The Lens: Enabling Open Access Innovation Cartography


Back in June, at the Seventh International Meeting for Synthetic Biology, I had the opportunity to speak with Professor Osmat Jefferson from Queensland University of Technology (QUT). Professor Jefferson is seconded to Cambia, a global non profit organization. Its mission is to create a more equitable and inclusive capability to solve problems using science and technology. Cambia is founded by the leading molecular biologist and social entrepreneur Richard A. Jefferson.

The Lens is an extension of Cambia’s early initiatives, Patent Lens, which was launched in 1999 and aimed at making the global patent knowledge more transparent. Currently, The Lens is a free, open and secure platform that merges global patents and research literature along with other patent metadata.

Brand New: QUT International Innovation and Industry Influence Mapping (In4M) Ranking system

An exciting initiative that The Lens has recently released, is the QUT In4M Ranking system. The influence of 200 global leading research institutions and 51 Australian institutions on industry and innovation was mapped and ranked using a new Lens methodology that relies on the extent to which the scholarly work has been cited in more than 100 million patent documents in The Lens database.

Most self-citations (i.e. if the applicant or owner of the patent was from the same institution as where the research was done) were manually removed, since the metric is primarily interested in whether scholarly work is relevant to external industrial or enterprise parties. From this, a normalized In4M rank was developed and applied to compare the influence of an institution relative to the other institutions within each of the global or Australian datasets.

Such an approach has the potential to expose institutional practices and thus inform or guide decision-making by parties throughout the innovation chain. This can potentially signal future investments and collaborations further down the line. The In4M metric is particularly exciting as it can be applied at various levels and allows institutions to evaluate the influence of their research on industry, improve it or engage them deeply in the innovation landscape. It also creates incentives for productive partnerships with entities sharing similar interests.

Source: QUT News

The In4M metric is a result of an international collaboration with PubMed, NIH, and Crossref and will be described in more details in an upcoming Nature Biotech article. The rankings of the 200 institutions were featured in the Nature Index supplement published on August 10th 2017 issue of Nature, a co-sponsored activity by The Lens and the Nature Index group.

PatSeq: Gene Patents Contentions and IP Rights Navigation

Another unique feature of The Lens platform is the Patent Sequence toolkit; it is no secret that gene patenting has been the subject of huge debates worldwide and with the availability of the public PatSeq platform, various stakeholders are now able to navigate the maze of gene patents using evidence-based tools.  The toolkit includes five interesting apps.

PatSeq Data serves and hosts the world’s most comprehensive and complete patent sequence publicly available database with more than 278 million patent sequences from 16 jurisdictions. PatSeq Finder is a unique app that allows users to perform sequence searches based on either nucleotide (DNA or RNA) or protein sequence and determine if such sequences have been referenced in a patent claim or simply disclosed.

PatSeq Explorer is a tool for navigating patent-disclosed sequences mapped onto genomes and chromosomes (currently offering 5 genomes; human, mouse, maize, soybean and rice). This enables the exploration of linkages between sequences and phenotypes and zooming in using the 4th app, PatSeq Analyzer to a gene region to compare patenting activity at the chromosomal locus or gene level.  This tool enables users to analyze the extent and scope of the invention using the sequences.  PatSeq Text Search allows users to search by text or by the declared organism name, the origin of a sequence.

All these tools, while daunting at first glance to the uninitiated, are extremely useful especially for researchers strapped for resources without access to traditional closed tools provided by proprietary sequence service providers. This will enable them to explore the space in which they can operate before dedicating resources to beginning their research or applying for patents on their potential discoveries. Such a tool also enables other patent professionals, biotech business analysts and even everyday citizens to be informed of the biotech and synthetic biological innovation landscape.

However, there are some jurisdictions* that still do not contribute their sequence listings to the PatSeq facility. While the challenge to achieve a complete global sequence patent database remains, The Lens team, in their recent publication, has outlined and offered many patent offices around the world, the opportunity to upload and share their listings publicly in PatSeq Data.

Authors’s Note: As of July 2017, the Intellectual Property Office of Singapore released the Patents Open Dossier (POD) which enables the public to view, monitor and manage patent profiles for applications that are of interest to them. Patent journals for the past 3 months are made available for free in .pdf format, and past issues will be available in CD-Rom format for a fee. This would hopefully enable PatSeq to strengthen their global patent database even further.

Moving from Academia to Activism

In my conversation with Professor Osmat, she spoke about what got her and Richard Jefferson into working in the open access space. Richard’s initial claim to fame within the scientific community was that he developed a reporter gene system called  ß-glucuronidase (GUS), which he adapted for use in plants and agriculture. GUS is now one of the most widely used tools in plant molecular biology, as well as in the development of transgenic crops worldwide.

However, in a presentation at the Skoll World Forum on Social Entrepreneurship in 2013, Richard described himself as not feeling at home within the scientific community as he did not seek the incentives and rewards that scientists traditionally did. He was tired of the fragmentation of the innovation landscape and the rush toward staking claims to discoveries for personal gain rather than to enrich the innovation space. Rather, he aimed to work towards democratizing the ability to innovate.

“If you want to control a society, there’s no better way than to suppress, harness or completely deny [the] fundamental biological imperative of innovation.”

Likewise, Professor Osmat has been working with UNESCO researchers on scientific projects that delivered public goods in Lebanon ever since she was an undergraduate. Her own experience meeting remarkable mentors working in those spaces gave her the belief that social change can be affected, and she is convinced that creating tools that enable innovation in neglected communities that are aware of their own constraints will empower them to make their own decisions, which brings the world halfway to the point of true innovation democracy.

With Cambia and the initiatives it has sprouted including The Lens, Professors Osmat and Richard have indeed found a space where they can both enable science and innovation worldwide and, by extension, call home.

Stay tuned for Biotechin.Asia’s interview with Professor Osmat this week.