His father Samuel Aboab was the Av Bet Din of Venice.
He paid especial attention to Biblical antiquities and natural science and conducted an active literary correspondence with Theophil Unger, a pastor, who was an enthusiastic collector of Hebrew manuscripts.
Aboab also maintained, from 1682 to 1692, a scientific correspondence with the learned imperial councilor Job Ludolf, at Frankfort-on-the-Main.
Lastly, Rabbi Jacob wrote a number of rabbinical decisions, which are preserved in the works of others such as "Pahad Yizhak" by Isaac Lampronti.
His son Abraham, was also a rabbinic scholar in Salonica, whose descendants settled in Turkey.