Open Source Drug Discovery for Malaria Meeting - Session 2, Part 1, Richard Jefferson

Published by MatTodd on 23 May 2012 - 12:41am



Part of the second session at the Open Source Drug Discovery for Malaria meeting at The University of Sydney, February 24th 2012. Speaker is Richard Jefferson, Cambia and the Institute of Open Innovation.




  1. set up about 20 years go with the aim of shifting the demographic of problem solving. The tools built were initially scientific – i.e. enabling technologies. This was an academic success but a practical failure. In an innovation system the rate limiting step is conversion of an idea to a solution.
  2. (2:12) The most important science is the science that fails but fails gracefully, since it provokes the most change. Cambia led to a biological open source movement to try to achieve more collaborative approaches. The latest moves are towards destroying information asymmetry, i.e. to de-risk innovation.
  3. (4:39) Innovation cartography. The power of an evidence base for self-interest. The analogy of trade. For trade one needs a map to reduce risk. The story of the Portugese/Spanish dominance of trade, owing to a very substantial investment in cartography. Maps identify risks. The quality of a map depends on the quality of surveying. The monopoly on maps gave rise to low levels of competition between powers. 1596 – a Dutchman was working in Goa, found the entire stock of Portugese maps. Copied them, went back to Netherlands and published them, open access. This gave rise to an explosion of activity, e.g. the founding of both the Dutch and English East India Companies, i.e. the publication of de-risking tools gave rise to huge commercial activity and innovation in ship building, and in associated areas such as insurance. Knowledge space is the key to business in the modern age, rather than moving commodities. The same metaphors apply. To bring the analogy back – those with money employ patent attorneys and business professionals who are gatekeepers to information. The have risks and expenditures. They recoup the expenses by targeting big innovations, not the small. We need a social revolution to democratize innovation.
  4. (12:25) Jefferson therefore built the Patent Lens. A transparent and inclusive innovation system. Patents are not the problem – they are part of the solution, as a great resource of our species’ technical knowledge. Patents are challenging to read, but still valuable. They are information, but not knowledge, which is more the aim of the Lens – how do we improve how we use patents? Solving a problem is like doing a jigsaw. The solution must be: A) Visualizable - Most important part of a jigsaw is the box – which shows the basic idea. B) Comprehensive – a jigsaw contains all the pieces and can be completed. C) Bounded – has corners and edges. D) Standardizable the pieces only come in certain shapes. These make innovation work. Currently we don’t provide these four requirements in many cases by default.
  5. (18:00) Patents are a right to sue, not a right to do. 80-100 million patents exist. They are public documents and a huge resource. To understand them we need survey points. In journalism this is the Who What When Where Why – these apply also to patents and innovation. The Lens added a Which. The front page of a patent typically has all this information. The Lens is a prototype – beta at the moment – but currently has 80 million patents in it.
  6. (21:13) Demonstration of the Patent Lens. Patents can be filtered easily by e.g. jurisdiction. Much of patent language is human-impenetrable. Need to allow automatic understanding of the text, allowing links between patents. Also need to be able to make links between patents and the academic literature.
  7. (26:30) How the lens facilitates collaboration. Can integrate patents with people. Can annotate patents and share them; can generate collections for projects. Can embed analyses in any other pages. Allows using patents to provide data to support assertions (or not).
  8. (29:28) Used this for Gates and malaria. Gates insist on a global access plan – how it’s clear that your work will find its way to the people who need it? Need to show impediments to delivery/partnerships appropriate. Recent appointment at Gates of new head of global development. Lens developed with agile development, here a pharma patent attorney working with software engineers, and this team was asked to develop a patent landscape for malaria vaccines. So currently has all candidates, with relevant patents, and human-enriched information. Is using an old content management system, and will have more tools soon. Cartography analogy again, that people focus on their local area of interest, and the broader map is built in aggregate. Comment made that most patents that could be enforced are not. They are a valuable resource, in aggregate.
  9. (35:44) Lens not yet live, so there will be bugs. Moving to Chinese, Korean and Japanese patents. Working generally with NCBI and Crossref, then want to move to the business literature, i.e. description of legal entities. The overall goal of the Lens is the removal of barriers to other people’s creativity.
  10. (38:10) Two questions from Mat Todd: 1) will the Lens include chemical structure searching? Jefferson: Yes, but technically challenging. Todd: Would be great if the innovation landscape around molecules could be visualized. Second Q: If we work on an antimalarial, and find that it’s a class of compounds covered by a patent, what do we do? Forbidden to research it? Palombi: Research exemption (low audio) but the clause is too narrow, because of the vagueness of the definition of “research” – there is little research not linked to anything commercial. Overall answer is that generally yes you’re allowed to research something that occupies the same area as an existing patent. The onus would be on the company to find us and ask us to stop, but there is so little incentive for them to do that. Patent infringement of this kind would apply to nearly every university. It actually could help the patent holders by making their methodology clearly more robust. The Lens is open source project. Can be licenced and internalised in companies, sure, but in return the community gets a search tool. Hence worth funding.
  11. (43:41) (Audio low) Observation from Palombi that it’s possible in future that infringing patents may become criminalizable, i.e. to ratchet up enforcement.
  12. (44:18) Jefferson demonstrates the Lens’ biological sequence tool. Sequence information listed associated with species, and which have been associated with patents. Valuable genetic resource for building an evidence base for policy.
  13. (47:00) Nico Adams (CSIRO) Chemical search tools have been developed by Peter Murray-Rust’s group. Chemical patents generally are not well-written. A particular problem is the intentional vagueness of chemical structures. Even if a patent can be read, it then needs to be understood. Jefferson: Mention of Surechem’s patent search tool. Many companies don’t need proprietary tools (don’t have resources to make them very good), they need proprietary outcomes (better information). Most companies frustrated by poor patent, poor tools available. “Companies are either doers or selective deniers”. NCBI can’t (at the moment) do things that are too disruptive in this area.
  14. (50:37) Question from Stuart Ralph. Patents generally awful but they do have a structured and limited vocabulary. Hence need natural language processing? Jefferson: Yes. Patent claims need to be translated into human language.
  15. (53:52) Moran, and others, questions (but audio unclear until 55:10). Nico Adams – Document summarization is important/relevant, e.g. Stephen Wam (CSIRO) interested in summarizing claims in science papers.
  16. (56:15) Final question from Luigi Palombi. Current negotiations are happening for the trans-pacific partnership agreement for the pacific rim, re IP. The Lens makes it easier for people to access information and is therefore relevant. People can’t currently get this information through government-funded patent sites. Should get in touch with e.g. DFAT negotiators. Jefferson: Yes, can become involved in these things when the Lens is ready (beyond beta), i.e. only when it’s comprehensive then it can be wedded to policy making. For example it needs to be at the point where it can understand patent claims.


cdsouthan's picture

Related to the question raised by  Mat, unfortunately  won't currently work on the Patent Lens full-text tab URL but I have left feedback on the PL site.  You therefore need  the corresponding FreePatentsOnline non-tabbed URL for to convert the IUPAC examples in a patent to their structures,  or, what is even easier if the patent is in SureChemOpen the chemistry is both extracted and searchable by structure.   Both these resources, and others, are mentioned in this slide set  (