root/trunk/org.bridgedb.webservice.cronos/WSREADME.txt

############################
# CRONOS-WebService README #
############################

WSDL for WebService is available at:
-----------------------------------

http://mips.helmholtz-muenchen.de/genre/proj/cronos/CronosWSService.wsdl
[http://mips.helmholtz-muenchen.de/CronosWSService/CronosWS?WSDL - doesn't not work for xjc]

Supported Methods:
------------------

public boolean isinRedList(String name,String organism3Letter)
returns true if name is an ambiguous gene or protein name, false otherwise.

public String cronosWS(String inputId, String organism3Letter, int queryIntId, int targetIntId)
returns the corresponding entry for 'inputId' in output type 'targetIntId' 

Parameters:
-----------

name: gene or protein name 
organism3Letter: Abbreviation for Organism

                organism                | organism3Letter
                ------------------------------------------
                Homo sapiens            | hsa
                Mus musculus            | mmu
                Rattus norvegicus       | rno
                Bos taurus              | bta
                Canis familiaris        | cfa
                Drosophila melanogaster | dme


inputId: EntryID of a particular Database (NM_12345, ENSMUST00004567, 
)
queryIntId: Type of the input-ID as integer value (for translation of input Types to integer values see tables below) (Example your inputId is NM_12345 then the queryIntId is 3)
targetIntId: Type of the targeted Database-Type as integer value (e.g. translation into Ensembl Gene ID is wanted then targetIntId is 5) 


Translation Tables for Query- and Target Database IDs
-----------------------------------------------------

1. Values for QueryId and TargetId: mostly used

|-----------------------------------------------|
| Integer value | Query/Target-Type             | 
|-----------------------------------------------|
|   1           | Gene Name                     |
|   2           | Protein Name                  |       
|   3           | RefSeq                        |
|   4           | UniProt                       |
|   5           | Ensembl/FlyBase Gene ID       |
|   6           | Ensembl/FlyBase Transcript ID |
|   7           | Ensembl/FlyBase Protein ID    |
|   8           | GI                            |
|   9           | GeneID                        |
|  10           | EMBL                          |
|  11           | PIR                           |
|  12           | DBSNP                         |
|  13           | UniSTS                        |
|  14           | HGNC                          |
|  17           | MfunGD                        |
|  18           | MGI                           |
-------------------------------------------------

2. Values for QueryId and TargetId: Expression-Analysis, human and mouse

|-------------------------------------------------------------------------------|
| Integer value | Query/Target-Type     | Integer value | Query/Target-Type     |
|-------------------------------------------------------------------------------|
| 200           | affy_hc_g110          | 500           | affy_mg_u74a          |
| 210           | affy_hg_u133_plus_2   | 510           | affy_mg_u74av2        |
| 220           | affy_hg_u133a_2       | 520           | affy_mg_u74b          |
| 230           | affy_hg_u133a         | 530           | affy_mg_u74bv2        |
| 240           | affy_hg_u133b         | 540           | affy_mg_u74c          |
| 250           | affy_u133_x3p         | 550           | affy_mg_u74cv2        |
| 260           | affy_hg_u95a          | 560           | affy_moe430a          |
| 270           | affy_hg_u95av2        | 570           | affy_moe430b          |
| 280           | affy_hg_u95b          | 580           | affy_mouse430_2       |
| 290           | affy_hg_u95c          | 590           | affy_mouse430a_2      |
| 300           | affy_hg_u95d          | 600           | affy_mu11ksuba        |
| 310           | affy_hg_u95e          | 610           | agilentprobe          |
| 320           | affy_hg_focus         |---------------------------------------|       
| 330           | affy_hugenefl         |       
|               |                       |               
| 350           | agilentcgh            |       
| 360           | agilentprobe          |       
----------------------------------------|

3. Values for QueryId and TargetId: Expression-Analysis, rat, cow and dog

|-------------------------------------------------------------------------------|
| Integer value | Query/Target-Type     | Integer value | Query/Target-Type     |
|-------------------------------------------------------------------------------|
| 700           | affy_rg_u34a          | 800           | affy_bovine           |
| 710           | affy_rg_u34b          |---------------------------------------|                       
| 720           | affy_rg_u34c          | 900           | affy_canine           |
| 730           | affy_rat230_2         |---------------------------------------|                       
| 740           | affy_rae230a          |                       
| 750           | affy_rae230b          |       
| 760           | affy_rn_u34           |       
| 770           | affy_rt_u34           |       
| 780           | agilentprobe          |
|---------------------------------------|       

3. Values for QueryId and TargetId: Expression-Analysis, fruit fly

|---------------------------------------|
| Integer value | Query/Target-Type     |
|---------------------------------------|
| 1000          | affy_drosgenome1      |
| 1010          | affy_drosophila2      |                       
| 1020          | BDGP_insitu_expr      |
| 1030          | DEBb                  |               
|---------------------------------------|       


Example for calling the WebService in Java
------------------------------------------
package call;

/**
 * @author brigitte
 */

public class Call
{
        public static void main(String []args)
        {
                try 
                {       // Call Web Service Operation
                        cronos.webservice.CronosWSService service = new cronos.webservice.CronosWSService();
                        cronos.webservice.CronosWS port = service.getCronosWSPort();
                        // TODO initialize WS operation arguments here
                        java.lang.String inputId = "eno1";
                        java.lang.String organism3Letter = "hsa";
                        int queryIntId = 1; //gene name
                        int targetIntId = 2;//protein name
                        // TODO process result here
                        java.lang.String result = port.cronosWS(inputId, organism3Letter, queryIntId, targetIntId);
                        System.out.println("Result = "+result);
                } 
                catch (Exception ex)
                {
                        System.out.println(ex);
                }

        }
}