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Module1 Session2 Assignment

This document provides instructions for an assignment on conducting advanced literature searches using PubMed. It includes tasks on understanding PubMed's advanced search features, building search queries, and using filters. The participant provides answers to the tasks, demonstrating searches on topics like ostriches, authors, dates, journals, and keywords for cancer in children.

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0% found this document useful (0 votes)
44 views

Module1 Session2 Assignment

This document provides instructions for an assignment on conducting advanced literature searches using PubMed. It includes tasks on understanding PubMed's advanced search features, building search queries, and using filters. The participant provides answers to the tasks, demonstrating searches on topics like ostriches, authors, dates, journals, and keywords for cancer in children.

Uploaded by

abaha93248
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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Introduction to Bioinformatics online course: IBT

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

Advanced Literature Searching


Introduction

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.

Tools used in this session

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: Understanding PubMed Advanced Searching

Task 1: Instructions

Go to http://www.ncbi.nlm.nih.gov/ and choose the PubMed link. PubMed is a


bibliographical database run by the NCBI covering a wide range of biomedical
literature, including bioinformatics. PubMed coverage includes MEDLINE. NCBI also
provides a very powerful way of searching the literature. Doing simple searches is
easy, but it is worth knowing about some of the powerful features that are available,
particularly as the same interface can be used for other parts of the NCBI site.
Remember that often finding useful things is easy to do — the problem is not being
swamped by irrelevant things. There are a few useful videos and help pages available
via the PubMed quick start link on the PubMed homepage.
Introduction to Bioinformatics online course: IBT

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.

Builiding a 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: Searching PubMed using the Advanced Search Query Builder

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.

Example of a search query and number of results : ((FOXP2[Title/Abstract]) AND


mutation[Title/Abstract]) AND language disorders[Title/Abstract] - 12 results

1. Any article dealing with ostrich


Introduction to Bioinformatics online course: IBT
2. Articles authored by T Hubbard (Careful: do you put this as Hubbard T or T
Hubbard?)
3. Articles authored since 2003 by the T Hubbard who works at the Sanger
Institute
4. An article by H.H.Erdemir published in 2014 in the journal J Biol Chem
5. Articles about schizophrenia risk (mentioned in the title), published in a
journal called Epigenomics, written by authors from the University of
Cambridge. Provide the citation/s in plain text format.
6. You would like to conduct a search for articles about cancer in children.
Search the MeSH database at NCBI to find out what the best keywords are to
use for both cancer and children when building up your search query.
Filters

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?

Remember Filters remain set until they are turned off!

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.

Task 2: participant’s answer


<start typing your answer here>

MyNCBI

Go to MyNCBI and register http://www.ncbi.nlm.nih.gov/sites/myncbi/. There are


tutorials on how to use this. The most useful features are:
Introduction to Bioinformatics online course: IBT

 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.

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