node = [['1001', '2008-01-06T02:12:13Z', ['']], 
        ['1002', '2008-01-06T02:13:55Z', ['']],
        ['1003', '2008-01-06T02:13:00Z', ['Lion', 'Rhinoceros', 'Leopard', 'Panda']],
        ['1004', '2008-01-06T02:15:20Z', ['Lion', 'Leopard', 'Eagle', 'Panda', 'Tiger']],
        ['1005', '2008-01-06T02:15:48Z', ['Lion', 'Panda', 'Cheetah', 'Goat', 'Tiger']],
        ['1006', '2008-01-06T02:13:30Z', ['']],
        ['1007', '2008-01-06T02:13:38Z', ['Cheetah', 'Tiger', 'Goat']]]


result = []
seenanimals = set()
for ident, _, animals in node: 
    for a in animals:
        if a not in seenanimals:
            result.append([ident, a])
            seenanimals.add(a)

print(result)