Databases for Biological Research

by Dave Heathcote, revised Fall 2007

1. PantherCat: UWM, Madison and other UW library catalogs.

2. Marquette/Medical College of Wisconsin/Other libraries: Library catalogs.

3. Table of Contents Alerts: Keeping up with what is new.

4. Electronic Journals: Full text articles and reprints on your computer.

5. Using Medline to find articles, sequences and structures: PubMed for searching the Medline from the 1960s to the present. It also searches many other databases maintained by NIH.

6. Funded Grants: Grant information including abstracts of all funded grants in the US.

7. Surfing for Biological Information: How to find information on the World Wide Web.

PantherCat---This is the web-based interface to the online catalog at UWM. It provides very simple searching of the library resources at UWM and even lets you see which books you have checked out and when they are due. You need to get connected to the internet and start a browser. You simply type in the URL for the page http://library.uwm.edu/ . If you are off campus, you will need to login with your UWM ID number to access library resources. Look in the Books & Other Resources section and click on the link to the Library Catalog (PantherCat). It looks the same and works the same on any computer. It is very intuitive and everyone should be able to figure out how it works in a few minutes.

The library in Madison and most of the other UW System libraries use the same software. Each library's page has a different appearance, so you can easily tell if you are in UWM’s catalog or another one. They all have the same functionality and can be searched in the same easy way. To get to these other catalogs, click on the other libraries tab on the top of the PantherCat page. Click on University of Wisconsin System Libraries located near the top of the list. Click on UW Madison to access the Madison online catalog or you can search multiple UW libraries and actually borrow materials from them. Click UW System Borrowing. Students can borrow books for 28 days and renew them once. They are available 1-5 days after you request them and you can pick them up at the Golda Meir Library. Try this out by searching for the current edition of our course books by Sanes, Reh and Harris and the one by Rao and Jacobson.

PantherCat also provides access to a large number of electronic databases purchased by the library. Simply select the databases a-z tab at the top of the page. You can search for article titles, abstracts and even full text articles from some of these databases. Under the Databases by Vendor/Publisher, click on Wilson. You can check any number of these databases and search them all at once. Alternatively you can go back to the databases page and use the Select a Subject click box to select Life and Health/Biological Sciences. This brings you to a list of databases covering the life sciences. You can search them using key words for articles or, in some cases, full text articles.

There are a number of journals available online. Some are freely available to everyone and others are available to the campus community because our library has a subscription. If we do have a subscription, you can get articles from a University computer or after logging in to the library’s web page from a computer off campus. Go back to the PantherCat main page and select the e-journals list tab on the top of the page. This is a list that includes a lot of non-science journals. You can click N and see how many of the Nature journals we have, including Nature Neuroscience and Nature reviews. Neuroscience. You can also go to D and find that we have Development but Developmental Cell is only available for all but the most recent year.

Marquette/Medical College of Wisconsin/Other libraries---You can search the holdings of most other libraries through the World Wide Web. Most that you will want to use can be accessed from the other libraries tab in PantherCat. You can see the holdings at Marquette or the Medical College of Wisconsin from the comfort of your computer without using the Upass or worrying about parking.

The easiest way to search them is to use the Web version of their catalogs. You can type in the URL for the Marquette library http://libus.csd.mu.edu/ or click on the PantherCat link. If you need a particular issue of a journal, (eg., Brain Research) click on the Title button and type in the journal name and Search. Click on the correct title in the list and the bibliographic record is displayed. To make sure they received the issue you want click on Latest Received. You will then also see which issues are bound, which are at the bindery and which are arrived and in the current periodical room. The previous page also shows that Marquette has an electronic subscription to Brain Research. You do need a password to access the last 12 months of the journal or you can go to the Marquette library and access the electronic version from one of their campus computers.

To get to the MCW library use the link on PantherCat or type in http://ils.lib.mcw.edu. Click on Go to the Library Catalog, select Title and search for Brain Research. Select it and you go to the bibliographic record with all available issues listed starting with volume 1. There is also a link to the Brain Research web site. If you go here, you find a list of all of the issues of the journal. You will be able to get an article if you are connected to the MCW network or are at their library.

You can also connect to the public library catalogs in Milwaukee County (CountyCat). To get to CountyCat type http://www.mcfls.org/. Although they don’t have the journal Brain Research, they do have a book on brain research and language. The previous record is on Brain Repair in case you are interested. It is a bit frightening that anyone can check out this nonfiction book. They also have audiobooks that you can download and listen to on your PC or MP3 player.

You can search the holdings of a huge number of libraries with both Wiscat and WorldCat. Both can be readily accessed from links on PantherCat. Wiscat covers all of the libraries in the state (academic and public) and makes it relatively easy to borrow items from them. WorldCat is very easy to use and extremely fast. It will locate items from all over the world, let you know if they are available at our library or which libraries in this and neighboring states have it. Try searching for the book by Sanes, Reh and Harris. It has 7 entries. 1 is the first edition of the book and shows that it is present at UWM. 2 is the second edition of the book. Clicking on the title in #1 gives you information about the book including a picture of its cover. If you click the libraries worldwide that own the item, it gives the closest libraries that have it on the top of the list.

Table of Contents Alerts--- The best way to keep up with a journal you are interested in is to go to its web site and sign up for an Alert service. The publishers want to know a little about you and they will send you emails of new issues with their Table of Contents several weeks before they mail out the printed version of the journal. Sometimes they will send you emails of articles in advance of publication. This can be useful or it can just fill up your email box. These emails usually contain links that will take you directly to the abstract of the article. Several journals that you might be interested in signing up for include Cell (http://www.cell.com/), Neuron (http://www.neuron.org/), Development (http://dev.biologists.org/), Journal of Neuroscience (http://www.jneurosci.org/) and of course the Nature series of journals (http://www.nature.com/nature/) and Science (http://www.sciencemag.org/).

Electronic Journals----Most journals are now available online. Publishers can release the electronic versions of their journals before they physically print them. This is a great help to researchers, who can get the latest information as soon as it is available and do not have to worry about delays by the printers, the post office or library processing. The publishers biggest concern is how to make sure that they get paid. Our library has made an effort to upgrade their subscriptions for many journals to include the online version. If we have an online subscription, anyone can access full text articles from a computer connected to the campus network. Most journals provide their articles in two formats, html (viewable with any browser) and pdf (viewable with the free Adobe Acrobat reader). The pdf version looks just like the printed copy and is preferable if you want to print a copy, while the html version can sometimes provide higher resolution graphics and movies on your computer screen. To find out which journals are available, you can use the Electronic Journals list in PantherCat. This includes both science and non-science journals, so you need to know what you are looking for. A third way is to look up the journal title in PantherCat. If it is available online, there will be an internet link in the bibliographic record that you can simply click on. Some publishers also make articles freely available after a certain time period even if you do not have a subscription. Some have them available after 6 months (Development and PNAS or the Proceedings of the National Academy of Sciences) or a year (Journal of Neuroscience, Cell, Neuron, Developmental Cell). Others occasionally have unlimited access in order to get people to subscribe. It is a lot like the cable companies offering a free week of the Disney channel to get you hooked on Mickey Mouse.

Electronic access is clearly the wave of the future. A number of influential people are trying to make electronic access free for everyone. The publishers don’t like that idea because they will then have to get money from the authors and authors would balk at paying fees that would maintain the profit margin of many publishers. A new independent enterprise encouraged by the NIH called BioMed Central is now publishing articles. The papers undergo the same kind of peer review as other journals but they are only published electronically. The articles are published immediately upon acceptance, Medline indexes their abstracts, the author keeps the copyright to the paper and anyone can get pdf copies for free from their web site. Their journals include BMC Developmental Biology and BMC Neuroscience as well as many other areas in Biology from Ecology to Medical Ethics. Check out their web page at http://www.biomedcentral.com/. Another online publisher is the Public Library of Science (PloS: http://www.plos.org/). It was started in 2003 and has a number of journals including the frequently cited PLoS Biology. NIH has instituted a policy that all researchers that receive NIH grants, should deposit articles dependent on funds from those grants in a centralized archive so that the public, who payed for the research and researchers can search the text of the articles. Other granting agencies have either followed suit or are considering a similar policy. Quite a few journals are now submitting their entire content after a certain period of time to the archive. You can check out the fairly extensive list at http://www.pubmedcentral.nih.gov/.

