org>

Hey Ben,

I'll check what's wrong with my GO service tomorrow AM when I get to work.  I left my computer there this evening so I can't check right now.  It is likely that the GO database has moved and that my script is unable to connect to it now.

In any case, I'll fix it first thing tomorrow.

M

-----Original Message-----
From: Benjamin Good <bmg at sfu.ca>
Date: Thu, 13 May 2004 10:04:39 
To:moby-l at biomoby.org
Subject: [MOBY-l] moby keyword services?

 Dear MOBY people,

 I am working on a moby client to be used in a demo two weeks from now. 
 If possible, I would like to use a service like 
"RetrieveGOfromKeywords" to take a keyword query and return a list of 
interesting things.  So far, the only service that I have found that 
both accepts a keyword query and seems to be working is "SearchPubMed" 
from prometheus.brc.mcw.edu .  SearchPubMed works from the Moby Browser, 
but I get an access denied message when I try to hit from my client 
(which works fine on other services).

 Does anyone have a service that accepts a keyword query, is working, 
and will allow me access to it?

thanks,
Ben

PS. This summer I'll be working on utilizing MOBY to integrate data 
sources for the International Rice Research Institute info system 
http://www.iris.irri.org/ .  I will undoubtedly have many questions for 
you, hopefully I'll eventually be able to answer some of yours!





_______________________________________________
moby-l mailing list
moby-l at biomoby.org
http://biomoby.org/mailman/listinfo/moby-l

!!!!!!!!!!!!!!!!
To respond to this message you MUST send your response to (note new address!)

markw_mobile2 at illuminae dot com

Responses to the reply-to address go directly to trash!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!


From barbara.re at studenti.unicam.it  Tue May 11 04:43:18 2004
From: barbara.re at studenti.unicam.it (RE BARBARA)
Date: Tue, 11 May 2004 10:43:18 +0200
Subject: [MOBY-l] Request information about MOBY
Message-ID: <1084264998.40a092261a199@mail.studenti.unicam.it>


Hi!
We are two students of university of Camerino (ITALY).
We are download and instal MOBY CENTRAL.
Now we study about perl and the different API but in the database of MOBY
CENTRAL there isn't any services.
How we do to insert the various services in our local MOBY?
And where do we find them?

Thanks you very match!

Barbara 
Chiara 



From icho at svsu.edu  Thu May 13 16:47:52 2004
From: icho at svsu.edu (Il-Hyung Cho)
Date: Thu, 13 May 2004 16:47:52 -0400
Subject: [MOBY-l] Java implemenation on
	Axis&In-Reply-To=s098f337.011@gw.svsu.edu
Message-ID: <s0a3a6da.022@gw.svsu.edu>

Hello Viji,
 
Here's what I have done successfully:
1. Installed Tomcat, Axis, jdk, mysql, ...
2. Ran over Axis user guide and successfully followed their examples
(in sample.userguide.example1~6).
3. Went over the Axis tutorial provided in www.ammal.com.
4. Implemeted a simple mysql access example by
    - setting up a simple database (not bioinformatics data) using
mysql 
    - providing a simple query server on axis
    - running a client sending a query to the server and receiving the
result
 
So, I think I basically went over most features needed in web services,
but what I am still not sure about is how to register my service to moby
so that clients can send inquiry to moby central and get the link to my
service.
Do my service have to be bioinformatics application? I am not a
bioinformatist, but just tring to see how biomoby works. Once I get my
simple service running on Moby, I can help my fellow bioinfomatist setup
their applications on Moby.
 
So far, I haven't been able to find a step by step procedure/tutorial
to register a service in Java to BioMoby.
 
Many thanks,
 
Il-Hyung Cho


From senger at ebi.ac.uk  Thu May 13 19:01:55 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Fri, 14 May 2004 00:01:55 +0100 (BST)
Subject: [MOBY-l] Java implemenation on
	Axis&In-Reply-To=s098f337.011@gw.svsu.edu
In-Reply-To: <s0a3a6da.022@gw.svsu.edu>
Message-ID: <Pine.OSF.4.10.10405132356330.613946-100000@ice.ebi.ac.uk>

> So far, I haven't been able to find a step by step procedure/tutorial
> to register a service in Java to BioMoby.
>
   There is no step-by-step- procedure for java. Sorry for that...
   Here is what you *can* do:

1) Make sure that you know enought about *your* service (name, type,
input/output data etc.)

2) Try: ./run-cmdline-client -h
It gives you following help:

 To register a service:

   -rs-name  <service-name>
   -rs-type  <service-type-name>
   -rs-categ <service-category>
   -rs-desc  <service-description>
   -rs-auth  <service-authority>
   -rs-email <service-contact>
   -rs-url   <service-URL>
   -rs-main  <service-authoritative>  use: 1 or 0

   -rs-in    <inputs>
      <inputs> are comma-delimited names of inputs;
      each of them is a pair of an input type and a namespace
      separated by an equal sign... sorry

   -rs-ifile <files-with-inputs>
      <files-with-inputs> are a comma-separated list of
      file names defining input data; the files should
      have format of Java properties, e.g...

   One can combine both methods: -rs-in and -rs-ifile.

   -rs-out   <outputs>
      <outputs> are comma-delimited names of output types

   -rs-ofile <files-with-outputs>
      <files-with-outputs> are a comma-separated list of
      file names defining output data; the files should
      have format of Java properties, e.g...

   One can combine both methods: -rs-out and -rs-ofile.

3) You can start ./run-cmdline-client with some of the mentioned
parameters to register your service. But...

4) You need to register *first* the pieces that the service consists of -
like service type, and input/output data typs, and namespaces. The
command-line clinent run-cmdline-client can register all of them.

If these instructions are too abstract try to send here/me info about your
service and I will try to be more concrete.

   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 mwilkinson at mobile.rogers.com  Thu May 13 21:07:59 2004
From: mwilkinson at mobile.rogers.com (mwilkinson)
Date: Thu, 13 May 2004 21:07:59 -0400
Subject: [MOBY-l] Request information about MOBY
Message-ID: <200405140115.i4E1Fd6B021945@portal.open-bio.org>

Hi Barbara and Chiara

You don't need to download and install the database unless you intend to set up a specialized registry just for yourselves.  Generally speaking you should be able to accomplish most of what you need by using the client-side libraries.

Have a look at the documentation for MOBY::Client::Cental, and Catherine has some excellent tutorials (follow the tutorials link on the website) for using Moby through the client libraries.

If you have more specific questions, or if I didn't answer your question adequately, please go ahead and ask!

Cheers!

Mark

-----Original Message-----
From: RE BARBARA <barbara.re at studenti.unicam.it>
Date: Tue, 11 May 2004 10:43:18 
To:moby-l at biomoby.org
Subject: [MOBY-l] Request information about MOBY


Hi!
We are two students of university of Camerino (ITALY).
We are download and instal MOBY CENTRAL.
Now we study about perl and the different API but in the database of MOBY
CENTRAL there isn't any services.
How we do to insert the various services in our local MOBY?
And where do we find them?

Thanks you very match!

Barbara 
Chiara 

_______________________________________________
moby-l mailing list
moby-l at biomoby.org
http://biomoby.org/mailman/listinfo/moby-l


!!!!!!!!!!!!!!!!
To respond to this message you MUST send your response to (note new address!)

markw_mobile2 at illuminae dot com

Responses to the reply-to address go directly to trash!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!


From bmg at sfu.ca  Mon May 17 05:38:08 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Mon, 17 May 2004 17:38:08 +0800
Subject: [MOBY-l] java client question
Message-ID: <40A88800.1090105@sfu.ca>

Dear Moby java developers,

 I am working on a java client and am having problems making it ask the 
question "what services exist that accept this kind of input"?   I see 
the example in the MobyCmdLineClient class, but can't seem to get it to 
work properly.  It seems that a couple lines that may once have caused 
the correct behavior have been commented out such that the service 
request actually ignores information pertaining to inputs.  It seems 
that perhaps this code is in the midst of a change???

Is there a newer version in progress somewhere?  

Here is what appears to be the pertinent code from MobyCmdLineClient:

                if ((param = cmd.getParam ("-fs-in")) != null ) {
                    String[] inputs = StringUtils.split (param, ",");
                       for (int i = 0; i < inputs.length; i++) {
                        String[] parts = StringUtils.split (inputs[i], "=");
                        if (parts.length >= 2) {
//                             pattern.addInput (parts[0], parts[1]);
                        } else {
//                             pattern.addInput (parts[0], "");
                        }
                    }

thanks
-Ben



From senger at ebi.ac.uk  Mon May 17 06:13:19 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Mon, 17 May 2004 11:13:19 +0100 (BST)
Subject: [MOBY-l] java client question
In-Reply-To: <40A88800.1090105@sfu.ca>
Message-ID: <Pine.LNX.4.44.0405171112040.7061-100000@bagheera.ebi.ac.uk>

Good point made.
I simply do not remember why the lines are commented out. Perhaps it was 
never finished - which is sad and blame me.
I will look at it this evening...

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 bmg at sfu.ca  Tue May 18 03:08:46 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Tue, 18 May 2004 15:08:46 +0800
Subject: [MOBY-l] MobyRequest or CentralImpl ?
Message-ID: <40A9B67E.9080001@sfu.ca>

Hello,

 When I want to execute a moby service from my java client, it seems 
that there are two choices present in cvs,  the invokeService() method 
from the MobyRequest class and the doCall method from the CentralImpl class.

  Any opinions about which one I should be using ?

thanks
-Ben



From senger at ebi.ac.uk  Tue May 18 04:04:03 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue, 18 May 2004 09:04:03 +0100 (BST)
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40A9B67E.9080001@sfu.ca>
Message-ID: <Pine.LNX.4.44.0405180853170.8181-100000@bagheera.ebi.ac.uk>

>   Any opinions about which one I should be using ?
>
   Actually, the third one - which does not exist yet :-)
   More seriously:

   1) The doCall of CentralImpl is there as a "side-effect". It was never 
meant to be used regularly but the life proved differently. The whole 
CentralImpl was meant to be used to access Moby registries, not the Moby 
services, but the method doCall was there so people started to use it. And 
it will still be there, so you are safe to use it.

   2) Then Paul started with MobyRequest. I have not used it myself so I 
cannot compare it - but I know that MobyRequest was meant to provide not 
only a simple call to a service (such as doCall in CentralImpl) but also 
to help with building the input XML query object and possibly to decode 
the returned result XML object.

