Helmsley Trust Supports Open Annotation in Biomedical Research

By dwhly | 11 January, 2015

Hypothesis, together with partners at the Neuroscience Information Framework (NIF) and ORCID, has been awarded a 3-year, $2.1M grant by the Leona M. and Harry B. Helmsley Charitable Trust to bring annotation to biomedicine. Web annotations, a new standard for digital notes on top of an existing online resource, are proving transformative in diverse fields from scholarly publishing to education, open government, and journalism. This project will bring these advances to biomedicine, where they have the potential to make a unique impact.

Biomedical researchers are faced with a rapidly growing body of literature and data, yet extracting, citing and sharing individual components in a digital and interactive way remains elusive. References to small data sets, embedded figures and widely catalogued research objects (such as proteins, structures and species) remain difficult to associate with contributors or commentary, surface to researchers and retrieve through open web search. Consequently, researchers are hampered in their ability to effectively discover, and leverage the information around them.

In 2014, the Helmsley Trust created a new program area, Biomedical Research Infrastructure (BRI), to improve the infrastructure for collaborative and cooperative research in biomedicine. As one of the largest private funders of biomedical research in the world, they are acutely aware of the inefficiencies and disincentives in biomedicine that limit research. This new program area strives to remove roadblocks to research collaboration where possible through the creation and adoption of open technologies.

This grant is one of three made by the new program office in their inaugural round, along with awards to the Mozilla Science Lab and Sage Bionetworks.

The potential of annotation

Annotations provide a powerful new way for researchers to organize their thoughts and notes on web content. These can be shared one on one, in small groups or publicly with other collaborators as preferred. Annotations can warn about quality issues, suggest modifications to experimental techniques or simply provide helpful background information.

Recent developments such as new identifiers for research objects (Research Resource Identifiers, aka RRIDs), researcher identities (ORCID) and a new open web annotation standard (W3C), are converging to increase knowledge discoverability, transfer, reproducibility and collaboration within biomedical research.

Already, projects such as the Neuroscience Information Framework (NIF) at UCSD have surfaced millions of annotations by aggregating associations between published papers and research objects or protocols. These annotations have been shared with literature discovery services, such as PubMed, but they remain difficult to discover. Migrating these associations into the open annotation model makes them available for reuse, consumption, and display through a variety of approaches, including standards compliant clients like Hypothes.is and others.

Annotations are an example of the new paradigm of micro­ or “nano­publication”­­ — new publishing capabilities that enable a more granular approach to research communication that hasn’t been possible until now. Micro­publishing permits a more rapid dissemination of experience, including details about aborted efforts or unsuccessful protocols. The enhanced visibility of small or one-off trials and bench experiments can suggest fruitful avenues to deepen an investigation for those better trained or resourced, along with the release of small amounts of data and statistical results.

Joining together annotations with RRIDs and the ORCID unique researcher identifier can transform biomedical research by creating an interlocking and interoperable set of open-source research assets that bring precision in location, attribution and reference.

Overview of partner collaboration

The partners will collaborate to incorporate ORCID contributor identifiers into annotations and into publisher workflows along with RRIDs, as well as exposing scholarly annotation activity in the ORCID interface.

Our proposal knits together identifiers and researcher ­driven commentary in a way that we hope will facilitate research activity and engagement with scholarly output in general. In addition, this proposal will enable the measurement and citation of annotation activity by researchers of scholarly research objects, making it possible to include such activity in institutional and individual research activity reporting.

The last key objective of our proposal is to facilitate the adoption of annotation generally in the biosciences. An early activity will be to organize and gather input from user groups and partners to better understand their needs, and evolve deliverables to meet them. We welcome interest by others that see the potential for this technology, and are eager to join forces with like-minded organizations and individuals.

With contributions from:
Dan Whaley, Hypothesis
Maryann Martone, UCSD
Laurel Haak, ORCID
Peter Brantley, NYPL

About The Neuroscience Information Framework

The Neuroscience Information Framework (NIF) at UCSD is an initiative of the NIH Blueprint for Neuroscience Research that provides an open networked environment researchers can use to search an inventory of Web­ based neuroscience data sources, research materials, and tools. NIF has three main indexes: the Registry, a catalog of 12,000 resources (including 2500 databases); the open access subset of the Literature, PubMed and PubMed Central services at the National Library of Medicine; and the Data Federation, a group of 200 databases that expose some 850 million data records. NIF and Hypothes.is will collaborate to develop services to expose plain text descriptions in the emerging Web Annotation standard. For more information on NIF, see http://www.neuinfo.org/.


The ORCID mission is to solve the name ambiguity problem in scholarly communications. To this end, ORCID provides an open registry of unique and persistent identifiers for researchers, and works with the community to ensure that these identifiers are collected during research workflows and become part of research works and activities. ORCID’s focus on researcher engagement, the provision of open APIs and software code, and collaborations with other standards organizations and persistent identifier initiatives, including RRID, makes ORCID a powerful tool for linking researchers with their annotation activity.

Share this article