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?

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Comments on “USPTO: Using Three Knowledge Bases To Diagnose Is Patentable”

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Anonymous Coward says:

Re: Re:

6 has got to be the worst troll ever. They normally pick less obviously retarded arguments to play with.

I have a patent for having an entirely numerical user name. It’s valid because its specifically for user names that are numbers that are written numerically and not alphabetically. Expect to receive word from my lawyer.

All your prior art is useless. The claim will hinge on something very complicated and you have no viable case against my claims on account of being a moron.

Frosty840 says:

Re: Re:

And you obviously haven’t RTFA.
Even though Mike quoted the relevant passage from Joe Mullin’s article, which in itself references the court ruling that separating a given knowledge base into three distinct entities is the patentable element of the system.

Let me make this quite clear: The prior art MYCIN system has three sections, each of which consults elements of a single database. The patentable element being disputed is the “invention” of splitting that single database into three separate databases.

Anyone with even a passing familiarity with database theory will see this as the absolutely trivial distinction that it actually is. The fact that the judge does not realise this distinction, and in fact argues against the case made for it, shows them to be insufficiently familiar with the art to be sitting on judgement on the case.

6 (profile) says:

I am not a troll. I do not even own a patent with which to go a trollin’.

We have seen neither the claims or the closest prior art. We have been given one quote. And that wasn’t even put into context very well.

Let’s take a sample claim.

1. A method for guiding the selection of a therapeutic treatment regimen for a patient with a chronic known disease or medical condition, said method comprising:

(a) providing patient information to a computing device, said patient information including prior therapeutic treatment regimen information for said chronic known disease or medical condition, said computer device comprising:
a first knowledge base comprising a plurality of different therapeutic treatment regimens for said disease or medical condition;
a second knowledge base comprising a plurality of expert rules for evaluating and selecting a therapeutic treatment regimen for said disease or medical condition;
a third knowledge base comprising advisory information useful for the treatment of a patient with different constituents of said different therapeutic treatment regimens; and
(b) generating in said computing device from said patient information and said first knowledge base a listing of available therapeutic treatment regimens for said patient; and
(c) generating in said computing device advisory information for one or more therapeutic treatment regimens for said patient in said listing based on said patient information and said expert rules.

Show me persuasive prior art against that. Go ahead. I’ll wait.

You might just happen to notice, while you’re being re tarded, that the three knowledge bases are each for a specific thing.

While I might agree with you if you merely said that it should be public policy to not allow claims to this sort of thing, Mike and others attacking it (or rather even more ridiculously, a broad generalization of the concept on display in the claim) on 103 grounds without any good evidence on display is ludicrous.

This OP is an embarrasment Mike. You need to change it.

nelsoncruz (profile) says:

Re: Re:


If different databases exist, for related purposes (in this case diagnostic and treatment), then using/consulting/merging them is totally an obvious thing. Even if there was no prior art, to me this should be an open and shut case.

If the fact that this is about “knowledge bases” or “data bases” confuses the issue, then think about them as books! Enough said!

fishbane (profile) says:

Re: Re: Re:

That HIVdb appears to be one database.

Well, that would be a big part of the problem. I shudder to think what sort of legal definition of “database” could end up coming out of this. Actual, you know, real world databases (here, the word used to mean an assemblage of information) can be composed as anything from one or more flat files, one or more logical sets of more or less structured information stored in whatever way by a DBMS… the list goes on. Put aside common usage of the word, what ‘database’ means varies based on the DBMS. Most commonly, “database” tends to mean separate namespaces in which sets of data are organized, but like anything else computer related, namespaces are mutable.

For that matter, go ask an accountant how many spreadsheets they have with exactly three tables in them. Do those become separate “databases” if they are saved as three logically distinct files?

Hell, the innovation of the URL was basically nothing more than coming up with a simple structure to append a protocol and global identifier to system-local file references. Of course, URLs also reference dynamic content. What do you call a system that compares a user’s GPS history with Google Maps and Starbuck’s store locations? Before you answer, tell me how many “databases” are used in Google Maps. And then ponder another system that uses this system to mash up the data with purchase history and a calorie lookup table.

