Module1 Session2 Assignment
Module1 Session2 Assignment
Practical Assignment
Module name: Introduction to Databases and Resources
Session name: Advanced Literature Searching
Trainer: Shaun Aron
Participant: NABIL SAID ABDALLAH
Date: 05/05/2024
Task 1 is a recap of the PubMed advanced search query builder. There are no
questions for this task but you are welcome to take your own notes as you run
through this task.
Please provide answers for Task 2 in this document.
NCBI www.ncbi.nlm.nih.gov/pubmed
Please note
Hand-in information If you are formally enrolled in the IBT course, please upload
your completed assignment to the Vula ‘Assignments’ tab. Take note of the final
hand-in date for each assignment, which will be indicated on Vula.
Task 1: Instructions
There are a number of options that can be selected to control searching strategies. A
simple search can be conducted using the search box on the PubMed homepage,
however the advanced search tab provides options for more specific searches.
• PubMed Advanced Search Builder: This is the most important section and is where
you can build up your query. You can create a query using a search term and field
and then add it to the query box. Based on the Boolean term used you can choose to
include and exclude terms searching specific fields.
• Filters: this has useful features for restricting a group of searches. There is some
overlap between the Filters and Search Builder, but usually you should use Search
Builder where you can and use Filters where you can’t. Also Filters is useful when you
want to affect how a group of searches is done. If you do set filters, don’t forget you
have done so! Filters stay in place unless you change them. You can remove a filter
by clicking on the tick next to it.
• History: shows all the searches you have done. The details section provides further
details on the query that was run for the search, while the action column allows you
to add the query to the search box again, delete or save your particular search
query.
Click on the advanced search link. You can now add terms to your search by selecting
which fields you want to search, and what terms/words/phrases you want to use. By
using AND, OR and NOT you can build up complex queries in the query box. Have a
look at the fields you can choose. The show index button button will provide
suggestions for search terms that you start typing. Note that when you do a search,
PubMed tells you how many papers were found in the history table. If you click on
the number found, the details of the papers are shown.
Task 2: Instructions
Each of the following examples should be conducted as individual search! Copy and
paste the search query that you generated for each search and the number of results
for questions 1 - 6.
Before setting any filters, using the advanced search page, search for papers that
deal with myopia.
7. Copy and paste your search query. How many papers are found?
Now set Filters to limit the search to clinical trials involving human males and where
there are links to free full text papers. How many papers do you retrieve once the
filters have been set?
8. Summarise the difference between setting restrictions using Filters and using
the features of the advanced search page?
Other features
Bring up the details of the papers found in the last search you did by clicking on
the number of papers found.
Look at the options for sending output to a file, to text, to email and so on.
Select the top 3 papers. Add them to the clipboard. Check under Clipboard to see
them.
MyNCBI
Saving search results. Once registered and logged in you can create and
save search results to specific collections. This is useful since you are able
to create collections to store the search results for different aspects of
your research.
Saving search queries. Useful if you wish to run the same or related
searches over a period of time.
Saving BLAST search results and options used. i.e. the particular BLAST
program used, the parameters, the database searched and the query
sequence
ANSWER
1. search query and number of results : ostrich[Author]-6
2. search query and number of results : (Hubbard T[Author]) OR (T
Hubbard[Author])-3718
3. search query and number of results : (((("2003"[Date - Create] :
"3000"[Date - Create])) AND (T Hubbard[Author])) OR (Hubbard
T[Author])) AND (Sanger Institute[Affiliation])-60
4. ((Erdemir[Author]) AND (("2014"[Date - Publication] : "2014"[Date -
Publication]))) AND ("J Biol Chem"[Journal]) /
5. Kirkbride JB, Susser E, Kundakovic M, Kresovich JK, Davey Smith G, Relton
CL. Prenatal nutrition, epigenetics and schizophrenia risk: can we test causal
effects? Epigenomics. 2012 Jun;4(3):303-15. doi: 10.2217/epi.12.20. PMID:
22690666; PMCID: PMC3970193.
6.
7.
a. search query and number of results: myopia[Text Word]-29620
b. 245 results
8. The fundamental difference between using filters and the functions on the
advanced search page on PubMed lies in the level of customisation and
accessibility. Filters, accessible on the results page after a basic search, allow
results to be limited according to predefined criteria such as publication date
or publication type, offering a quick and simple approach. Advanced search
functions, on the other hand, offer more granular control over search criteria,
Introduction to Bioinformatics online course: IBT
allowing the use of Boolean operators and the specification of specific fields
for more complex or specialised searches.