[MOBY-l] help in registering a new service

[maliha aziz]

  As suggested by Mark Wilkinson I am emailing on this list to get some input on this issue ....


We are interested in registering a BIPASS service with BioMoby.We have some questions about registering new data types such as "cluster" and "variant".
  (BIPASS http://bip.umiacs.umd.edu:8080 is a alternative splice database server.
 It has been registered with NAR in 2007.
 /http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933140)
    The variables used are as follows
  ·   Identifier (input)
  ·   OrganismName (input)
  ·   ClusterID (input and output)
  ·   Variant
  ·   TranscriptID 
  ·   Chromosome
   
  The four services that we are planning to deploy are as follows 
  
   BIPSearchTranscriptsByTranscriptID – takes transcript Id as      input and generates cluster ids as output
   BIPSearchTranscriptsByAnnotation – takes Annotation as      input and generates cluster ids as output
   BIPSearchTranscriptsByAnyField – takes either Annotation or transcript      Id as input and generates cluster ids as output
   BIPGetClusterInfo – takes cluster Id as      input and generates the corresponding Variant, TranscriptID ,Chromosome as      outputs.
   
   
  The only two things that I find to be new and generated only by BIPASS as they are relevant to BIPASS only ( I dont know how useful they are to the community as they can only be consumed by the BIPASS service next inline) are as follows 
 
 Cluster - generated by 
  
   BIPSearchTranscriptsByTranscriptID
   BIPSearchTranscriptsByAnnotation
   BIPSearchTranscriptsByAnyField      
  This object needs to be of the following format
 
 Cluster ID ISA Object HAS string
 
 Variant -  which tells us whether the particular cluster generated by the  BIPASS tool  contains an alternative splicing case 
 
 This object needs to be of the following format 
 
 Variant ISA Object HASA  BOOLEAN type
 
 
 For registering both of these we would also have to register a new namespace 
 Namespace : BIPASS
 
 
 So for the rest of the inputs and outputs what i think needs to be done is as follows
  \u003cbr\>\u003c/span\>INPUTS\u003c/span\>\u003cbr\>\u003cbr\>\n\n\n1. Identifier\u003cbr\>article name \u003d Identifier\u003cbr\>class \u003d Global_Keyword\u003cbr\>namespace \u003d  Genbank etc (multiple namespaces can be selected... it depends on which repository are we including in BIPASS )\u003cbr\>\u003cbr\>2. OrganismName\u003cbr\>\n\n\narticle name \u003d OrganismName\u003cbr\>\nclass \u003d TaxonScientificName\u003cbr\>\nnamespace \u003d  Genbank  etc (multiple namespaces can be\nselected... it depends on which repository are we including in BIPASS )\u003cbr\>\n\u003cbr\>\u003cspan style\u003d\"font-weight:bold\"\>OUTPUTS\u003c/span\>\u003cbr style\u003d\"font-weight:bold\"\>\u003cbr\>1. ClusterID\u003cbr\>article name \u003d ClusterID\u003cbr\>\n\n\nclass \u003d Cluster\u003cbr\>\n\n\nnamespace \u003d  BIPASS\u003cbr\>\n\n\n\u003cbr\>2. Variant\u003cbr\>article name \u003d Variant\u003cbr\>\n\n\n\nclass \u003d Variant\u003cbr\>\n\n\n\nnamespace \u003d 
 BIPASS\u003cbr\>\u003cbr\> 3.TranscriptID \u003cbr\>article name \u003d TranscriptID \u003cbr\>\n\nclass \u003d object\u003cbr\>\n\nnamespace \u003d  Genbank  etc (multiple namespaces can be\nselected... it depends on which repository are we including in BIPASS )\u003cbr\>\n\n\u003cbr\> 4.Chromosome\u003cbr\>article name \u003d Chromosome\u003cbr\>\n\nclass \u003d GeneticElement\u003cbr\>\n\nnamespace \u003d  BIPASS\u003cbr\>\u003cbr\>As\nfar as the issue about how would the user know which web service takes\nannotation as an input and which takes transcript idz we can name the\nservice in such a way that it becomes explicit that this webservice\ntakes annotations and this takes transcript ids and this third one take\ntranscripts or annotations.\n\u003cbr\>\u003cbr\>Hopefully if this line of thought is approved we can get the webservices registered before the end of this month\u003cbr\>\u003cbr\>regards\u003cbr\>",1] );  //--> 
 INPUTS
 
 1. Identifier
 article name = Identifier
 class = Global_Keyword
 namespace =  Genbank etc (multiple namespaces can be selected... it depends on which repository are we including in BIPASS )
 
 2. OrganismName
 article name = OrganismName
 class = TaxonScientificName
 namespace =  Genbank  etc (multiple namespaces can be selected... it depends on which repository are we including in BIPASS )
 
 OUTPUTS
 
 1. ClusterID
 article name = ClusterID
 class = Cluster
 namespace =  BIPASS
 
 2. Variant
 article name = Variant
 class = Variant
 namespace =  BIPASS
 
  3.TranscriptID 
 article name = TranscriptID 
 class = object
 namespace =  Genbank  etc (multiple namespaces can be selected... it depends on which repository are we including in BIPASS )
 
  4.Chromosome
 article name = Chromosome
 class = GeneticElement
 namespace =  BIPASS


Your feedback would be highly appreciated 

Thanks
Maliha Aziz

       
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