The Specify Collections Consortium (SCC), founded in 2018, is a collaborative, open-source software community of engaged collection institutions with a vision to advance research and education uses of biological specimen and sample information. A Board of Directors, along with Research and Technology Advisory Committees drawn from member institutions, govern the Consortium and determine its software and technical service priorities. The Consortium advances the interests of its members through engineering, deployment, and support of software technologies that facilitate the creation, curation, discovery, and scientific utilization of the information and knowledge associated with biological collections.
The consortium produces the Specify Collection Management System and offers related technical services for processing the data associated with specimens and samples in biological collections used for research. We have partnered with natural history museums and biological repositories for more than 30 years. Today, Specify handles research data at biological collections institutions and consortia around the globe.
The Specify Software Project is pleased to offer Specify 7, a web implementation of our biological collections data management platform. Specify 7 server code is open source and available from GitHub.
We encourage members to use our Dockerized compositions of Specify 7. You can choose a version, make the necessary adjustments and then run a single command to get everything working. It is very simple and can be easily updated when new versions are released. Members can contact us at email@example.com to gain access to this repository.
The new generation of Specify combines the interface design components and data management foundation of Specify 6 with the efficiency and ease-of-use of web-based data access and cloud computing. The Specify 7 web application uses the same interface layout language as Specify 6, so any user interface customization made in one product is mirrored in the other. Also Specify 6 and Specify 7 use the same data model and can work from the same Specify MySQL database, which means they can be run simultaneously with any Specify collection. By providing an easy migration path to the web, Specify 7 helps transition Specify 6 collections to cloud computing. It is also a great starting platform for collections which prefer zero workstation software installation and ubiquitous web browser access.
Specify 7’s server/browser architecture open the door for computing support of collaborative digitization projects and for remote hosting of institutional or project specimen databases. Without the need for a local area or campus network to connect to the MySQL data server, Specify 7 gives you and your collaborators access to a shared specimen database through any web browser. Without adequate IT support to maintain a secure database server? With the Specify 7 server software supported on generic Linux servers, museums can utilize a server hosting service to provide support for the technical complexities of systems administration, security management, and backing-up. Want to create a joint database with remote collaborators for a collaborative digitizing effort? No problem! Host, hire a hosting service or use our Specify Cloud service for your Specify database, set up accounts and go. We provide the same efficient user interface and printed reports and labels customization, and help desk support for Specify 7 as we do for Specify 6.
Support for Single Sign-On (SSO) integrates Specify 7 with a campus or institutional identity providers. It supports all identity providers (IdPs) that have an OpenID endpoints.
The Security and Accounts tool allows administrators to give access based on roles and policies. Create, edit, and copy roles among collections and databases. Administrators can give users as many or few permissions as desired, from guest accounts to collection managers.
It is important that web applications work for people with disabilities. Specify 7 is developed with this top of mind, not only meeting international accessibility standards but also providing a better experience for everyone.
Specify 7 is largely compliant with the main WWW accessibility standard – WCAG 2.1 (AA). It supports screen readers and allows each user to customize their color scheme and appearance as well as reduce motion and resize all elements.
This accessible design respects system and web browser preferences for date formats, language, theme, and animations.
Specify 6 is a database platform for museum and herbarium research data. It manages species and specimen information for computerizing biological collections, tracking museum specimen transactions, linking images to specimen records and publishing catalog data to the Internet. Specify 6 is written in Java for Windows, Mac OS X, and Linux computers and uses the relational data manager, MySQL, as its data engine. Specify, Java, and MySQL are free and open-source. Specify 7 works with the same MySQL database design as Specify 6, they can run simultaneously on the same collection database.
Specify supports data from specimens, taxonomic and stratigraphic classifications, field notebooks, DNA sequence runs, literature references, as well as from other primary sources. It also manages the information associated with repository agreements, accessions, conservation treatments, collection object containers, images, and document attachments.
