Per Wikipedia entry Opposite (semantics), pairs of words that are complementary in meaning within a context are called relational antonyms.
Quote from the entry:
A relational antonym is one of a pair of words with opposite meanings, where opposite makes sense only in the context of the relationship between the two meanings. There is no lexical opposite of teacher, but teacher and pupil are opposite within the context of their relationship.
This term is relevant for the first few examples given (certainly boys-girls, arguably also man-machine and data-control; with some simplification (forgetting about fungi for the moment) also plants-animals). I cannot think of a context where shoes and socks would be relational antonyms.
A related post at Linguistics.SE provides further, if somewhat opinionated, discussion of a closely related topic, namely, how to classify the pair mother-father. A document linked in one of the comments, authored by Rick Morneau, quotes Lexical Semantics by D.A. Cruse (Cambridge University Press, 1986) for the following finer classification of antonyms (two items from a list):
Relational: doctor-patient, predator-prey, parent-child
Counterparts: male-female, ridge-groove, heaven-hell