1. Phenotype annotation Chris Mungall Lawrence Berkeley Labs NCBO GO

2. Outline Principles of Compositionality Tour of PATO Pre vs post composition Quantitative phenotypes Next steps

3. Phenotype annotation: why? To shed light on the relationships between genes, environment and phenotype To compare genes and phenotypes across organisms To improve human health and wellbeing

4. Difficulties Phenotypes can be complex –Descriptions are often composite –Encompass relationships between different kinds of entities, at different levels of granularity –Different ways of describing the same thing Descriptions must be rigorous and unambiguous –Ensures meaningful analyses and comparisons within and between organisms

5. Compositionality is essential for describing phenotypes Compositionality is a principle of good ontology design –aka building blocks, cross-products, normalised/modular design –Create complex descriptions (definitions) from simpler ones Descriptions can be composed at any time –Ontology construction time (pre-composition) –Annotation time (post-composition)

6. An example of compositionality Plasma membrane of spermatocyte Plasma membrane [GO CC] Spermatocyte [OBO Cell] Formal means of composition Genus-differentia a plasma membrane which is part_of a spermatocyte GO-CCOBO-RELCell GenusDifferentia

7. Compositionality and ontology tools Composition supported by: –Phenote –OBO-Edit Cross-product plugin –Protégé-OWL –SWOOP –…and others

8. Advantage: Automatic DAG calculation a plasma membrane which is part_of a spermatocyte a membrane which is part_of a germ cell

9. The building blocks of phenotype descriptions: EQ Entities and qualities (EQ) –(Bearer) Entity E.g: compound eye, spermatocyte, blood, wing growth, scale morphogenesis –Quality (aka property, attribute) A kind of dependent continuant Defined in PATO E.g: green, hot, squamous, rugose, edematous, light- sensitivity, luminescent, ectopic, arrested, decomposed

10. Formal treatment of EQ We must be clear about what we mean when we compose an E and a Q –Otherwise we will have incomplete query results and erroneous statistics in annotations –The meaning must be computable Formally, an EQ description defines: a Quality which inheres_in a bearer entity a bearer entity which bears a Quality Which implicitly refers to:

11. Example normaleya[1]/eya[1] EQ Cell death in eye Increased rate Eye disc cellsmall Eye disc cellrefractile

12. Kinds of entities which can be bearers of biological qualities Continuants (3D entities) –Cell parts (GO) –Cells (OBO Cell ontology) –Gross anatomical entities (CARO, FMA, flyAO, MA, zfishAO, …) –Aggregates of organisms (?) Occurrents (4D entities) –Biological processes (GO)

13. normaleya[1]/eya[1] EQ Cell death in eye Increased rate Eye disc cellsmall Eye disc cellrefractile GOFlyAO PATO

14. Tour of PATO Tour from the top-down The top level of PATO has been built according to formal ontological principles –This helps us define terms in a consistent and unambiguous way –The top level can be hidden from end- users by means of ontology views (aka slims) –Still subject to change Feedback welcome!

15. PATO: Top level division Quality Quality of a continuant A quality which inheres In a continuant Quality of an occurrent A quality which inheres In a process or spatiotemporal region arrested color premature delayed duration morphology physical quality densityshapesizestructure Note: some nodes omitted for brevity cellular quality rate

16. Divisions by granularity Monadic quality of a continuant Physical quality A quality that exists through action of continuants at the physical level of organisation Cellular quality A quality that exists at the cellular level of organisation potency color hot nucleate quality ploidy temperaturemass … … cold diploid haploid aneuploid multipotent totipotent oligoptent green pink yellow anucleate binculeate large mass small mass

17. Monadic vs relational quality of a continuant Monadic quality of a C A quality of a C that inheres solely in the bearer and does not require another entity Relational quality of a C A quality of a C that requires another entity apart from its bearer to exist Displacement (with) Physical quality Connecte d-ness (to) Sensitivity (to) Cellular quality morphology … … shapesizestructure

18. Example relational quality Sensitivity –Directed towards some entity type E.g. –Sensitivity of an eye to red light The quality inheres_in the eye With respect to (towards) red light –Pheno-syntax: E= eye Q= sensitivity E2= red_light

19. On absence Annotation patterns for absence, counts are currently under discussion “spermatocyte devoid of asters” –E= CL:spermatocyte Inheres in the spermatocyte –Q= PATO:lacks_part The quality/relation of missing some part or parts –E2= GO-CC:aster The quality is with respect to the type “aster”

20. Pre- vs post- composition When do we build the phenotype description? –In the ontology –During annotation? Reconciling pre and post composition: An analysis of the plant_trait ontology

21. When do we build the phenotype description? Early? –Pre-composed phenotype definitions MP:0000017 “big ears” TO:0000227 “root length” TO:0000029 “chlorine sensitivity” Late? –Post-composed phenotype definitions E= MA:ear Q= PATO:big E= PO:root Q= PATO:length E= organism Q= PATO:sensitivity E2= CHEBI:chlorine

22. Is this comparable? MP:0000285 “abnormal cardiac valve morphology ” MP:0000287 “heart valve hypoplasia” E= MA:heart_valve Q=PATO:hypoplastic PATO:0000141 “structure ” PATO:0000645 “hypoplastic” PATO:0000051 “morphology ” ?