Data fields in Specify’s form windows can be selected, organized, re-named, and re-sized to suit your curatorial preferences and to eliminate the need for tabbing through multiple data forms. Specify’s “tree” data windows for taxonomy, geography, storage location, chronostratigraphy and lithostratigraphy provide intuitive access to hierarchical data for editing, drag-and-drop synonymization, re-parenting, and for discovering linked collection objects.
Retrieving data is facilitated by Specify’s full-text ‘Simple Search’. For complex fielded queries, the ‘Query Builder’ provides access to every data table and field. The Query Builder includes the expected complement of comparison operators for each search field, along with display, sort, distinct, and count options. Frequently-used query templates can be saved for quick re-execution. Records resulting from searches and queries may be exported to a Microsoft Excel format file, printed as labels or reports, or saved in a Specify ‘Record Set’. Record Sets are logical containers which hold links to batches of specimen records for later review or action.
Field or legacy bulk data uploads are supported from Microsoft Excel files through the Specify ‘WorkBench’. The WorkBench presents a spreadsheet data entry screen which checks and validates keystroked or uploaded data against your existing database content to improve incoming data quality. Specify 6 also provides embedded georeferencing with the Tulane University’s ‘GEOLocate’ service, custom printed label and report design, and specimen data exporting.
For collections that need to publish their collections catalog information publicly, the Specify Web Portal is a full-featured web interface for read-only, public access to specimen data and images. It is an optional component of a Specify installation. Working from an exported copy of a Specify collection database, the Web Portal provides full-text indexed searches, structured, and spatial queries of specimen holdings. Express searches are fast, while structured queries allow precise specification of the search scope and support multi-field queries with AND or OR logic. Searches can be qualified to return only records with geo-coordinates or with attached images.
The Specify Web Portal displays specimen information in three views–Records, Images, and Maps. On the “Records” tab specimen data are shown in a traditional grid view. The choice and number of data fields to display in the web interface is determined by each collection, and web users can sort and re-arrange data columns during a session. The search panel is customizable with an institutional logo or brand image, and pages can be embedded into institutional content management systems or web platforms by a web programmer.
The Specify Web Portal is an effective tool for publishing specimen data. Specify’s Schema Mapper and Data Export tools make issuing updates to the web portal from a Specify collection database easy. The Web Portal is intended for institutional web server computers; setup requires the technical expertise of a server admin. Installation information is available on Github.
The Specify Cloud hosting service provides access to Specify 7 databases including linked media file attachments, through any web browser with no Specify or MySQL software to install or database server computer to maintain. With Specify Cloud, we pre-install Specify 7 on a fast, high-availability, internet server to create a secure, managed platform for hosting and serving your collection data.
Both Specify 6 and Specify 7 are entirely free to download and use. Specify is licensed under the GNU General Public License 2.0 (License).
Joining the Specify Collections Consortium as a member enables individual collections or entire institutions to receive incredible support, help with data conversion and importing, form customization, label and report creation, and unlocks hundreds of exclusive pieces of documentation for IT staff and users.
Members of the Specify Collections Consortium sustain the software, maintenance, and support services of the Specify Software Project. A commitment to join the consortium ensures continuous access to all technical support services.
Please contact us at firstname.lastname@example.org to join us!
For museums and consortia of vision who see the strategic and long-term research value of their collections and for guiding the future of collections informatics, Founding Members assume a stand-up, leadership role in Consortium governance and operations. As research collections community leaders with a seat on the governing board, Founding Members will engage their vision and grow the informatics future of the biological collections community.
With insight, commitment, and leadership, Founding Members leverage their collection informatics investment to positively impact hundreds of smaller yet significant collections around the world that contribute specimens and data to the collective knowledge of earth’s biological diversity.
