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Web-based, platform-independent, multi-user interface for managing scientific literature and citations Refbase is a web-based bibliographic manager which can import and export references in various formats (including BibTeX, Endnote, MODS XML, and OpenOffice). Refbase can make formatted lists of citations and offers RSS, rich metadata and powerful searching. Here are some key features of "Refbase": Main features: · A clean and standardized interface that attempts to be as web standards compliant as possible. · A multitude of search options, including quick, simple, advanced as well as powerful SQL search options. · Various display options: list view, citation view, details view and print view · Search within results functionality which provides an easy way of refining your search query (alternatively, power users can refine any query result by directly editing the raw SQL query). · The ability to extract literature cited within a text and build an appropriate list of citations. Direct download links & easy upload of files: · Direct download links are provided for all records that link to a file. Download links can be made available to either everyone, logged-in users only or on a user-specific basis. In addition, the admin can optionally specify a condition where files will be always made visible. Files can be easily uploaded to the server when adding/editing records, and uploaded files can be automatically moved into subdirectories and renamed according to a customizable naming scheme. File links are included in file exports so that clients such as Zotero are able to automatically download the attached files. Output formatted citation lists: · Refbase can make formatted lists of citations in HTML, RTF, PDF, LaTeX, structured text (Markdown) or plain text (ASCII), and supports common citation styles such as AMA, APA, Chicago, Harvard, MLA or Vancouver. This allows for easy integration with desktop applications when writing a term paper or scholarly article. Citations can be grouped by year or resource type (i.e., peer-reviewed publications, monographs, book contributions, theses, etc). Using this, refbase can be used to generate automatically updating author/group bibliographies for your web site or the yearly report of your organization. Import records: · Refbase offers batch import of records via the web interface or from the command line, and automatically detects records in various common bibliographic formats (BibTeX, Endnote (tagged text & XML), RIS, PubMed (MEDLINE & XML), MODS XML, RefWorks, ISI Web of Science, CSA Illumina, Copac and SciFinder). Records from PubMed can be imported directly via their PubMed ID. In addition, an Endnote style file and PHP script is provided which allows Endnote users to transfer data into refbase at the command line. (more info) Export records: · Refbase supports export of records to common bibliographic formats (ADS, BibTeX, Endnote, ISI Web of Science, RIS, Word XML) by use of Bibutils (bibliography conversion utilities), and can output records in MODS XML format, a bibliographic XML standard developed by the Library of Congress. In addition, refbase can export an OpenDocument Spreadsheet (ODF XML) for use with OpenOffice.org. Upon export, refbase can automatically generate user-specific cite keys which allows users to use the exported data with their desktop reference managers. (more info) Automatic email announcements: · The database can inform you automatically about any newly added records: For each record that has been added to the database, an announcement email will be sent to a mailing list (or any other email address) containing the main record data as well as a direct link to the details page of that particular record entry. This enables users to easily keep track of new database entries. (more info) RSS support: · Users can track queries using RSS, i.e., users are able to convert any query into a dynamic RSS feed and subscribe to it using their favorite news aggregator. The feed will display all recently added/edited records matching the users query. This enables users to easily track modifications to the database. (more info) User-specific fields: · Refbase offers nine record fields that are specific to each user: Marked, Copy, Selected, User Keys, User Notes, User File, User Groups, Cite Key and Related. You can use these fields to store personal information for a particular record, for example your personal keywords or notes. These fields are only provided to logged in users and can't be viewed by other users. User-specific fields are available in details view and can be optionally displayed in list & citation view. User-specific groups & saved queries: · Logged-in users can add records to user-defined groups. A drop-down menu on the main page (or any search results list) provides quick access to all records belonging to a particular group. Users will benefit from this feature when collecting literature for a particular seminar or when writing a scientific paper. · In addition, logged-in users are able to permanently save any search query together with the current display settings. Saved queries can be easily recalled or edited from the main page. SRU/W, unAPI, OpenURL and COinS: · Refbase supports modern search and bibliographic standards which can be utilized by the next generation of bibliographic clients and which allow for better