Microbiology: Find Articles
What are articles and where can I find them?
When your professors say something like "find five articles for your reference list", they are typically asking you to track down peer-reviewed publications from an academic or research journal. These journals usually have names like Journal of Experimental Biology, Science, or Annual Review of Plant Biology.
There are hundreds of journals for different subjects and disciplines, so to save researchers time and energy trying to search through all of them individually, many of them are collected and made available through literature databases like BIOSIS Previews or Environment Complete. These databases offer streamlined searching and in many cases also provide access to the full-text of articles. In cases where the full-text is not available in that database, the Libraries often can provide access through other resources.
Keyword searching using Boolean operators
Keywords
Keep in mind that the literature databases you will most likely be using do not function like Google or other search engines. Google relies on natural language processing to find quick answers; literature databases require you to be a little more thoughtful and purposeful with your search strings in order to pull together sources for in-depth research. You will have better luck finding what you need if you have a basic understanding of keyword searching using Boolean operators.
A basic keyword search in most databases will look for your terms in a few different places, most often in the article title, author, subject terms, and abstract fields. Keep in mind that, with very few exceptions, literature databases will not search in the full-text of an article! So if you want to find a wide array of sources on a particular topic, you will need to spend a little time brainstorming synonyms for some of your keywords.
VIDEO TUTORIAL: How to Search: Topic Breakdown
Boolean operators
Once you've got your starting list of keywords, you need to think about how to input them into the database's search interface, which often requires a basic understanding of Boolean operators and how they work. Simply put, Boolean operators tell the database how the keywords you're searching for are or are not related. The operators you'll want to become familiar with are OR, AND, and NOT. (Note: you don't have to capitalize your operators when you go to type in your search strings, but it can help visually separate your terms and is highly recommended.)
| Boolean Operator | When to use it | Example search string | What it does |
|---|---|---|---|
| OR | Use OR when you want to search for synonyms or similar concepts | vaccination OR inoculation |
Will bring back results that mention either "vaccination" or "inoculation". Will increase the number of search results; search is more comprehensive. |
| AND | Use AND when you want to connect two or more different concepts | cancer AND lethargy |
Will only bring back results that mention "cancer" together with "lethargy" (but not necessarily adjacent to each other). Will decrease the number of search results; search is more focused. |
| NOT | Use NOT when you want to exclude a concept from your search results. Use very sparingly! | dementia NOT Huntington |
Will bring back results that mention "dementia", but will exclude those that mention "Huntington". Best to only use if you notice the same irrelevant concept coming up in your search results, as it may potentially exclude some relevant information. Will decrease the number of results. Order matters with this one! "dementia NOT Huntington" will bring back a different set of results than "Huntington NOT dementia". |
VIDEO TUTORIAL: How to Search: Boolean Operators
Advanced search techniques
There are lots of other techniques you can use to effectively and efficiently search literature databases. Most will allow you to use all the techniques listed below but may have slightly different characters or syntax. Be sure to check the databases' help pages to find the correct syntax for each resource!
| Strategy | What it does | Example |
|---|---|---|
| Truncation |
Uses an asterisk to search for results that include the selected prefix with any word endings VIDEO TUTORIAL: How to Search: Truncation |
nurs* Will include results that mention "nurse", "nurses", "nursing", etc. |
| Wildcards |
Uses a symbol (most often $ or #) to search for terms that may have alternate spellings or additional characters. Check the help page for the database you're searching to make sure you're using the correct symbol. |
an$esthesia Will include results that mention "anesthesia" (American spelling) or "anaesthesia" (British spelling) |
| Phrase searching |
Uses quotation marks to enclose a group of terms that must show up exactly as typed. VIDEO TUTORIAL: How to Search: Phrase Searching |
"cancer fatigue" Will only include results that mention "cancer fatigue" exactly (but not necessarily "cancer-related fatigue"). |
| Proximity searching |
Uses an operator and a number (e.g., "N3", "NEAR/3") to find terms that appear in close proximity to each other. Some databases, like PubMed, do not allow for proximity searching, and others use different syntax. Be sure to check the help page for the database you're searching to make sure you're using the correct syntax. VIDEO TUTORIAL: How to Search: Proximity Operators |
blood N3 collection Will include results that mention "blood collection", "collection of blood", "blood was collected", etc. |
| Nesting |
Uses parentheses to group terms and more effectively use Boolean operators. VIDEO TUTORIAL: How to Search: Boolean Operators (starting at 2:09) |
(cancer OR neoplasm) AND (chemotherapy OR radiation) Will return search results that mention "cancer" together with either "chemotherapy" or "radiation", as well as "neoplasm" with either "chemotherapy" or "radiation". |
| Subject headings | Uses predefined subject terms (also called controlled vocabulary) to help account for different spellings, synonyms, and other related concepts. Typically more limiting than keyword searching. Different databases use different terms, so be sure to check the resource's thesaurus to select the best headings. |
"dementia"[Mesh] Will return search results that have been tagged with the Medical Subject Heading (MeSH) term "dementia". MeSH is used primarily in PubMed; other resources have similar headings. |
Additional literature databases and indices for biology
- Academic Search Complete This link opens in a new windowASC is the MU Libraries' general-purpose database. It includes material from most disciplines, so can be a good place to start if you're not sure what index to use. (However, don't rely on it exclusively for serious research in biology.) It can be particularly helpful if you are looking for "popular science" magazine or newspaper articles.
