Remarks

• Lack of an AUTO_INCREMENT id for this table – The PK given is the ‘natural’ PK; there is no good reason for a surrogate.
• MEDIUMINT – This is a reminder that all INTs should be made as small as is safe (smaller ⇒ faster). Of course the declaration here must match the definition in the table being linked to.
• UNSIGNED – Nearly all INTs may as well be declared non-negative
• NOT NULL – Well, that’s true, isn’t it?
• InnoDB – More effecient than MyISAM because of the way the PRIMARY KEY is clustered with the data in InnoDB.
• INDEX(y_id, x_id) – The PRIMARY KEY makes it efficient to go one direction; the makes the other direction efficient. No need to say UNIQUE; that would be extra effort on INSERTs.
• In the secondary index, saying just INDEX(y_id) would work because it would implicit include x_id. But I would rather make it more obvious that I am hoping for a ‘covering’ index.

You may want to add more columns to the table; this is rare. The extra columns could provide information about the relationship that the table represents.

You may want to add FOREIGN KEY constraints.