Difference between revisions of "International C. elegans Meetings - UCLA"

From WormBaseWiki
Jump to navigationJump to search
Line 35: Line 35:
 
****year
 
****year
 
****journal
 
****journal
****identifier = evowm2014
+
****identifier
  
 
=Proofreading=
 
=Proofreading=

Revision as of 21:37, 5 January 2015

Contact Information and File Specifications

  • Contact Anne Marie Mahoney at the Genetics Society of America. The GSA has worked with us in the past to get International Meetings into WormBase.
  • They will send us a parseable file of abstracts in which each abstract is a separate file, named according to its program number.
  • Also ask for a participants list, containing names, addresses, email addresses, and institutions, for Cecilia's records.
  • Juancarlos can parse the abstracts into mangolassi where we can proofread them before entering them into the editor on tazendra.

File Format

  • The International Meeting Abstracts are sent to us in a specific file format, with tag:value attributes that are readily parsed into the paper tables (pap_).
  • Each abstract is sent as an individual file, named according to the abstract number, e.g. 826C.txt
  • Below is the list of tag names. Authors and Institutions are listed sequentially, with increased numerical values, if needed.
    • AbstractNo :
    • Title :
    • Author 1 :
    • Presenting Author :
    • Study Group :
    • Author 1 Affiliation :
    • Institution 1 :
    • Body of Abstract :

Parsing Scripts

  • Meeting abstracts are located in directories, named according to the meeting, here: /home/postgres/work/pgpopulation/pap_papers/abstracts
  • There are two scripts that we run for processing the abstracts:
    • unaccent.pl - this script converts accented characters to unaccented ones
    • parse.pl - this script parses the abstract information into the correpsonding paper tables
      • The parse.pl script has some values that need to be set for each specific meeting:
        • year
        • journal
        • identifier

Proofreading

Things to check for in parsed files:

  • Does the abstract number in the identifier match the abstract number in the program?
  • Are author names correct, i.e. are there any foreign characters not translated correctly?
  • Does the text of the abstract start and stop at the right places?
  • Are symbols represented properly, e.g. 3'UTR?


Back to Paper pipeline