Groklaw reported the notifications on Friday. See the full filing here. These patent reexaminations are a routine part of patent lawsuits. One party, usually the one that’s alleged to be infringing, asks the patent office to reexamine the patent and decide whether or not the patent should have been issued in the first place. A rejection isn’t by any means a final nail in the coffin in Oracle’s infringement case against Google. But it doesn’t exactly help Oracle, either.

Oracle has six months to appeal the patent office’s finding, and it can also, as a final step, sue the patent office itself. But these things rarely go that far.

And these rejections are sometimes meaningless to the final outcome of a lawsuit. In 2005, as part of its epic patent litigation against NTP — the case that nearly barred the import of BlackBerry devices into the United States — Research In Motion won several rejections from the patent office, like this one, which I wrote about at the time, only to suffer later defeats in court that led it to pay a $612 million settlement.

Oracle has claimed that Google owes it more than $6 billion for parts of its Java software that were used in the Android mobile operating system; Oracle took over Java after it acquired Sun Microsystems last year. Google has argued that Oracle’s claims for damages are flawed. After face-to-face talks between Oracle CEO Larry Ellison and Google CEO Larry Page failed in September, the trial had been expected to begin in October. But it was delayed, and is now expected to get underway in 2012.

Some of the best known companies are those that have built up huge war chests of patents and then go after companies that refuse to license their technologies. In this group of “non-practicing entities” are companies like Nathan Myhrvold’s Intellectual Ventures; and NTP, the company that successfully sued Research In Motion.

There are other patent-collecting companies that use their patent power to help companies that are already the target of patent litigation. And, of course, there are the armies of attorneys to litigate all the various disputes.

One lesser-known approach is the one taken by Article One Partners, a firm that helps companies being targeted for attack by seeking to invalidate the patents being asserted. Article One does this by tapping a global network of contributors that search for similar ideas that predate a patent — so-called “prior art.” Article One gets a flat fee or subscription from those who seek its services, while contributors that find prior art are given a monetary reward.

While Microsoft has publicly said it is tapping Article One’s services, most of the company’s more than 100 clients prefer not to advertise their association with Article One. That said, the demand for its services is huge, according to Ray Felts, who is president of the company’s North America practice.

“We are assisting clients in the middle of just about every major litigation out there,” Felts said in a recent interview.

To expand its practice and be closer to the majority of its customers, Felts has relocated to Silicon Valley, and Article One has opened an office in Palo Alto.

Although the company’s clients tend to be in high-tech circles such as Silicon Valley, Felts said those that that ferret out prior art have come from all over the world. Some $2 million in rewards has been paid out, he said, with one person in the Southeast U.S. having taken in more than $100,000. The privately held company has been doubling its revenue year over year, Felts said, without disclosing numbers. Its backers include Marshall Phelps, the lawyer that built up the intellectual property licensing businesses at Microsoft and IBM.

Much of Article One’s work is around protecting the makers of products against suits by the nonpracticing entities, such as Lodsys. However, more and more, the company is seeing disputes from one manufacturer suing another.

“You have what we call the circular firing squad of operating companies killing each other,” Felts said.

The mobile industry in particular has seen a surge in such litigation. Of the 250 patent studies that Article One has done for clients, more than half have been in the mobile and wireless areas.

“It’s driving our growth,” Felts said.

With the deal, RIM will now have access to Intellectual Ventures’ collection of 30,000 patents as it winds its way through the murky litigious waters of the smartphone market. Financial terms of the deal were not disclosed.

“Intellectual Ventures offers an efficient way to access the invention rights companies need to stay competitive within the market,” Intellectual Ventures’s telecom licensing head Mario Obeidat said in a statement Wednesday. “RIM has always been an innovator on the forefront of the mobile communications world, and by becoming a licensing customer of IV, they can have access to a broader set of patents to assist them in the management of their IP-related business matters.”

RIM knows firsthand what it is like to be on the wrong side of a patent infringement verdict, having been through a long and costly battle with NTP.

The smartphone market battle continues to be fought in the courthouse as well as in the marketplace. Apple and Nokia are locked in courtroom battles, as are Microsoft and Motorola, and Google and Oracle, just to name a few.

Intellectual Ventures, the IP shop started by former Microsoft exec Nathan Myhrvold, has thousands of patents, including at least some in the smartphone space.

On Friday NTP filed patent infringement lawsuits against Apple (AAPL), Google (GOOG), HTC, LG Electronics, Microsoft (MSFT) and Motorola (MOT) claiming–just as it did in the suit that nearly shut down RIM’s BlackBerry service–that their mobile wireless email devices infringe upon its technology. The suit asks that the companies be prevented from selling and operating such products and slapped with punitive damages (see document below).

“Use of NTP’s intellectual property without a license is just plain unfair to NTP and its licensees,” NTP co-founder Donald Stout said in a statement. “We took the necessary action to protect our intellectual property.”

And wring every last bit of value out of it. NTP’s key patents expire in 2012, so this really seems a last-ditch attempt to use them to win one last big payday.

And if it does, the big names in the smartphone industry could find themselves in the same unpleasant position RIM (RIMM) Chairman and co-Chief Executive Jim Balsillie found himself in back in 2006.

“It’s a lot of money for patents that will not survive, for sure, but that doesn’t do us any good if there’s a court that doesn’t wait,” Balsillie said after agreeing to a $612.5 million settlement with NTP. “No question, we took one for the team here. It wasn’t a good feeling to write this kind of check.”

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[Image credit: Bob MacNeil / WIPO Magazine]

Last Friday the patent holding firm sued AT&T, Verizon, Sprint and T-Mobile for infringing on its portfolio of mobile email-services patents and demanded they pay royalties on the sales of BlackBerries and other devices that send and receive email. Apparently NTP feels that because Good Technology, Visto and RIM have licensed the same patents, these big wireless carriers should as well. Said the company in its complaint against Verizon: “Verizon’s continued infringement with its present knowledge of NTP’s patent rights and their relevance to defendant’s operations is reckless and willful.”

NTP’s lawsuit will no doubt again raise questions about the validity of its patents, a number of which are still under re-examination by the U.S. Patent and Trademark Office–those, that is, that haven’t already been rejected.