Papers Page Code

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** Papers Master **
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*Papers Master  
<Labid> - id by which to refer to the article <br />
<Labid> - id by which to refer to the article <br />
<PMID> - PubMed id<br />
<PMID> - PubMed id<br />
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<Citation> - citation of the article (author, journal, year, etc) (If pubmed id exists, leave blank)<br />
<Citation> - citation of the article (author, journal, year, etc) (If pubmed id exists, leave blank)<br />
<preprint> - URL of the preprint file<br />
<preprint> - URL of the preprint file<br />
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<subjects> - specifies the grant(s) funding the paper (e.g. "cegs,keck") (refer to Papers Subjects)<br />
<website> - supplemental website<br />
<website> - supplemental website<br />
<Year> - published year of an article (must fill in) <br />
<Year> - published year of an article (must fill in) <br />
<footnote> - footnote of this article <br />
<footnote> - footnote of this article <br />
<website2> - second supplemental website<br />
<website2> - second supplemental website<br />
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** Papers Subject **
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*Papers Subject  
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<Category> - name of subject areas<br />
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<Category> - classification of research areas<br />
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<LabID> -name of subject areas <br />
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<LabID> -name of grants <br />
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<grant> - specifies the grant(s) funding the paper (e.g. "cegs,keck")<br />
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<Title> - brief description of grants <br />
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<Website> - website of research grants <br />
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<Html> - content appears on webpage <br />
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</blockquote>
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The tags can conceptually be divided into two groups: ones such as PMID and labitle, which serve to identify the paper, and tags such as website and subject which supply supplemental information about the paper. There are three ways to identify a paper (in order of decreasing precedence):
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The tags can conceptually be divided into two groups: ones such as PMID and labitle, 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):
# PMID
# PMID
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# labtitle, labcite
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# Title, Citation
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# labtitle, Authors, Journal and optionally Year, Volume and Pages
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For the proper display of the paper, at least on of these methods must be specified in citation.xml. 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.
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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.
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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 <tt><grant></tt> and <tt><preprint> </tt> is strongly encouraged. (Please consult Mark for guidelines on citing grants.)
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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 <tt><subjects></tt> and <tt><preprint> </tt> is strongly encouraged. (Please consult Mark for guidelines on citing grants.)
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'''CGI and Perl scripts:''' These are invoked from a password-protected directory on the server ([/papers_template click here to access]). You can view the source code [scripts here]. The most important script that most people will use is <tt>papers.cgi</tt>. This simply invokes two other scripts:
 
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* <tt>importEprint.sh</tt> creates the directory <tt>/web/papers/skel</tt> which is used for collecting citation info later on. It will back up the existing copy of <tt>/web/papers</tt> to <tt>/web/papers_template/backup/skel_DATE.tar.gz</tt>, which can later be recovered.
 
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* <tt>papers.pl</tt> is a script that takes a main XML file containing a list of articles in NCBI format, and collects information contained in the copies citation.xml files found in <tt>/web/papers/skel</tt> which specify supplimental information for the articles in the main file. It will add any papers not in the list downloaded from the NCBI to the overall list, which is saved in the file <tt>/web/papers/papers.xml</tt>. The following files are produced by this script: 
 
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<blockquote>
 
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/web/papers/index.html<br/>
 
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/web/papers/paper-tags.htm<br/>
 
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/web/papers/paper-ids.htm<br/>
 
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/web/papers/papers-simple.html<br/>
 
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/web/papers/papers.xml<br/>
 
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/web/papers/[labid]/index.html<br/>
 
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/web/papers/grant/index.html<br/>
 
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/web/papers/grant/[grantid].html<br/>
 
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</blockquote>
 
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The other scripts of importance:
 
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* <tt>downloadXML.cgi</tt> obtains a complete listing of Mark's publications from PubMed. This is a non-trivial task (and currently relies on the NCBI not changing any aspect of their site). The downloaded file is <tt>/web/papers/NCBIData.xml</tt>. This script should be invoked whenever a new paper is published.
 
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* <tt>rollback.cgi</tt> recovers an earlier copy of <tt>/web/papers</tt> in case of disaster. Backups are stored in <tt>/web/papers_template/backup </tt>.
 
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Revision as of 14:09, 12 September 2011

Contents

New Stuff

MBGLab--Papers-Master

Papers-Subjects

Automatic generation of publication documents from SpreadSheet

Return to index

Introduction and guidelines: All papers are defined by a unique "labid" such as "pgenes-nar" or "genome-transposon-nature". Ideally, the labid should contain the abbreviated subject and journal name as shown. To add a paper, you simply need to go to MBGLab--Papers-Master (Link above) , then fill in the corresponding columns. If you also want to add a new subject area, go to Papers-Subjects (Link above). After finishing adding new papers, go to Private Wiki and find the rebuild link (under Papers / Manuscripts ), then click it.

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 (If pubmed id exists, leave blank)
<Citation> - citation of the article (author, journal, year, etc) (If pubmed id exists, leave blank)
<preprint> - URL of the preprint file
<subjects> - specifies the grant(s) funding the paper (e.g. "cegs,keck") (refer to Papers Subjects)
<website> - supplemental website
<Year> - published year of an article (must fill in)
<footnote> - footnote of this article
<website2> - second supplemental website
  • Papers Subject
<Category> - classification of research areas
<LabID> -name of grants
<Title> - brief description of grants
<Website> - website of research grants
<Html> - content appears on webpage

The tags can conceptually be divided into two groups: ones such as PMID and labitle, 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):

  1. PMID
  2. 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.)

Rebuild Link

Rebuild Link on private wiki

Old Code Page

Redirect Papers Page Code Old

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