A San Diego scientist and two taxpayer groups that challenged the patents, claiming they are too broad and therefore stifle embryonic stem cell research in the United States, said the fight is not over.

“We think we’ve come out of this process with some substantial gains for the stem-cell-research community,” said John Simpson of the Foundation for Taxpayer and Consumer Rights. “As far as we are concerned, this fight is long from over.”

At issue are patents held by the University of Wisconsin’s Alumni Research Foundation, or WARF, which holds the rights to work by James A. Thomson, a professor who was the first to patent his work isolating and culturing human embryonic stem cells.

On Tuesday, the patent office upheld the two older of three patents on Thomson’s work. On Feb. 25, the patent office upheld the third, most recently issued WARF patent.

All three patents were challenged in July 2006 by the Foundation for Taxpayer and Consumer Rights, a Santa Monica nonprofit; the New York-based Public Patent Foundation; and Jeanne Loring, a stem cell researcher now at the Scripps Research Institute in La Jolla.

Under the patents, anyone doing work in the United States with human embryonic stem cells needs to obtain a license from WARF, which could entail paying a fee. The challengers argued the WARF patents are driving vital stem cell research overseas.

The challengers also have argued that Thomson’s work was “obvious” in the light of previous research, making his work unpatentable. To receive a patent, something must be new, useful and not obvious.

In April 2007, the patent office issued a preliminary ruling invalidating the patents. After that, WARF filed applications to narrow the scope of the patents to stem cells created from an embryo before implantation.

“What the patent office accepted today were narrower, modified versions of the patents we originally challenged,” Dan Ravisher, a lawyer with the Public Patent Foundation, said Tuesday. “Therefore, what’s being upheld today has a decreased chilling effect on research than the original patents.”

Carl Gulbrandsen, managing director of WARF, praised the ruling for protecting the intellectual property that is critical to stimulating private-sector investment.

“Dr. Thomson’s groundbreaking work already has led to additional scientific breakthroughs and this latest ruling affirms that his pioneering discoveries are patentable inventions,” Gulbrandsen said in a statement.

WARF referred to the patent office decision as final.

Ravisher said he is considering new challenges that can be brought against the two patents upheld Tuesday. By law, the ruling cannot be appealed.

The narrower patents now may not cover embryoniclike stem cells created from a new and developing technology, Loring said. Those so-called pluripotent stem cells are created by coaxing skin cells, or other so-called adult cells, to move backward down the development process until they once again become like embryonic stem cells.

The narrower patents also should not cover embryonic stem cells derived from fetal tissue, Loring said.