preliminary description of requirements for has_part and inference rules

2. Motivation for has_part : An example of an incorrect use of part_of chromosome nucleus mitochondrion part_of part_of all chromosome part_of some nucleus all chromosome part_of some mitochondrion

3. Current GO: part-specific subtypes chromosome nucleus mitochondrion part_of nuclear chromosome miotchondrial chromosome part_of ABF1 MGM101 is_a is_a

4. propagation over part_of chromosome nucleus mitochondrion part_of nuclear chromosome miotchondrial chromosome part_of ABF1 MGM101 is_a is_a ABF1 MGM101

6. Another example: erroneous use of part_of with complexes core TFIIH complex holo TFIIH complex NEF3 complex part_of TFB1 part_of we would not do this!!

7. core TFIIH complex (CURRENT GO) core TFIIH complex holo TFIIH complex NEF3 complex TFB1 part_of part_of core TFIIH portion of holo TFIIH complex core TFIIH portion of NEF3 complex is_a is_a

8. Problem: annotations to more generic term core TFIIH complex holo TFIIH complex NEF3 complex TFB1 part_of part_of core TFIIH portion of holo TFIIH complex core TFIIH portion of NEF3 complex is_a is_a

9. Problem: additional semi-redundant annotations required to capture necessary gene products core TFIIH complex holo TFIIH complex NEF3 complex TFB1 part_of part_of core TFIIH portion of holo TFIIH complex core TFIIH portion of NEF3 complex is_a is_a TFB1 TFB1 ABF1 MGM101

11. We would like to propagate gene products in this case – but can we do this universally ? core TFIIH complex holo TFIIH complex NEF3 complex has_part has_part TFB1 TFB1 TFB1

12. thought experiment: use has_part for location-specific chromosomes chromosome nucleus mitochondrion has_part has_part ABF1 MGM101

13. no reliable propagation of gene products over has_part chromosome nucleus mitochondrion has_part has_part ABF1 MGM101 ABF1 MGM101 MGM101 ABF1

14. So what’s the difference in ontology structure? core TFIIH complex holo TFIIH complex NEF3 complex has_part has_part TFB1 chromosome nucleus mitochondrion has_part has_part ABF1 MGM101

15. So what’s the difference in ontology structure? there is no structural difference the computer needs some additional knowledge that is currently IMPLICIT core TFIIH complex holo TFIIH complex NEF3 complex has_part has_part TFB1 chromosome nucleus mitochondrion has_part has_part ABF1 MGM101

16. What’s the difference in annotations? core TFIIH complex TFB1 chromosome ABF1 MGM101 SOME instances of MGM10 proteins are part of SOME chromosomes SOME instances of TFB1 proteins are part of SOME core TFIIH complexes

17. What’s the difference in annotations? core TFIIH complex TFB1 chromosome ABF1 MGM101 SOME instances of MGM10 proteins are part of SOME chromosomes SOME instances of TFB1 proteins are part of SOME core TFIIH complexes ALL instances of core TFIIH complexes proteins has_part SOME TFB1 protein (in this species) TFB1 is integral to core TFIIH complex complex This crucial piece of knowledge is IMPLICIT NOT ALL instances of chromosome has_part SOME MGM10