[MOBY-l] sequence retrieve service active & auto-discovered & auto-executed!!

[Mark Wilkinson]

Okay, all is up and running now :-)

By telling MOBY that you have a GenbankGI number and that you are
looking for a "Retrieve" service it will auto-discover my Test Sequence
Retrieve service.  You tell it to execute and it does so, returning a
MOBY envelope containing sequence object(s).  The one thing it doesn't
do, yet, is to auto-create the objects themselves... this is going to be
a fun job!

So...  the first step is finished!  I think we need to have a serious
look at the object hierarchy as it stands and make some decisions ASAP
about the structure of some of the basic objects.  In particular, get
some GO objects specified, and have some useful way of getting "into"
the GO objects... for example a 'Keyword" namespace:

        <Object  namespace="Keyword"  id="Serine/Threonine Kinase">

Of course, we need to set up more services too.  I also need to document
my code, and change some of it so that it doesn't do bad things in nasty
ways...

In any case, it is an exciting day!  I think I'll blog this on the
website :-)

below is a transcript from a complex_client.pl session:

Cheers all!!

Mark


perl complex_client.pl

This client must begin with base Objects containing only a namesapce and
an ID.
Which namespace do you have in-hand?

0. EMBL/AC : EMBL Accession number
1. GenBank/GI : GenBank GI number

Select number: 1


What is the GenBank/GI ID number you have?

ID=168257


What type of service do you want?

0. tBlastx : Marks Test Blast Service type
1. Service : root object for services
2. Retrieve : Basic retrieve service based on a namespace and id
3. Blast : Marks Test Blast Service type

Select number: 2


Looking for services that use GenBank/GI ID's as input to a Basic
retrieve service based on a namespace and id...Found!
Service 0:  MarksTestSequenceRetrieveService : Authority:
bioinfo.pbi.nrc.ca  -  Retrieves a sequence from our local GenBank
database using the fastacmd function of Blast
Select number: 0
Executing Service: MarksTestSequenceRetrieve
RESULT:

<MOBY AuthURI='http://bioinfo.pbi.nrc.ca'>
   <Sequence namespace='GenBank/GI' id='168257'>
      <Length>5582</Length>