- AGRICOLA This link opens in a new windowAgricola is the index of the National Agriculture Library. It includes the Animal Welfare Information Center and so is an important source for animal welfare and rights information (including IACUC applications at Miami). Agricola can also be useful for searches relating to plant science, fisheries, ecology, nutrition, environmental sciences, and veterinary science.
- All the World's Primates This link opens in a new windowAll The World’s Primates includes contributions from more than 300 scientists, most of whom have done research on primates in their natural habitats. Containing all of the 505 species and 195 subspecies recognized by the International Union for Conservation of Nature (IUCN), ATWP details habitat, social behavior, diet, physical measurements, risks of extinction, and other facts critical to understanding primate lives. Users can organize primates by multiple methods that best suit their needs. Fully referenced with over 10,000 citations, the data accompany more than 3,000 photographs, as well as interactive maps for each species and subspecies, video, audio, links, search tools, multilingual glossaries, review articles, and other resources.
- bioRxivAn open access preprint repository for the life sciences. Articles initially posted in bioRxiv HAVE NOT gone through the peer review process, so be careful. Some older articles may have links to the final published version.
- Environment Complete This link opens in a new windowOffers deep coverage in environmental aspects of agriculture, ecosystem ecology, energy, natural resources, marine & freshwater science, geography, pollution & waste management, environmental technology, environmental law, public policy, social impacts, and urban planning.
- medRxivAn open access preprint repository for the health sciences. Articles initially posted in medRxiv HAVE NOT gone through the peer review process, so be careful. Some older articles may have links to the final published version
- PsycINFO (EBSCOhost) This link opens in a new windowThe principal literature database for basic and clinical psychology. Includes excellent coverage of animal behavior and neuroscience literature.
- SciFinderN This link opens in a new window
Users must create an account, providing your @miamioh.edu e-mail address, in order to use SciFinderN. The same login will work for either SciFinder or SciFinderN.
SciFinder-n is a newer version of SciFinder, and still provides access to journal articles, dissertations, abstracts, and patents in chemistry and biomedicine. Search for literature or for chemical records by research topic, author, chemical substance or reaction, document identifier, and company/organization name. New features include MethodsNow Synthesis and PatentPak.
- SSRNAn open access preprint repository. Contains primarily social sciences, but is rapidly expanding to include life sciences and other STEM disciplines. Like bioRxiv, when articles are initially posted, they HAVE NOT gone through peer review, so be careful.
Key literature databases and indices for biology
If you're looking for journal articles on a particular topic, this is the place to start. Literature databases, or indexes, track the individual articles published in the thousands of research journals available in biology. Some indexes are built for very particular fields of study, while others are broad (but less comprehensive).
- Web of Science (Core Collection) This link opens in a new windowAlso known as Science Citation Index. This is an interdisciplinary database, best-known in the natural sciences. Web of Science's key feature is citation tracking, which allows you to look up a given article and find additional related papers which have cited it. Our coverage includes 1965-present. Web of Science is part of the Web of Knowledge site, which enables simultaneous searches of BIOSIS, MEDLINE, and Web of Science together.
- PubMed This link opens in a new windowBased on the MEDLINE literature index, the PubMed web site is a freely-accessible database provided by the National Library of Medicine. It connects to about 30 other genetics and biomedical databases in the larger NCBI system. PubMed's coverage extends from 1950-present.
- BIOSIS Previews This link opens in a new windowPart of the Web of Knowledge site. Also known as Biological Abstracts, this index gives the most comprehensive coverage of literature in the life sciences, including journal articles, meeting abstracts, and books. Covers basic and applied biology broadly, e.g. agriculture, biochemistry, ecology, medicine, neuroscience, and physiology. Our coverage includes 1969-present.
Get to Full Text with Find It!
Most literature indexes do not have the actual journal articles included within them. Instead, these indexes just contain information about the article, e.g. titles, authors, abstract.
When you find an article of interest in an index, click the "Find It" button by that entry to get to the full text. If we have a subscription, "Find It" will provide a link to the journal article. (Or if we have the print, it will provide a link to the catalog with the location and call number.)
(A few databases, like Academic Search Complete, include full text for some articles. These databases may allow you to search only for articles available in full text, but be aware that you are only searching a small portion of the articles we actually subscribe to.)
Using Journal Literature
Most indexes in biology will label at least two different types of research articles:
Primary article: A primary article will directly report the authors' research findings. The details of experiments they conducted will be reported. Most primary articles follow the "IMRAD" format familiar to students from writing lab reports: Introduction, Materials and Methods, Results, and Discussion.
Review article: This type of article will summarize the research that has been done in a certain research area. Reviews can be a good entry point into reading on a particular research topic, since some terms will be defined, and important experiments and results discussed. Web of Science is an excellent database for locating reviews.