Microsoft's announcement Tuesday that a federal ruling has deemed its Windows file-storage systems patents valid, is raising concerns in the open source community.

The software giant's victory in the file allocation table (FAT) patents battle could demonstrate that global patents systems can be dangerous to the health of Linux and the open source community at large.

"This is now a situation in which Microsoft could cause major problems to Linux vendors and users," said Florian Mueller, the leader of an anti-software patents initiative in Europe Wednesday. "The example of the FAT patents shows that all those patent quality initiatives and patent pledges have no significant value to open source developers, vendors and users if Microsoft ever wants to go for Linux's throat," he said in an email.

The FAT filesystem, sometimes called the DOS file system, contained patents that were deemed patentable by the USPTO because they were "novel and non-obvious." The patents had been challenged by some individual computer users and by the Public Patent Foundation. Last year, it appeared that the open source community, which maintains there was "prior art" inherent in the patents, had prevailed.

But in a decision filed last week, examiners sided with Microsoft, which noted Tuesday that a "patent re-examination certificate," signifying conclusion of the issue, is being prepared. Microsoft had argued that it developed the FAT in 1976.

Eben Moglen, general counsel of the Free Software Foundation, had said if Microsoft was successful in licensing the patents, it could add "millions of dollars annually to consumers' expenses for digital photo storage, and (raise) the cost of digital cameras throughout the world."

The patent decision could represent a proverbial Sword of Damocles hanging over the open source community, because Microsoft could, at least in theory, seek royalties for Linux. Microsoft has given no indication it plans to use the patents against the open source community.

David Kaefer, Microsoft director of business development, said his firm was pleased with the USPTO decision. "This result underscores the validity of these patents but also the importance of allowing third parties to request re-examination," he said, according to published reports.

Mueller said the decision "gives Microsoft the strategic option" to cause problems for the Linux and open source community. "The USPTO and even the European Patent Office continue to grant new patents to Microsoft daily, and some of them may be equally dangerous to open source as the FAT patents," he said