<Sequence>AGCTTCTCTCCGATCTCAGGGAAGAGAAGGGAAGTGGAGGCAGCGAACCCTTGCCCGATCTCAGGGTCCTTTGAGAGGACGAGGATAGAGTATAGTAGTATGTACAGTATGTACAGAATGTACATGGACATACATGGACCATGGACAGCCCGCATCTGGGGAACGGAACCAACAAGGTTATGCTTTGTGAGTGGTTGGCACGTGCCTCGGCAGGGGAGATACTGTCCACAGCTCCCTAGCTCGAGGAAGAAGAAAAGAAGAAAAGAAGAAGCAAAAAACAAATAAGAAACCAGAACCCCCTTGTGCCGTGGATGTGCGGATTGTGGAGATGTGAGATGTGAGATGTGGATGTGTCAGCAGCAGAGAGCAGAAAAATCCCTCGTACGATGTACCATTGTATATCGTACCGTATTGTACTGTCATGTACTGTCCTTGCTATGCCGACGGCCCCGCGCTGGCCAATGGCACGGCCCAAGCGCGGTGGTTGTCAGCAGCGCGCGGATAAACGGTGGTCACTGGGCAGCGCGCTGGGACCGGTACCGAGAGCGATACCGGTACTGTCACGGTATTGGCTGCTGCCACCTGGAAAATTGCGCATACAATCAAACTGGGTCTGCAGCGTGGGGCCCTGTATTGTATTTGTGTATTTTCTCGTTTTCTCGCTGTTTTCCCTCTTTCCCTGCTGTAATTTTCCCCTTCCCTCTCCTCTTATATTCGCTCGCCTCCGCTCTTCTCCTCTGCCCCGACAATCCGTTTTCCTCGCTTCTGCTGGTTTCTTTTTCGTCGTCGTCGTCGTCGTCTCATCTTCTCTTCCTCATCCTCTTCTCTTCATCCTCTTCTTCTCTCTCCCACCCTCATCTTCATCTCAATTCTCCCTCCTCTCCCTCCTCTCTCTCCCCTCTCTCCCCTCTCCCCTCTCCTCTCCGCCATCTGTTTTCGGAGGACCGTTCCAGTCAATTACCACCCCCCCCCCACAATCCCCCTCCCTACCCTCAAAACAGTAGCAGAAGAAGAAGAAGAAGGAAATACTGCTGCTCCATGCTCGCCGTTTGTTCCAGAAGAGACTGAAATAGGTCGGAAATCCACTCCATTCGGTTGCCCTGTTGATTGATATCATATCTTCAAATACACCCATCATCCAGCAAATATCACCCAGAGCAGCAGAATAATGGCACACTCCGCTGCTTCGGGCGCCGCCTCCGCCGCCCACTTCGAGAAGAAGACCCCCGAGGTCGCCCACGAGGAGAAGAAGCCGCCGCTCCCCGAGGAGGAGGATGAGGACGAGGACATGGACGCCCTCATCGAGGAGCTCGAGTCCCAGGATGGCCACATCGACATTGAGGACGACGAAGACGGCGAGCCTGGCGGTGCCCGCCCCGTGCCCGACGAGCTGCTCACCACCGACACGCGCCACGGTCTGACCGATGCCGAAGTCGTCGCCCGCCGCAAGAAGTACGGCCTCAACCAGATGAAGGAGGAGAAGGAAAACCTGGTCTTGAAGTTCCTCAGCTACTTCGTGGGGCCCATCCAGTTCGTCATGGAGGTGAGTGGCGATTCTCCTATTGTTTTATATATATATATATATATATATATATATATATGTGTGTGTGTGTGTGTGTGTTATTGGCATATAAACCTAATTGATTGAAAATAAAAAGGCCGCCGCCATTCTTGCCGCCGGTCTCGAGGACTGGGTCGATTTTGGTGTCATCTGCGCGCTTCTCCTGCTCAACGCCTGTGTCGGGTTCGTCCAGGAATTCCAGGCTGGCTCCATCGTCGACGAATTGAAGAAAACCCTCGCGCTCAAGGCGGTCGTGCTCCGCAATGGCCGTCTGACTGAGGTCGAGGCCCCCGAGGTCGTGCCCGGCGATATCCTCCAGGTCGAGGAGGGCACCATCATCCCCGCTGACGGCCGCATCGTCACCGAAGAGGCCTTCCTGCAAGTCGATCAGTCTGCCATCACCGGTGAGTCGCTGGCCGTCGACAAGCACAAGGGTGATACCTGCTATGCGTCCTCTGCCGTCAAGCGTGGTGAGGC
CTCCGCCGGCACTGGCCATTTCACTGAGGTGCTCAACGGCATTGGCACTGTTTTGCTCATCCTTGTCATCCTCACTCTGCTGGTCGTCTGGGTTTCCTCCTTCTACCGTTCCAACTCCATTGTCACCATTCTCGAGTTCACCCTGGCCATCACCATCATCGGTGTCCCGTCGGTCTCCCCGCGGTCGTGACCACCACCATGGCTGTCGGCGCCGCTTACCTGGCCAAGAAGAAGGCCATTGTCCAGAAACTGTCCGCCATCGAGTCCCTTGCCGGTGTGGAGATCCTCTGCTCCGACAAGACCGGTACTTTGACAAAGAACAAGCTCTCCCTCGCCGAGCCGTACTGCGTTTCTGGCGTTGACCCCGAGGATCTGATGCTGACCGCCTGTCTGGCTGCCTCCCGCAAGAAGAAGGGTATCGATGCCATCGACAAGGCGTTCTTGAAGTCTCTCCGCTACTACCCCCGCGCCAAGTCCGTCCTCACTCAGTACAAGGTCCTCGAGTTCCATCCCTTCGACCCCGTCTCCAAGAAGGTCAGCGCCGTCGTGCTGTCCCCCCAGGGCGAGCGCATTACCTGCGTCAAAGGTGCCCCCCTCTCGGTCCTCAAGACCGTCGAGGAAGACCACCCCATCCCCGACGAAGTCGATAGCGCCTACAAGAACAAAGTCGCCGAGTTCGCAACCCGTGGTTTCCGCTCTCTCGGTGTTGCCCGCAAGCGCGGTGAGGGTTCCTGGGAAATCCTTGGAATCATGCCCTGCTCCGATCCTCCCCGCCACGACACCGCCAAGACCATCAATGAGGCTAAGACGCTCGGTTTGTCCATCAAGATGTTGACCGGTGACGCGGTCGGTATCGCCCGTGAAACTTCTCGCCAGCTCGGTCTCGGAACCAATGTTTACAACGCTGAGCGTCTTGGTCTCGCCGCCGGCGGAACCATGCCTGGCTCGGAGGTGTACGATTTCGTTGAGGCCGCCGATGGTTTCGCGGAGGTTTTCCCCCAGCACAAGTACAACGTCGTCGAGATCCTGCAACAGCGTGGTTACCTCGTCGCCATGACGGGTGACGGTGTCAACGACGCCCCATCCCTCAAGAAGGCCGACACCGGTATCGCCGTCGAGGGTGCCTCCGACGCCGCCCGCTCCGCCGCCGACATCGTCTTCCTCGCCCCCGGTCTCTCTGCCATCATCGACGCGCTCAAGACCTCCCGTCAGATCTTCCACCGCATGTACGCCTACGTCGTCTACCGTATTGCCCTGTCTCTCCACTTGGAAATCTTCCTGGGTCTCTGGATCGCCATTCTCAACACATCCCTCAACCTCCAGCTTGTCGTCTTCATCGCCATCTTCGCTGATATCGCCACCCTCGCCATCGCCTACGACAACGCCCCTTTCTCCAAGACGCCCGTCAAGTGGAACCTGCCCAAGCTATGGGGAATGTCCGTCCTCCTCGGCATCGTCCTCGCCGTCGGCACCTGGATCACCCTCACAACCATGCTCGTCGGTTCCGAGAACGGCGGTATCGTCCAGAACTTCGGTCGAACGCACCCGGTCCTCTTCCTCGAAATCTCCCTGACCGAGAACTGGCTCATCTTCATCACCCGCGCGAACGGGCCCTTTTGGTCCTCGATCCCGTCGTGGCAACTGTCCGGTGCCATCCTGCTCGTCGACATCATCGCCACCTTGTTCACGATCTTCGGTTGGTTCGTGGGTGGGCAGACGTCCATCGTCGCCGTGGTTCGCATTTGGGTTTTCTCGTTTGGCTGCTTCTGCGTCCTTGGTGGACTGTATTATCTGCTCCAAGGCTCGGCGGGCTTTGACAACATGATGCATGGGAAGAGTCCGAAGAAGAATCAGAAACAGAGATCATTGGAGGATTTCGGTAAGCATATCTATCTATCTCTCCTGATTTCAATTTGGCTTTCAACGTTTCAGATAACTATTACATATATACGTAAATGGCTTCATTCTAACCAAAGTCCACTCCGTACTTTACAGTTGTTTCACTCCAACGAGTCTCCACACAACACGAGAAGAGCTCATGATCCGCG
CATCATCCCGCACTTAAAAATAAAAGGAGGATTGGAGGGGAGGATTTGATAATCTTTGTATTTTTTTTTGTGGTTTTCTTTTGTTTCCTGTTCATACTTTTTTTTTTTTTTTTGTCTTTCACTTTTCTTTCCTTTTCTATTTTCTTTTCCAAACCATACACATACATCTTGGTTGGGGGGTTGGGTTTGGTCAATCAGCTGGAACAGGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCACTCCATCTCTTTCTCTGTGTGTCTCTGCCCAGCTTGTATCCGTGTGGAGGCAATTTTGAATATGCAGGGACAAGAAAGATGGATGCTGGTGGCCCCCCCCCCCCCCCCCGAACTTGGAAACGCAAGATATAGAAGGGGAATAATTTAGACGGGGGAATGAAAAGGGGAGAGAGGAAGAAGCAAAAGACAATGTATAGCCAGACCTGGTCAAACCAGCTCAACCCTTTCTCCCCCTGGGAAAACAAAAAAAATGTTGCCAAAAGAAAAAAATCCAGATCAACCAACCAACCAGCCAACATGCCCGCCGTAAATAAAATTTTTCTTTTTCTCTTTTCTTTCTCTTTTTCATTTTCTTCTTTTCTTCATGTGTTTAATTTTTTTTTTTTTTTTAATAACTATGTTATTTAATAATCACTGTTTACGTATTACTTTATTTTAATCCCTGTTATCTTCTGCGGCGTTTGTTCTCTTCAATATTCACTTCACTACTACTATGGCTGGTATATATATTGCTTAACTGCGGAGTTATATGTTGTTACTTCGATAGCCTGAGAGAGACCGACGAGATAGGCAAGACACCACACACCAACAACCGCCAGTAAGCGCTGAATAAGCAAACCAACGCAACCTCTTCTTCTCTCTTCGGTTTTCAGTTCCCAGTTCCCATGAAATATACCTACCACCATAGAAGAACCTCAGCACAGCTCAGCCTAGCAAAGCCTAGGCCGCGGGCTAAATTCTGCTATATACAAATGGAATTGAAATCTACAGTGCTGCATGGGACGGGTGGACGGGTGGACGGGTGGATGGGTGGATGGATGGATGGCAGGGCGCGGTGCGTGCGGTGCGGTGCGGTACGGTACGGTGCGGAGAGTTCGATGACAGCGTAGCGACGTCATGGATCCCGGGAGGAGGAGGAGGAGGAAGAGGAAGAGGAGGAATGGGAGTGCGCGCGGGTTGATTGATATCGTGTGCTGTGTGTTTAGTTGATGGTGTCGTCTGTATAGGTTGGGTGAGTTCGTTCGTTCGTTAGTTTGTGCCTGTTATGCCGCCCCCCGATGCAAGTGTATATATATATATATATATGTATATATATAGATGCGCTGGCTAAGCTT</Sequence>

   </Sequence>
</MOBY>


--
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"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada