Category Archives: Proteus

The Knowledge Last Mile Problem

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File:Ancients repository of knowledge.jpg

Colonel Jack O’Neill, the intrepid leader of the Stargate SG-1 taskforce of the eponymous popular Sci-Fi TV show, in his time took some remarkably astute decisions, oftentimes in situations of great stress, saving our galaxy from being overrun by nasty alien races more than a few times. Now, O’Neill is a great generalist and thinks fast on his feet but he never was a paragon of erudition nor does he have any such pretensions. Indeed, he harbors a robust disdain for anything resembling scholarly pursuit. However we all know, in intergalactic matters our gut-level decisions are not always enough. From time to time we have to invoke a higher body of knowledge. When the Replicators were on the verge of exterminating humans and no weapon in possession of humans and their alien allies seemed to be having any lasting impact on the ferocious onslaught, it was clear a new kind of weapon was desperately needed if the Replicators were to be thwarted. Fortunately for the earthlings, Colonel O’Neill very recently, had downloaded into his brain the entire knowledge repository of an incredibly advanced race, the Ancients. Armed with this knowledge he could quickly devise a weapon capable of annihilating the Replicators. Needless to say, once again the Milky Way Galaxy was saved.

Note that O’Neill did not learn from the Ancients. Instead his mind just imbibed the knowledge. He ‘acquired’ countless skills, including those needed to deal with the Replicator emergency, without having to go through the arduous process of learning. I shudder to think what would have happened if O’Neill had had to read countless PDFs and WebPages before he was suitably equipped.

In short, the Ancients had developed the perfect technology to bridge the last mile knowledge gap, the gap between existing knowledge and its translation into practice, the gap that every human institution that works with knowledge has struggled with. No matter the amount of conclusive findings clinical research throws up, if the clinicians do not integrate them into their care-delivery is it worth anything?

Since beginning there has been the gap, the gap between research findings and how it is applied in practice.


The good intentioned knowledge producing people and institutions reduced it by making it easier for people to access the results of the research. This was done by using journals, monographs, textbooks and such, and later on making much of it available for little or no cost by the medium of internet.


But soon the realization dawned upon the knowledge producers and providers that just providing easier access to the research results is never going to be enough. The outputs of research efforts need to be sifted through to allow only the reliable information to impact practice. What came to be known as Evidence Based Medicine was driven by such meta-analysis. Besides vetting research for quality, the research results have to be articulated in actionable terms, which, in the field of medicine, came be known as clinical guidelines. The users of the knowledge, such as the clinicians, do not usually have time and inclination to undertake such analyses and translations. So it seemed to make sense that pre-processing the research results into meta-research and guidelines before it is made available will lead to improved application of the research into practice.

These efforts did result in narrowing the gap but not remarkably. The original enthusiasm for guidelines and meta-research seems to have lost steam.


What if a clinician’s mind had access to a knowledge repository just like the Ancients’, and had the ability to simply suck in on demand, the most appropriate pieces of knowledge? That would surely eliminate the gap.

A clinician with access to such a knowledge repository would be able to manage almost any condition using the best evidence and recommended practices. For such a scenario to unfold will take a very long time because we do not yet possess that level of ability to tinker with minds. However, we do possess reasonable knowledge of computers. After all we created them. Can we then think of a way in which all human wisdom, expressed into actions, be made available in a shared knowledge repository. The computer of the clinician can then access this knowledge on demand to get precise advice about what next needs to be done about the patient on hand. The wisdom in such a repository could be deposited, over course of time, by clinicians themselves to be shared with other clinicians. The clinicians would enhance the knowledge to work for themselves but will also be able to share it to be able to make significant difference to others.

What will be the form of knowledge contained in such a knowledge repository? Remember, the knowledge should be able to modify behavior of a computer system to be able to advise the clinicians about individual patients. Software has been used for a long time as the standard way of altering the behavior of computers. However, software is created by programmers with special skills using sophisticated development tools. If the knowledge repository has to acquire the necessary knowledge that evolves with the understanding of the experts and clinicians, it will need to be modifiable by people with clinical expertise who normally do not possess software development skills.


This is where knowledge form like Proteus comes in. The Proteus knowledge is executable and yet modifiable by clinicians. We are in the process of building early mechanisms to allow clinicians to deposit such knowledge in a publicly available repository, which will allow clinicians to integrate, on demand, any part of knowledge they need to modify behavior of the Proteus Engine, a software module which interprets the knowledge and provides advice to the clinicians about individual patients based on the data from those patients.


Proteus Open Source Now!

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This is to announce the availability of source code for tools related to clinical decision support guidelines model, Proteus under an open source license (EPL). The open source development will proceed under the new Proteus Intelligent Processes (PIP) project.

With this announcement, we are also opening up the project for general participation. The code and related information can be found at  The home for Proteus will remain at Introductory information about the rule authoring system GreEd is available at

This also coincides with the release of the version 2.7 (beta), which has several new features to make knowledge authoring more exciting and easy.  Take the new application for a spin by downloading it from

What’s New

I list some of the new features in Version 2.7 below:

Protean (Clinical Workflow Authoring Tool)

  • Sharing executable knowledge
  • Unlimited undo and redo
  • Promotion and demotion
  • Move an item from one location to another
  • Search your library of components

GreEd (Rule Authoring Tool)

  • Undo and Redo
  • Default Inference
  • Semantic Guidance and constraints
  • New operators for your expressions, like [N of M] and [Between]
  • Date Fields and Operations

Read more about the new features here:

This is a major milestone for Proteus which was made possible by contributions from many wonderful people. Much of the development for this version was done in the Semantic Data Capture Initiative project of Henry Ford Health System, my employer. Besides Henry Ford, Lister Hill Center of National Library of Medicine played a critical role at the nascent stage of Proteus. Several ideas related to metadata usage and rule authoring were developed at City of Hope National Medical Center.

We will be scheduling a web seminar to provide a quick introduction to Proteus, GreEd and the PIP project and demonstrate the tools. Please let me know if you are interested in participating.

I will be at the upcoming AMIA annual symposium, in San Francisco and will be happy to meet you if you are planning to attend.

We welcome your participation and feedback.

Feel free to contact me.


Can the Fun Apps of Web 2.0 World be Useful Apps for the Healthcare World?

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Many a conference have been organized and quite a few more papers and articles have been written about how Web 2.0 can revolutionize healthcare. The thought leaders have declared that Healthcare 2.0 is here – A new era where the Web 2.0 paradigm influences healthcare. It is said that connectivity between people and crowdsourcing that these new approaches facilitate will deeply influence how providers and consumers exchange information and make decisions.

All of which is true, notwithstanding the fact that the technology to do all that already existed – it’s just that the awareness of its power has reached the tipping point where everyone has started chanting the same mantra, in unison. No doubt these are powerful shifts and will have profound impact on healthcare. But, I have always felt that these cheerleaders have missed something fundamental. There has been so much emphasis on the social networking aspect (fuelled in no small measure by the sheep mentality of the venture capital and angel funds), that the other important aspect that can inspire new things in healthcare has not been given enough attention. That aspect being the component approach that the Web 2.0 has popularized. So many interesting tools have been created by the intrepid developers of Web 2 world that probably many of them can be mashed together to create really useful apps to do things in healthcare which were not easily possible or even conceivable earlier. It is also encouraging to see that so many have been brave enough to allow what they have developed to be used by others in ways which might be quite different than for which they were originally created. Continue reading