Papers Page Code

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(Generate publication documents from SpreadSheet)
(Generate publication documents from SpreadSheet)
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*Build Papers Page  
*Build Papers Page  
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update.py : Generate whole website from spreadsheet[[Build Papers Page Code]]
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update.py : Generate whole website from spreadsheet, see [[Build Papers Page Code]]
==Rebuild and Further (private) Info==
==Rebuild and Further (private) Info==

Revision as of 11:30, 16 September 2011

Contents

SpreadSheet Structure

  • "Papers Page" is generated from two google spreadsheets, "Papers Master" and "Papers Subjects". "Papers Master" stores basic information about each paper. "Papers Subjects" stores information about each grant.

Here is a list of the tags and their meanings:

Papers Master:
<labid> - id by which to refer to the article
<PMID> - PubMed id
<title> - title of the article
<citation> - citation of the article (author, journal, year, etc)
<preprint> - URL of the preprint file
<subjects> - specifies the grant(s) funding the paper (e.g. "cegs,keck")
<website> - supplemental website
<Year> - year the article was published
<footnote> - additional information
<website2> - second supplemental website

The tags can conceptually be divided into two groups: ones such as PMID and title, which serve to identify the paper, and tags such as website and subject which supply supplemental information about the paper. There are two ways to identify a paper (in order of decreasing precedence):

I. PMID
II. title, citation

You should always include the PMID if a paper is known to be listed in PubMed. Option 2 should be used for papers that are in press.

The other group of tags supplies additional information about the paper specified by the first group of tags. All of these tags are optional, however used of <subjects> and <preprint> is strongly encouraged. (Please consult Mark for guidelines on citing grants.)

labid PMID title citation preprint subject website Year footnote website2
metamembrane20430783http://archive.gersteinlab.org/papers/e-print/metamembrane/preprint.pdfinteractionshttp://metagenomics.gersteinlab.org/membrane2010


Papers Subjects:
<category> - classification of grants
<labid> - name refer to each grant
<title> - description of each grant
<website> - external website
<html> - additional information	

We encourage you to sort <category> after adding new grants because of coding issues. <website> should also be reflected in <html> section. For example, "don" has <website> "http://www.donaghue.org", also "URL: <A HREF=http://www.donaghue.org> http://www.donaghue.org</A>" in <html> section.

category labid title website html
Research GrantsdonDongahue Young Investigatorhttp://www.donaghue.org/Young investigator award from Donaghue Foundation to M Gerstein (PI), "Comparative Genomics of Microbial Pathogens," (DF98-113, 1/1/99-12/31/03). URL: <A HREF=http://www.donaghue.org> http://www.donaghue.org</A>Articles funded by this grant:

Generate publication documents from SpreadSheet

Two steps:

  • Download XML file from NCBI using PubMed ID to generate pubmed_spreadsheet. This step is done by scripts automatically.

GoogleSpreadsheet.py : grab googlespreadsheet with python, see Grab_GoogleSpreadsheet_with_a_Python
Other Code: see PubmedSpreadsheet_Generation_Code

First obtain pubmed_result.xml from papers medline query
   parse_pmids.py
curl `cat ncbiquery.txt` > NCBIData.xml Reformat NCBIData.xml to tab delimited file to upload to Google python import.py replace PubMed Import XML spreadsheet with export_out.tab (this can be added to the bottom of PubmedHandler.py instead of exporting the export.tab file using the NewGoogleSpreadsheet.py API)
  • Build Papers Page

update.py : Generate whole website from spreadsheet, see Build Papers Page Code

Rebuild and Further (private) Info

http://wiki.gersteinlab.org/labinfo/Papers_Page_Documentation


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