Entrez Learn how to use Limits, History and Previewing
To do: Find all the papers written in French that have been entered into PubMed during the last 5 years and contain the words alpha synuclein, human, and parkinson.
A few hints:
In the text box at the top of the page enter alpha synuclein.
Click on the Go button and explore some of the links to see all the hits in the many Entrez resources.
Go back to the main results page and then select Pubmed.
Click on the Preview/Index link below the text box. You can add terms in the text box below and select Language from the drop down menu and then click the Index button. You will see a long list of languages for articles in PubMed.
Select french. (Notice that there are nearly 600,000 French papers indexed in PubMed.) and click on the AND button. Notice that the term appears in the text box at the top of the page.
Now select Preview to the right of text box at the top of the page.
Notice that you started with over 1400 articles and approximately 17 are written in French. Add the terms human and parkinson to your search terms and click on Preview.
Finally click on Limits and select 5 years from the Entrez Date drop down menu and click on the Go button.
How many articles do you end up with? Click on History to see how you got to this answer.
Batch entrez, a useful way to download multiple entries from entrez. These entries can be nucleotides, proteins, citations, etc. You need to start with GI or accession numbers appropriate for the database you wish to query.
Create a text file named npids.txt using Word or a text editor with the following protein IDs and save it as text only format on the Desktop (note: NCBI can only upload plain text files):
NP_054643
NP_054642
NP_004553
Upload the file npids.txt into the Batch entrez web page and click on Retrieve to download the 3 protein sequences.
Choose FASTA from the Display drop down menu.
Then choose the File option on the Send to drop down menu and click on Send to. Save the file to your Desktop noting the name given to the file. Open it using Word. (Note: You may need to select the 'Show All Documents' option.) You can now use this file as input for other analyses.