The IBIS specification uses voltages relative to ground for drive-low (pulldown), but voltages relative to the appropriate supply rail for drive-high (pullup).
To convert to ground-relative voltages, take the nominal I/O supply voltage and subtract the voltage value listed in IBIS.
For example, a voltage shown as 6.6V in the [pullup] section of an LVCMOS33 I/O type is 3.3V - 6.6V = -3.3V Many IBIS tools have an option to show the data relative to either Vcc or Gnd.