indexing by search engines. refbase offers an SRU/W web-service that allows clients to access a refbase database using a standard query syntax and retrieve results in structured XML format. In addition, refbase embeds bibliographic metadata within web pages (COinS) and advertises bibliographic formats associated with database records via it's unAPI service. This allows clients such as Zotero to automatically discover and extract bibliographic data from a refbase database (screenshot). Using these features, visitors to your site will be able to use it more efficiently with the resources they have access to. Link records to each other: · The user-specific field Related enables users to link records to other records in the database. Links can be either static (by explicitly linking to particular record serial numbers) or dynamic (by entering queries like "author:lee; title:ecosystem" which will link to all records that contain "lee" within the author field or where the title field contains "ecosystem"). Power users may even specify full MySQL WHERE clauses to define a dynamic link. User management: · refbase provides a convenient user management interface to the database admin where one can add or remove users and modify any user data (like changing a user's password or address information). Additionally, the interface allows to group particular database users and offers information about when and how often a user logged in. User-specific permissions: · The admin can assign access rights individually for each user. Permission settings are provided for basic actions such as whether one may add, edit or delete records or whether they may upload or download files. Using this, the admin can provide guest accounts with limited access rights (e.g., browse/download only) to non-members of his site. In addition, permission settings are provided to enable or disable certain parts or functionality of the refbase interface (such as the different views, import, export, etc) for particular users. Batch SQL modifications: · The database admin is allowed to execute SQL queries other than just SELECT statements. By that, one can easily apply batch changes to thousands of records at once. As an example, executing a SQL query like UPDATE refs SET publication = "Polar Research" WHERE publication RLIKE "^Polar Res.?$" would modify every record whose publication field equals either "Polar Res" or "Polar Res." by setting its publication field to "Polar Research". Requirements: · Apache · PHP 4.4.0 or later · MySQL 4.1 or later What's New in This Release: Feature additions: · New resource types: Abstract, Conference Article, Conference Volume, Magazine Article, Manual, Miscellaneous, Newspaper Article, Patent, Report, Software · Import from Endnote XML and SciFinder · Direct import from arXiv IDs, DOIs and OpenURLs · Direct upload of references from Bookends Improved interface: · Redesigned main page, page footer/header & forms on results pages · Quick Search form now always available in the page header · Search suggestions for text entered by the user · Forms on results pages can be hidden · Search results can be browsed & searched in three different views: List view, Citations, Details · Additional record info (keywords, abstract, etc) and links to cite or export the record can be displayed underneath each citation · OpenSearch support (which e.g. enables Firefox & IE users to search refbase directly from their browser's toolbar) · Initial support for searching & managing of duplicate records · New query history with links to any previous search results · New customizable "main fields" search option that allows to search across multiple fields at once · New option to customize the default number of records per page · Results can be dynamically included in foreign web pages · New export formats: ADS, Atom XML, ISI Web of Science, OAI_DC XML, SRW_DC XML, Word XML · New citation styles: AMA, APA, Chicago, Harvard (3 variants), MLA, Vancouver · Output of citations in LaTeX bibliography (.bbl) format · Cite, group or export ALL found records (instead of just the selected ones) · For PDF output, US letter is now supported as page format · The 'headerMsg' URL parameter adds a header to any of the citation formats · Upon export, links to corresponding files are now included if the export format and user permissions allow so · Added chinese localization · Added support for all new export formats · Added new options that allow to append found records to a local BibTeX or MODS/SRW XML file (if they don't yet exist in that file), and update existing records in that file if their modification date on the server is more recent · Added new option to extract citation IDs from a file and retrieve matching records from refbase (supported file types: .aux, .bbl, .bib, .enw, .ris, .tex, (MODS|SRW|Endnote) .xml) · Added a refbase extension for MediaWiki which allows to place a serial number within ...' markup tags; metadata for the reference is retrieved from refbase and marked-up according to a MediaWiki citation template · Added support for the sitemaps.org protocol which allows for better indexing by search engines · Added unAPI support for the new export formats 'atom', 'oai_dc' and 'srw_dc' Changes: · Introduced measures to better prevent cross-site scripting (XSS) attacks · For security reasons, HTML tags are now stripped from the 'headerMsg' URL parameter; string formatting can now