Jrosen (profile) says:

More stupidity, and idiocy spreads

With things like this, it’s stopped being ‘how to innovate’, it’s turned into ‘how can I be even more petty in f’ing over other businesses that compete with mine’. Now given, that is, to a degree what companies do. Compete with each other. But it’s no longer free-market competition of ‘who can make the better product that people want, so they’ll buy it’, it’s simply become ‘who can we sue, legally f*** over, or worse’.

Using three databases/knowledgebases is NOT new, NOT innovative, NOT hard to do and should NOT be f’ing patent-able. Hell, you take anyone in the country, or world, who’s done searches for computer problems, and they likely do 3-6 knowledge/database searches each time!

6 (profile) says:

“Even if there was no prior art, to me this should be an open and shut case.”

That’s because you have no exposure to the nightmares of your own legal system apparently. Or you don’t realize that those same nightmares apply to examination.

Change the courts if you want to change decisions like this. Till then, just go with the flow plebs.

hmm says:

time to face a simple truth?

Yes, perhaps its time to face the awful possibility that…. the USPTO is entirely and completely in the hands of the industry lobbyists. i.e. they will do whatever their paymasters want.
Its pretty much the ONLY explanation why they allow pathetically obvious patents to continue.
OK, Here’s a challenge to ANYONE from the USPTO…tell me WHY patents for already-existing things (such as human DNA which has prior art going back MILLIONS of years (or thousands if you’re a creationist)) can be patented unless someone somewhere high up in the USPTO is accepting bribe money?

Glenn says:


we already know that the USPTO is staffed by idiots, so what do you expect?

I think I’ll patent “new math”: 2 + 2 = 5 (you know, because it’s not really ‘2’ but only somewhere around ‘2’ so ‘4’ or ‘5’ or ‘6’ or even ‘3’ are all possible correct answers to the equation… I’ll make billions! you know, as ‘2’ or ‘3’ or …)

6 (profile) says:

“You know you create change? By making people aware of bad results such as this one. Yet, you’re the one insisting that we shouldn’t be writing about it… Funny…”

You can’t just say “it’s a bad result” without telling them 1. The law is messed up and we should demand for the courts to change it or 2. There is a lawful case against this patent under the current law.

Make up your mind. It appears you’re trying to say 2 in your article, but you don’t provide the necessary meat to substantiate it.

If you want to say 1 then by all means, add in some things about how the judiciary needs to change things. Don’t just leave them out.

They are the ones with POWER. They are the ones that need to make the changes. And no amount of “public awareness” is going to change that. The judges on the CAFC/BPAI are appointed, not elected. And the USSC rarely weighs in on these issues (and even they are not elected). The elected district court judges (in the rare event that they were elected) have little to no power to set precedent that could change the system.

6 (profile) says:

“Its pretty much the ONLY explanation why they allow pathetically obvious patents to continue.”

The much better, and real, reason is that there are stringent legal requirements to invalidate a claim.

Nobody in this thread has yet to provide me with art on the claim posted above. I’m still waiting. Since it is so easy, and I’d have to be an idiot not to be able to invalidate this claim as obvious, by all means, provide me with the references and the exact wording that an examiner should supply to invalidate it.

Keep in mind that your response must hold up under judicial scrutiny and comply with all the precedents.

Go ahead hotshots. Get right on it.

6 (profile) says:

“OK, Here’s a challenge to ANYONE from the USPTO…tell me WHY patents for already-existing things (such as human DNA which has prior art going back MILLIONS of years (or thousands if you’re a creationist)) can be patented unless someone somewhere high up in the USPTO is accepting bribe money?”

I’ll be 100% honest with you in that I have issues with gene patenting as well, along the same lines as your own. However, it was decided by a court, a long time back, that the ISOLATED gene does not occur in nature. If you can show that it does, then by all means, have a court invalidate the claim, set a precedent, and we will follow suit. As a side note, I don’t think we patent DNA itself, we allow patenting of genes however, so I presume that is what you are referring to.

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