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I managed to solve the issue by doing the following:

In "application.properties" I put the following lines

spring.jpa.hibernate.naming.physical-strategy=org.springframework.boot.orm.jpa.hibernate.SpringPhysicalNamingStrategy\n\nspring.jpa.hibernate.naming.implicit-strategy=org.springframework.boot.orm.jpa.hibernate.SpringImplicitNamingStrategy\n

In the connection string I added ";INITIALIZATIONSTRING=set schema 'PUB'" at the very end. It looks like this now:

spring.datasource.url=jdbc:datadirect:openedge://HOM-DB-01:25475;databaseName=ems2esp;INITIALIZATIONSTRING=set schema 'PUB'\n

Also, I had to ensure that "schema" property in @Table annotation should NOT be defined:

@Table(name = "INTEG_TABLE_003C", schema="DO NOT DEFINE SCHEMA")\n

\n"}}],["$","$L14",null,{}],["$","ul",null,{"className":"list-group","children":[["$","li","0",{"className":"list-group-item","children":["$","$Lf",null,{"href":"/answer/32745585","className":"text-primary","children":"Postgres selecting from table row"}]}],["$","li","1",{"className":"list-group-item","children":["$","$Lf",null,{"href":"/answer/9208532","className":"text-primary","children":"To find the next work day"}]}],["$","li","2",{"className":"list-group-item","children":["$","$Lf",null,{"href":"/answer/19727786","className":"text-primary","children":"SQL Server Left Join With 'Or' Operator"}]}],["$","li","3",{"className":"list-group-item","children":["$","$Lf",null,{"href":"/answer/79073595","className":"text-primary","children":"How to exclusivley select a record from different tables"}]}],["$","li","4",{"className":"list-group-item","children":["$","$Lf",null,{"href":"/answer/55535359","className":"text-primary","children":"Add user to table and use users id while adding data to second table while user registration"}]}],["$","li","5",{"className":"list-group-item","children":["$","$Lf",null,{"href":"/answer/79071949","className":"text-primary","children":"Selecting the earliest row where a specified date value falls between a date range (two columns) when multiple rows may match"}]}],["$","li","6",{"className":"list-group-item","children":["$","$Lf",null,{"href":"/answer/11106209","className":"text-primary","children":"SQL AVG returning an int"}]}],["$","li","7",{"className":"list-group-item","children":["$","$Lf",null,{"href":"/answer/16369331","className":"text-primary","children":"Using two tables. 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