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csv_import_format

JournalMap CSV Bulk Import Format

Bulk uploads of articles into JournalMap can be accomplished through importing formatted CSV files. Citation information is put into an articles.csv file and location information for each article is in a separate locations.csv file. The two-file format allows for us to easily accommodate situations where there are multiple locations for a single article. The article DOI and title are the linking fields between the articles.csv and locations.csv file; thus it is crucial that these two fields be identical between files.

It is recommended that you use a spreadsheet program, scripting environment, or text editor that writes in unicode UTF-8) for preparing these CSV import files. I will often used Google Sheets for this purpose or write scripts in Python to format the CSV files. Microsoft Excel uses a different text encoding which can mess up special characters in names, titles, or abstracts.

Listing of fields for the CSV files (bolds are fields names). Field names must be input exactly as listed below and in the same order (the CSV importer in JournalMap is finicky).

Article CSV Fields

  • doi - Article DOI number if it has one (blank otherwise)
  • publisher_name - Journal title (e.g., Ecological Applications). Cannot have semi-colons in the title.
  • publisher_abbreviation - Optional (vestigial) - We don't really use this anymore
  • citation Optional (vestigial) - The fully formed citation for the article.
  • title - Article title.
    • It is critical that this match the title in the locations.csv file exactly!
    • When no DOI is present the title is the linking field between the article and its locations.
  • publish_year - year the article was published
  • first_author - First author (e.g., “Karl, J.W.”)
  • authors_list - comma-separated list of all authors in the form of “Karl, J.W., Gillan, J.K., Herrick, J.E.”
    • (with or without periods OK, but separated by commas)
  • volume_issue_pages - fully formed statement of volume, issue, and pages (e.g., “12(3):45-67”)
  • volume - if present, otherwise blank
  • issue - if present, otherwise blank
  • start_page - if present, otherwise blank
  • end_page - if present, otherwise blank
  • keywords_list - comma- or semi-colon separated list of article keywords if present. Otherwise blank.
  • no_keywords_list - Required
    • true = keywords not present
    • false = keywords present
  • abstract - text of abstract if one is given. Otherwise blank.
  • no_abstract - Required
    • true = abstract not present
    • false = abstract present
  • url - Optional - Article URL if one is given.
    • Sometimes an article will have a DOI that will point to a publisher's page for that article, but an organization may also have a page/record for that article on their system. The URL field gives an opportunity to point to that page as well. Can also be used for articles that have no DOI.

Location CSV Fields

  • title - Article title (as it appears in the articles.csv table)
  • doi - Article DOI (if it has one)
  • latitude - Latitude value in geographic decimal degrees
  • longitude - Longitude value in geographic decimal degrees
  • place - Text-based location description as it was given in the article.
  • no_recorded_place - Required
    • true - No text-based location description given
    • false - Text-based location description WAS given
  • coordinates - Coordinates as recorded in article (copy/paste). Blank if no coordinates given.
  • coordinate_type - Optional - if coordinates were reported, what was the coordinate system?
    • Geographic Coordinate System (GCS)
    • Universal Transverse Mercator (UTM)
    • Universal Polar Stereographic (UPS)
    • Military Grid Reference System (MGRS)
    • US Public Land Survey (PLSS)
    • Great Britain Ordnance Survey National Grid (GBOS)
  • no_recorded_coordinate - Required - Flag for no coordinates were reported in an article.
    • true - no coordinates reported
    • false - coordinates were reported
  • location_type - Optional - What was the location type reported?
    • point
    • linear feature
    • bounding box
    • polygon/area
    • other
  • location_scale - Optional - What was the area represented by the location reported?
    • site
    • local
    • landscape
    • state
    • region
    • continent
  • location_reliability - Optional - How reliable was the location information?
    • 1 - Study approximately mapped from vague place name or coordinates
    • 2 - Study location automatically assigned from JournalMap location parser
    • 3 - Study mapped from a specific place name or high-precision reported coordinate
    • 4 - Study mapped from coordinates and verified by place name
    • 5 - Study accurately located by the author
  • location_conformance - Optional - How well does the reported location match the intended scale?
    • 1 - Poor
    • 2 - Fair
    • 3 - Good
    • 4 - Great
    • 5 - Excellent
  • error_type - Optional - Were there any errors in the location information reported?
    • Unknown coordinate system
    • Text formatting error
    • Incomplete coordinates
    • Invalid coordinate values
    • Other
  • error_description - Optional - Description of any coordinate error.

Notes

For articles missing a DOI just supply a title and the article will validate. The abstract and keywords_list fields will be required unless the no_abstract and no_keywords_list are set to true. The url is always optional. To tie locations to a DOI-less article, the title field in the location CSV must match the article title exactly. The article CSV file must be uploaded before the locations CSV file or at the same time as the locations CSV file. A couple of the “type” fields don't currently do hard checks to make sure the values supplied by a CSV file are those listed above.

csv_import_format.txt · Last modified: 2015/06/10 13:51 by jkarl

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