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SANGAM DEMO Plan Execution

The current user interface consists of two distinct phases:

  • Phase 1:  Locates all matching entries for a specified search condition on both the term and species, e.g., term = “crh” and species = “rno”.
  • Phase 2:  Retrieves information on the records selected from Phase 1.  The user-interface allows a user to select a subset of records identified during Phase 1 for submission during Phase 2.

 We describe each phase in turn.

 

Phase 1

 Phase 1 employs the following autonomous Web Services:

1)     KEGG find (K-Find) Web Service: It takes the term and species parameter and call the find webservice provided by the KEGG which then returns the list of matching records.

2)     NCBI e-search (N-eSearch) Web Service.  It also takes the term and species and retrieves the matching record list by using the URL retrieval in XLM format.

 The results of these two web services are combined using Sangam’s internal Web Services.  These are:  Branch, Iterator, IUnion, and Join.  The plan that consists of these operators along with the autonomous Web Services is as follows:

 

Sangam’s Web Services provide the following functionalities.

  • Branch operator(B) : it takes the input from the SANGAM user interface and branches it out as inputs to the branches of K-Find/N-eSearch webservice and N-eSearch webservice.
  • Iterator Operator(I): It takes the all the inputs (in this case term and species) and shower them across all the available instances of K-Find/N-eSearch webservice.
  • Iunion Operator(IU): this is a pair operator for the Iterator webservice it joins all the results returned from all the K-Find/N-eSearch sub-branches and forward it to the Join operator
  • Join Operator(J): Join operator will join the results from the both the main branches and give it to the SANGAM user-interface as list of DNA and Protein records returns by K-Find and N-eSearch respectively.

 

Phase 2

The user employs an interface to specify those DNAs (from KEGG) and Proteins (from NCBI) of interest.  This list is submitted to Phase 2 of the system, which employs the following external Web Services:

 

1)     KEGG Get (K-Get) webservice: It uses the Get webservice supported by KEGG to returned the detailed information about all the records by the users

2)     NCBI eFetch (N-eFetch) webservice: It uses the eFetch URL utility provided by the NCBI to get the information of all the selected records in the XML format.

 

 

Once again, phase 2 employs Sangam’s internal Web Services as glue to combine these autonomous Web Services together. In addition to the autonomous webservices used in Phase1, Phase 2 uses one more autonomous webservice called Project.

 

·        Project Operator (P): it is placed in between the Branch and Iterator webservice so that it filters out record-ids irrelevant for the particular branch (e.g. in the above diagram P2 will filter out all the records returned by K-Find webservice)

 

This whole process consisting two phases is iterative, so that user can perform the same operation again for different <term, species> pair through SANGAM