Endnote Stye for Bibliometic Analysis of PubMed Reference

Dear All,

I am novice to EndNote, and recently start using Endnote. Can anyone suggest me any endnote style format that gives the detailed information of a reference to extract reference from PubMed in order to analyses biblimetrically.

I Need Information in Following Format

  1. Author/s

  2. No fo Authors

  3. Title of the Paper

  4. Name of Journal

  5. Year of Publication

  6. Author/s Affiliation (if two authors with different affiliation then separated by ‘;’

  7. Country

  8. Vol, Issue, Page information

  9. ISSN

10 Citation if available

i have tried to extract he reference in xml then change to excel, but it is not producing the desired result.

Please help this i need for my PhD work.

Thanks and Regards

I don’t think PubMed has all that information in a downloadable format?  I think the Affiliation field is only given for the corresponding author.  Perhaps Endnote counts the authors somehow, but I don’t think it ends up in a field.  It must count, as it knows when to show the … Last Author for the newest APA 6th style requirements?   


What is the difference between “citation if possible” and the other parsed information? 


You would probably want to obtain the Medline formated records, save the file and run a script to count the authors, insert the number of authors for each record and then import with a modified filter to collect the additional information into a correctly set up reference type with the additional fields you need. 


this would be exported from Endnote in an excel friendly format (tab delimited?)


  1. Author/s parsed into record
  1. No of Authors  would need a script outside to count them? (unless this is coded somewhere?)
  1. Title of the Paper parsed into record
  1. Name of Journal parsed into record
  1. Year of Publication parsed into record
  1. Author/s Affiliation (if two authors with different affiliation then separated by ‘;’ don’t think more than one address is commonly given in PubMed - my current Pubmed connection file doesn’t parse this into record, but a source address is available in PubMed
    7. Country could be parsed Into record
  1. Vol, Issue, Page information: these are individually parsed into Endnote records
  1. ISSN: this is parsed into Endnote records

10 Citation if available ? This can be exported from endnote in any style you like.  - but it is given together, as the last SO item as well. 


An example of most of a Medline text for a record is below. 

PMID- 17237784
DA - 20070130
DCOM- 20070423
LR - 20091119
IS - 1061-4036 (Print)
IS - 1061-4036 (Linking)
<font color="#ff0000">VI - 39 <br></font><font color="#ff0000">IP - 2 <br></font><font color="#ff0000">DP - 2007</font>Feb
<font color="#ff0000">TI - PTEN-deficient intestinal stem cells initiate intestinal polyposis.<br></font><font color="#ff0000">PG - 189-98<br></font>AB - Intestinal polyposis, a precancerous neoplasia, results primarily from an abnormal increase in the number of crypts, which contain intestinal stem cells (ISCs). In mice, widespread deletion of the tumor suppressor Phosphatase and tensin homolog (PTEN) generates hamartomatous intestinal polyps with epithelial and stromal involvement. Using this model, we have established the relationship between stem cells and polyp and tumor formation. PTEN helps govern the proliferation rate and number of ISCs and loss of PTEN results in an excess of ISCs. In PTEN-deficient mice, excess ISCs initiate de novo crypt formation and crypt fission, recapitulating crypt production in fetal and neonatal intestine. The PTEN-Akt pathway probably governs stem cell activation by helping control nuclear localization of the Wnt pathway effector beta-catenin. Akt phosphorylates beta-catenin at Ser552, resulting in a nuclear-localized form in ISCs. Our observations show that intestinal polyposis is initiated by PTEN-deficient ISCs that undergo excessive proliferation driven by Akt activation and nuclear localization of beta-catenin.
<font color="#ff0000">AD - Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.<br></font>FAU - He, Xi C
<font color="#ff0000">AU - He XC <br></font>FAU - Yin, Tong
<font color="#ff0000">AU - Yin T <br></font>FAU - Grindley, Justin C
<font color="#ff0000">AU - Grindley JC</font>
FAU - Tian, Qiang
AU - Tian Q
FAU - Sato, Toshiro
<font color="#ff0000">AU - Sato T<br></font>FAU - Tao, W Andy
<font color="#ff0000">AU - Tao WA<br></font>FAU - Dirisina, Raminarao
<font color="#ff0000">AU - Dirisina R<br></font>FAU - Porter-Westpfahl, Kimberly S
<font color="#ff0000">AU - Porter-Westpfahl KS<br></font>FAU - Hembree, Mark
<font color="#ff0000">AU - Hembree M<br></font>FAU - Johnson, Teri
<font color="#ff0000">AU - Johnson T<br></font>FAU - Wiedemann, Leanne M
<font color="#ff0000">AU - Wiedemann LM<br></font>FAU - Barrett, Terrence A
<font color="#ff0000">AU - Barrett TA<br></font>FAU - Hood, Leroy
<font color="#ff0000">AU - Hood L<br></font>FAU - Wu, Hong
<font color="#ff0000">AU - Wu H<br></font>FAU - Li, Linheng
<font color="#ff0000">AU - Li L<br></font>LA - eng
SI - GEO/GSE6078
GR - R01 DK070001/DK/NIDDK NIH HHS/United States
PT - Journal Article
PT - Research Support, N.I.H., Extramural
PT - Research Support, Non-U.S. Gov't
DEP - 20070121
<font color="#ff0000">PL - United States<br></font>TA - Nat Genet
<font color="#ff0000">JT - Nature genetics<br></font>JID - 9216904
<deleted some mesh and date fields>
<font color="#ff0000">SO - Nat Genet. 2007 Feb;39(2):189-98. Epub 2007 Jan 21. </font>

Thanks for Valuable information.

Please one more query, which fomat of .enl i should use to extract data in this format i mean MEDLINE format. If you have this format with you kindly send me and explain the process to import and use this format


Dear respondant

By Citation i mean how many papers have citated a paper “A” in their articles.

i.e. to say “A” is being cited in how many references if it is there is PubMed.


So you want citation index data as well, which would change over time, and endnote doesn’t currently have a way to update a field automatically with new information. Anyway, PubMed doesn’t provide this metric: http://www.nlm.nih.gov/services/cite.html.  Proprietary databases that you have to pay for, do (i.e. Scopus, Web of Science)

With regard to numbers of authors, I found this cite: http://www.nlm.nih.gov/bsd/authors1.html which might be of interest to you, but doesn’t solve the problem of retrieving the info for individual records. 

I don’t think I can or should provide step by step instructions in a reply to this thread! There are many variations, and it is just too complicated to explain, sorry

You can edit a connection or filter file to include the address and the country location, and use that when you connect to Pubmed from inside Endnote or you can work from PubMed and export the file in the display setting MEDLINE

Or it is probably easier to send to “file” in the format MEDLINE to a text file.  You would then edit the Pubmed filter to include the additional fields when importing the file, and tell endnote what field to send them to.  You probably will also first need to edit the reference types in Endnote to make a field to save the info to.   (some instruction on how to edit connection file are available - for different application).

I recommend you consult the PDF document installed with the Endnote software, the tutorials and webinars that the software vendor provides (see the training forum below these and the www.endnote.com for the support & training website) for help, and the help and tutorials for Pubmed.  For example see - 

http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.How_can_I_save_my_re to learn how to save the results in the different formats.  The PubMed Quick Start Guide is available from here http://www.ncbi.nlm.nih.gov/sites/entrez/

Good luck!


Thats great, I am really thankful to you for providing me such a illustrative  suggestions and guiding me through endnote.

Keep it you, catch you later with some more problems

Shri Ram