Using PubMed to find articles, sequences and structures.

The National Center for Biotechnology Information (NCBI), which is part of the National Library of Medicine and NIH indexes the entire Medline (back to the early 1960s) as well as amino acid and nucleotide sequences, genome data and structural information from databases around the world. All of the databases, including Medline are free to everyone. There are a number of third party services that will let you search the Medline, but NCBI provides a very fast, easy and free way to do it directly from the browser on your desktop. It is called PubMed.

PubMed is a powerful tool for retrieving information from the various NCBI databases. The data is on a fast, dedicated computer run by NIH. Articles, abstracts, sequence information, genome maps and molecular structures can be rapidly searched using it. One of the most powerful features of PubMed is that it uses an algorithm that compares key words and MESH (Medical Subject Heading) terms to find articles "related" to ones you have chosen. Related papers can be quickly retrieved by simply clicking the link with your mouse. This is very useful for finding out about a particular area quickly and easily. PubMed is available at http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed. You can select the database you want to search from the scroll box on the upper left (PubMed=Medline, protein sequences, nucleotide sequences, structures, genomes, etc.) and enter a search term. You can refine your search by clicking the Limits or Preview/Index tabs beneath the search box. For example, lets say you want to find a recent paper that you saw in Science about zebrafish. Type in zebrafish and go to the Preview/Index tab. On the bottom of the page, click the scroll box and select Journal name. In the box next to it, type in Science. Below the two boxes are three buttons. Click the AND button and it will be added to your search on the top of the page. Now select Publication Date in the clickdown box, type this year into the box next to it and click the AND button. Now click the Preview button at the top of the page and you will see how many items match your criteria. To see those items, click the Go button or the number in the Results column. When you see the reference you are looking for, click the Related articles link. The articles are ordered based on its score from the algorithm, but you can sort the related articles by author, journal or date with the click box at the top of the results. You can read abstracts of the articles that look interesting, save them to the clipboard and print them out. If it seems complicated you might want to view the online tutorials for PubMed (they are available from the blue bar on the left). There are also tabs at the top of the page that give All related articles and one that gives related Reviews. Reading a couple of recent reviews can quickly get you up to speed in a particular field.

To search the other databases, select them from the Search box on the upper left of the PubMed page. Both protein and nucleotide databases can be searched like the Medline using Preview/Index. So search for the protein dystroglycan AND rabbit[organism]. Click on the last one, which was the first one reported. The Display box shows it is in the GenPept format, which shows a lot of information about the protein, its original submission, the Nature paper where it was published and the all-important amino acid sequence of the protein. You can view it in other formats including the last one, which is Graph. This shows the sequence and the known domains of the protein in a graphical format. The nucleotide database can be searched and viewed in the same way. If you want to view molecular structures, you need to download and install the Cn3D structure viewer. It either works as a standalone application or it is a helper application that works in your browser. With it you can view different renderings of protein structures, spin them around and get an idea of how function might be related to structure.

Funded Grants---You can find information about funded grants at the web site of the funding agency. The National Institutes of Health (NIH) has a database called CRISP with information about funded grants. You can search for grants that were funded between 1972 and the present on this database. Go to http://crisp.cit.nih.gov/ and search for key phrases, geographical locations or for individuals. You can get the public abstract of the awards and other information about the grants. You can get the same information about NSF grants. Go to their search page at http://www.nsf.gov/awardsearch/. Although the interface is different from that of NIH, you can enter search terms and get the same information about awarded grants.