be done using the refbase markup syntax · Improved support for PHP installations running with 'safe_mode=On' · The 'edition' field now accepts string values · After any add/edit/delete action, refbase now includes a link to the last multi-record search results list in the feedback message if the previous query resulted in a single record; Along with other changes, this obviates 'receipt.php' · When importing multiple records, ALL records are now imported by default · Improved UTF-8 handling on import so that e.g. a best-effort conversion is done for UTF-8 data which are imported into a latin1-based database · When importing (or exporting) RIS records, the type of thesis (such as "Masters thesis" or "Ph.D. thesis") is now taken from (or exported to) the 'U1' field (as is supported by Bibutils v3.35 or greater) · Upon import, if the given URL actually is a DOI prefixed with , we'll extract the DOI and move it to the 'doi' field · Improved recognition of PubMed resource types · refbase now remembers many more search & display options while navigating or refining the results list · Changed the HTTP transfer method in most forms from POST to GET; this helps to avoid warnings about re-sending POST data in some browsers (such as Firefox) · When linking to particular records via 'show.php', one can now use consecutive serial number ranges as values of the 'records' URL parameter; examples: or · One can now specify 'creation-date' as value for the 'citeOrder' parameter in 'show.php' URLs (or the '--order' option of the 'refbase' CLI); this allows to sort records such that newly added/edited records get listed top of the list · One can now specify 'Mobile' as value for the 'viewType' URL parameter (or the '--view' option of the 'refbase' CLI); this will return results in simple HTML suitable for mobile devices or any postprocessing · Refined layout of 'user_receipt.php' · Added many CSS attributes (id/class names) to HTML output where appropriate; this allows to easier refine the CSS styling of the refbase interface · By default, export via the refbase GUI is now enabled for anonymous users · By default, the SRU formats SRW_DC XML and SRW_MODS XML are now transformed to HTML via XSL stylesheets · MODS XML exports include file links that Zotero is able to download · Renamed the Bibutils 'xml2word' command line tool to 'xml2wordbib' according to the name changes in Bibutils v3.40; note that if you're using a Bibutils version prior to Bibutils v3.40, you must revert this change in file 'export/bibutils/export_xml2word.php' · The citation output options (previously located in the results footer) have been moved to the Display Options form of the results header in Citation view · The admin can now define any of the supported views (List view, Citations, Details) as the default view · For each view, the admin can now define whether the results header & footer should be displayed open or closed by default, or whether they should be entirely hidden from the interface · The admin can now customize the list of fields that are displayed by default in List & Details view; similarly, the list of fields that are available in dropdown menus of the results header can also be customized · The admin can now define 'accesskey' values which allow for keyboard navigation of the main parts of the refbase interface · The '$databaseBaseURL' in 'ini.inc.php' is now auto-generated by default · The refbase logo image files have been updated to the new refbase logo, and the logo URL path & dimensions can now be customized easily via 'ini.inc.php' · The session/temp dir path can now be specified explicitly in 'ini.inc.php'; this allows you to define a custom directory path that's used on your server to save session data and to write any temporary files · Improved internationalization and added many additional localization strings · Changed or merged some localization strings to allow for better translations to languages such as Spanish or Chinese · Underline fontshape markup is now supported in various import and citation formats as well as in refbase markup (use: '__underlined text__') · For the "Extract citations" functionality, refbase now checks whether the extracted serial numbers and cite keys exist in the database and report any missing record identifiers Bug fixes: · Fixed bug that prevented correct directory creation/renaming and/or file upload on some platforms · Fixed 'preg_match()' compilation errors when importing BibTeX records into a refbase UTF-8 database · Worked around an error in Internet Explorer when importing single records via the web interface · When importing PubMed MEDLINE source data, refbase now extracts author information from the 'AU' field if the 'FAU' field is not available · refbase now converts Endnote XML text style markup into appropriate refbase markup · Upon RIS import, refbase now makes sure that HTML encoded source data (such as 'ä', 'ö' or 'é') get decoded before import · Fixed an issue were it wasn't possible to correctly import (or cite) records which contained non-ASCII characters in author's given names · Records of unrecognized resource type were omitted upon citation output; fixed · When outputting to LaTeX or RIS, curly brackets are now escaped to avoid incorrect output · Fixed an error when exporting data to ODF XML and when the user-specific fields were missing from the SQL query

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