   So, if you are looking just how to call a service, both methods will do 
it for you (but as I said I may be mistaken because I have not used 
MobyRequest myself).

   3) So, why did I start this reply with the third option? Because I 
still hope to write a code that will help service providers hopefully 
more that any of the two methods you mentioned. But it does not exist 
yet...

   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  Tue May 18 06:02:38 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue, 18 May 2004 11:02:38 +0100 (BST)
Subject: [MOBY-l] java client question
In-Reply-To: <40A88800.1090105@sfu.ca>
Message-ID: <Pine.OSF.4.10.10405181057210.716676-100000@ice.ebi.ac.uk>

>  I am working on a java client and am having problems making it ask the 
> question "what services exist that accept this kind of input"?
>
   I fixed that (actually I have added it, it was never finished :-)).
Try it please if it does what is expected.
   Using this opportunity I also add few new options to the 'find
services' in MobyCmdLineClient:
   -nc ... do not include in the search result services that are child
           types (more specific) than the service type you requested
   -np ... do not include in the search result services operating on
           the parent types of the data types you requested
   -on ... print only names of the fou8nd services

   With 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 gordonp at cbr.nrc.ca  Tue May 18 09:33:12 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Tue, 18 May 2004 07:33:12 -0600
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40A9B67E.9080001@sfu.ca>
References: <40A9B67E.9080001@sfu.ca>
Message-ID: <40AA1098.7060205@cbr.nrc.ca>

Benjamin Good wrote:

> Hello,
>
> When I want to execute a moby service from my java client, it seems 
> that there are two choices present in cvs,  the invokeService() method 
> from the MobyRequest class and the doCall method from the CentralImpl 
> class.
>
>  Any opinions about which one I should be using ?

MobyRequest is designed specifically for this purpose.  If you look at 
the ChangeLog, there is an example:

    // Assumes you already have a service (mobyService) and data 
(mobyInputData) around
    mobyRequest = new MobyRequest(new CentralImpl());
    mobyRequest.setDebugMode(true);
    mobyRequest.setService(mobyService);
    mobyRequest.setInput((MobyDataInstance[]) mobyInputData);
    try{
        mobyRequest.invokeService();
    } catch(MobyException mobye){
        System.err.println("Failure in MOBY protocol: " + mobye);
    } catch(SOAPException soape){
        System.err.println("Failure in SOAP transaction: " + soape);
    } catch(NOSuccessException nse){
        System.err.println("Failure in MOBY logic (input was not 
acceptable " +
                           "for this service)" + nse);
    }


You can reuse the MobyRequest object as many times as you like...

>
> thanks
> -Ben
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>




From bmg at sfu.ca  Wed May 19 23:56:49 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Thu, 20 May 2004 11:56:49 +0800
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AA1098.7060205@cbr.nrc.ca>
References: <40A9B67E.9080001@sfu.ca> <40AA1098.7060205@cbr.nrc.ca>
Message-ID: <40AC2C81.6090108@sfu.ca>


 Hi Paul,

 I'm trying to get your method running but am having some trouble 
creating the mobyInputData for my request.  Running with Martin's method 
I built the query object directly as a string of xml as shown below. 
 I've been trying to create a MobyData instance, but am getting a bit 
lost.    What is the best procedure for creating a useful MobyData object ?

Sorry for being a little slow on the uptake here, but I'm sure a 
complete example would also be helpful for others in the future.

cheers
-Ben

    private String mobyQuery(String ns, String query){
        return "<?xml version='1.0' encoding='UTF-8'?> "+
        "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>" +
              "<moby:Query>" +
                  "<moby:queryInput moby:articleName=''>"+
                        "<moby:Simple>"+
                            "<Object namespace='"+ns+"' id=\""+query+"\"/>"+
                        "</moby:Simple>"+
                    "</moby:queryInput>"+
               "</moby:Query>"+
        "</moby:MOBY>";
    }



Paul Gordon wrote:

> Benjamin Good wrote:
>
>> Hello,
>>
>> When I want to execute a moby service from my java client, it seems 
>> that there are two choices present in cvs,  the invokeService() 
>> method from the MobyRequest class and the doCall method from the 
>> CentralImpl class.
>>
>>  Any opinions about which one I should be using ?
>
>
> MobyRequest is designed specifically for this purpose.  If you look at 
> the ChangeLog, there is an example:
>
>    // Assumes you already have a service (mobyService) and data 
> (mobyInputData) around
>    mobyRequest = new MobyRequest(new CentralImpl());
>    mobyRequest.setDebugMode(true);
>    mobyRequest.setService(mobyService);
>    mobyRequest.setInput((MobyDataInstance[]) mobyInputData);
>    try{
>        mobyRequest.invokeService();
>    } catch(MobyException mobye){
>        System.err.println("Failure in MOBY protocol: " + mobye);
>    } catch(SOAPException soape){
>        System.err.println("Failure in SOAP transaction: " + soape);
>    } catch(NOSuccessException nse){
>        System.err.println("Failure in MOBY logic (input was not 
> acceptable " +
>                           "for this service)" + nse);
>    }
>
>
> You can reuse the MobyRequest object as many times as you like...
>
>>
>> thanks
>> -Ben
>>
>> _______________________________________________
>> moby-l mailing list
>> moby-l at biomoby.org
>> http://biomoby.org/mailman/listinfo/moby-l
>>
>
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>




From p.lord at russet.org.uk  Thu May 20 06:06:09 2004
From: p.lord at russet.org.uk (Phillip Lord)
Date: 20 May 2004 11:06:09 +0100
Subject: [MOBY-l] CFP: The Seventh Annual Bio-ontologies Meeting
Message-ID: <vfhdubmmzy.fsf@rpc71.cs.man.ac.uk>







Apologies for those of you who get this more than once. 

The deadline for submissions is now approaching. 









The Seventh Annual Bio-ontologies Meeting Call For Submissions
==============================================================

Key Information
===============      


Organisers: Robert Stevens(1), Robin McEntire(2),
      Phillip Lord(1), and James.A.Butler(2)

(1) Dept of Computer Science, University of Manchester
(2) GlaxoSmithKline

Submission Deadline: 31st May 2004      
Contact:  bio-ontologies at lists.man.ac.uk    
Website:  http://bio-ontologies.man.ac.uk
Location: Glasgow, Scotland.
Date: 30th July
Main Conference: http://www.iscb.org/ismbeccb2004/
Registration: http://www.iscb.org/ismbeccb2004/reg.html
Registration Costs:  80 Academic, 110 Corporate, 60 Student
   (Prices in UK Pounds. 17.5% VAT will be added. Coffee and lunch included)



General Information
===================
      
The Bio-Ontologies workshop has been in existence since 1998, and now
operates as a Special Interest Group at the ISMB Conference.
Bio-Ontologies is well established as one of the key meetings for
dissemination of the latest information and research on ontologies in the
life sciences and has drawn the key researchers in the field.

After last year's highly successful theme of "Ontologies and Text
Analysis", we will follow with the timely theme of "Ontologies and
Bio-Images". Work is currently being done in the area of ontologies of
images, especially in the domain of developmental biology and
medicine. A prime example of this work is the Bio-Image databank,
which makes extensive use of ontologies.

Our guest speaker for this year's topic will be Dr. David Shotton, who
will talk about the use of ontologies within the BioImage database.


New this year
=============

This year, Comparative and Functional Genomics will publish selected
presentations from the Seventh Annual Bio-Ontologies
Workshop. Previously we have published Conference Reviews in CFG. We are
very pleased that last year's Workshop had enough substantial,
high-quality work to enable such a special issue this year. We do, however,
believe that a level of informality is critical to the success of this
Workshop, and so we hope the meeting offers a venue for news and
views, perhaps less developed, but up to the minute work. All are
welcome!

      
Submissions
===========
We invite the submission of two A4 page abstracts for presentation along
this theme. Suitable topics include, but are not restricted to:

The content of bio-images;
The technical origins  of images
Support for image analysis (e.g., change in shape, colour,
texture, etc.)

We wish, however, not to restrict the topics presented to the theme
alone. So, we are also interested in:

Shared experiences in using ontology tools, development methodologies, 
comparing ontologies, and reusing other people's ontologies; 

Current research in ontology languages and ontology exchange
languages;

Updates on ontologies in development by members of the life
sciences community, including genomics, proteomics and
metabolomics;

Practical uses of ontologies in research and drug discovery
especially pre-competitive ontologies for the industry.


Submission details at http://bio-ontologies.man.ac.uk
-- 
Phillip Lord,				Phone: +44 (0) 161 275 6139
PostDoctoral Research Associate,        Email: p.lord at russet.org.uk
Department of Computer Science          http://www.russet.org.uk  
Kilburn Building                        http://www.cs.man.ac.uk/~phillord
University of Manchester                
Oxford Road
Manchester
M13 9PL


From markw at illuminae.com  Thu May 20 11:24:50 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 20 May 2004 08:24:50 -0700
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AC2C81.6090108@sfu.ca>
References: <40A9B67E.9080001@sfu.ca> <40AA1098.7060205@cbr.nrc.ca>
	<40AC2C81.6090108@sfu.ca>
Message-ID: <1085066689.7946.5.camel@myhost.mydomain>

Hi Ben, 

heads up that the Query and queryInput tags are deprecated.  Please see
the API documentation.