Founding Member status ensures immediate access to Consortium technical staff, and a complete suite of technical support services for all the institution’s collection databases. Your institutional IT staff will benefit from direct access to Specify engineers for problem resolution, joint code development, proposal and project planning. Consortium intellectual and technical resources will ensure that your collection digitization initiatives are achievable, effective, and successful. For large institutions with multiple collections, investment in a Founding Membership realizes considerable cost savings over the expense of commercial software licenses, or the salaries of in-house programmers. Institutional benefits of Founding Memberships include:
- Two permanent seats on the Consortium Board of Members, one permanent seat on each Consortium standing committees: Science and Technology.
- Priority access to all technical support services, including Consortium shared hosting, direct unlimited access to Consortium help desk and engineering staff, including remote login sessions, for an unlimited number of collections.
- Collaborative proposal and project development planning for software innovation, collection data analysis, integration, or digitization initiatives.
- Preferred and priority access to all new software products and releases, including BETA testing, opportunity to contribute code and capabilities to Consortium software projects.
- Two paid seats at the annual Specify Research Summit.
For biological collections that prefer to be proactively engaged in shaping the priorities and technology directions of the Consortium, Full Membership offers a leadership opportunity. You will be at the table to participate in the critical discussions that will determine the cyberinfrastructure support capabilities for your collection, as well as more generally impact the direction of biological collections computing, worldwide.
- Your IT staff will benefit from direct access to Consortium engineers for assistance and project development, extending the influence and reach of your own bioinformatics activities by leveraging the technical activities of the Consortium. Your collections researchers and IT staff will receive comprehensive software support, at considerable savings relative to the costs of commercial software licenses, or maintaining bespoke in-house software. Specific benefits for Full Members include:
- Access to a rotating seat on the Consortium Board of Members, priority for one seat on either of the Consortium’s Science and Technology Advisory Committees.
- Priority access to consortium technical support services, including direct access to Consortium help desk, for one collection, and access to engineering staff for remote login sessions. This includes advanced support for User Interface changes, field mapping, label and report creation and database setup as necessary during data conversion projects.
- Collaborative proposal writing and new project planning.
- Preferred access to all new software products and releases, opportunity to contribute code and capabilities to Consortium software projects.
- One paid seat at the annual Specify Research Summit.
For collections that want to utilize Consortium’s setup services in the first year to migrate legacy collection data into the Consortium data model and software, and those that require additional technical services for conversion, or for maintenance of their data in the Consortium’s database hosting service. When joining as a Solutions Member, we will work with you to define your collection’s digitization workflows and configure software to fit them. Benefits include:
- Access to rotating seats on Consortium Science and Technology standing committees (Science, Technology).
- Access to the suite of Consortium extended technical support services, which may include software platform customization, installation, mapping and migrating legacy data into the consortium data model and eligibility for Consortium data shared hosting and On-Site Consulting and Training.
- Technical advice for proposal development and new project planning.
- Timely access to all Consortium software tools and updates.
- A paid seat at the annual Specify Research Summit.
For institutions that want to continue to advance their collection data management and mobilization of collection information for scientific use, Associate Membership offer comprehensive support and opportunities for collaboration. Collections that are Associate Members get the comprehensive core software and technical support benefits of the Consortium, including:
- Access to rotating seats on Consortium standing committees (Science, Technology).
- Full access to the Specify forum, help documents and videos, and answers to incidental technical support questions.
- Technical advice for funding proposal and project development.
- Access to all Consortium software tools and updates.
- A paid seat at the annual Specify Research Summit.
- The University of Kansas
- Florida Museum of Natural History
- University of Michigan
- Danish Natural History Museums
- Commonwealth Scientific and Industrial Research Organisation
- Consejo Superior de Investigaciones Científicas
- Le Muséum d’histoire naturelle de Genève
- Paleontological Research Institute
- Royal Botanic Garden Victoria
- Royal Botanic Garden Edinburgh
- Natural History Museum of Geneva
- Santa Barbara Museum of Natural History
- Queensland Dept. of Environment and Science
- Natural Science Collections Facility, SANBI
- Cornell University Museum of Vertebrates
- Western Australia Herbarium
Any many more member collections and institutions.