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Getting Started: PCB3063 Term Project and NCBI’s OMIM, PubMed and Sequence Resources. Michele R. Tennant, Ph.D., M.L.I.S. Health Science Center Libraries/ U.F. Genetics Institute PCB3063, General Genetics [email protected] Today’s Session. Your term project
Michele R. Tennant, Ph.D., M.L.I.S.
Health Science Center Libraries/
U.F. Genetics Institute
PCB3063, General Genetics
Click on “Databases” from HSCL Website
Limit so that your terms reside only in the “title”
Link to discussion of Sipple Syndrome
Link to OMIM Gene Map
Record was retrieved via these words in title
Link to record for the RET Oncogene
Use the MeSH Database as a dictionary to find the appropriate MeSH term, and then to refine your search
You typed “breast cancer” into MeSH database
Use “breast neoplasms” rather than breast cancer
Click on the link to refine the search
Check here and your topics will be the main point of the articles you find – you won’t get peripheral citations. Not recommended the first time you search a topic – if there are few papers in existence for your topic, you may be left with no articles at all
MeSH automatically builds the search for you – in this example, you are looking for papers in which the immunological aspects of breast cancer are the main point of all the articles you retrieve
Click “Search PubMed”
Note that this is the search the MeSH Database built for you – it used the MesH term “breast neoplasms”, glued “immunology” directly to the search by using the slash, and picked up all the different types of breast neoplasms. MeSH also retrieved only the papers where these topics were the main points of the articles. You did not need to do any of this yourself – MeSH did it for you once you found the proper MeSH term, and clicked on subheading. Now we need to complete the second half of the search – vaccines
You’ve now found articles on cancer vaccines, but you need to combine the breast cancer and cancer vaccines concepts
The Advanced Search screen displays your PubMed history; from here you can combine your two searches using the appropriate Boolean operator
For Part B, print the PubMed history, which shows your searches.
Click on “Catalog” from HSCL Website
“Definition” field acts as record title – search [titl]
Unique identifier; assigned by NCBI; required by journals/grants
Link to PubMed citation/abstract
Numbers indicate location on the nucleotide sequence
Search for HUMAN presenilin 1
But end up with rat, mouse, etc.
The typical RefSeq accession number format: 2 letters, an underscore, and then numbers