M


On Wed, 2004-05-19 at 20:56, Benjamin Good wrote:
>  Hi Paul,
> 
>  I'm trying to get your method running but am having some trouble 
> creating the mobyInputData for my request.  Running with Martin's method 
> I built the query object directly as a string of xml as shown below. 
>  I've been trying to create a MobyData instance, but am getting a bit 
> lost.    What is the best procedure for creating a useful MobyData object ?
> 
> Sorry for being a little slow on the uptake here, but I'm sure a 
> complete example would also be helpful for others in the future.
> 
> cheers
> -Ben
> 
>     private String mobyQuery(String ns, String query){
>         return "<?xml version='1.0' encoding='UTF-8'?> "+
>         "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>" +
>               "<moby:Query>" +
>                   "<moby:queryInput moby:articleName=''>"+
>                         "<moby:Simple>"+
>                             "<Object namespace='"+ns+"' id=\""+query+"\"/>"+
>                         "</moby:Simple>"+
>                     "</moby:queryInput>"+
>                "</moby:Query>"+
>         "</moby:MOBY>";
>     }
> 
> 
> 
> Paul Gordon wrote:
> 
> > Benjamin Good wrote:
> >
> >> Hello,
> >>
> >> When I want to execute a moby service from my java client, it seems 
> >> that there are two choices present in cvs,  the invokeService() 
> >> method from the MobyRequest class and the doCall method from the 
> >> CentralImpl class.
> >>
> >>  Any opinions about which one I should be using ?
> >
> >
> > MobyRequest is designed specifically for this purpose.  If you look at 
> > the ChangeLog, there is an example:
> >
> >    // Assumes you already have a service (mobyService) and data 
> > (mobyInputData) around
> >    mobyRequest = new MobyRequest(new CentralImpl());
> >    mobyRequest.setDebugMode(true);
> >    mobyRequest.setService(mobyService);
> >    mobyRequest.setInput((MobyDataInstance[]) mobyInputData);
> >    try{
> >        mobyRequest.invokeService();
> >    } catch(MobyException mobye){
> >        System.err.println("Failure in MOBY protocol: " + mobye);
> >    } catch(SOAPException soape){
> >        System.err.println("Failure in SOAP transaction: " + soape);
> >    } catch(NOSuccessException nse){
> >        System.err.println("Failure in MOBY logic (input was not 
> > acceptable " +
> >                           "for this service)" + nse);
> >    }
> >
> >
> > You can reuse the MobyRequest object as many times as you like...
> >
> >>
> >> thanks
> >> -Ben
> >>
> >> _______________________________________________
> >> moby-l mailing list
> >> moby-l at biomoby.org
> >> http://biomoby.org/mailman/listinfo/moby-l
> >>
> >
> >
> > _______________________________________________
> > moby-l mailing list
> > moby-l at biomoby.org
> > http://biomoby.org/mailman/listinfo/moby-l
> >
> >
> 
> 
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre


From gordonp at cbr.nrc.ca  Thu May 20 11:10:51 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Thu, 20 May 2004 09:10:51 -0600
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <1085066689.7946.5.camel@myhost.mydomain>
References: <40A9B67E.9080001@sfu.ca> <40AA1098.7060205@cbr.nrc.ca>	
	<40AC2C81.6090108@sfu.ca> <1085066689.7946.5.camel@myhost.mydomain>
Message-ID: <40ACCA7B.2090907@cbr.nrc.ca>

Mark Wilkinson wrote:

>Hi Ben, 
>
>heads up that the Query and queryInput tags are deprecated.  Please see
>the API documentation.
>  
>
Actually, with the Java client, you don't need to put any of that in 
your code anyway :-)  I'm creating a Wiki document with a complete 
example right now, will send the URL as soon as I'm done...



From fgibbons at hms.harvard.edu  Thu May 20 11:23:57 2004
From: fgibbons at hms.harvard.edu (Frank Gibbons)
Date: Thu, 20 May 2004 11:23:57 -0400
Subject: [MOBY-l] New MOBY application: "BioGraphNet: a distributed forum for
 heterogeneous biological networks"
Message-ID: <5.2.1.1.2.20040520110235.01a0a610@email.med.harvard.edu>

Hey fellow MOBYers,

Below is an abstract I've submitted for BOSC (Bioinformatics Open Source 
Conference) and BioPathways, satellite conferences of ISMC/ECCB in Glasgow, 
Scotland this year. BioGraphNet is our 'sandbox' within the BioMOBY 
'playground', in which we're looking at ways to share and view biological 
networks.

At this point, Gabriel Berriz and I have a working prototype: a registered 
object for describing fairly generic pairwise interactions, half a dozen 
working services, and an application that runs in a web-browser to allow 
end-users to play with the interaction data. A key element of this is that 
anyone can make their data available at any time, and it will be discovered 
and included in the webpage displayed to users (bench biologists). There's 
no installation, no updating of databases. I'd appreciate your giving it a 
try (http://llama.med.harvard.edu/cgi/BioTrawler) and letting us know what 
you think. We're looking for feedback on a number of levels:

* Does the overall idea, (being able to view an interactive graphical 
display of your chosen data sources for your favorite genes), seem useful 
to you? What pitfalls do you see in the near or distant future?
* So far we've got correlated expression, synthetic lethality, homology, 
transcription-factor/target (known and predicted), as well as experimental 
protein-protein interaction results. What kinds of data would make it more 
useful?
* Do you have some data you'd like to share? We've developed tools to 
facilitate making data available as a MOBY service: drop a text file in the 
right place, enter the textual description of your service - BOOM, it's 
registered and available to the world. One goal of this project is to make 
it easy for people with data to put it out there.
* Anything else that strikes you....

We're really keen to get input on this, just reply to me: 
mailto:fgibbons at hms.harvard.edu

I'm looking forward to seeing some of you again in Glasgow!

-Frank Gibbons

--------------------------------------- ABSTRACT 
---------------------------------------

TITLE: BioGraphNet, a distributed forum for heterogeneous biological networks.
AUTHORS: Francis D. Gibbons, Gabriel F. Berriz, and Frederick P. Roth
Dept. of Biological Chemistry and Molecular Pharmacology, 250 Longwood 
Ave., Harvard Medical School, Boston MA 02115, USA

ABSTRACT:
Biological network information is increasingly abundant.  The combination 
of biological networks may be viewed as a multicolor graph, with each color 
representing a different gene-gene or protein-protein relationship, e.g., 
protein interaction, sequence homology, correlated expression, 
transcriptional regulation, genetic interaction (sensu synthetic 
lethality), or metabolic relationship.  Relationship types may be further 
stratified by type of evidence supporting the relationship, by 
directionality or by confidence measure.  Furthermore, each organism has 
its own collection of networks.  Although this information's complexity 
argues for its maintenance by distributed groups, much of its value is 
derived through network integration.

BioMOBY has established a 'playground' for distributed services.  We have 
developed a 'sandbox' within BioMOBY called BioGraphNet.  BioGraphNet is a 
common standard and collection of services for sharing distributed network 
information.  We now serve several network data types, and encourage others 
to participate, using the common standard objects we have registered in 
BioMOBY's ontology.

As an example application illustrating the use of BioGraphNet, we provide 
BioTrawler, a web-based biological network browser that dynamically 
discovers suitable distributed data sources within BioGraphNet, integrates 
those selected by the end-user 'just in time', and visualizes the graph 
neighboring a user-defined set of genes. Graph layout is handled by the 
open-source GraphViz package (modified to handle multiple edges between a 
pair of nodes). BioTrawler also exports graph representations in several 
commonly used formats (GIF by default, but also Pajek, Cytoscape, and PDF).

The combination of BioMOBY and BioGraphNet represents a distributed network 
annotation system analogous to the Distributed Annotation System (DAS) for 
sharing genome annotation.

LICENSING:
The object descriptions and service interfaces are already available to all 
BioMOBY users. We plan to release BioTrawler under the Artistic License.

URL: http://llama.med.harvard.edu/cgi/BioTrawler


PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
617-432-3557       http://llama.med.harvard.edu/~fgibbons 



From simont at mcw.edu  Thu May 20 12:00:54 2004
From: simont at mcw.edu (Simon Twigger)
Date: Thu, 20 May 2004 11:00:54 -0500
Subject: [MOBY-l] New MOBY application: "BioGraphNet: a distributed forum
	for heterogeneous biological networks"
In-Reply-To: <5.2.1.1.2.20040520110235.01a0a610@email.med.harvard.edu>
References: <5.2.1.1.2.20040520110235.01a0a610@email.med.harvard.edu>
Message-ID: <DF90F624-AA76-11D8-812A-000A959D1D82@mcw.edu>

Hi Frank,

This looks very nice - is it possible to view the graph data into 
something like a java graph-viewing applet so people could zoom in and 
select things, etc? The image that comes back is nice but too small to 
see anything. Im cc'ing this to Vijay Narayanasamy in my group as he 
has built tools like this that display interaction data using this type 
of applet and he might be able to offer some suggestions and show you 
what he has done previously so you can see if it would be of use.

I wonder if it would be worth coloring the genes (grey elipses) as well 
as the lines connecting the genes? It might give a better overview of 
the types of interacting partners if they were colored light green, 
light pink, etc. rather than all being grey.

I'd be interested in getting you some rat data, we're working on some 
rat services here so perhaps we can chat more about that and see what 
makes sense. I'd love to see the tools you have for making text files 
available - I've done similar stuff myself but its not very generic, if 
you have something like that we can certainly make use of it.

I have to run to a meeting but will probably write some more later on.

Cheers,

	Simon.


On May 20, 2004, at 10:23 AM, Frank Gibbons wrote:

