Difference between revisions of "Entering WBG Articles"

From WormBaseWiki
Jump to navigationJump to search
Line 21: Line 21:
 
''Journal  Worm Breeder's Gazette''
 
''Journal  Worm Breeder's Gazette''
  
Volume  nn (where n = a number)  '''(We currently don't have a field for number in postgres, so should we create Volume numbers that are 18.2 or 18.3 using information from the Number of the latest Gazette issue?  Or ignore the number field entirely?  --K.)'''
+
Volume  nn (where n = a number)  (We currently don't have a field for number in postgres, so should we create Volume numbers that are 18.2 or 18.3 using information from the Number of the latest Gazette issue?  Or ignore the number field entirely?  --K.)''' we do, it's between pages and year, and it has an 18 for this set from Daniel's file -- J'''
  
 
Year  20nn (where n = a number)
 
Year  20nn (where n = a number)
Line 31: Line 31:
 
Author  listed as Last Name, First Name//Last Name, First Name//Last Name, First Name  etc.
 
Author  listed as Last Name, First Name//Last Name, First Name//Last Name, First Name  etc.
 
    
 
    
Affiliation  list all affiliations  '''(How do we want to handle multiple affiliations?  Comma separate? --K.)'''
+
Affiliation  list all affiliations  (How do we want to handle multiple affiliations?  Comma separate? --K.) '''It's a multivalue field, so if the data file had them in separate lines with their own tag, it would presumably work, but I haven't tested that.  The file, at a glance, has one affiliation entry per paper entry -- J'''
  
 
URL - corresponds to the URL of the article in the PDF document
 
URL - corresponds to the URL of the article in the PDF document

Revision as of 18:27, 13 January 2011

Entering WBG Article into Postgres

We would like to enter WBG articles to postgres as soon as they become available on line so they can be incorporated into WormBase as WBPapers.

  • Check text files of abstract titles, authors, and affiliations for special characters (e.g. vowels with accents) and convert them to standard characters before reading into the database, since ACeDB doesn't allow special characters.
  • Articles can be read into the development database and checked using the paper editor on mangolassi.caltech.edu

General File Format

Here is a general file format for uploading to postgres, followed by a specific example.

Note that for WBG articles, there are some values that do not change, e.g. Status (Valid), Type (Gazette_article), Journal (Worm Breeder's Gazette), and Primary_data (not_designated). Also, the identifiers are created according to the information in the volume, number, and page. These special fields are italicized below.

Identifier wbg.nn.n.nnnn (where n = a number)

Status Valid

Title First letter capitalized

Journal Worm Breeder's Gazette

Volume nn (where n = a number) (We currently don't have a field for number in postgres, so should we create Volume numbers that are 18.2 or 18.3 using information from the Number of the latest Gazette issue? Or ignore the number field entirely? --K.) we do, it's between pages and year, and it has an 18 for this set from Daniel's file -- J

Year 20nn (where n = a number)

Month nn (where n = a number)

Page n or nn (where n = a number)

Author listed as Last Name, First Name//Last Name, First Name//Last Name, First Name etc.

Affiliation list all affiliations (How do we want to handle multiple affiliations? Comma separate? --K.) It's a multivalue field, so if the data file had them in separate lines with their own tag, it would presumably work, but I haven't tested that. The file, at a glance, has one affiliation entry per paper entry -- J

URL - corresponds to the URL of the article in the PDF document

Type Gazette_article

Primary_data not_designated

Specific Example

A specific example with all information dispayed:

Identifier wbg18.2.0002

Status Valid

Title Antibiotic markers for rapid selection and easy maintenance of transgenic nematodes

Journal Worm Breeder's Gazette

Volume 18

Year 2010

Month 06

Page 2

Author Giordano-Santini, Rosina//Semple, Jennifer//Dupuy, Denis//Lehner, Ben

Affiliation Genome Regulation and Evolution, Inserm Unit 869, and Institut Europeen de Chimie et Biologie, Bordeaux, France

URL http://www.wormbook.org/wbg/volumes/volume-18-number-2/pdf/wbg-volume-18-number-2.02.pdf

Type Gazette_article

Primary_data not_designated


Back to Paper Pipeline