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BIOD20: Special Topics in Virology

This guide is for students in BIOD20 to help them locate topics and articles for their journal club assignment, as well as guidance on analyzing articles.

Workshop FAQ

Getting Started

Q: What do you do when you don't know where to start, i.e. don't have a specific topic?
A: Getting started is often the hardest part! Take some time to think back on past courses and assignments; which topics have been most interesting to you? You can also do some background research in virology-related resources (e.g. books, journals, etc.). This page has some places you can go to get started.

Q: Are we always specifically searching for a topic of interest? What if you just want to learn the basics about a topic?
A: Typically you will start off broadly, reading up on the basics of a topic before focusing in on a particular subset of that topic. Literature searching is often a back-and-forth process of refining your topic so that a) it's not so broad that it becomes impossible to survey the literature and b) it's not so focused that it becomes impossible to find any literature at all!

Q: How do we determine what is considered "important" in terms of concepts to include in the search?
A: Generally I would say focus on concrete terms and nouns, while avoiding "squishy" words that are ill-defined (e.g. things like "effects"). This FAQ page on How do I choose good keywords? may also be useful.

Selecting Databases

Q: Is there overlap between PubMed and MEDLINE?
A: Yes, PubMed draws content from the MEDLINE database, but also includes some additional content such as select journals, book citations, etc. The National Library of Medicine has a fact sheet outlining their key differences if you'd like to read more.

Q: Are there more resources than PubMed?
A: You betcha! Check out the "Selecting Databases" page for additional resources that you can use for literature searching.

Q: Does using the "Start your search" bar on the library homepage provide coverage for all articles within the university's databases?
A: Unfortunately no! Despite appearing to be an "all search" option, this tool does not capture everything and will often bring back loooots of irrelevant results, which is why I recommend searching within databases directly.

Searching Databases

Q: Are there more shortcuts to use when searching, e.g. using "quotation marks" around words to keep them as one term?
A: Definitely! Check out the "Building a Search Strategy" page for some sample tips and tricks. Note that not all of these will work in every database and that databases don't always use the same symbols. If you want help on how to search a particular database, feel free to shoot me an email!

Q: Is using the # method to combine searches applicable to all databases?
A: Not all databases, but some such as PubMed and MEDLINE allow you to combine searches using their number; for other databases, you will need to manually combine terms using AND/OR.

Example of a numbered combination search in PubMed:

screenshot of a search strategy in PubMed

Example of a manual combination search in PubMed:

screenshot of a search strategy in PubMed

Q: How do we exclude specific types of articles? When I clicked only Journal Articles, reviews and clinical trials still came up.
A: Certain databases allow you to apply exclusion filters where you can select specific types of studies to be removed from your search results. Others, such as PubMed, only allow you to filter by inclusion, such as with the "Journal Articles" article type filter. Unfortunately, I've also found that this filter doesn't function perfectly and will sometimes pull in unwanted doc types, so it's important to carefully review results to make sure retrieved articles match your assignment specifications.

Reviewing Results

Q: Is it worth it to go to the 2nd, 3rd, 4th (etc.) page of results, are they still relevant?
A: 100% yes!! Most databases have "sort by" features you can use to try to bring the more relevant stuff towards the top of your results, but I recommend taking a look through everything to make sure you don't miss anything important. This is why it's helpful to aim for a manageable search set (e.g. ~100 results) when finalizing your research topic, so you won't make yourself miserable having to look through thousands of results!

Q: I still sometimes have difficulty finding full articles.
A: If you hit any snags in finding the full-text of an article, feel free to email the citation to me or stop by the Information and Reference Desk in the library. We'll check to see if UofT has it, and if not, we can request a copy for you free of charge!