> Hey fellow MOBYers,
>
> Below is an abstract I've submitted for BOSC (Bioinformatics Open 
> Source Conference) and BioPathways, satellite conferences of ISMC/ECCB 
> in Glasgow, Scotland this year. BioGraphNet is our 'sandbox' within 
> the BioMOBY 'playground', in which we're looking at ways to share and 
> view biological networks.
>
> At this point, Gabriel Berriz and I have a working prototype: a 
> registered object for describing fairly generic pairwise interactions, 
> half a dozen working services, and an application that runs in a 
> web-browser to allow end-users to play with the interaction data. A 
> key element of this is that anyone can make their data available at 
> any time, and it will be discovered and included in the webpage 
> displayed to users (bench biologists). There's no installation, no 
> updating of databases. I'd appreciate your giving it a try 
> (http://llama.med.harvard.edu/cgi/BioTrawler) and letting us know what 
> you think. We're looking for feedback on a number of levels:
>
> * Does the overall idea, (being able to view an interactive graphical 
> display of your chosen data sources for your favorite genes), seem 
> useful to you? What pitfalls do you see in the near or distant future?
> * So far we've got correlated expression, synthetic lethality, 
> homology, transcription-factor/target (known and predicted), as well 
> as experimental protein-protein interaction results. What kinds of 
> data would make it more useful?
> * Do you have some data you'd like to share? We've developed tools to 
> facilitate making data available as a MOBY service: drop a text file 
> in the right place, enter the textual description of your service - 
> BOOM, it's registered and available to the world. One goal of this 
> project is to make it easy for people with data to put it out there.
> * Anything else that strikes you....
>
> We're really keen to get input on this, just reply to me: 
> mailto:fgibbons at hms.harvard.edu
>
> I'm looking forward to seeing some of you again in Glasgow!
>
> -Frank Gibbons
>
> --------------------------------------- ABSTRACT 
> ---------------------------------------
>
> TITLE: BioGraphNet, a distributed forum for heterogeneous biological 
> networks.
> AUTHORS: Francis D. Gibbons, Gabriel F. Berriz, and Frederick P. Roth
> Dept. of Biological Chemistry and Molecular Pharmacology, 250 Longwood 
> Ave., Harvard Medical School, Boston MA 02115, USA
>
> ABSTRACT:
> Biological network information is increasingly abundant.  The 
> combination of biological networks may be viewed as a multicolor 
> graph, with each color representing a different gene-gene or 
> protein-protein relationship, e.g., protein interaction, sequence 
> homology, correlated expression, transcriptional regulation, genetic 
> interaction (sensu synthetic lethality), or metabolic relationship.  
> Relationship types may be further stratified by type of evidence 
> supporting the relationship, by directionality or by confidence 
> measure.  Furthermore, each organism has its own collection of 
> networks.  Although this information's complexity argues for its 
> maintenance by distributed groups, much of its value is derived 
> through network integration.
>
> BioMOBY has established a 'playground' for distributed services.  We 
> have developed a 'sandbox' within BioMOBY called BioGraphNet.  
> BioGraphNet is a common standard and collection of services for 
> sharing distributed network information.  We now serve several network 
> data types, and encourage others to participate, using the common 
> standard objects we have registered in BioMOBY's ontology.
>
> As an example application illustrating the use of BioGraphNet, we 
> provide BioTrawler, a web-based biological network browser that 
> dynamically discovers suitable distributed data sources within 
> BioGraphNet, integrates those selected by the end-user 'just in time', 
> and visualizes the graph neighboring a user-defined set of genes. 
> Graph layout is handled by the open-source GraphViz package (modified 
> to handle multiple edges between a pair of nodes). BioTrawler also 
> exports graph representations in several commonly used formats (GIF by 
> default, but also Pajek, Cytoscape, and PDF).
>
> The combination of BioMOBY and BioGraphNet represents a distributed 
> network annotation system analogous to the Distributed Annotation 
> System (DAS) for sharing genome annotation.
>
> LICENSING:
> The object descriptions and service interfaces are already available 
> to all BioMOBY users. We plan to release BioTrawler under the Artistic 
> License.
>
> URL: http://llama.med.harvard.edu/cgi/BioTrawler
>
>
> PhD, Computational Biologist,
> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 
> 02115, USA.
> Tel: 617-432-3555       Fax: 617-432-3557       
> http://llama.med.harvard.edu/~fgibbons
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>
--

Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw



From gordonp at cbr.nrc.ca  Thu May 20 12:19:08 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Thu, 20 May 2004 10:19:08 -0600
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AC2C81.6090108@sfu.ca>
References: <40A9B67E.9080001@sfu.ca> <40AA1098.7060205@cbr.nrc.ca>
	<40AC2C81.6090108@sfu.ca>
Message-ID: <40ACDA7C.7000000@cbr.nrc.ca>

I've created two TWiki documents to explain the usage and interaction of 
the jMOBY classes:

http://www.biomoby.org/twiki/bin//view/General/MOBYJavaClient

and

http://www.biomoby.org/twiki/bin//view/General/ServiceInvocationjMOBY

Hopefully this will help!

>
> I'm trying to get your method running but am having some trouble 
> creating the mobyInputData for my request.  Running with Martin's 
> method I built the query object directly as a string of xml as shown 
> below. I've been trying to create a MobyData instance, but am getting 
> a bit lost.    What is the best procedure for creating a useful 
> MobyData object ?





From willy_valdivia at orionbiosciences.com  Thu May 20 12:22:47 2004
From: willy_valdivia at orionbiosciences.com (Willy Valdivia-Granda)
Date: Thu, 20 May 2004 09:22:47 -0700
Subject: [MOBY-l] New MOBY application: "BioGraphNet: a distributed forum
	for heterogeneous biological networks"
Message-ID: <20040520162247.16792.qmail@webmail07.mesa1.secureserver.net>



From bmg at sfu.ca  Fri May 21 00:06:06 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Fri, 21 May 2004 12:06:06 +0800
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40ACDA7C.7000000@cbr.nrc.ca>
References: <40A9B67E.9080001@sfu.ca>
	<40AA1098.7060205@cbr.nrc.ca>	<40AC2C81.6090108@sfu.ca>
	<40ACDA7C.7000000@cbr.nrc.ca>
Message-ID: <40AD802E.1090502@sfu.ca>

Thanks, your example was very helpful.  I have two questions now,

1)  Why do I keep getting this message and is there a way to stop it?
- No returnType was specified to the Call object!  You must call 
setReturnType() if you have called addParameter().
2) How do I specify a query object for a Moby object such as 
genericSequence?
For example,
<moby:Simple moby:articleName=''>
         <moby:GenericSequence namespace='' id=''>
                    <moby:String namespace='' id='' 
articleName='SequenceString'>ATATATATATATATATA</moby:String>
         </moby:GenericSequence>
 </moby:Simple>

I've tried to start building it like this

        MobyDataType the_type = new MobyDataType("");
        the_type = central.getDataType("GenericSequence");
        System.out.println(the_type.toString());       
        MobyDataSimpleInstance mobySimpleInstance = new 
MobyDataSimpleInstance(the_type,"","");

but it is not working as I would expect.  I would think at this point I 
would have an empty genericSequence object, but when I get he XML at 
this point it doesn't know anything about being a Sequence.

<Simple xmlns="http://www.biomoby.org/moby" 
xmlns:moby="http://www.biomoby.org/moby" moby:articleName=""><Object 
namespace="" id=""/></Simple>

Is it necessary to create a DOM object for the instantiation?  (What is 
the best way to do that :) ?)

thanks
-Ben

ps.  I'm trying to a build a nice clean implementation because its going 
to form the guts of a bunch of applications..



Paul Gordon wrote:

> I've created two TWiki documents to explain the usage and interaction 
> of the jMOBY classes:
>
> http://www.biomoby.org/twiki/bin//view/General/MOBYJavaClient
>
> and
>
> http://www.biomoby.org/twiki/bin//view/General/ServiceInvocationjMOBY
>
> Hopefully this will help!
>
>>
>> I'm trying to get your method running but am having some trouble 
>> creating the mobyInputData for my request.  Running with Martin's 
>> method I built the query object directly as a string of xml as shown 
>> below. I've been trying to create a MobyData instance, but am getting 
>> a bit lost.    What is the best procedure for creating a useful 
>> MobyData object ?
>
>
>
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>




From bmg at sfu.ca  Fri May 21 04:11:18 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Fri, 21 May 2004 16:11:18 +0800
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AD802E.1090502@sfu.ca>
References: <40A9B67E.9080001@sfu.ca>	<40AA1098.7060205@cbr.nrc.ca>	<40AC2C81.6090108@sfu.ca>	<40ACDA7C.7000000@cbr.nrc.ca>
	<40AD802E.1090502@sfu.ca>
Message-ID: <40ADB9A6.9080803@sfu.ca>

In response to my own question regarding building a GenericSequence 
query object, the following bit of code does the job but I feel like I'm 
missing something.  

        MobyDataType the_type = new MobyDataType("");
        the_type = central.getDataType("GenericSequence");
        String seq_object =    "<moby:GenericSequence namespace='' id=''>"+
            "<moby:String namespace='' id='' 
articleName='SequenceString'>"+query+"</moby:String>"+
            "</moby:GenericSequence>";
        MobyDataSimpleInstance mobySimpleInstance = new 
MobyDataSimpleInstance(the_type,"","");
        mobySimpleInstance.setValue(seq_object);       

It looks like the only alternative is to build the object as a DOM, but 
not being familiar with DOM building this seems like more trouble than 
its worth.  Please, show me the path to enlightenment and intelligent 
creation of moby objects in Java.

-Ben




Benjamin Good wrote:

> Thanks, your example was very helpful.  I have two questions now,
>
> 1)  Why do I keep getting this message and is there a way to stop it?
> - No returnType was specified to the Call object!  You must call 
> setReturnType() if you have called addParameter().
> 2) How do I specify a query object for a Moby object such as 
> genericSequence?
> For example,
> <moby:Simple moby:articleName=''>
>         <moby:GenericSequence namespace='' id=''>
>                    <moby:String namespace='' id='' 
> articleName='SequenceString'>ATATATATATATATATA</moby:String>
>         </moby:GenericSequence>
> </moby:Simple>
>
> I've tried to start building it like this
>
>        MobyDataType the_type = new MobyDataType("");
>        the_type = central.getDataType("GenericSequence");
>        System.out.println(the_type.toString());              
> MobyDataSimpleInstance mobySimpleInstance = new 
> MobyDataSimpleInstance(the_type,"","");
>
> but it is not working as I would expect.  I would think at this point 
> I would have an empty genericSequence object, but when I get he XML at 
> this point it doesn't know anything about being a Sequence.
>
> <Simple xmlns="http://www.biomoby.org/moby" 
> xmlns:moby="http://www.biomoby.org/moby" moby:articleName=""><Object 
> namespace="" id=""/></Simple>
>
> Is it necessary to create a DOM object for the instantiation?  (What 
> is the best way to do that :) ?)
>
> thanks
> -Ben
>
> ps.  I'm trying to a build a nice clean implementation because its 
> going to form the guts of a bunch of applications..
>
>
>
> Paul Gordon wrote:
>
>> I've created two TWiki documents to explain the usage and interaction 
>> of the jMOBY classes:
>>
>> http://www.biomoby.org/twiki/bin//view/General/MOBYJavaClient
>>
>> and
>>
>> http://www.biomoby.org/twiki/bin//view/General/ServiceInvocationjMOBY
>>
>> Hopefully this will help!
>>
>>>
>>> I'm trying to get your method running but am having some trouble 
>>> creating the mobyInputData for my request.  Running with Martin's 
>>> method I built the query object directly as a string of xml as shown 
>>> below. I've been trying to create a MobyData instance, but am 
>>> getting a bit lost.    What is the best procedure for creating a 
>>> useful MobyData object ?
>>
>>
>>
>>
>>
>> _______________________________________________
>> moby-l mailing list
>> moby-l at biomoby.org
>> http://biomoby.org/mailman/listinfo/moby-l
>>
>>
>
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>




