Papers Page Code

• • 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
<website> - supplemental website
<Year> - published year of an article (must fill in)
<footnote> - footnote of this article
<website2> - second supplemental website

• • Papers Subject **

<Category> - name of subject areas
<LabID> -name of subject areas
<grant> - specifies the grant(s) funding the paper (e.g. "cegs,keck")

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):

1. PMID
2. labtitle, labcite
3. labtitle, Authors, Journal and optionally Year, Volume and Pages

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.

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 <grant> and <preprint> is strongly encouraged. (Please consult Mark for guidelines on citing grants.)

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 papers.cgi. This simply invokes two other scripts:

• importEprint.sh creates the directory /web/papers/skel which is used for collecting citation info later on. It will back up the existing copy of /web/papers to /web/papers_template/backup/skel_DATE.tar.gz, which can later be recovered.
• papers.pl 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 /web/papers/skel 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 /web/papers/papers.xml. The following files are produced by this script:

/web/papers/index.html
/web/papers/paper-tags.htm
/web/papers/paper-ids.htm
/web/papers/papers-simple.html
/web/papers/papers.xml
/web/papers/[labid]/index.html
/web/papers/grant/index.html
/web/papers/grant/[grantid].html

The other scripts of importance:

• downloadXML.cgi 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 /web/papers/NCBIData.xml. This script should be invoked whenever a new paper is published.
• rollback.cgi recovers an earlier copy of /web/papers in case of disaster. Backups are stored in /web/papers_template/backup .