I590 Exercise 5

Subject: Medical databases, PubChem, Biomolecule Sequences and Structures

Updated: 23 April 2006 Ok to print out now
Due: 25 April 2006
1. On the Find Information page of the IU Libraries at:


select the "Search Onesearch @ IU" option.

a. Search ABI/INFORM Global Suite, Academic Search (EBSCO), IngentaConnect, and Lexis-Nexis Academic for plasminogen activator inhibitor 1 or PAI-1. How many total references did you find, and how many were retrieved?

Scan through the first 30 records retrieved and circle the databases above which retrieved records on the topic.

b. Change the search settings to remove duplicates by title and re-run the search. How many total references did you find now?

Note that Medline OVID and Web of Science are included in the list of databases.

2. Repeat this search on Ovid Medline, 1966- for PAI-1 (i.e., do not use the full phrase), including the option to "Map Term to Subject Heading". Notice the option that Ovid's implementation of MEDLINE gives you to explode or focus the search. Choose the focus option and include all subheadings. How many records did you find?

3. Compare and contrast the searches performed in 1 and 2, listing the advantages and disadvantages of each type of search and indicating when it would be appropriate to use each approach.

4. T. Ventura-Holman published an article in the journal Genomics in 1998 on the murine Fem1 gene family. Use Science Citation Index Web of Science to find the reference to the article.

a. In the view that shows the abstract, choose the option to view the record in Medline, and you will see a couple of GenBank record numbers. Copy each of those and paste into the Entrez nucleotide search. Print out those records and hand in.

5. Use the Entrez Structure database and search Mus musculus at a computer that has Cn3D loaded.

Choose one of the answers and look at the 3D structure. Use the Zoom and other features to get a better view of the molecule. (Nothing to hand in or answer for this one.)

6. Use the SMILES tool at:


to generate the SMILES code for isatin (what else!). Click on the smiley face after you draw the molecule.

SMILES code:

Now copy your SMILES string, go to PubChem at:


and do a structure search using the SMILES as input.

Did you find it?

If not, try a name search for isatin. Once found, look at the MeSH Tree Structure for the compound and list it below.

The record includes the Canonical SMILES for Isatin. What is it?

Re-try your structure search using the Canonical SMILES for isatin and see if PubChem finds Isatin.

Notice the link to a protein structure. Try that and view the structure with Cn3D. Zoom in and see if you can find the isatin (I did!).

7. Go to the NLM Gateway at:


Choose the TOXNET option, and search HSDB for PCB.

How many records were found?

Click on the first record and note the many topics included, ranging from Human Health Effects to Administrative Information. Browse through some of the entries and give me your impression of HSDB as a reliable information source for data on hazardous substances.