From gordonp at cbr.nrc.ca  Fri May 21 10:12:48 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Fri, 21 May 2004 08:12:48 -0600
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40ADB9A6.9080803@sfu.ca>
References: <40A9B67E.9080001@sfu.ca>	<40AA1098.7060205@cbr.nrc.ca>	<40AC2C81.6090108@sfu.ca>	<40ACDA7C.7000000@cbr.nrc.ca>
	<40AD802E.1090502@sfu.ca> <40ADB9A6.9080803@sfu.ca>
Message-ID: <40AE0E60.5030605@cbr.nrc.ca>


> In response to my own question regarding building a GenericSequence 
> query object, the following bit of code does the job but I feel like 
> I'm missing something. 
>        MobyDataType the_type = new MobyDataType("");
>        the_type = central.getDataType("GenericSequence");
>        String seq_object =    "<moby:GenericSequence namespace='' 
> id=''>"+
>            "<moby:String namespace='' id='' 
> articleName='SequenceString'>"+query+"</moby:String>"+
>            "</moby:GenericSequence>";
>        MobyDataSimpleInstance mobySimpleInstance = new 
> MobyDataSimpleInstance(the_type,"","");
>        mobySimpleInstance.setValue(seq_object);      
> It looks like the only alternative is to build the object as a DOM, 
> but not being familiar with DOM building this seems like more trouble 
> than its worth.  Please, show me the path to enlightenment and 
> intelligent creation of moby objects in Java.

This is indeed the way to build the object, as per the comments in my 
example class. I was hoping that by making direct string XML input 
inconvenient, people would pay more attention to making sure the 
declared data type and XML corresponded, and were correct.  The fact 
that you can't build an instance directly from a string is explicitly 
stated in the javadocs, you have to call setValue().  But if you really 
want to add a constructor with an extra argument you can, it's open 
source.  Even better, someone could make setValue() parse the XML string 
and check it against the Moby Object ontology for validity :-)

There is a error in your XML: according to 
http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects , GenericSequence is 
a subclass of VirtualSequence, which hasa Integer(Length).  So you 
should also have in the encapsulating GenericSequence a tag like

<moby:Integer moby:namespace="" moby:id="" ></moby:Integer>

This brings up a new issue though that requires a policy formulation on 
the part of the community:  Suppose VirtualSequence had two Integer 
members, how would these be distinguished in the XML (i..e the Length 
field vs. the foo field)?  There are no examples in the 0.7 API 
distinguishing object members by name.  Should we not make articleName a 
required attribute when there is more than one component to an object?

Once we've resolved this, I'll make the automatic creation of XML for 
primitives part of the MobyDataSimpleInstance (like base Object creation 
is now), so creating more complicated objects is just a question of 
collating other instance of the same class.  This should avoid a lot of 
the query formulation issues, as you'll never be inputting XML directly 
(unless of course your object is a subclass of the text-xml object).





From senger at ebi.ac.uk  Fri May 21 10:24:03 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Fri, 21 May 2004 15:24:03 +0100 (BST)
Subject: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AE0E60.5030605@cbr.nrc.ca>
Message-ID: <Pine.LNX.4.44.0405211520500.3173-100000@bagheera.ebi.ac.uk>

> This brings up a new issue though that requires a policy formulation on 
> the part of the community:  Suppose VirtualSequence had two Integer 
> members, how would these be distinguished in the XML (i..e the Length 
> field vs. the foo field)?
>
   Articles can be named. The API says: "Articles are, optionally, named 
using the articleName attribute. This might be used if, for example, the 
service requires named inputs. The order of non-named articles in a single 
Input or Output set MUST not be meaningful.".
   Mark, is this correct answer? I am still not sure about calling 
services :-(

   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  Fri May 21 11:38:41 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 21 May 2004 08:38:41 -0700
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <Pine.LNX.4.44.0405211520500.3173-100000@bagheera.ebi.ac.uk>
References: <Pine.LNX.4.44.0405211520500.3173-100000@bagheera.ebi.ac.uk>
Message-ID: <1085153921.9874.7.camel@myhost.mydomain>

Martin is 100% correct.  In fact, the articleName attributes of
sub-objects really defines an ontology of their own, with the
articleName being the "relationship predicate" linking the sub-object to
its parent object.

M


On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
> > This brings up a new issue though that requires a policy formulation on 
> > the part of the community:  Suppose VirtualSequence had two Integer 
> > members, how would these be distinguished in the XML (i..e the Length 
> > field vs. the foo field)?
> >
>    Articles can be named. The API says: "Articles are, optionally, named 
> using the articleName attribute. This might be used if, for example, the 
> service requires named inputs. The order of non-named articles in a single 
> Input or Output set MUST not be meaningful.".
>    Mark, is this correct answer? I am still not sure about calling 
> services :-(
> 
>    Martin
-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre


From gordonp at cbr.nrc.ca  Fri May 21 12:20:15 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Fri, 21 May 2004 10:20:15 -0600
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <1085153921.9874.7.camel@myhost.mydomain>
References: <Pine.LNX.4.44.0405211520500.3173-100000@bagheera.ebi.ac.uk>
	<1085153921.9874.7.camel@myhost.mydomain>
Message-ID: <40AE2C3F.6000007@cbr.nrc.ca>

Then perhaps we should have some examples of that in the API (i.e. data 
*instances* with articleName attributes)?  Under the MOBY Data Class 
Ontology section, none of the examples have articleNames, even though 
the GO objects contain several sibling String elements... or am I 
missing something?


Mark Wilkinson wrote:

>Martin is 100% correct.  In fact, the articleName attributes of
>sub-objects really defines an ontology of their own, with the
>articleName being the "relationship predicate" linking the sub-object to
>its parent object.
>
>M
>
>
>On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
>  
>
>>>This brings up a new issue though that requires a policy formulation on 
>>>the part of the community:  Suppose VirtualSequence had two Integer 
>>>members, how would these be distinguished in the XML (i..e the Length 
>>>field vs. the foo field)?
>>>
>>>      
>>>
>>   Articles can be named. The API says: "Articles are, optionally, named 
>>using the articleName attribute. This might be used if, for example, the 
>>service requires named inputs. The order of non-named articles in a single 
>>Input or Output set MUST not be meaningful.".
>>   Mark, is this correct answer? I am still not sure about calling 
>>services :-(
>>
>>   Martin
>>    
>>




From mwilkinson at mobile.rogers.com  Fri May 21 12:20:26 2004
From: mwilkinson at mobile.rogers.com (mwilkinson)
Date: Fri, 21 May 2004 12:20:26 -0400
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
Message-ID: <200405211626.i4LGQsKr015549@portal.open-bio.org>

Point me to what you are looking at.
-----Original Message-----
From: Paul Gordon <gordonp at cbr.nrc.ca>
Date: Fri, 21 May 2004 10:20:15 
To:mobyl <moby-l at biomoby.org>
Subject: Re: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?

Then perhaps we should have some examples of that in the API (i.e. data 
*instances* with articleName attributes)?  Under the MOBY Data Class 
Ontology section, none of the examples have articleNames, even though 
the GO objects contain several sibling String elements... or am I 
missing something?


Mark Wilkinson wrote:

>Martin is 100% correct.  In fact, the articleName attributes of
>sub-objects really defines an ontology of their own, with the
>articleName being the "relationship predicate" linking the sub-object to
>its parent object.
>
>M
>
>
>On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
>  
>
>>>This brings up a new issue though that requires a policy formulation on 
>>>the part of the community:  Suppose VirtualSequence had two Integer 
>>>members, how would these be distinguished in the XML (i..e the Length 
>>>field vs. the foo field)?
>>>
>>>      
>>>
>>   Articles can be named. The API says: "Articles are, optionally, named 
>>using the articleName attribute. This might be used if, for example, the 
>>service requires named inputs. The order of non-named articles in a single 
>>Input or Output set MUST not be meaningful.".
>>   Mark, is this correct answer? I am still not sure about calling 
>>services :-(
>>
>>   Martin
>>    
>>


_______________________________________________
moby-l mailing list
moby-l at biomoby.org
http://biomoby.org/mailman/listinfo/moby-l

!!!!!!!!!!!!!!!!
To respond to this message you MUST send your response to (note new address!)

markw_mobile2 at illuminae dot com

Responses to the reply-to address go directly to trash!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!


From gordonp at cbr.nrc.ca  Fri May 21 12:39:40 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Fri, 21 May 2004 10:39:40 -0600
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <200405211623.i4LGNN62007555@furry.cbr.nrc.ca>
References: <200405211623.i4LGNN62007555@furry.cbr.nrc.ca>
Message-ID: <40AE30CC.5040701@cbr.nrc.ca>

mwilkinson wrote:

>Point me to what you are looking at.
>
The GO_Term example looks like:

<GO_Term namespace="GO/Acc" id="GO:0005575">
  <String namespace="" id="">cellular component</String>
  <String namespace="" id=""> That fraction of cells, prepared by 
disruptive biochemical
      methods, that includes the plasma and other membranes.</String>
</GO_Term>

Should probably look something like:

<GO_Term namespace="GO/Acc" id="GO:0005575">
  <String namespace="" id="" articleName="Term">cellular component</String>
  <String namespace="" id="" articleName="Definition"> That fraction of 
cells, prepared by disruptive biochemical
      methods, that includes the plasma and other membranes.</String>
</GO_Term>

My CDN $0.02 :-)

