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Im trying to obtain historical datasets of public transports like train, bus and also bikesharing provider. While api.citybik.es provides almost all APIs of these providers, i struggle to actually find a database with compiled data throughout a year. My big goal is to compare the capacity usage of two or more of these public transports in one city(preferably Germany).

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motivateco, the firm charged with operating the city's now-public Bike Share program, have a list of XML and JSON feed for each city they operate in. They also release the General Bikeshare Feed Specification (GBFS) which they are trying to push as a standard for bike sharing data publication.

If you are looking for time series data check out:

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Capital Bikeshare's AWS server has data from 2010 4q - Current
Cambridge, MA has data from 2015 - Current

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