Intern:Reference



During data import, the relation between a data set and its reference is set. Several references can be related to a data set but in principle, real primary data should be supplementary to one reference only.

Prior to a data import, the reference has to be defined in the reference table. If a paper has a persistent identifier (DOI), it is entered in the URI-field; if no identifier exists, a link to the paper in pdf-format should be given instead (see the pdf-article on how to prepare and link pdf-files for Pangaea).

To add a new reference in 4D, click on Reference, click new. As a first step (if known), you should enter:


 * URI: should be a DOI, urn:nbn, hdl etc. or any other persistent identifier. NO links to web pages - use persistent identifier when ever available! (add the 'protocol' to the URI with ':', e.g.
 * pdf-files can be stored in the repository ePIC which provides a handle for persistent linking or any other repository with persistent identification.
 * pdf-files can be stored in the repository ePIC which provides a handle for persistent linking or any other repository with persistent identification.
 * pdf-files can be stored in the repository ePIC which provides a handle for persistent linking or any other repository with persistent identification.

You can now click on "Get Metadata" which will try to extract all of the following information from the given URI. This works with DOI Names (provided by Crossref or DataCite), some Handle types (only if provided by ePIC), but also with plain URLs to PDF/HTML/... files. For DOIs the metadata is requested from the publisher through web services. Otherwise it is extracted from the ePIC website for handles pointing to ePIC or, as a last chance, extracted directly from the PDF or HTML page (title, sometimes also authors and year) using Apache TIKA (see the webpage for all supported file formats).

It may happen that some of the information below needs to be completed, e.g., if the authors do not yet have entries in the staff table:


 * Author(s): Names must already be defined in the staff table and will be added by multiple choice selection
 * Title: full title (not abbreviated, lower case for all words but for proper nouns, no full stop at end)
 * Source: this field should be used for monographs, e.g.
 * Books - In: Bleil, U & Thiede, J (eds.), Geological History of the Polar Oceans, NATO ASI Series, Kluwer Academic Publishers, London
 * grey literature like special reports, etc. not published in a series
 * disseration thesis, self published and issued just by the university
 * Journal: relational field to a table with 16500 most common journals (new journals can be added to the Journal table via menu View/Journal)
 * Volume: 53(2)
 * Pages: 34-67 or 123 pp for complete books, thesis, reports etc.
 * Year: 1998 (for papers 'submitted' or 'in press' leave empty)
 * Status: contains the "prepublication" status of a reference. If this is set to something != "published", like "in press", the citation is formatted using this status instead of the year.
 * Serial No (optional): proprietary publication number, e.g. AWI publ No 1234 or PKDB56789
 * Type: choose as appropriate from the Publication type choices list
 * Keywords (optional): select from thesaurus or define new as required

! If using copy/paste to fill the fields, avoid to add carriage returns, redundant spaces or spaces at the end of an entry.

Import
A list of references can be imported as tab-delimited ASCII-file. A format and header template is provided in the 'IMPORT FORM FOR REFERENCES' by using Menue File/Import, choose References. Authors are also recognized by staff IDs. Author in the import list will be recognized if:
 * name and first name are identical, notification if several similar names
 * name and initials are identical, notification if several similar
 * name identical and initial identical with initial of first name (first letters of several first names are added for comparison)
 * name identical and 1. initial identical with initial of 1. first name (only if no other similar names are archived, e.g. Shackelton, N is recognized because Shackelton, Nicholas J is the only record with name Shackelton in the staff list.

For the reference management software EndNote an export style is provided: which produces a file ready for import to 4D/pangaea.

Delete
Attention is required when a reference is deleted! Even if relations to data sets exist, the reference can be deleted. While pressing  the curator is prompted with a requester: x related records in 'DATA SET' - do you want to delete relations?  will delete reference and relations.

Citation
Supplementary data should be submitted and imported before a paper is in press. After import and proofread of the data, the author is provided with a DOI for data citation/identification to be used in the publication. The paper should not just refer to the Pangaea domain, but give the link precisely pointing to the relevant data.

Examples:
 * as a link to one specific data set or
 * as a link to a number of data sets (childs), grouped in a parent set or
 * http://www.pangaea.de/search?q=@Ref896 (896 is the PANGAEA internal reference ID) to show many data sets related to a publication without a parent definition. This link may be used if many data sets (some thousand) are related to one reference.

For refering in a publication to its primary data, the author should refer to the data by using a note like (example): Supplementary data are available at 

Import from DOI metadata

 * Check carefully all fields (no returns, no empty spaces, special characters
 * The capitals (initial capital, all caps) can be kept from the paper publisher

Links

 * Connotea Free online reference management (provided by Nature, operation stopped in 2013)
 * refbase Web Reference Database
 * example: Literature Database SK Ozeanographie (not valid anymore in 2014)
 * ISO standard for bibliographic referencing