Today, we will focus on searches of literature data banks and of
other databanks at NCBI's entrez. Related to this are
bibiography softwares. If you write scientific or other academic
articles, you frequently need to cite the literature. It is a good
idea to get used to using a bibliography program ASAP. This makes it
easier to incorporate citations into an article, to reformat the
bibliography, and to download citations from the internet. Popular
choices are Endnote, Refwork, Zotero and Mendeley.
Endnote is popular, but expensive, and old versions usually stop
working when you update your operating system. Also, citations
incorporated into a text document cannot be used by other citation
programs. Refwork also is a commercial software, but UConn has a
subscription.
Mendeley and Zotero are similar, but no longer compatible. - You
still can export your personal library from one program and load it
into the other, but the two softwares can no longer be used on the
same document. Mendeley is popular, it also can be used to keep
track of pdf versions of articles, and it is updated within reasonable
time, when Microsoft office or the operating system becomes
incompatible with an older version.
Your instructor currently uses Mendeley, maintained by Elsevier. The
software can be downloaded here.
After you create a free account, your database of references is stored
online, you can share folders with others, and you can use your
references from different computers. The software comes with three
important features: A) a bookmark for your browser that automatically
downloads citation (and pdf, if available, from the cite you are
visiting (e.g. pubmed, journal page, scopus, ...), a plug-in for
microsoft word, the allows you to insert citations into the text you
are writing, and the Mendeley desktop, that allows access to your
references, and different bibliography style sheets. I strongly
encourage you to install either Mendeley
or Zotero on
your personal computer.
1. (less than 20minutes)
Use Pubmed
in NCBI's Entrez to find an article written by
Carl R. Woese (famous scientist,
co-discoverer of the Archaea), published in the journal
Proceedings of the National Academy of Sciences of the United States
of America with the words primary kingdoms
in the title of the paper. Try to use Boolean operators
(AND, OR, NOT)
and field
tags; if you cannot recall the tags, use the pull-down menus
under "advanced"
(link below the search text window).
| What query did find the 1977 article? |
|
If your search resulted in multiple matches, click on the link to the
PNAS article. You should see a page with the title, the abstract
and a listing of similar articles. How many similar articles
(click on the link in right hand bar, scroll down and click on view
all) are linked to this article?
When was the most recent published (Hint: In the Display Options
pull-down menu set the "Sort by" option to Pub
date)?
How many articles cite the Woese 1977 PNAS paper, how many of these
are publicly available? (click on "Cited by" in the right bar,
then select "See all Cited by articles". the bar on the left hand
allows to select "Free Full Text")
2. (ca. 5 minutes) (Note: If Entrez'
pulldown menus do not work well, use another browser)
In NCBI's
Entrez/pubmed find the earliest paper co-authored by Senejani and
Gogarten. What is the topic of the paper?
To learn about inteins, in NCBI's
Entrez select books as the target database to search (pulldown menu to
the left of the search bar) and search for intein homing - the image
in the right column is somewhat informative. For more information
check the books (the first one has a nice chapter on inteins although
most are much longer than the 150 aa that is mentioned as size in the
book), or Wikipedia
on inteins
3. (ca. 5 minutes)
Dr. Johann Peter Gogarten seems obsessed with ATP synthases and
Inteins. Is he interested in anything else? How many articles has he
published that are NOT related to the ATP synthase OR
ATPase OR intein OR inteins?
(Note, a complication is that there is a proliferation of authors with
the same family name :)) - As usually happens, there is more
than one way to formulate the search - parentheses are important.
What query did you assemble?
How many articles did you find?
4. (13 minutes)
Comparing search engines and databases (you want to open pubmed,
google
scholar, and Scopus
in different tabs in your browser. (UConn has a subscription to
Scopus. To use it, you either need to be on campus, or establish a vpn
connection to uconn. Instructions on how to do the latter are here.
Aside, this can slow down your connection to huskyCT and Webex):
For a scientist of your choice (e.g., your advisor, or someone who
publishes in your field of interest), use pubmed, Google scholar, and
Scopus and to search for articles by this author.
Which scientist did you choose?
How many articles authored by this person did you find in pubmed,
google
scholar, and Scopus
(comma separated, if your author of choice does not have a google
scholar profile enter --)
How often was your author cited according to his Google Scholar
profile?
What is the H-index for the author of your choice according to his
Google Scholar profile? (At top in the right column of the Google
Scholar profile)
What is the H-index (google or on the google scholar page, hover the
pointer over the "h-index")?
In Scopus,
search for your author, click on the name(s) of your author, wait ...
Click on citation overview. How many articles did scopus find?
Click on "view H-graph" (link is in the upper right). How often were
these articles cited according to scopus (below the graph)?
What is the H-index for the author of your choice according to Scopus?
5. (15 minutes)
Using Pubmed,
search for articles co-authored by Taiz and
Gogarten.
a) How many articles did you retrieve?
b) select the article by L Zimniak, P Dittrich, J P Gogarten, H
Kibak, L Taiz. Scroll down to associated data, what is
listed?
.
c) Select search in nucleotides. Then select "run blast" in the right
hand column. On the form under organisms enter flowering plants
(start typing, then select from the offered choices). Under
algorithm options, increase the number of matches to 5000, and
decrease the expect threshold to 0.0001. Place a check-mark in
"show results in a separate window" and click on BLAST. Check
"select all".
How many matches did you obtain?
d) Go back to the nucleotide entry (or here).
Click on the link behind "Protein_id". Scan through the genbank
entry for this protein, then select "run blast" in the right hand
column. Under algorithm options, increase the number of matches to
5000, and decrease the expect threshold to 0.0001. Place a check-mark
in the "show results in a separate window" and click on BLAST.
Once the search is done (which takes time), it will take some more
time to completely load the results. Check "select all"
How many matches did you obtain?
e)What might explain the difference in the number of matches
from the two searches?
6. (10 minutes)
Using Entrez,
search Protein (use drop-down box to select
the Protein database) for 19888400 (this is
a gi number, see historical
note)
Run a BLAST search (same parameters as above) except select
the taxon Thermoplasmatales (taxid:2301). Select the graphic tab
once the search is done (the results are displayed piece by piece, you
need to wait until the graphics tab shows up).
Do you notice anything interesting about the alignments? (think
intein)
Click on the Taxonomy Tab and then on Taxonomy. For which genus and
species are most homologs to 19888400 reported?
7. (5 minutes)
To what domain (super kingdom), phylum (kingdom), and family does Thermoplasma
belong? (Use the Taxonomy
Search. or click on Thermoplasma in the taxonomy report from the
last exercise. In the line labeled lineage, if you hover the mouse
pointer over the names, it tells you which taxonomic category you are
pointing at. )
How many protein and genome sequences are available for Thermoplasma
acidophilum, how many are available for the genus Thermoplasma?
(In the taxonomy browser go to Thermoplasma and check
protein and genome in the header, then click on <Display>)
Check the appropriate radio button below before pressing the submit
button: