GrinderServlet | Systems Biology Group

--++ Using the Grinder Servlet

Base URL:

Eventually it will be at

http://grinder.soe.ucsc.edu/data/GrinderServlet?request=

Currently

http://disco.cse.ucsc.edu:8089/Grinder/data/GrinderServlet?request=

Possible Requests
- ```
species
```
  Get a list of all available species
- ```
keyspaces
```
  Get a list of all keyspaces for a species, or for all species
  - Optional parameter:
```
species=
```
    To restrict to one species
- ```
map
```
  Map ids from one keyspace to another
  - Parameter:
```
source=
```
    Source keyspace
  - Parameter:
```
target=
```
    Target keyspace
  - Parameter:
```
ids=
```
    Comma separated list of ids
- ```
mapfile
```
  Map ids in a file on the server's file system from one or more keyspace(s) to a single target keyspace
  - Parameter:
```
source=
```
    Source keyspace (Optional, but must have either this or ksCol)
  - Parameter:
```
target=
```
    Target keyspace
  - Parameter:
```
file=
```
    Path to the file. Must have this, and the file must exists
  - Parameter:
```
idCol=
```
    0-based. Which column in the file holds the ids. Required if have more than one column
  - Parameter:
```
ksCol=
```
    0-based. Which column in the file holds the keyspace the ID belongs to. Must have this or source
  - Parameter:
```
columnSeparator=
```
    Optional. What you use as a column separator if you aren't using
  - Parameter:
```
copyCols=
```
    Optional. copyCols=true if you want the Grinder to copy over all the columns other than the id column
Result : Text file, one id per line

Sample commands

Get all the Species available

http://disco.cse.ucsc.edu:8089/Grinder/data/GrinderServlet?request=species

Get all the Keyspaces available

http://disco.cse.ucsc.edu:8089/Grinder/data/GrinderServlet?request=keyspaces

Get all the Keyspaces available for Humans

http://disco.cse.ucsc.edu:8089/Grinder/data/GrinderServlet?request=keyspaces&species=Human

Map ids from UCSC IDs to Human EntrezGene? IDs

http://disco.cse.ucsc.edu:8089/Grinder/data/GrinderServlet?request=map&source=UCSC_IDs&target=Human_EntrezGene&ids=uc003bdb.1,uc003uiz.1

Map all the ids in the first column of a file from GenBank? EST Accession Numbers to Human EntrezGene? IDs, and copy all the rest of the columns untouched.

http://disco.cse.ucsc.edu:8089/Grinder/data/GrinderServlet?request=mapfile&source=GenBank_EST_Accession_Numbers&target=Human_EntrezGene&file=<path the server can read>&idCol=0&copyCols=true

-- Main.gregd - 15 Feb 2008