The advantage of looking at grant abstracts is that you can see who has similar interests to you. This could be very valuable when you look for a place to get your Ph.D. or a mentor for your postdoc. It also tells you what people are planning on doing before they publish it.

Surfing for Biological Information---There are many sites with information useful to researchers. You can visit these sites using any browser. A good place to start is on the Department of Biological Sciences Home page http://www.uwm.edu/Dept/Biology/ under Biological Links. Then go to Links to other Biological Sites. There are many different kinds of databases available. Some are set up by individuals, academic departments, professional societies, government agencies and companies. There are also a number of sites that maintain lists of sites with different information. A good example is Yahoo Science. Click on Biology and then Neuroscience to find a large number of Neuroscience sites. Another useful list is The World-Wide Web Virtual Library: Bioscience. It contains hundreds of different Biology sites and links to other lists like Developmental Biology, Neurobiology, Physiology and Biophysics, Microbiology, Botany, and even Whales.

As an example of the kinds of information available, someone has set up a page called Xenbase: a Xenopus web resource (http://www.xenbase.org/). It contains information about the Xenopus genome and expression patterns of specific genes as well as information about where to get animals and specific reagents and protocols used for research. It also maintains a set of white pages with names and addresses of people working on Xenopus. There are several other Xenopus pages on the web. One is a company that sells frogs and has information about Xenopus care and diseases as well as links to other sources of information (http://www.xenopus.com/). Another link is to a tutorial on amphibian development that I have used as optional reading for my Developmental Biology class. It is maintained by Jeff Hardin at UW Madison (http://worms.zoology.wisc.edu/frogs/welcome.html). This interesting site also has movies of different aspects of amphibian development.

The Society for Neuroscience site (http://web.sfn.org/) contains extensive information for lay audiences about a wide variety of nervous system diseases as well as publications of the society and information about its annual meeting: including the abstracts of all presentations. The Nobel Prize committee has a web site where they put out press releases on recent winners. Go to http://www.nobel.se to find the names of all Nobel laureates and their acceptance speeches. The 2004 winners in Physiology or Medicine were Neuroscientists Richard Axel and Linda Buck. They will announce this year’s (2007) winners on October 8 (Physiology or Medicine, 9 (Physics) and 10 (Chemistry). Check back soon. The US National Academy of Sciences has a site that includes a listing of its members. If you need to find someone to submit your paper to PNAS, check out this site at http://www.nas.edu/ (choose the Directories button on the left side of the page). You can get the contents, abstracts, and full text of articles from PNAS and other academy books and publications from the Publications button.

Many companies have their catalog online. Some contain more information than their paper catalog. An example is the Fisher Catalog. You can look in their chemical catalog for any chemical they sell. You can get ordering information, and the material data safety sheet as well as the chemical properties. Other companies, like Sigma, Gibco, Promega, Beckman, and the American Type Culture Collection also have pages with information useful for research.

One of the best ways to find specific companies is the Google search engine (http://www.google.com). It ranks sites with your search criteria based on how many other sites link to it. So a big company or a critical resource used by many people will be near the top of the list. Google is good at finding lots of other things. You can also install the Google Toolbar on your browser. This lets you do searches without having to first go to the Google site. Many of the newer browsers, like Firefox, have this built in as well as toolbars for other search engines like Yahoo. Another cool service provided by Google is Google Scholar. You can get to it from the main Google page by clicking more>> or going to http://scholar.google.com/. You can type in the name of an author (or select the Advanced Scholar Search) and it will find the papers published by that person. At the end of the listing is a link that tells you how many papers listed this paper in their bibliography. If you click that link, it will give you all of the citing papers. This can be very helpful in drilling through the literature in the same way as the Related Papers function of PubMed.

A newer search engine that also prioritizes its results is called Clusty (http://clusty.com/). It arranges the results into similar clusters. If you type in Developmental Neuroscience, it provides a list of sites, but on the left side of the page are groupings of all the hits into a collapsed outline form. This makes it easier to find groups of relevant sites and not just the huge numbers of redundant and irrelevant sites that are collected by other search engines.

Happy surfing!!!