Joombib Publications

Joombib Publications Component for Joomla 4.x

Purpose

Joombib is a Joomla component designed to manage and disseminate a library of SCI Institute publications and related bibliographic information in a bibtex-oriented format.

Provide a searchable database of publications with bibliographic information, abstracts, PDF downloads, and citations available in bibtex format.
Provide a method of tagging publications as relevant to various areas of research, SCI sub-projects, and research grants in order to
facilitate filtering lists by such categories.
Provide an efficient method of gathering publications relevant for research grant proposals and progress reports.
Provide a single database that may be shared among various sub-project websites that display only project related publications in order to avoid redundant entry of information.
To enforce collection and maintenance of bibliographic data in a bibtex-comlpient format required by funding agencies.
Provide a way of generating custom lists of publications by author for linking on author profile pages.

Presentation

The publications library is found on the SCI website under "Publications" on the main menu. At the top of the page is a search tool which will find publications matching the search term in the title, authors, journal name, abstract, tagged categories and research and funding grant. Visitors may also filter by publication type or the year of publication. By default, publications are listed by year of publication in descending order and by first author's last name so normally the current year is listed first and an author with a last name starting with "A" may be at the top. Below the search box are pagination links to allow browsing through the search results. By default 20 citations are displayed per page. Below that are buttons to download the entire database of citations in bibtex format or view a printer-formatted bibliography. At the time of this writing over 2,800 publications are contained in the library.

Each citation is accompanied by icons for downloading the publication itself (when available) in PDF format and the bibtex citation. The SCI Institute provides all of its publications to download for free. Whenever possible, the DOI (Document Object Identifier) or other digital identifier is provided and linked to the official landing page provided by the Journal of publication.

Below each citation is a button to expand or hide an abstract of the publication. Abstracts may consist of one or more paragraphs of HTML formatted text as well as any number of images.

Once a publication has been added to the library and tagged appropriately, it may also be listed on the Publications page of any Joomla-based sub-project website that has the (read-only) Joombib Pubs component installed provided that the database server allows connections from that site. By setting the relevant tag name in the component the listing will display only project relevant publications from the database. This allows the listing to display as part of the project's own website consistently with the site's look and feel.

If the database server cannot accept outside connections or the Pubs component cannot be used then sub-projects may still access customized lists of publications simply by linking to the SCI Publications page with a group filter provided. For example, a link for a listing of publications related to the CEDMAV project (Center for Extreme Data Management Analysis and Visualization) is structured as:

https://www.sci.utah.edu/scipubs/all-pubs/pubs.html?groupFilter=cedmav

Users may create custom links to the library that display a list of publications in which they are a coauthor. For example, on Dr. Chris Johnson's profile page there is a link labeled "My Publications" that lists only his publications. The URL just needs the author's name included as a search term and is structured as:

https://www.sci.utah.edu/scipubs/search.html?schTerm=C.R.+Johnson

One additional feature for making followers of SCI aware of SCI's growing library of publications is the weekly Events emailer which is sent out each Monday morning to the SCI mailing list. Along with announcing SCI related events occurring in the following week, the script also checks the publications database for any new publications added in the past week. A list of new publication citations is included in the emailer. This service is provided by the eventsEmailer.php script which is run each morning by cron on the server.

Administration

Publications in Joombib are managed in the Joomla back-end. The Joombib management interface is found under Components in the left side column. The user is initially shown a list view of citations similar to the listing in the front-end. Buttons at the top allow the user to create a new publication, edit an existing one or delete one or more from the database. Below them are search tools and pagination links similar to the front view. The major differences are that rather than the expandable section for the abstract, a list of Search Group checkboxes is displayed as well as an expandable section with a table of Research Group checkboxes is available. The search groups allow publications to be tagged as related to particular funding agencies and research projects. The Research Groups table allows tagging by major and sub-fields of research such as Biomedical Computing and Computational Electrophysiology respectively. Tagging in these sections is Ajax-driven, meaning tags are applied instantly without needing to save or reload the page. This allows whole pages of citations to be tagged at a time for maximum efficiency.

Directly to the left of each citation are icons for editing and changing the published status of each publication. Clicking the green checkmark switches it to a gray "x" and temporarily removing the publication from the front-end website. Clicking again restores it. Above that, a little pencil in a box icon allows editing the publication data.

The Publication Details form is designed not only to collect bibliographic information but also to enforce compliance with bibtex and SCI conventions. An important feature for maintaining this compliance is dynamic form transformation based on Entry Type. The Bibtex convention supports 14 entry types for such things as books, articles, technical reports, and conference proceedings. Each entry type its own set of required fields, optional fields, and ignored fields. When entering a new publication, once an Entry Type is selected from the drop down select the rest of the form changes to include the required and optional fields while hiding others not supported for that type. The form also indicates which fields are required and will not allow submission until those fields are filled. The form also enforces compliance to the SCI format for the bibtex key which should begin with "SCI:" followed by the first three letters of the first author's last name, then the year of publications, followed by a letter of the alphabet. Upon submission, the Key is analyzed, comparing it with the year entered in the Year field, and will not submit if the formatting is incorrect. Digital identifiers such as DOI, ISSN, PMID, etc. will automatically be linked to their official landing pages.

A PDF version of the publication itself and any relevant images may be uploaded on this form. Images uploaded here will be shown along with the abstracts in the front-end but may be clicked on to display full sized pop-up versions. While the Abstract field supports HTML formatting for web display, any HTML elements and certain non-supported characters are stripped out for inclusion in the bibtex citations.

Once a new publication has been added to the library or a change to an existing one has been made, a script is triggered that will update the full SCI bibliography bibtex file as well as the print-formatted HTML bibliography. Since these are larger files that take some seconds to generate, it provides much faster performance to have them generated behind the scenes rather than as part of the saving process. For this to work, the dedicated bib-update.php script must be in place on the server and run by cron regularly to check for changes.

Component Settings

In the upper right hand corner of the Joombib Manager listing page is a button labeled "Options" to access the component settings panel. These are settings that need to be configured once the component is installed or when changes to component behavior are needed. The "Library Title" will appear at to top of the Publications listing page. The "Archive base URL" sets the base URL of where publication files (PDFs) are stored. This allows flexibility in cases where a different than usual path is needed. "Archive base folder" sets the path on the server where files are uploaded in the edit form. The filenames for the bibliography bibtex and HTML files may be specified in the next two lines.
"Preferred Abbrev Form" is related to a feature that is no longer used. Joombib supported specifying types of abbreviations for Journal names as has been requested by certain funding agencies. In cases where this was used, a code was entered in place of the Journal name which would automatically be replaced by either the full name or an abbreviated form in the desired format. For example, "c-CinC" could be translated to "{IEEE} Computers in Cardiology" or "{IEEE} Comp. in Card." This feature, however, has proven too difficult to maintain as it required continual adding of new abbreviations/translations and a way to find the many codes. It has not been used much and is no longer maintained.

"Select Categories" specifies the list of publication types to be included in the search tool's drop down selector. "Search Groups" specifies the list of funding agencies and research project tags to which publications may be tagged in the edit form. "Max image width" and "Max image height" specifies the maximum size of image files that will be stored when uploaded through the edit form. Larger images will be scaled down to this size when uploaded.