The word Substance refers to a homogeneous chemical composition. This may be an element (e.g. Nitrogen, Oxygen), a compound (e.g. Nitrogen Dioxide, Benzene) or a complex mix of different compounds (Vodka, Blood). Substances are not directly interacted with by players during the game - they are simply a data template. A Substance is specific to its state - for example: Water and Ice are considered different substances.
This is mostly relevant the most to Chemistry, but in terms of atmos we can see part of this system as a combination of gasses flowing and mixing in the atmosphere of the station, as they might have reactions with each other.