We introduce topological phases of matter defined by skyrmions in the ground state spin -- or pseudospin -- expectation value textures in the Brillouin zone, the chiral and helical topological skyrmion phases of matter. These phases are protected by a symmetry present in centrosymmetric superconductors. We consider a tight-binding model for spin-triplet superconductivity in transition metal oxides and find it realizes each of these topological skyrmion phases. The chiral phase is furthermore realized for a parameter set characterizing Sr$_2$RuO$_4$ with spin-triplet superconductivity. We also find two types of topological phase transitions by which the skyrmion number can change. The second type occurs without the closing of energy gaps in a system described by a quadratic Hamiltonian without breaking the protecting symmetries when atomic spin-orbit coupling is non-negligible and there is a suitable additional degree of freedom. This contradicts the flat band limit assumption important in use of entanglement spectrum and Wilson loops, and in construction of the ten-fold way classification scheme of topological phases of matter.
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