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The dataset for "transport, passenger car, EURO 5" includes the construction, operation, maintenance and disposal of the vehicle and road infrastructure. Is there a way to only model the effects from the operational phase?

I have modelled the data from Simons (2013) for the exhaust emissions, but when I model the outputs the results don't show up in the Product system calculation.

I was trying to assess just the effect of exhaust emissions and hence did not model Petrol as input. So basically my process had only the emissions modelled.

But when I add the fuel i.e. Petrol as input the results start showing up in the impact assessments. Why is that the case? I did not quite understand that.

Simons 2013: Road transport: new life cycle inventories for fossil-fuelled passenger cars and non-exhaust emissions in ecoinvent v3

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Of course the use phase can be modelled separately. Input fuel, car, effort for maintenance, output emissions of (depending on fuel) engine, tyres, brakes.

There are also databases (like ecoinvent) which contain unit processes that represent the use phase of passenger cars (not sure which database you are referring to with the dataset you mention).
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I added the additional information from your comment to your question (https://ask.openlca.org/37/how-does-ask-openlca-work#a38)
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