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Mexico City's chief prosecutor disputed a volunteer group's claims that human remains and other evidence had been found at the site.
It marks the first time in recent memory that anyone claimed to have found such a body disposal site in the capital.
Police in Juarez, Mexico, on Tuesday pulled three bodies buried under the floor of an abandoned house next to a downtown auto parts store.
More than 111,000 people have gone missing in Mexico since the war between drug cartels ramped up in 2007, a Mexico City think-tank reported this week.
The new integrated database, mandated by law in 2017, is designed to address Mexico's crisis of disappearances and unidentified remains.