iDigBio Specimen Portal Technology Preview 2012


iDigBio Specimen Portal Technology Preview 2012

iDigBio, a National Science Foundation (NSF) funded project charged with integrating digitized biological collections from institutions across the United States, will be releasing a preview of technology developed during the inaugural year of the project. Working with over 130 collaborating institutions, through the leadership of the Advancing Digitization of Biodiversity Collections (ADBC) community and with international support from the Global Biodiversity Information Facility (GBIF) and it's supporting partners, iDigBio's technology preview is the first release of a semi-annual release cycle for a specimen portal that will eventually contain over 1 billion vouchered specimen records. This technology preview contains sample datasets provided by Morphbank and the Florida Museum of Natural History, some of which is research quality specimen data. These datasets allow iDigBio to share its development efforts with the community for feedback and guidance. You can access the technology preview here:

Highlights from the technology preview include:

Inside the Box

iDigBio's specimen portal architecture incorporates the work of the free and open source software community. This allows iDigBio to incorporate new features and technology quickly and with the support of a very active and robust development community. Software projects leveraged by iDigBio:


Search Technology 

Integrating data across institutions and disciplines has always been a difficult problem. In this technology preview, iDigBio has leveraged the Solr project to index specimen data across all available specimen meta-data terms allowing for a more productive search by end-users.

Although search facets can greatly improve our search productivity, iDigBio's technology preview includes full text search of both specimen and media record meta-data. Also, word clouds are created based on search facets for Scientific Name, Country, and Recorder.



iDigBio's technology preview puts species distribution data at the tip of your fingers. Utilizing mapping technology provided by CartoDB, a Vizzuality product, users will have specimen level distribution data for all meta-data records containing geographical information.


Cyberinfrastructure Roadmap

iDigBio Cyberinfrastructure decisions and activities are the primary responsibility of the Advanced Computing and Information Systems Laboratory (ACIS) at the University of Florida, under the leadership of co-PI Dr. José Fortes. Ongoing project decisions are evaluated based upon the experience and expertise of ACIS personnel, industry research, biodiversity community and information technology community input, and internal project input from the iDigBio project team at Florida State University. The Cyberinfrastructure domain is tasked with the implementation of six primary objectives:

  • Implement a horizontally scalable cloud infrastructure for object (media) storage
  • Implement a horizontally scalable cloud infrastructure for text (data/metadata) storage
  • Implement infrastructure to enable hosting for the web services/websites of strategic partners
  • Deploy iDigBio appliances and services via multiple channels (e.g., web services, locally-run virtual machines, Infrastructure-as-a-Service cloud implementations) to enhance, simplify and/or improve activities completed by data providers and data consumers
  • Implement a Graphical User Interface (GUI) to enable end-users, including data contributors and data consumers, access to search/visualize/download text and media data from the cloud infrastructure
  • Implement a comprehensive authentication and access control system to enable data tracking and a cohesive user experience among the systems listed above, as well as the iDigBio collaboration and communication website.


Feedback and Comments

Users of the Specimen Portal Technology Preview are encouraged to provide feedback to iDigBio. Submitted comments, questions and suggestions will be used to improve the product and give support as necessary. You can access the contact form here: