USPTO: Using Three Knowledge Bases To Diagnose Is Patentable

from the three-databases-makes-a-difference dept

Back in June, we wrote about the rather horrifying situation that Dr. Bob Shafer found himself in, facing a patent lawsuit over a fantastic resource of HIV-related data that he had been putting together for years, and which the community of HIV researchers have used for years. Shafer's employer, Stanford University, was threatened by a company, Advanced Biological Laboratories, claiming that the database violated its patents (6,188,988 and 6,081,786) on using databases for diagnostic decisions -- even though HIVdb predated either patent. There was some back and forth, and Stanford settled the dispute (much to Shafer's dismay) and a separate lawsuit commenced against Shafer himself, after he refused to abide by the terms of the original settlement.

Joe Mullin has an update on the situation and the one bit of good news is that the lawsuit itself has been settled, and Shafer really just needs to post a link to ABL's "response" to his claims.

But the more disturbing part is that the USPTO has upheld the '988 patent in question, despite over 200 pages of prior art submitted by Shafer and his lawyers. Why?

Even though doctors had used databases to help choose therapies to treat various ailments for decades before the first relevant patent application at issue was filed in 1998, Hughes said the '988 patent should be allowed. Her reasoning: the prior art references didn't distinguish a system with exactly three "knowledge bases." And that distinction alone--having three "knowledge bases"--is a patentable advance, Hughes decided.

Yes, you read that right. Even though people have used such knowledge bases for decision making for quite some time, the fact that we're talking about three knowledge bases suddenly makes it patentable. Because without patents, no one would have ever thought to use exactly three knowledge bases. Shafer and others are already pushing back on that and hoping to still invalidate the patent. Mullin notes that Ted Shortliffe, president of the American Medical Informatics Association, has joined Shafer in pointing out how ridiculous the idea that "three" knowledge bases makes some sort of meaningful difference:

This is a trivial distinction without a practical difference since multiple knowledge bases could be merged into a single entity and have long been separated into multiple representations largely for computational convenience and clarity.

Honestly, can someone explain how the USPTO is employing people who think that having three knowledge bases turns using knowledge bases for diagnostic purposes into a patentable invention?

Filed Under: bob shafer, hiv, knowledgebases, patents