Stone, iron, and logs can be directly gathered from the ground using the destruction & removal tools, but will soon run out (although trees will very slowly spread outwards from existing forests).
Once these materials run out, they can only be obtained either through trade, or from foresters which plant trees, quarries which mine stone, and mines which produce iron and coal. Quarries and mines only produce a finite amount of resources, and will eventually run out - they cannot be removed once built.
Wool is produced from sheep in pastures, while leather is produced both from cows and from deer, hunted at hunting cabins.
Herbs are produced at an herbalist, and help keep your citizens healthy.