Saturday 15 December 2018

Reference Management Tools


Bibliographic management software is Referral software designed to establish, store, sort and use bibliographic references of articles, books or even websites to facilitate the citation and to automate the production of bibliographies for various publications scientists



Principle of operation

Bibliographic reference management tools are based on the principle of data separation and formatting. Indeed, all the information and data are stored in a database in separate fields (author, title, place of publication,) which makes it possible to use it by applying for each text a different and adapted formatting the constraints of publishing houses, research institutions, journals etc. In concrete terms, the information stored in the database is therefore, for example, as follows:

For your thesis you must for example apply the style of the German standard DIN 1505-02:
For the publication of an article in a magazine, you are asked to respect another particular style (here that of the journal trajectories):

And for a presentation of a thematic bibliography of your university, you must provide references in accordance with yet another style (here that of the EHESS):
These three different layouts can be produced in just a few clicks and seconds with a bibliographic reference management tool.

The features of bibliographic reference management tools
 1. Feed the database

The tools allow you
 to add bibliographic records manually
 retrieve records from a library catalog
 to import and export bibliographic records
2. Work with bibliographic references

You can
 Search and sort records
 Organize records into folders and subfolders
 Work with keywords in the bibliography
 Annotate bibliographic records
3. Exploit bibliographic references

It is possible to
 Generate on the fly a bibliography of references selected according to different predefined styles
 Integrate bibliographic references into a word processor (Word / OpenOffice) to quote references in the text

The different types of applications

1. Specific software
Software that installs on a personal computer and stores all data locally. For example :
Endnote (paid software)
Jabref (free software)

Advantage: This solution guarantees independence from an internet connection because all information is stored on a personal computer. It is therefore possible to work on and with the data even without having an internet connection.

Disadvantage: If one often changes working environment (on a desktop computer, at home, a laptop, a computer at the library etc.), specific software installed locally is not suitable, because the data is precisely stored on a computer and remote access is not possible.

2. An online platform
An internet application that stores all data on a server. Access is through a personalized account. For example:

Ref works (paying, inquire for a campus license from his university)
Sign up for free

Advantages and disadvantages are reversed compared to the locally installed software solution. The online platform allows optimal synchronization for someone who works on several different workstations, but is a disadvantage in case of work situation without internet connection.
 3. Plugin / extension in the Firefox browser

The application is an add-on module to install in the Firefox web browser.
The zotero tool can nowadays be installed as standalone software or as an extension for some internet browsers, especially Firefox. Thanks to a custom account system on the zotero server, this tool combines the advantages of the two previous solutions. The data is stored on a personal computer, but is synchronized with a remote server which allows to use its bibliographic references of any workstation while also having them locally on his own computer.

Criteria of choice for a tool

For the practical work of our seminar, we have chosen zotero as a working tool, but we encourage our participants to also check with their university and research center about the tools and licenses available. Here is a short list of criteria for choosing a tool:
Compatibility for automatic record retrieval with popular catalogs of libraries and databases
Compliance with standard formats for import / export

Minimum desired features

The cost of software and possible access to campus licenses through his university
The complexity / time of training to use
Personal work mode (on one or more computers)
Compatibility with its operating system (Windows, Mac, Linux)
The variety / adaptability of bibliography styles
Automatic recovery, import and export
The first two criteria are undoubtedly the decisive criteria and deserve to be briefly developed. Automatic retrieval of bibliographic records from library catalogs and databases is fundamental. It can be done in different ways.

1. A transfer function between the search tool and the bibliography management tool
                        This is the case for zotero for example: if the search tool is compatible, a function allows to recover in a few clicks either a list of results or a single bibliographic record.

2. An export function in the search tool and an import function in the bibliography management tool
                      The import / export feature is doubly important. Firstly, it also allows automated retrieval of bibliographic records from a search tool (especially in the catalogs of German library networks) to its bibliographic reference management tool. The recognized computer formats are BibTex, Endnote, RDF, RIS; some bibliography management tools also manage the MARC librarian format. If the bibliography management software that we choose reads and exports in these formats, we keep - secondly - also a freedom vis-à-vis the different software, because we can change software at any time without losing references already collected previously.

