Pubmed is relatively new retrieval system for the biomedical publications that has the special advantage of being able to retrieve new citations much sooner than can be done from the standard MEDLINE database. This service, which is offered through the National Center for Biotechnology Information (NCBI), makes it possible to do a single search both for newly published articles that have not yet been fully processed for inclusion in MEDLINE and for papers already in that database. The search strategy combines into a single search a title word search that covers both the newly published papers and those already in MEDLINE plus a subject heading search of MEDLINE. It also has an extremely useful feature that allows a search to be limited to the most recent additions. Thus, for example, if you search a topic once a month, you can limit each search to items added in the last 30 days.
Access to PubMed: The PubMed system is on the internet and is available without charge to be searched by anyone who wishes to use it. It can be reached at
Searching PubMed: The PubMed search engine is organized around title words and standard MEDLINE headings. It is quite powerful, but not totally user-friendly. When you connect to the web address listed above, you will be ready to do a simple search for a single term in a fairly straightforward manner.
Selecting a database: The default state specifies a MEDLINE search, but if you click on the window that says MEDLINE, several other options are offered. Most of these involve searches of various sequence and genomic databases. You will generally want to stay with the MEDLINE search unless you haver specialized needs.
Selecting a search word or phrase: Just below the database window, there is a blank window. When you click on it, a cursor appears and you can enter the term you want to search. If the term is a single word, there are no special problems. However, if you try to search for a phrase that contains two words, such as Alzheimer's disease, the default setting treats your request as a search for papers that contain the word "Alzheimer*" (there is a built in truncation of the possessive) and the word "disease". If you wish to keep the two words together as a phrase (or as a subject heading), it is necessary to enclose them in quotation marks ("Alzheimer's disease").
New papers do not have subject indexing: For recent papers, the system generally works better when you do not force a linkage between words by using quotation marks. Thus, for example, in a search done on January 13, 1998 for Alzheimer's disease (no quotes), limited to the last 30 days, 67 citations were found, whereas none were found for "Alzheimer's disease" (with quotes). The reasons are complex, but at least partially they reflect the fact that modern papers are more likely to refer to "Alzheimer disease". A search for that phrase (with quotes) yielded 27 citations from the last 30 days. By contrast, "Alzheimer's disease" did not find any papers until enough time had gone by so they were indexed under that heading. Another difference is that without quotations marks Alzheimer's is automatically truncated to Alzheimer*. Beyond that, the search without quotation marks also finds papers on subjects such as Alzheimer's dementia and papers that do not have either Alzheimer* or disease in the title. This is probably achieved as an abstract word search, but for some unknown reason a search with quotation marks fails to find papers with "Alzheimer's disease" in the abstract but not the title. Although it is not clear exactly why, pragmatic experience clearly says do not use the quotation marks on searches for recent papers.
Number of documents to display per page: The default setting brings the citations up in groups of 20, after which you must go to the next page of results. By clicking on the window, you can make a wide range of adjustments in the number of citations that will come up at once (up to 5000).
Publication date limit: A window near the one for entering the search terms determines the time period to be covered by the search. The default setting is no limit. Clicking on it brings out a pop-up menu, with options including the last 30, 60, 90 or 180 days, as well as last 1, 2, 5 or 10 years. This feature is particularly useful when looking for papers that may have been added since the last time you searched.
Activating the search: The next step is to click on the search button. The simple search works well if you expect to bring up a manageable number of items, for example searching presenilin*. (The asterisk works the same way here as in Paperchase, allowing you to find all terms starting with the combination of letters that precedes the asterisk). If the number of citations that comes up is too large, you may need to use an advanced search, as described below.
Listing of citations: At this point, PubMed will display the first page of citations, and also tell you the total number found and the number of "pages" they are distributed over. You have three ways to obtain detailed displays of the cited articles.
Online help: If you experience trouble with PubMed, try clicking on help at the left of the search page. A substantial set of instructions and information will be displayed.
Advanced Searching: If you need more than a simple search, click on "Advanced Search" at the left side of the search page. This will give you a different page format, which allows you to specify items like search field. As an example, to do a search for papers on Alzheimer disease published in 1997, click on the enter terms window and type alzheimer*. Leave search fiield on "all fields" and click on search. You will be told how many alzheimer* citations have been found and presented with another enter terms window. Click on the window and type 1998. Click on the search field window, hold down the mouse button, pull down the menu to publication date, and release the button. Click on search again. This adds a line to the display saying that 12 citations were found (as of 1/13/98) that contain both alzheimer* and a 1998 publication date. Click on the retrieve button (near top of page) and all 12 citations will be displayed on a "page" that you can scroll through. A little later in the year, the number of citations will be much larger, and you will get multiple pages of 20 citations each. At that point, you may want to expand the page size or further limit the search.
Modify Current Search: You can add a third item to the search if you want (for example, presenilin*). This will initially be displayed as a separate line, not combined with the previous pair at the bottom of the page in the Modify Current Search section. You can combine items from two separate lines by highlighting each of them (this is done by holding down the shift key and clicking first on one and then on the other, which on my computer only works for two adjacent items, although in theory it is supposed to work for any two). You can then search for the intersection (AND) of the two items simply by clicking on search or you can alter the type of Boolean operator by clicking on that window and selecting alternatives, such as union (OR) and difference (BUTNOT). In all cases, the actual search is done by clicking on the search button.
Search Field Window: PubMed gives you the option of doing searches in a variety of fields including major and minor topic fields (called MESH for MEdical Subject Heading), authors, journals, dates, and even the affiliation (laboratory address) of the first author. These features tend to be particularly useful when you want to narrow or expand a search. Examples include limiting your search to papers published in a particular year and searching for additional papers by the author of a particularly interesting paper that you have found.
Displaying complete citations: The complete citations from an advanced search are displayed in exactly the same way as those for the simple search described above.
Reasons for using PubMed: The primary advantage of PubMed over PaperChase is its coverage of very recent publications. As this is being written on January 13, there are already 12 cited publications about Alzheimer disease listed with 1998 publication dates, and many more that have been entered into the system in the last 30 days. Generally, you will find it most convenient to take advantage of the many useful features of PaperChase during your initial collection of references, followed by use of PubMed to find the most recent papers.