>-----Original Message-----
>From: Paul Gordon <gordonp at cbr.nrc.ca>
>Date: Fri, 21 May 2004 10:20:15 
>To:mobyl <moby-l at biomoby.org>
>Subject: Re: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
>
>Then perhaps we should have some examples of that in the API (i.e. data 
>*instances* with articleName attributes)?  Under the MOBY Data Class 
>Ontology section, none of the examples have articleNames, even though 
>the GO objects contain several sibling String elements... or am I 
>missing something?
>
>
>Mark Wilkinson wrote:
>
>  
>
>>Martin is 100% correct.  In fact, the articleName attributes of
>>sub-objects really defines an ontology of their own, with the
>>articleName being the "relationship predicate" linking the sub-object to
>>its parent object.
>>
>>M
>>
>>
>>On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
>> 
>>
>>    
>>
>>>>This brings up a new issue though that requires a policy formulation on 
>>>>the part of the community:  Suppose VirtualSequence had two Integer 
>>>>members, how would these be distinguished in the XML (i..e the Length 
>>>>field vs. the foo field)?
>>>>
>>>>     
>>>>
>>>>        
>>>>
>>>  Articles can be named. The API says: "Articles are, optionally, named 
>>>using the articleName attribute. This might be used if, for example, the 
>>>service requires named inputs. The order of non-named articles in a single 
>>>Input or Output set MUST not be meaningful.".
>>>  Mark, is this correct answer? I am still not sure about calling 
>>>services :-(
>>>
>>>  Martin
>>>   
>>>
>>>      
>>>
>
>
>_______________________________________________
>moby-l mailing list
>moby-l at biomoby.org
>http://biomoby.org/mailman/listinfo/moby-l
>
>!!!!!!!!!!!!!!!!
>To respond to this message you MUST send your response to (note new address!)
>
>markw_mobile2 at illuminae dot com
>
>Responses to the reply-to address go directly to trash!
>!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>
>  
>




From markw at illuminae.com  Fri May 21 13:47:49 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 21 May 2004 10:47:49 -0700
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AE30CC.5040701@cbr.nrc.ca>
References: <200405211623.i4LGNN62007555@furry.cbr.nrc.ca>
	<40AE30CC.5040701@cbr.nrc.ca>
Message-ID: <1085161668.10201.6.camel@myhost.mydomain>

Well would you believe it - nobody has ever noticed that before (or at
least, never mentioned it)!

I'll fix that as soon as I can!  It should be exactly as you say.

my bad...

M



On Fri, 2004-05-21 at 09:39, Paul Gordon wrote:
> mwilkinson wrote:
> 
> >Point me to what you are looking at.
> >
> The GO_Term example looks like:
> 
> <GO_Term namespace="GO/Acc" id="GO:0005575">
>   <String namespace="" id="">cellular component</String>
>   <String namespace="" id=""> That fraction of cells, prepared by 
> disruptive biochemical
>       methods, that includes the plasma and other membranes.</String>
> </GO_Term>
> 
> Should probably look something like:
> 
> <GO_Term namespace="GO/Acc" id="GO:0005575">
>   <String namespace="" id="" articleName="Term">cellular component</String>
>   <String namespace="" id="" articleName="Definition"> That fraction of 
> cells, prepared by disruptive biochemical
>       methods, that includes the plasma and other membranes.</String>
> </GO_Term>
> 
> My CDN $0.02 :-)
> 
> >-----Original Message-----
> >From: Paul Gordon <gordonp at cbr.nrc.ca>
> >Date: Fri, 21 May 2004 10:20:15 
> >To:mobyl <moby-l at biomoby.org>
> >Subject: Re: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
> >
> >Then perhaps we should have some examples of that in the API (i.e. data 
> >*instances* with articleName attributes)?  Under the MOBY Data Class 
> >Ontology section, none of the examples have articleNames, even though 
> >the GO objects contain several sibling String elements... or am I 
> >missing something?
> >
> >
> >Mark Wilkinson wrote:
> >
> >  
> >
> >>Martin is 100% correct.  In fact, the articleName attributes of
> >>sub-objects really defines an ontology of their own, with the
> >>articleName being the "relationship predicate" linking the sub-object to
> >>its parent object.
> >>
> >>M
> >>
> >>
> >>On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
> >> 
> >>
> >>    
> >>
> >>>>This brings up a new issue though that requires a policy formulation on 
> >>>>the part of the community:  Suppose VirtualSequence had two Integer 
> >>>>members, how would these be distinguished in the XML (i..e the Length 
> >>>>field vs. the foo field)?
> >>>>
> >>>>     
> >>>>
> >>>>        
> >>>>
> >>>  Articles can be named. The API says: "Articles are, optionally, named 
> >>>using the articleName attribute. This might be used if, for example, the 
> >>>service requires named inputs. The order of non-named articles in a single 
> >>>Input or Output set MUST not be meaningful.".
> >>>  Mark, is this correct answer? I am still not sure about calling 
> >>>services :-(
> >>>
> >>>  Martin
> >>>   
> >>>
> >>>      
> >>>
> >
> >
> >_______________________________________________
> >moby-l mailing list
> >moby-l at biomoby.org
> >http://biomoby.org/mailman/listinfo/moby-l
> >
> >!!!!!!!!!!!!!!!!
> >To respond to this message you MUST send your response to (note new address!)
> >
> >markw_mobile2 at illuminae dot com
> >
> >Responses to the reply-to address go directly to trash!
> >!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> >
> >  
> >
> 
> 
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre


From VNarayan at mail.brc.mcw.edu  Fri May 21 12:58:18 2004
From: VNarayan at mail.brc.mcw.edu (Vijay Narayanasamy)
Date: Fri, 21 May 2004 11:58:18 -0500
Subject: [MOBY-l] New MOBY application: "BioGraphNet: a distributed fo
	rum for heterogeneous biological networks"
Message-ID: <295CC5EB4257D411B34D00D0B7748F4432E02F@baldar.brc.mcw.edu>

Hi Frank,

If you are interested in Java Graphlayout Applet look at the following links
http://java.sun.com/applets/jdk/1.0/demo/GraphLayout/

Several groups have modified this program to suit their needs.

A modified version for my application TransMiner
(http://www.bisti.nih.gov/2003meeting/Abstracts/III45.pdf) can be found at

http://sifter.cs.iupui.edu/~sifter/transMiner/BCTrans1.html 

Let me know if you are interested in this Graphlayout applet.

Cheers,

Vijay


-----Original Message-----
From: Simon Twigger [mailto:simont at mcw.edu] 
Sent: Thursday, May 20, 2004 11:01 AM
To: Frank Gibbons
Cc: 'moby-l at biomoby.org'; vnarayan at mcw.edu
Subject: Re: [MOBY-l] New MOBY application: "BioGraphNet: a distributed
forum for heterogeneous biological networks"

Hi Frank,

This looks very nice - is it possible to view the graph data into 
something like a java graph-viewing applet so people could zoom in and 
select things, etc? The image that comes back is nice but too small to 
see anything. Im cc'ing this to Vijay Narayanasamy in my group as he 
has built tools like this that display interaction data using this type 
of applet and he might be able to offer some suggestions and show you 
what he has done previously so you can see if it would be of use.

I wonder if it would be worth coloring the genes (grey elipses) as well 
as the lines connecting the genes? It might give a better overview of 
the types of interacting partners if they were colored light green, 
light pink, etc. rather than all being grey.

I'd be interested in getting you some rat data, we're working on some 
rat services here so perhaps we can chat more about that and see what 
makes sense. I'd love to see the tools you have for making text files 
available - I've done similar stuff myself but its not very generic, if 
you have something like that we can certainly make use of it.

I have to run to a meeting but will probably write some more later on.

Cheers,

	Simon.


On May 20, 2004, at 10:23 AM, Frank Gibbons wrote:

> Hey fellow MOBYers,
>
> Below is an abstract I've submitted for BOSC (Bioinformatics Open 
> Source Conference) and BioPathways, satellite conferences of ISMC/ECCB 
> in Glasgow, Scotland this year. BioGraphNet is our 'sandbox' within 
> the BioMOBY 'playground', in which we're looking at ways to share and 
> view biological networks.
>
> At this point, Gabriel Berriz and I have a working prototype: a 
> registered object for describing fairly generic pairwise interactions, 
> half a dozen working services, and an application that runs in a 
> web-browser to allow end-users to play with the interaction data. A 
> key element of this is that anyone can make their data available at 
> any time, and it will be discovered and included in the webpage 
> displayed to users (bench biologists). There's no installation, no 
> updating of databases. I'd appreciate your giving it a try 
> (http://llama.med.harvard.edu/cgi/BioTrawler) and letting us know what 
> you think. We're looking for feedback on a number of levels:
>
> * Does the overall idea, (being able to view an interactive graphical 
> display of your chosen data sources for your favorite genes), seem 
> useful to you? What pitfalls do you see in the near or distant future?
> * So far we've got correlated expression, synthetic lethality, 
> homology, transcription-factor/target (known and predicted), as well 
> as experimental protein-protein interaction results. What kinds of 
> data would make it more useful?
> * Do you have some data you'd like to share? We've developed tools to 
> facilitate making data available as a MOBY service: drop a text file 
> in the right place, enter the textual description of your service - 
> BOOM, it's registered and available to the world. One goal of this 
> project is to make it easy for people with data to put it out there.
> * Anything else that strikes you....
>
> We're really keen to get input on this, just reply to me: 
> mailto:fgibbons at hms.harvard.edu
>
> I'm looking forward to seeing some of you again in Glasgow!
>
> -Frank Gibbons
>
> --------------------------------------- ABSTRACT 
> ---------------------------------------
>
> TITLE: BioGraphNet, a distributed forum for heterogeneous biological 
> networks.
> AUTHORS: Francis D. Gibbons, Gabriel F. Berriz, and Frederick P. Roth
> Dept. of Biological Chemistry and Molecular Pharmacology, 250 Longwood 
> Ave., Harvard Medical School, Boston MA 02115, USA
>
> ABSTRACT:
> Biological network information is increasingly abundant.  The 
> combination of biological networks may be viewed as a multicolor 
> graph, with each color representing a different gene-gene or 
> protein-protein relationship, e.g., protein interaction, sequence 
> homology, correlated expression, transcriptional regulation, genetic 
> interaction (sensu synthetic lethality), or metabolic relationship.  
> Relationship types may be further stratified by type of evidence 
> supporting the relationship, by directionality or by confidence 
> measure.  Furthermore, each organism has its own collection of 
> networks.  Although this information's complexity argues for its 
> maintenance by distributed groups, much of its value is derived 
> through network integration.
>
> BioMOBY has established a 'playground' for distributed services.  We 
> have developed a 'sandbox' within BioMOBY called BioGraphNet.  
> BioGraphNet is a common standard and collection of services for 
> sharing distributed network information.  We now serve several network 
> data types, and encourage others to participate, using the common 
> standard objects we have registered in BioMOBY's ontology.
>
> As an example application illustrating the use of BioGraphNet, we 
> provide BioTrawler, a web-based biological network browser that 
> dynamically discovers suitable distributed data sources within 
> BioGraphNet, integrates those selected by the end-user 'just in time', 
> and visualizes the graph neighboring a user-defined set of genes. 
> Graph layout is handled by the open-source GraphViz package (modified 
> to handle multiple edges between a pair of nodes). BioTrawler also 
> exports graph representations in several commonly used formats (GIF by 
> default, but also Pajek, Cytoscape, and PDF).
>
> The combination of BioMOBY and BioGraphNet represents a distributed 
> network annotation system analogous to the Distributed Annotation 
> System (DAS) for sharing genome annotation.
>
> LICENSING:
> The object descriptions and service interfaces are already available 
> to all BioMOBY users. We plan to release BioTrawler under the Artistic 
> License.
>
> URL: http://llama.med.harvard.edu/cgi/BioTrawler
>
>
> PhD, Computational Biologist,
> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 
> 02115, USA.
> Tel: 617-432-3555       Fax: 617-432-3557       
> http://llama.med.harvard.edu/~fgibbons
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>
--

Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw


From 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-l] 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  Fri May 21 18:10:08 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 21 May 2004 15:10:08 -0700
Subject: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
In-Reply-To: <40AE30CC.5040701@cbr.nrc.ca>
References: <200405211623.i4LGNN62007555@furry.cbr.nrc.ca>
	<40AE30CC.5040701@cbr.nrc.ca>
Message-ID: <1085177408.10201.21.camel@myhost.mydomain>

Fixed.

