Access to databases of interest.
Chest Pain Dataset
1. There is a subset of the Children's Hospital medical record system
containing about 300 patient records in an Oracle 7.3.2 database on the
machine Gray.lcs.mit.edu. This is actual patient data downloaded from Children's
Hospital in Boston, which has been "scrubbed" to remove identifying
information about the patients. Nevertheless, treat the data as confidential,
because potential errors in scrubbing or others' abilities to correlate
apparently innocuous facts about these patients with other knowledge could
lead to compromise. In particular, do not leave the data or any data extracted
from it in places where others could gain access to it.
There is an incomplete description of the data
model available.
To access these data from a PC running Windows95 or WindowsNT, the following
components need to be installed:
- Oracle software from CD labelled Workgroup Server 7.3.2.1.1 NT. This
disk contains the full server software for Oracle running under NT, but
for our purposes the stuff of interest is the client software for either
95 or NT, depending on your workstation setup.
- One of the components that is installed by the above setup should be
SQL*Net V2. This needs to be configured by running the program "SQL
Net Easy Configuration" (under he Start menu). You need to select
"Add Database Alias" and do the following:
- Choose a name for the database. I suggest CHDB.
- Choose the TCP/IP network protocol, when asked.
- In the next dialog box, put gray.lcs.mit.edu for TCP/IP host name,
and EMRS2 for Database Instance
- When asked to confirm, say "Yes".
- Oracle's ODBC (Open Database Connectivity) drivers must also be installed
in order to give you convenient access to the database. These may be obtained
from Oracle's Web site, or from anonymous FTP on medg.lcs.mit.edu/pub/6.872/ORACLE_ODBC.
That directory contains two files, n116315.exe, and runme.bat. (The .exe
file is about 10MB in size, so don't try this over a slow modem!) Download
them both and run the latter. It will expand the former into three subdirectories
that install the ODBC drivers for Windows95, Windows3.1 and WindowsNT/x86,
respectively. From the appropriate subdirectory, run Setup.exe. Tell it
just to install the ODBC drivers; the rest of what it proposes should already
be in place.
- You then need to configure the ODBC driver. From the Oracle menu under
your Start menu, select "32-bit Administrator" (euphoneous, no?).
When it lists data sources, select "Add...". Select the "Oracle73
driver." In the next dialog box, for Data Source name type OCHDB,
for SQL*Net String type CHDB (from step 2, above). (Description is for
your pleasure.)
- You can test out your installation thus far by using the 32-bit ODBC
Test program under the Oracle hierarchical menu. When you Connect, choose
OCHDB and type your Oracle User Name and Oracle Password. (Note: You must
obtain these from the instructor before you can connect to the Oracle database!)
- A more capable way to browse the database than by using the above test
program is to set up the Microsoft Access database program to connect to
OCHDB. This lets you use the facilities of Access to view the data, prepare
reports, design forms, run queries, etc. Unfortunately, the "standard"
installation of Access (which is part of Microsoft Office Professional)
does not install the ODBC drivers needed by Access. You need to select
"custom install" and tell it to do so.
- In Access, you need to create a new database, Then select File/Get
External Data/Link Tables..., and under Files of type, select ODBC Databases.
Then select or type OCHDB for Select Data Source. This will ask you to
log on to Oracle, so use your Oracle User Name and Oracle Password. You
then can select all of (or a subset of) the tables in the next selection
list. You will get a handout showing the tables and fields in them. Access
then maps each selected Oracle table to an Access table that it creates.
In this process, it will ask you what are the primary key(s) of each table.
Once this process is completed, you can use all of Access' facilities to
explore this database.
- Other means of accessing the Oracle database involve programming in
various scripting or programming languages. Some of these require installation
of additional "bridging" software. For example, Java access requires
JDBC, which in turn uses ODBC, which in turn uses SQL*Net! We do not have
instructions (or licenses) for how to use all these, but here is a list
of some possibilities:
- Visual Basic, using ODBC.
- Java (e.g., Symantec Cafe or Visual Cafe), using JDBC
- Java using DBAnywhere
- Oracle's Pro*C and Pro*C++, which use SQL*Net calls directly from C
code to provide the most efficient access.
- DBPerl, which runs on Gray itself (it's the Unix scripting language
Perl with the Oracle library compiled in).
Any of these methods can be used, in turn, with various Web server technologies
to build Web-based applications. These are challenging implementation problems.