Importing records

From refbase

This document describes how to import records into your refbase database.

Contents

Supported import formats

refbase-0.9.0 and above features a generic import script (import.php) which allows to (batch) import records from various common bibliographic formats and online databases. Supported import formats:

(*) Formats marked with an asterisk are provided via Bibutils.

Records from arXiv.org, CrossRef.org and PubMed.gov can be imported directly via their identifiers — simply enter one or more arXiv IDs, DOIs/OpenURLs or PubMed IDs (PMIDs), and refbase will fetch & import the corresponding record metadata.

If you'd like to see support for any additional format, contact us and we'll see what we can do.

Import from other reference managers & bibliographic databases

Please see here for instructions on how to get bibliographic data from desktop reference managers or online reference management services into a refbase database. See here for instructions on how to import data from bibliographic databases (such as PubMed, ISI Web of Science or publisher-specific database services like ScienceDirect).

Alternatives to web-based import

Besides import of records via the web interface, refbase provides a 'refbase_import' command line client to (batch) import records via the command line or directly from PubMed. There are also other methods to perform a manual batch import via the command line, such as an Endnote style file and PHP script which allows Endnote users to transfer data into refbase at the command line.

In addition, refbase allows PHP developers to write their own import parsers and use the provided templates to import their records into a refbase database.

Import road map

On the programming side, we'd like to provide a standardized import interface (such as a uniform PHP array or object structure) and make this standard among the bibliographic projects of the Bibliophile initiative. This would enable developers of different bibliographic projects to develop importers that would be interchangable among applications.

Similar to the current export integration, we'd like to develop a native MODS XML importer and tightly integrate with Bibutils for standardized conversion into other bibliographic formats.

Future versions of refbase may provide for duplicate detection methods upon import and offer integration with bibliographic desktop applications so that users could upload their data directly from within their desktop apps.

Format-specific notes

Problems with special characters when exporting RIS from Reference Manager

The RIS format, as exported by Reference Manager (we've tested version 9.5), does not seem to support higher ASCII characters (such as accented characters or umlauts). If you know how to export these special characters from Refman to RIS, please let us know. Additionally, the RIS format is a common format available for export on journal websites (such as from Elsevier). All of these citation exports in RIS format do not contain higher ASCII characters. As a result, you should check the correct spelling of all of your RIS imports to have correct references in your database.

Note that this is not a problem of refbase. I.e., if your RIS files display special characters correctly, these files should get imported correctly.

Besides RIS, Reference Manager does support other export formats (like MEDLARS and comma/tab-delimited text), which correctly support output of special characters. In the future, we'll hopefully find a workaround to import one of these formats. Don't hesitate to contact us, if you're experiencing this problem.

Import from CSA Illumina

In former versions of refbase, the complete CSA export text could be copied into the import form. Due to the integration of support for other bibliographic formats, this procedure had to be changed in the last versions. Now, you have to delete all text before the line Record x of xx. As an example, here's the beginning of a typical CSA record:

Thu May 18 1:47:09 EDT 2006
CSA

Record 1 of 1

DN: Database Name
    ASFA: Aquatic Sciences and Fisheries Abstracts
TI: Title
    Mesoscale features of phytoplankton and planktonic bacteria in a
    coastal area as induced by external water masses.
AU: Author
    Casotti, R; Brunet, C; Aronne, B; D'Alcala, MR
AF: Affiliation
    Stazione Zoologica 'A. Dohrn' Villa Comunale, 80121 Naples Italy
SO: Source
    Marine Ecology Progress Series [Mar. Ecol. Prog. Ser.]. Vol. 195, pp.
    15-27. 2000.
IS: ISSN
    0171-8630
DE: Descriptors
    Phytoplankton; Flow cytometry; Chlorophylls;

In this example the first three lines must be deleted before import.

Example records of supported formats

This section presents examples of supported bibliographic formats. These examples may help to check your installation. If you encounter problems when importing records into your local refbase database, you may want to compare your own source records with the sample records given below (which should get imported correctly). This may help to track down whether your problem is caused by your installation or by some incorrectly formatted source records (e.g., CSA is known to output some records incorrectly).

Sample records of supported formats:

You should be able to copy the complete sample text and paste it into the import form of import.php.

Let us know, if you run into any problems!