On Fri, 2004-05-21 at 09:39, Paul Gordon wrote:
> mwilkinson wrote:
> 
> >Point me to what you are looking at.
> >
> The GO_Term example looks like:
> 
> <GO_Term namespace="GO/Acc" id="GO:0005575">
>   <String namespace="" id="">cellular component</String>
>   <String namespace="" id=""> That fraction of cells, prepared by 
> disruptive biochemical
>       methods, that includes the plasma and other membranes.</String>
> </GO_Term>
> 
> Should probably look something like:
> 
> <GO_Term namespace="GO/Acc" id="GO:0005575">
>   <String namespace="" id="" articleName="Term">cellular component</String>
>   <String namespace="" id="" articleName="Definition"> That fraction of 
> cells, prepared by disruptive biochemical
>       methods, that includes the plasma and other membranes.</String>
> </GO_Term>
> 
> My CDN $0.02 :-)
> 
> >-----Original Message-----
> >From: Paul Gordon <gordonp at cbr.nrc.ca>
> >Date: Fri, 21 May 2004 10:20:15 
> >To:mobyl <moby-l at biomoby.org>
> >Subject: Re: [MOBY] Re: [MOBY-l] MobyRequest or CentralImpl ?
> >
> >Then perhaps we should have some examples of that in the API (i.e. data 
> >*instances* with articleName attributes)?  Under the MOBY Data Class 
> >Ontology section, none of the examples have articleNames, even though 
> >the GO objects contain several sibling String elements... or am I 
> >missing something?
> >
> >
> >Mark Wilkinson wrote:
> >
> >  
> >
> >>Martin is 100% correct.  In fact, the articleName attributes of
> >>sub-objects really defines an ontology of their own, with the
> >>articleName being the "relationship predicate" linking the sub-object to
> >>its parent object.
> >>
> >>M
> >>
> >>
> >>On Fri, 2004-05-21 at 07:24, Martin Senger wrote:
> >> 
> >>
> >>    
> >>
> >>>>This brings up a new issue though that requires a policy formulation on 
> >>>>the part of the community:  Suppose VirtualSequence had two Integer 
> >>>>members, how would these be distinguished in the XML (i..e the Length 
> >>>>field vs. the foo field)?
> >>>>
> >>>>     
> >>>>
> >>>>        
> >>>>
> >>>  Articles can be named. The API says: "Articles are, optionally, named 
> >>>using the articleName attribute. This might be used if, for example, the 
> >>>service requires named inputs. The order of non-named articles in a single 
> >>>Input or Output set MUST not be meaningful.".
> >>>  Mark, is this correct answer? I am still not sure about calling 
> >>>services :-(
> >>>
> >>>  Martin
> >>>   
> >>>
> >>>      
> >>>
> >
> >
> >_______________________________________________
> >moby-l mailing list
> >moby-l at biomoby.org
> >http://biomoby.org/mailman/listinfo/moby-l
> >
> >!!!!!!!!!!!!!!!!
> >To respond to this message you MUST send your response to (note new address!)
> >
> >markw_mobile2 at illuminae dot com
> >
> >Responses to the reply-to address go directly to trash!
> >!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> >
> >  
> >
> 
> 
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre


From barbara.re at studenti.unicam.it  Mon May 24 13:07:07 2004
From: barbara.re at studenti.unicam.it (RE BARBARA)
Date: Mon, 24 May 2004 19:07:07 +0200
Subject: [MOBY-l] Request about ontologi
Message-ID: <1085418427.40b22bbbcb942@mail.studenti.unicam.it>



Hi!

we have installed in local the moby central and after some interrogations in 
perl I esteem there interesting in the ontological part. 
 
We have read the whole material found in the directory /moby-live/docs but we 
have not understood as biomoby it interacts with these ontologies. 
 
Do you have some information in respect? 

Do you know how to interact with the ontologies? 

Do you have some documentation in respect? 

thanks very much!

BACHI



From bmg at sfu.ca  Tue May 25 06:55:46 2004
From: bmg at sfu.ca (Benjamin Good)
Date: Tue, 25 May 2004 18:55:46 +0800
Subject: [MOBY-l] java xml parsing
Message-ID: <40B32632.2060908@sfu.ca>

Say I have a Query response like this

"<?xml version='1.0' encoding='UTF-8'?>"+
        "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' 
xmlns='http://www.biomoby.org/moby'>"+
        "<moby:mobyContent 
moby:authority='illuminae.com'><moby:serviceNotes>This is provided by 
SeqHound</moby:serviceNotes>"+
                "<moby:mobyData moby:queryID='1'>"+
                    "<moby:Simple moby:articleName=''>" +
                    "<genbank-flatfile namespace='NCBI_gi' 
id='111076'><![CDATA[LOCUS D31461 32 aa linear   ROD 30-MAY-1997"+
        "DEFINITION  T-cell receptor delta chain BDN7, thymus - mouse 
(fragment)."+
        "ACCESSION   D31461"+
        "PID         g111076"+
        "ORIGIN"+
         "       1 atyfcalmer vsrrgapdkl vfgqgtqvtv ep"+
        "//]]></genbank-flatfile></moby:Simple>"+
                "</moby:mobyData>"+
                "</moby:mobyContent></moby:MOBY>";       

Any suggestions regarding the best way to extract the gi id or the CDATA 
?  It seems there are many options, just wondering if the Java group has 
already settled on an approach.

thanks
-Ben



From gordonp at cbr.nrc.ca  Tue May 25 10:45:41 2004
From: gordonp at cbr.nrc.ca (Paul Gordon)
Date: Tue, 25 May 2004 08:45:41 -0600
Subject: [MOBY-l] java xml parsing
In-Reply-To: <40B32632.2060908@sfu.ca>
References: <40B32632.2060908@sfu.ca>
Message-ID: <40B35C15.8080006@cbr.nrc.ca>

If you are using MobyRequest, the getOutput will return a Vector with 
one element (corresponding to the one response).  This element is a 
MobySimpleDataInstance array of length one.  The MobySimpleDataInstance 
will just contain the genbank-flatfile tag and its nested contents.  
Unfortunately, for now this is as far as the autoparsing goes.  
Hopefully soon
MobySimpleDataInstance will soon give you its constituent members as 
other MobySimpleDataInstances, down to the primitives of the ontology. 

But for now, you can parse the XML response in an XML parser (determined 
by Java using the runtime libraries available) and run an XPath.  I 
haven't tried to compile the following code, but it should give you an 
idea of how to parse robustly (given that your XML object 
genbank-flatfile is not attributed to the MOBY namespace):

import javax.xml.parsers.*;
import org.w3c.dom.*;
import org.apache.xpath.XPathAPI; // xpath statement execution env

try{
  // Insert your code to get the XML string

  // Get a parser and parse the document
 DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
 DocumentBuilder docBuilder = dbf.newDocumentBuilder();
 Document document=docBuilder.parse(new 
java.io.StringBufferInputStream(xmlString));
 Element mobyPayload = document.getDocumentElement();

  // Now run the XPath statement that will be used fetch data from the 
server response   
  Node idAttr = XPathAPI.selectSingleNode(mobyPayload, 
"//genbank-flatfile/@id");
  if(idAttr != null){
        System.out.println("Output of XPath was " + idAttr.getNodeValue());
  }
}
catch(TransformerException te){
  // Insert your favourite death scene here
}
catch(ParserConfigurationException){
  // Ditto
}
catch(org.xml.sax.SAXException saxe){
  // Ditto
}
catch(java.io.IOException ioe){
  //Ditto
}


Benjamin Good wrote:

> Say I have a Query response like this
>
> "<?xml version='1.0' encoding='UTF-8'?>"+
>        "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' 
> xmlns='http://www.biomoby.org/moby'>"+
>        "<moby:mobyContent 
> moby:authority='illuminae.com'><moby:serviceNotes>This is provided by 
> SeqHound</moby:serviceNotes>"+
>                "<moby:mobyData moby:queryID='1'>"+
>                    "<moby:Simple moby:articleName=''>" +
>                    "<genbank-flatfile namespace='NCBI_gi' 
> id='111076'><![CDATA[LOCUS D31461 32 aa linear   ROD 30-MAY-1997"+
>        "DEFINITION  T-cell receptor delta chain BDN7, thymus - mouse 
> (fragment)."+
>        "ACCESSION   D31461"+
>        "PID         g111076"+
>        "ORIGIN"+
>         "       1 atyfcalmer vsrrgapdkl vfgqgtqvtv ep"+
>        "//]]></genbank-flatfile></moby:Simple>"+
>                "</moby:mobyData>"+
>                "</moby:mobyContent></moby:MOBY>";      
> Any suggestions regarding the best way to extract the gi id or the 
> CDATA ?  It seems there are many options, just wondering if the Java 
> group has already settled on an approach.
>
> thanks
> -Ben
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>