3. A remote database query function in the bibliography management tool
                          Ref Works offers a third way to automatically retrieve bibliographic records from catalogs, bibliographies and databases: it is the bibliography management tool that acts as a metamotor by directly querying resources via a Ref Works common interface. By going through the protocol Z39.50, an interconnection protocol used in the world of librarianship, we have in Ref Works access to the catalog of the BNF for example, while a recovery of records of the BNF is not possible with zotero . However, this search interface also has the disadvantage of all metamotors: since the search is not performed in the interface of the resource in question, but in an interface implanted above.

What is the use of bibliographic reference management software?


Referral software has 3 main functions:

Easily collect references, either one by one or in batches, by clicking a button or importing a file, from an existing database, connected websites or from publisher sites,


Manage their references, classify them, annotate them, tag them, and export them,

Quote a reference within a text, from a classic office automation tool or from Latex, and generate a bibliography, while adopting a style (format) of presentation (chosen or imposed by a review).
There are dozens of tools of this type, free or paid, each having developed some features more than others according to the needs of a community, the operating system for which it works, the interest also of the funders of their developments.

How to choose?

Since some LGRBs allow the creation of bibliographies or collaborative collections and that this idea interests you, it is advisable to inquire about the habits of your community, your laboratory or the members of your research project and to choose the same tool. In the same vein, the fact that the tool is also a form of social network can count if you want to expose your bibliography to identify new collaborators.

Being able to annotate PDFs and even share notes with collaborators is a feature that is generally appreciated. Some tools integrate this functionality directly, others allow it by using a third-party PDF reader. This is the case of Zotero for which there is also the possibility of using the ZotFile application (which also allows a Zotero mobile operation).

Being free, free or paid can also be a criterion, as can the limits of file storage space (to be distinguished from the limits in the number of possible references). To work around the problem if you have a large library of PDFs, you have to check if the tool allows outsourcing the storage by using another service like Google Drive, Drop Box or Box. For Mendeley, it is necessary to simply indicate a directory in the "cloud" as being an "watched folder"; for Zotero, it will be a question of setting up a WebDav server.

The operating system of your usual computer and the use of LaTeX are also 2 fundamental criteria in your choices, like the compatibility with your favorite browser, or the fact that the tool works entirely from the web.

The existence of an application for tablets and smartphones now counts more and more, even if it is especially here to be able to read and annotate the documents rather than to quote them in a text.
The fact that the DirDoc IST Cluster can organize Zotero trainings in your lab can also influence you. That said, if you want to opt for another tool, or migrate from one tool to another, Le Lab can help you in your approach.

There are comparators that can help you make your choice:

   The dedicated page of Wikipedia ,
   The most complete comparator is probably that made and updated by the library of the Technical University of Munich,
   The comparator of the Imperial College ,
   this post which presents the advantages and disadvantages of Zotero, Mendeley, EndNote, Papers, Ref Works,
·         A very detailed comparison of Zotero, Mendeley and Docear (by Docear),
·         A comparative table of Endnote, Mendeley and Zotero developed by MIT.

Migrate from one tool to another

If you want to change bibliographic reference management tools, you will need to export your database and then re-import it into the new environment. Check the Wikipedia page to identify the format (s) that are both exported to your starting tool and imported by your new tool.
Do not hesitate to contact Le Lab for help with a major migration operation.

Style

A style (output style) is used to format the rendering of a reference call (examples: (Doe 2015) or (Doe, 2015) or a number referring to the complete reference) and also the rendering of the complete bibliography at the end of document. You can choose the one you like the most, but in most cases it will be imposed by the magazine or conference to which you submit a paper, for example.

Many tools include the ability to choose from a library of styles that can be expanded by downloading a new style. Zotero proposes for example to visualize the format of a style and to download it then to integrate it to the tool, to see this page. They can be installed in other tools as they are developed in a standard CSL format. EndNote also offers a catalog.

The cloud, synchronize its data

Some tools only work from a computer, but more and more, they are connected to a platform. This means that after creating an account, it becomes possible to access via an Internet browser all its references and sometimes even the full text. It is also what allows access from several computers, his smartphone or his tablet. However, care must be taken to synchronize the possible modifications made on a terminal so that they are reflected in the opening of others.

EndNote allows you to synchronize your database with the EndNote Web version embedded in the Web of Science bibliographic database.

Zotero provides online access to its library but the online interface remains minimalist.
Mendeley also allows synchronization with an online account that powers the user profile that allows you to take advantage of social networking features.