Zoological Society of San Diego (2014)

Enhancing Access to Peruvian Plant Specimens through Herbarium Digitization

Project Details

Grantee Organization: Zoological Society of San Diego
Grant Amount: $70,748
Contact: Mathias Tobler
Contact Email: mtobler 'atsign' sandiegozoo.org
Funding Dates: 12/15/2014 - 12/31/2016

For information on the preceding phase of this grant, please click here.


The Zoological Society of San Diego (ZSSD) manages the San Diego Zoo Institute for Conservation Research, a leader in endangered species research. International programs across the globe include conservation projects in Peru, which is a hotspot of floristic diversity. While decades of plant collections have produced thousands of plant specimens in Peruvian herbaria, these records are virtually inaccessible to researchers, conservation planners, students, and the general public. ZSSD set out to solve this, and with prior support from JRS in 2012-2013, they implemented a digitization project with the goal of making Peruvian plant collections openly available to the public through a web portal. This work has produced more than 50,000 specimen images from three national herbaria, through which 25 staff and students have been trained in digitization techniques. ZSSD plans to focus on continuing their work of enhancing global access to Peruvian plant specimens with more digitization in two major Peruvian herbaria. They will also make major updates to the Atrium Biodiversity Information System, particularly with respect to integration standards and data sharing.

Key Objectives and Activities

Objective 1: Complete the digitization of plant specimens in the Molina Forestry Herbarium (Universidad Nacional Agraria La Molina) and Cuzco Herbarium (Universidad San Antonio Abad) and make all images and metadata accessible to the global community.

Objective 2: Finalize training of at least four herbarium staff and 20 students. Produce written protocol in order to achieve autonomy in herbarium digitization.

Objective 3: Create training manual and videos for end users of Atrium to facilitate use of images and data for conservation initiatives and research in Peru. The user manual and demonstration videos will provide instructions on independent use of, and contribution to, the growing set of plant specimen information and images.

Planned Outputs

The proposed project will build on the ongoing digitization activities in two important Peruvian herbaria (La Molina and Cuzco). 50,000 Peruvian plant specimens will be digitized and added to the existing database, resulting in a total of at least 100,000 plant records available to the international community. Combined with the 74,000 images of primarily Peruvian plant species from other projects already in the Andes-Amazon Atrium system, the result will be one of the most detailed baselines of information and richest collections of images regarding flora of the country, and will be an important contribution to the knowledge of the flora in Peru. To develop capacity and sustainability within the Atrium user community, the group will emphasize training and instructional resources. Staff and students trained in curation and digitization during the first phase of the project will conduct on-site trainings to improve the general daily workflow, and produce user manuals and demonstration videos to allow users and contributors to engage independently. The project will be promoted in Peru through meetings, workshops, publications, and demonstrations.

Planned Outcomes

This information will have an impact on conservation-driven research because all major national protected areas and research sites in the country are well represented in the plant specimen holdings of the collaborating herbaria. The shared data and photos are an essential step toward digital treatments of the floras of multiple long-term research sites. Because many of these species exist in other regions, the resulting dataset will have impacts extending beyond national boundaries. One important set of results will relate not just to the number of images digitized and shared through Atrium, but also to the continued growth of the community of data users. It is predicted that both the data and the user community will grow over time as more images are added.

Primary Software Platforms

  • All information from this project is integrated with tens of thousands of existing plant specimen records and images in the Atrium Biodiversity Information System for Peru: http://atrium.andesamazon.org/
  • Atrium provides free global access to all the specimen data and images.
  • Atrium uses the IIPImage server to serve static and high-resolution zoomable images from a single JPEG2000 master file.
  • Collection data are served to the the Global Biodiversity Information Facility (GBIF).

Results to Date

The project capitalized on delays in digitization early in the project that were caused by annual holidays and university strikes to fine-tune the digitization workflow. This investment paid off and the Peruvians working on the herbaria collections at Cuzco and La Molina made up for lost time, completing digitization of all the public holdings from both institutions. This has yielded a total of more than 81,000 specimen records which are ready to be published on Atrium pending a server update. The server hosting Atrium has been migrated to the San Diego Zoo which will contribute to the sustained availability of the resource.

A total of 30 people, mostly undergraduate students, has been trained in imaging and digitization through this project. As outreach to publicize the resource is ongoing, and training resources are still in development, staff and students at La Molina are already using the information to assess which localities, habitats, and types of plants are under-sampled in the collections. Identifying and addressing these weak spots in the floristic knowledge will facilitate improved conservation and resource management for Peru.

Lessons Learned

The thoughtful and systematic approach taken to improving the workflows of digitization was a large asset of the project. The team has reflected on a number of lessons learned in the process of initiating their specimen imaging project:

  • Herbarium specimens often require more curation and refurbishment, before imaging can even start, than might be expected.
  • “Existing” collection databases don’t always mean “good” or “reliable” data.
  • Specimen imaging workflow starts slowly and improves over time.

Ably navigating both these challenges, and delays due to external forces, the team exploited the opportunity to hone the digitization workflow. Hands-on participation by the project leaders has resulted and a true transfer of technology and know-how to Peruvian herbarium colleagues, such that they were working entirely independently on digitization. They have also implemented policies to help sustain the workflows and avoid repeated collections backlogs in the future; La Molina is requiring all students who collect specimens as part of their thesis research to process and digitize the records themselves. This increases the value of the collection as well as the digitization capacity in Peru.

Related Publications

Householder, JE; F Wittmann; MW Tobler; JP Janovec (2015) Montane bias in lowland Amazonian peatlands: Plant assembly on heterogeneous landscapes and potential significance to palynological inference. Palaeogeography, Palaeoclimatology, Palaeoecology. 423: 138-148. (link)

Shearer, CA; SE Zelski; HA Raja, JP Schmit; AN Miller; JP Janovec (2015) Distributional patterns of freshwater ascomycetes communities along an Andes to Amazon elevational gradient in Peru. Biodiversity & Conservation. 24(8): 1877 – 1897. (link)

Project Director’s Biography

The proposed project is rooted in 12 years of collaboration and partnership between Drs. Mathias Tobler and John P. Janovec. Dr. Tobler is a Scientist at the San Diego Zoo Global Institute for Conservation Research where Dr. Janovec is positioned as a Research Fellow. Dr. Janovec is also a Research Professor at the Universidad Cientifica del Sur and a Research Associate at the Universidad Nacional Agraria La Molina, in Lima, Peru. Both Dr. Tobler and Janovec have combined studies of flora, fauna, and ecosystems, and have directed large projects funded by the Gordon and Betty Moore Foundation and the National Science Foundation (US). They are also the developers of the Atrium Biodiversity Information System, a central component of the project.

Notes from JRS

This grant is a continuation of the prior award to the San Diego Zoo and the team of Tobler and Janovec.  The initial project was fantastically productive and its success reflects the long-time relationship between the project directors and the collaborators and particularly Dr. Janovec’s deep integration into local institutions and botanical exploration in Peru. The project has helped to inform how JRS designs and assesses other projects that propose training and collaboration among national herbariums. We hope that this phase helps to solidify the past training and collaboration and helps the team to transition to local support through outreach and partnerships.  2016 will be a key for the project as Dr. Janovec transition’s out of full-time engagement and the work will be transferred more fully to Peruvian partners.  We keep our foundation fingers crossed as there is emergent interest from government to sustain the digitization work.

Last Updated: February 28th, 2017

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