Difference between revisions of "Entering WBG Articles"
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''Journal Worm Breeder's Gazette'' | ''Journal Worm Breeder's Gazette'' | ||
| − | Volume nn (where n = a number) | + | 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 | + | 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
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