From markw at illuminae.com  Wed May 26 12:18:56 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 26 May 2004 09:18:56 -0700
Subject: [MOBY-l] [Fwd: [MISC] [bioped-l] Help me! (fwd)]
Message-ID: <1085588336.7304.11.camel@myhost.mydomain>

-----Forwarded Message-----
> From: Jason Stajich <jason at cgt.duhs.duke.edu>
> To: Mark Wilkinson <markw at illuminae.com>
> Subject: [MISC] [bioped-l] Help me! (fwd)
> Date: Wed, 26 May 2004 09:37:55 -0400
> 
> this went to the wrong list I guess.
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
> ---------- Forwarded message ----------
> Date: Wed, 26 May 2004 15:32:24 +0200
> From: ERCOLI CHIARA <chiara.ercoli at studenti.unicam.it>
> To: bioped-l at open-bio.org
> Subject: [bioped-l] Help me!
> 
> 
> 
> Hi,
> I'm BACHI, I have installed biomoby and I have developed some interrogations
> in perl.
> Besides I have noticed the presence of ontologie in the directory /moby-
> live/Docs but I have not understood their role.
> 
> Do you know how to tell me where and does as biomoby use the ontologies?
> 
> If it uses her, where are they considered?
> 
> Thanks you.
> 
> BACHI
> 
> _______________________________________________
> bioped-l mailing list
> bioped-l at open-bio.org
> http://open-bio.org/mailman/listinfo/bioped-l
-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre


From gberriz at hms.harvard.edu  Wed May 26 09:50:24 2004
From: gberriz at hms.harvard.edu (Gabriel Berriz)
Date: Wed, 26 May 2004 09:50:24 -0400
Subject: [MOBY-l] Namespaces
Message-ID: <5.2.1.1.2.20040526094806.02897fd0@email.med.harvard.edu>

Hi, all.

What's the official list of valid BioMOBY namespaces?

Provisionally I have been referring to 
http://www.geneontology.org/doc/GO.xrf_abbs , but I'm not sure if this is 
actually/exactly what BioMOBY goes by.

Thanks,

Gabriel



From markw at illuminae.com  Wed May 26 13:49:18 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 26 May 2004 10:49:18 -0700
Subject: [MOBY] [MOBY-l] Namespaces
In-Reply-To: <5.2.1.1.2.20040526094806.02897fd0@email.med.harvard.edu>
References: <5.2.1.1.2.20040526094806.02897fd0@email.med.harvard.edu>
Message-ID: <1085593758.7304.16.camel@myhost.mydomain>

Hi Gabriel, 

You can find this by making a call to MOBY::Central->retrieveNamespaces,
or from the following quick-link (ugly... but effective)

http://mobycentral.cbr.nrc.ca/cgi-bin/types/Namespaces

M


On Wed, 2004-05-26 at 06:50, Gabriel Berriz wrote:
> Hi, all.
> 
> What's the official list of valid BioMOBY namespaces?
> 
> Provisionally I have been referring to 
> http://www.geneontology.org/doc/GO.xrf_abbs , but I'm not sure if this is 
> actually/exactly what BioMOBY goes by.
> 
> Thanks,
> 
> Gabriel
> 
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre


From senger at ebi.ac.uk  Fri May 28 06:59:04 2004
From: senger at ebi.ac.uk (Martin Senger)
Date: Fri, 28 May 2004 11:59:04 +0100 (BST)
Subject: [MOBY-l] LSAE - Life Sciences Analysis Engine
In-Reply-To: <1083263157.1632.41.camel@myhost.mydomain>
Message-ID: <Pine.LNX.4.44.0405281149391.28763-100000@bagheera.ebi.ac.uk>

Dear Moby users and developers,
   I am sorry to bother you with a topic that is not directly connected to 
BioMoby - but I hope that it is relevant.
   BioMoby defines its own, very interoperable, standard for the
BioMoby-native web services interface. But:
   1) The BioMoby regitry also includes, at least theoretically now, 
possibility to register other web services, and
   2) The service implementation is up to the service providers - it is
hidden from the outside world, but the LSAE topic I am going to talk about
here, can help with the service implementation (I believe).
   So, that was the rationale why to bother you...

   Now, the LSAE (if you are still reading).
   I have put together (with the De Novo Pharmaceutics) a revised
submission of an OMG spec for the LSAE (Life Sciences Analysis Engine).
With few additional features, it actually carves in stone what we already
have in myGrid (Soaplab).
   This revised submission is due to be considered by OMG in August. But I
have put it together already now because I would like to have as many
comments as I can collect from various communities (BioMoby is a 
significant one for me).
   Therefore, if you have time to look into the spec and give me any 
comments and suggestions, it would be marvelous.

   Last but not least: The spec has two submitters - this cannot be
changed now. But any spec is considered stronger if it has other
organizations as "supporters". The role of a supporter is only that the
name of an institute/company is in the spec - it does not give it any
rights (e.g. to vote on the spec), but neither any responsibility. So if
you consider that your institute could appear as a supporter of this spec,
please let me know and I will be very glad to list it in the spec.

   Now, where you can find it: the documents have been posted to the OMG
server today, so they will appear there later today, or on Monday:
   http://www.omg.org/cgi-bin/doc?lifesci/2004-05-01
   http://www.omg.org/cgi-bin/doc?lifesci/2004-05-02
Before they are available there, I have also put them here:

http://industry.ebi.ac.uk/~senger/storage/lsae/LSAE_AccompaniedFiles.zip
http://industry.ebi.ac.uk/~senger/storage/lsae/LSAE_Revised_submission_1_final.doc

   With best 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 mwilkinson at mrl.ubc.ca  Fri May 28 17:57:26 2004
From: mwilkinson at mrl.ubc.ca (Mark Wilkinson)
Date: Fri, 28 May 2004 14:57:26 -0700
Subject: [MOBY-l] new features in the MOBY browser
Message-ID: <1085781445.12321.102.camel@myhost.mydomain>

Hi all, 

Those of you who are using it will notice some new features in the MOBY
browser.  It is now possible to limit service discovery by service type,
service provider, output type, or keyword.  This helps to clean up the
increasing mass of services that are discovered by default... which I
guess is a sign of success, so we shouldn't bemoan it :-)

I have played with it for a couple of hours and haven't noticed any
obvious bugs, but please let me know if you do.  The code is committed
to the Gbrowse project, if you want to get it for yourself.

Cheers all!  Have a great weekend, 

M
-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre


From markw at illuminae.com  Mon May 31 13:55:27 2004
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon, 31 May 2004 10:55:27 -0700
Subject: [MOBY-l] Attn. all those interested in the Service Ontology
Message-ID: <1086026127.2973.8.camel@myhost.mydomain>

This gem has been floating around the GO-friends mailing list.  If they
have a bioinformatics tools ontology already, we should be using it and
working with them to extend it.  It seems to be at exactly the level of
resolution that we require for our Service Ontology...

M


-----Forwarded Message-----
> From: Michael Ashburner (Genetics) <ma11 at gen.cam.ac.uk>
> 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: [MISC] Re: Draft evidence code ontology
> Date: Mon, 31 May 2004 14:14:07 +0100
> 
> I should also add that I did not take into account this very useful
> email from Steffen Moeller, tho I would like to.
> Michael
> 
> 
> Envelope-to: m.ashburner at gen.cam.ac.uk
> Delivery-date: Mon, 22 Mar 2004 20:48:49 +0000
> Date: Mon, 22 Mar 2004 21:48:38 +0100
> To: m.ashburner at gen.cam.ac.uk
> Subject: Evidence Ontology - Bioinformatics tools suggestion
> Mime-Version: 1.0
> Content-Disposition: inline
> User-Agent: Mutt/1.3.28i
> From: Steffen Moeller <moeller at pzr3.pzr.uni-rostock.de>
> X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/
> X-Cam-AntiVirus: No virus found
> X-Cam-SpamDetails: scanned, SpamAssassin (score=-2.5, USER_AGENT_MUTT -2.49)
> 
> Dear Michael,
> 
> below you find my revised suggestion of an ontology for bioinformatics
> tools. I perceive the world as a combination of known sources of
> information and various methods that may be applied to get to this
> source.
> 
> Difficult are cases when the language does not distinguish between the
> approach and the tool. Taking "Blast" as an example, Blast certainly
> is an algorithm with many flavours (PSI-...). This has
> multiple implementations (NCBI and WU spring to mind). The method is a
> pairwise sequence comparison. The implementation is an application.
> 
> Hope to have helped to some extend. If you consider this usable and you
> want me to fill the gaps then please tell me.
> 
> Many greetings
> 
> Steffen
> 
> * in-silco analysis
>   & source-of-information (part-of)
>     + application (is-a)
>       + sequence-analysis (is-a)
> 	+ sequence-comparison (is-a)
>         + structure-prediction (is-a)
>           + fold-prediction  (is-a)
>   	  + transmembrane-topology prediction (is-a)
> 	    - TMHMM (part-of) is-a hidden markov model
> 	    - HMMTOP (part-of) is-a hidden markov model
> 	    - PHD (part-of) is-a neuronal network
> 	  + contact prediction
>       + structure-comparison (is-a)
>       + interaction-prediction (is-a)
>       + visualisation (is-a)
>     + databases (is-a)
>       + literature (is-a)
>       + sequence database(is-a)
>         + DNA database (is-a)
> 	  + SNP database (is-a)
>         + RNA database (is-a)
>         + protein database (is-a)
>       + databases connecting other databases (is-a)
>         + protein-interaction (is-a)
> 	+ metabolism (is-a)
>         + abstraction (is-a)
>           + Protein Domain database (is-a)
> 	    + PFAM (instance-of)
> 	    + InterPro (instance-of)
> 	    - Prosite (instance-of) is-a Regular expression, is-a Profile
>   & techniques (part-of)
>     + molecular modeling (is-a)
>     + sequence-similarity (is-a)
>       + direct-comparisons (is-a)
>       	+ pairwise (is-a)
> 	  + global
> 	  + local
> 	+ multiple (is-a)
> 	  + global
> 	  + local
>       + abstraction (is-a)
>         + neuronal network (is-a)
>         + hidden markov model (is-a)
> 	+ Profile (is-a)
> 	+ Weight matrix (is-a)
> 	+ Regular expression (is-a)
> 
> 
> --
> This message is from the GOFriends moderated mailing list.  A list of public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: owner-gofriends at geneontology.org
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> Web:          http://www.geneontology.org/
-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre