MyWEST: My Web Extraction Software Tool
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(Andrea Stella, MS and Marco Masseroli, PhD)
  http://www.medinfopoli.polimi.it/MyWEST/


DATABASE CONFIGURATION FILE 
============================

DATABASE WHERE TO SAVE THE EXTRACTED DATA 
___________________________________________

- Set "DRIVER" with the name of the driver used for connecting the database storing the 
  extracted data. 

  Examples:
  . For ODBC connection (default option also for MS-Access databases) set 
    "DRIVER=sun.jdbc.odbc.JdbcOdbcDriver". 

  . For direct connection to MySQL Server databases using the MyWEST provided driver 
    set "DRIVER=com.mysql.jdbc.Driver".

  . For direct connection to MS-SQL Server 7 databases using the MyWEST provided driver 
    set "DRIVER=com.inet.tds.TdsDriver".


- Set "DBURL" with the URL for accessing the database storing the extracted data. 

  Examples:
  . For databases accessible through the ODBC connection set "DBURL=jdbc:odbc:DATABASE_NAME" 
    (e.g. DBURL=jdbc:odbc:DBgene. DBgene is the default name of the MS-Access database storing 
    the extracted data).

  . For databases accessible using specific drivers through direct TCP/IP connection, set 
    "DBURL=jdbc:DRIVER_NAME:DATABASE_FULL_URL" 
 
  Examples:
  . DBURL=jdbc:mysql://111.111.111.111:3306/GeneData for the GeneData MySQL database 
    listening on the default door 3306 of a computer with IP 111.111.111.111, and using 
    the MySQL above described driver.

  . DBURL=jdbc:inetdae7://111.111.111.111:1433/GeneDB for the GeneData MS-SQL Server 7 
    database listening on the default door 1433 of a computer with IP 111.111.111.111, and 
    using the above MS-SQL Server 7 described driver.


- In case an user ID and password are required for the connection, set "USER" and "PASSWORD" 
  labels accordingly. Otherwise let these unset, i.e. USER=  , PASSWORD=  ,(default values).


DATABASE SETTINGS
-------------------------------

DRIVER=sun.jdbc.odbc.JdbcOdbcDriver

DBURL=jdbc:odbc:DBgene

USER=
PASSWORD=



PROXY CONFIGURATION
_____________________

To use a proxy for accessing the Web interfaced databanks to extract the data from, set accordingly 
"PROXYSERVER" with the proxy IP number or name, and "PORT" with the proxy port.

If no proxy is used, set "PROXYSERVER=NOPROXY" and "PORT=". This is the default setting.


PROXY SETTINGS
--------------------------

PROXYSERVER=NOPROXY
PORT=



WEB INTERFACED DATABANKS TO EXTRACT DATA FROM 
____________________________________

For each Web interfaced databank to extract data from, set as it follows.

- Set "NAME" with an unique name for the Web interfaced databank (e.g. NAME=GeneCards).

- Set "BASEURL" with the complete URL (excluded the page identifying code) for linking a Web 
  page containing data to extract of the Web interfaced databank 
  (e.g. BASEURL=http://genome-www.stanford.edu/cgi-bin/genecards/cardsearch.pl?search=). 

- Set "PARAMETER" with the identifying code of the reference page to use for creating templates
  for the Web interfaced databank. 
  (e.g. PARAMETER=H59260, where H59260 is the accession number of the nucleotide sequence 
  whose data are contained in the reference page). 

- If linking the Web interfaced databank with the URL set in "BASEURL" and the code set in "PARAMETER"
  an intermediate Web page containing a link to the desired Web page is retrieved, set the 
  "URL1" and "LINK" labels.

    . Set "URL1" with the base URL of the following page, excluded the URL inside the <A Href=""> tag 
      of the link identifying the Web page containing data to extract.
      (e.g. URL1=http://genome-www.stanford.edu/cgi-bin/genecards/).

    . Set "LINK" with the text of the link, in the intermediate Web page, to the desired Web 
      page (e.g. LINK=Display).

      If the text of the link is equal to the identifying code used to link the Web interfaced databank, 
      set "LINK=@@@@".

- Set "CODE_TYPE" with a short for the type of page identifying code used to set "PARAMETER". 
  (e.g. CODE_TYPE=AN    for Accession Number codes, CODE_TYPE=LL     for LocusLink codes). 

- The "END" label defines the end of a Web interfaced databank settings. 

When adding a new Web interfaced databank, be sure that its setting information are contained within the 
"NAME" and "END" labels.

Use a different "NAME" for each Web interfaced databank in the setting list.


WEB INTERFACED DATABANKS SETTINGS
-----------------------------------------

NAME=UniGene 
BASEURL=http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ACC=
PARAMETER=M27396
if using proxy add  URL1=http://www.ncbi.nlm.nih.gov/UniGene/
if using proxy add  LINK=here
CODE_TYPE=AN
END

NAME=LocusLink
BASEURL=http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=
PARAMETER=4898
CODE_TYPE=LL
END

NAME=Swiss-Prot
BASEURL=http://www.expasy.org/cgi-bin/niceprot.pl?
PARAMETER=P09581
CODE_TYPE=SP
END

NAME=SourceSearch
BASEURL=http://genome-www4.stanford.edu/cgi-bin/SMD/source/sourceResult?organism=Hs&option=Number&choice=Gene&criteria=
PARAMETER=T53775
CODE_TYPE=AN
END

NAME=GeneCards
BASEURL=http://bioinfo.weizmann.ac.il/cards-bin/cardsearch.pl?search=
PARAMETER=NM_000135
LINK=Display
URL1=http://bioinfo.weizmann.ac.il/cards-bin/
CODE_TYPE=AN
END

NAME=Mouse Genome Informatics (MGI)
BASEURL=http://www.informatics.jax.org/searches/accession_report.cgi?id=
PARAMETER=MGI:87895
CODE_TYPE=MGI
END