Exercises on Pubmed

Go to parent Basic bioinformatics concepts, databases and tools#Exercises_during_the_training

PubMed is the most consulted database with references to the scientific literature. The abstracts of most scientific articles are freely available.

Exercise 1

Search in the Pubmed database for the articles written by Ghysen.

go to http://http://www.ncbi.nlm.nih.gov/

select "Pubmed" in the databases selector

enter "ghysen" in the search term box

click "Search"
This search returns more than 100 articles and probably you are looking for one specific article.
So to refine your search, click on the "Advanced" link

This opens the Advanced search builder that allows you to refine your search in a user-friendly manner.

Use the Advanced search builder to search for publications in which Ghysen is the last author.
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This search still returns more than 40 articles.
Suppose you know that Gautier is also an author of the paper.

Search for publications with Ghysen as last author and Gautier as co-author.
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This search returns the article that you were looking for.

Exercise 2

Suppose you want to find reviews on the relation between amyloid and prion diseases. First try a regular Pubmed search using "prion" and "amyloid" as search terms.

This search returns more than 2500 articles but at the left menu you can click "Review" to filter the reviews from the list of results

Select the review entitled "Is tau ready for admission to the prion club?". You can add more search terms to the search. Once the "Review" filter is activated it stays active until you remove it.

Retrieve the protein sequences of the protein tau isoforms that are mentioned in this article in fasta format.
In the right menu go to the links to related info in other databases. Click the "Protein (Refseq)" link In the resulting list of Protein entries, expand "Send" and download the sequences to a FASTA file

View the location of the tubulin-binding domains of protein tau isoform 1 in the NCBI sequence viewer.
Return to the "Summary" list of Protein entries Click the "Graphics" link of isoform 1

Depending on the content of the article, Pubmed will link to different databases.
Select the review entitled "Rottlerin and curcumin: a comparative analysis".

View the structures of rottlerin and curcumin.
In the right menu go to the links to related info in other databases Click the "Compound (MeSH keyword)" link. This leads to a list of Pubchem Compound entries that are featured in this article, including the structures of the compounds You can click the structures to display them in more detail.