Dr. David Blumenthal, one of the nation’s leading health information technology experts, will leave Partners HealthCare at the end of this year to head The Commonwealth Fund based in New York City.

Blumenthal is a professor at Harvard Medical School and chief health information and innovation officer at Partners. He was US National Coordinator for Health Information Technology under President Obama from 2009 to 2011, with the charge of building a nationwide health information system.

Previously, he worked as a primary care doctor and health policy expert at Massachusetts General Hospital and other Partners institutions for more than 30 years. He returned to Partners just seven months ago.

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In an e-mail to the Partners community Thursday, Chief Executive Dr. Gary Gottlieb said Blumenthal “provided remarkable leadership in directing the process of modernizing Partners’ electronic health information system,’’ including helping the large hospital and doctors network select Epic as the vendor for Partners eCare, its new information system.

The Commonwealth Fund is a large private philanthropy that funds research on health care issues.