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					Exercises – Web of Science and Beilstein/Gmelin

1. Finding articles in Web of Science

While discussing your research with your advisor, she mentions a useful article from
2005 by Gothelf & LaBean. She doesn‘t remember the exact title, just that it was about
DNA and nanostructures. You‘d like to find the article to read more. Use Web of
Science to find it.

What is the name of the article?             __________________________________

What is the name of the journal it appears in?
                                              __________________________________

How many times has it been cited?                                           __________

How many references does it cite?                                           __________

Do we have this available online?                                           __________

Occasionally a journal won‘t be available online. Where can you find the printed edition
in the DH Hill Library (call number and floor)?

                                             __________________________________


2. Working with results

Do a search for cytochrome* and electrochem*. Click on the result number (about 2,400)
to return to the result list.

In the blue ‗Refine Results‘ box along the left, look under Document Types to see the
breakdown. How many review articles are available?
                                                                         ____________

Sort the full result list (not just review articles) by Times Cited. How many times has the
top article been cited?
                                                                            ___________

Now use the Analyze button to analyze by author. Who has the most papers? (Make
sure you analyze ALL papers in the list: to do so, change the default number being
analyzed so it‘s at least as large as the result set.)
                                                                    _________________
Also Analyze by Source Title. Which journal has published the most papers on this
topic?
                        _____________________________________________________
Beilstein/Gmelin

3. Basic searching in the Commander: Finding a substance, navigating

We‘re going to search for information on caffeine, an organic chemical. First choose a
database. Click the Select Database button along the top. Which one should you choose?
                                                                  ________________

Use the Search All Text box (under the structure editor) to search for caffeine. Click
Start Search to get results.

How many substances?                                                 __________
How many reactions?                                                  __________
How many citations?                                                  __________

Uncheck Reactions and Citations in the Search Status Report pop-up box (this will speed
things up for the next step) and click View. You should be looking at the Substances.
Double-click on one of them to see the details. You‘ll be using the buttons along the top
bar for navigation:




Click the Query and Results buttons. Note how this takes you back and forth between
those screens. We don‘t have access to a lot of the Reports functionality so let‘s ignore
this for now. We‘ll talk about Alerts during the Keeping Up seminar in a few weeks.

Looking at the Results, only one of these is actually caffeine. So what are the others?
Double click one of them to see details. By default you will be seeing all information
about that substance: the View drop-down menu near the top of the screen will probably
be set to View:all. Change it to View:hit only to see where caffeine is mentioned within
the data. Click Grid and Details to navigate to and from the listed results.

Return to the query editor by clicking Query at the top of the screen. Use the Clear Table
button to erase our old query, we‘ll start fresh. This time, use the fields available in the
left column. Make sure the Search Fields button is selected (it might default to
Predefined Search Forms—these are useful but we‘ll hold off on using them for now).

Expand the Substance Identification part of the hierarchy, then double-click Chemical
Name to add it to the query near the bottom of the screen. In the field content box, type
caffeine. Click the drop down arrow under Relation to see your options—if this was a
numerical search, say, for a melting point value, we could change the relation to ―<‖ or
―>‖ if we wanted. In this case, we‘ll keep it as ―is‖. (So, we will search for substances
which the ―Chemical Name (CN) IS caffeine‖. Makes sense, right?) Click Start Search.

How many substances do you get with this search?                      _________________

Double click the first structure to see details. Notice that caffeine is
indeed listed as one of the chemical names. Use the left and right
arrows on the far left of the navigation bar to move through the results.

All of these results do use caffeine as a name, but have different alternate names, CAS
numbers, and formulae.


4. More basic searching

Search Beilstein/Gmelin for information on the solubility of acetic acid in water. Start by
doing a search for acetic acid, as you did for caffeine in the last exercise. Once you find
the substance, view the details and scroll through the field availability list. Look for
Solubility. Click the field code to jump to that data.

How many solubility references are there for acetic acid?             ________________

One citation with water as a solvent gives a temperature of 15 C. What is the solubility
value?                                                             ________________

Click the home button within a citation (looks like a house) to return to the top of the list.
Now look for data on enthalpy of vaporization. Click that field code to see the
information here. One citation is from the Journal of the American Chemical Society.

