In a potential setback for the pharmaceutical and biotechnology industries, a federal appeals court Friday revived certain controversial new rules aimed at curbing abuse of the U.S. patent system and reducing the backlog of unexamined patent applications.

The mixed court ruling upheld some of the rules changes adopted by the U.S. Patent and Trademark Office in 2007.

GlaxoSmithKline PLC (GSK) and an independent inventor challenged the rules before they went into effect, arguing that Congress had not given the patent office the authority to make substantive changes to the patent process.

Glaxo, backed by the pharmaceutical and biotechnology industries, said the rules would undermine patent rights that encourage firms to take significant financial risks in developing new drugs.

A federal trial judge in Virginia sided with Glaxo in 2007 and invalidated the rules, but the U.S. Court of Appeals for the Federal Circuit on Friday overturned much of the trial judge's decision.

In a 2-1 ruling, the Federal Circuit upheld a patent office rule that would require an inventor who makes a large number of claims about what a patent covers to provide detailed information on why the invention is eligible for patent protection.

The appeals court also upheld a new rule that would limit the number of times a company or inventor can request a re-examination of a rejected patent application.

The Federal Circuit, however, struck down a patent office rule that would have limited the number of times an inventor can file a patent "continuation," the process used to amend a patent application.

The patent office has said its new rules would stop opportunistic patent applicants from flooding and abusing the system.

An array of consumer groups and law professors supported the patent office in the case, saying the current patent system creates uncertainty in the marketplace and makes it all too likely that dubious patents will eventually be approved.

Friday's ruling sent the case back to the trial judge for further study. The appeals court said Glaxo still has the opportunity to make different legal arguments against the new patent rules.

Bradley Wright, a Washington patent attorney with Banner & Witcoff, said the ruling could have a significant negative impact on pharmaceutical, biotechnology and chemical companies, which frequently file patent applications that contain a large number of claims.

"It will increase the cost of filing for new patents," Wright said.

Glaxo said in a statement that it is reviewing the decision and assessing its options. The company said it was pleased the court found one of the rules invalid but disappointed in other portions of the decision.

The patent office did not return a call for comment.

The top trade associations for the pharmaceutical and biotechnology industries had filed friend-of-the-court briefs supporting Glaxo. General Electric Co. (GE), Elan Corp. (ELN) and Monsanto Co. (MON) also supported the drug maker.

-By Brent Kendall, Dow Jones Newswires; 202-862-9222; brent.kendall@dowjones.com