Can you get the original article this data is from online?            ________________


5. Building a search in Beilstein

You can also use the Beilstein/Gmelin databases to identify chemicals that have desired
characteristics. In this exercise, build a search to find all substances that have the
following properties:

              NMR spectroscopy available (―exists‖)
              Melting point > 250
              Refractive index > 1.44

Search the hierarchy to find NMR, melting point, and refractive index. Click the
Predefined Search Form button to start with, we‘ll try this approach instead. Use the
―Find Field or Form‖ button to locate the desired fields in the hierarchy. Double click on
a form to open it, and add parameters, then click OK to add the field to the query. Do so
for each of the three fields listed above.
   How many matching substances are in the database?                         __________


6. Structure Searching

Let‘s continue by exploring the structure searching power of this database. Double-click
one of the results from a previous exercise (click Results to get back to it if necessary) to
see details. Use the Copy() button to send the structure back to the query editor. In the
options in the upper right, click the button to search ―as structure‖ and uncheck all of the
―Allow‖ variables you can if this isn‘t already done. Use the Clear Table button to
reduce the search only to the structure. If we search now, for a particular structure,
without allowing for any variation, how many results do you think you‘ll get? (May not
be exactly one, but it won‘t be very many single-component results.) Notice that you can
also search for reactions.

Now try again, and check all the ―Allow‖ variables. Also check the Free Sites: hetero
atoms box. Do you see what happens to the molecules in the structure? Check and
uncheck the box a few times if you missed it. Start the search. You get more results,
because we‘re allowing for some variation on the original structure search. Click View
to see the results to understand how the results have changed.

Click Query again to get back to the query editor. Check the Free Sites: all atoms box
and search again. Notice it might take a few seconds because it‘s doing some very
complex work to match structures while allowing so much variation. You should get
substantially more results. Have a look at them, and scroll through the structures to
understand how this search is working.

7. Structure Editing and Reaction Searching

                               Go back to the Query screen, clear the structure, and
                               uncheck all of the boxes again. Double click the structure
                               to enter the editor. Draw the structure on the left. Do your
                               best – use the tools that seem logical, including the eraser.
                               We‘ll go through it together afterwards.

                               Click the ―To Commander‖ button when you‘re ready
                               (looks like two crossed red arrows). This should send the
                               structure back to the Commander for searching.

                                Change the search to a reaction search: search ―as product‖
                                instead of ―as structure.‖ How many reactions do you
                                find?
                               _________________
Solutions
Note the specific numerical answers will change over time as new items are added to online databases. The
answers provided are accurate as of October 2009.

1. Finding articles

    What is the name of the article? DNA-programmed assembly of nanostructures
    What journal did it appear in?   Organic & Biomolecular Chemistry
    How many times has it been cited?        92
    How many references has it cited?        108
    Do we have this available online?
    Yes. Click on the red/white ―Find Text @ NCSU‖ button. This pops up a new window that links the
    article back to NCSU‘s holdings. A link to online access is available here, to the Royal Society of
    Chemistry Archive. Clicking that should take you to the article.
    Where can you find the printed edition in the DH Hill Library (call number and
    floor)? 6th floor, QD241 .O649. You probably won‘t ever need the print edition with the online
    version available, but for some journals or volumes, electronic editions aren‘t available.

2. Working with results

    Sort the result list by Times Cited. How many times has the top article been cited?
    1140

    How many review articles are available?                                                         185

    Now use the Analyze button to analyze by author. Who has the most papers?
    Bianco, P.

    Also Analyze by Source Title. Which journal has published the most papers on this
    topic?
                                          Journal of Electroanalytical Chemistry


3. Basic searching in the Commander: Finding a substance, navigating

First choose a database. Click the Select Database button along the top. Which one should you choose?
         Beilstein. This is used for organic chemistry. Gmelin is for inorganic chemistry. Don‘t use
both—this may seem like a good idea, but it creates a few problems. First, it can be a lot slower. And
second, and more important, it drastically limits how you can search for information. The only fields you
can search are those that are common to both databases. Always choose the most appropriate database (it‘s
easy to switch back and forth) unless your work specifically demands that you use both.

Use the Search All Text box (under the structure editor) to search for caffeine. Click Start Search to get
results.

How many substances?                         1440
How many reactions?                          422
How many citations?                          1363
===

How many substances do you get with this search?   (caffeine as chemical name?)     8



4.      More basic searching

How many solubility references are there for acetic acid?           3 solubility, 30 solution
behavior

One citation with water as a solvent gives a temperature of 15 C. What is the solubility
value?                2.7 percent

Can you get the original article this data is from online? Yes. Click the Full Text
link—although at this writing it‘s not behaving correctly. You can verify by clicking on
the Journals link on the Libraries‘ page and searching for the journal there.


5.      Building a search in Beilstein

How many matching substances are in the database?                           114


7.      Structure Editing and Reaction Searching

How many reactions do you find?                                             2

				
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