23. Yes: if term is decomposable MP:0000285 “abnormal cardiac valve morphology ” MP:0000287 “heart valve hypoplasia” E= MA:heart_valve Q=PATO:hypoplastic PATO:0000141 “structure ” PATO:0000645 “hypoplastic” PATO:0000051 “morphology ” = Def: a hypoplasticity which inheres_in a heart valve

24. Comparing phenotypes We want to compare and query both within and across species –For gross anatomical phenotypes to be compared across species, descriptions must be decomposed or decomposable to anatomical terms Anatomical terms must be comparable –Homology links –CARO: Common Anatomy Reference Ontology

25. Case study: Defining plant traits with PATO OBO Plant Trait ontology Pre-composed phenotype terms –Analagous to OBO mammalian_phenotype ontology Task: Define these terms with PATO –A good test of PATO –Demonstration of compositional approach –Allows meaningful comparison across plant species –Pilot study before applying to metazoans http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating

26. Methods Creation of genus-differentia definitions –First pass: Obol –Second pass: manual editing Ontologies used –PATO –Plant anatomical entities (PO) –Gramene environment (GEO) –Chemical entities of biological interest (CHEBI) –GO

27. Basic phenotype terms “root length” (TO:00000227) –E= PO:root Q= PATO:length –Formally: Def: a length which inheres_in a root

28. Relational qualities involving types of chemical “Chlorine sensitivity” [TO:0000029] Directed towards an additional entity type –Q= PATO:sensitivity E2= CHEBI:chlorine Def: a sensitivity which is directed towards chlorine [ inheres_in organism ]

29. Relational qualities involving the environment “drought sensitivity” [TO:0000029] –Directed towards an additional entity type –Q= PATO:sensitivity E2= EO:drought Def: a sensitivity which is directed towards drought [ inheres_in organism ] OBO needs a good environment ontology

30. Complex phenotypes “Chinsura boro” –"Abortion of microspore development at trinucleate stage” Def: a arrested which inheres_in ( microspore development which during trinucleate stage )

31. Results of plant_trait analysis 252/784 terms provided with genus- differentia definitions so far Helped find inconsistencies and problems in the ontology New term suggestions for PATO –proportionality Approach should work for animal phenotype ontologies

32. Bacterial phenotypes Performed similar analysis on bacterial phenotype terms –Provided by Garrity & Hozzein Results (morphological only): –26 new terms added to PATO –Rugose, rhizoidal, lobate, filamentous, … –Todo: chemical utilization phenotypes Required: –Ontologies for aggregates of organisms –Assay ontology

33. Measurements Ontologies provide qualitative partitions on the kinds of entities we find in nature We may also want to record quantitative information –Comes from measurements of qualities –The measurement is not the phenotype Phenotypes exist independently of our measurements of them

34. Measurement schema A measurement record consists of –The quality being measured E.g. the length of a particular mouse tail –The unit type From PATO UO –A magnitude Floating point number Error measure [optional]

35. Sample of PATO UO Unit –Base unit Length unit –Angstrom –meter Mass unit –Dalton –Gram Substance unit –Derived unit Concentration unit –pH Quality –Morphology Size length –Physical quality Mass

36. Phenotype exchange formats Genotypes and phenotypes: –Pheno-syntax –Pheno-XML General purpose –OWL (using canonical EQ encoding) Also has Obo equivalent GO annotation files –Works with pre-coordinated terms only

37. OBD-Phenotype A database for phenotype associations Built on OBD framework –Tuned for inference and reasoning –Graph traversal built in from the start Results –Annotations on data from OMIM, ZFIN and FlyBase –Currently too small a dataset to do analysis

38. Next steps Get PATO & Phenote used across multiple organisms and projects –MODs, BIRN, OMIM, Collect annotation data from multiple sources in one repository (OBD) –Both pre + post composed –Demonstrated improved analysis of annotation data using PATO

41. filamentous - having thin filamentous extensions at its edge pleomorphic - a quality inhering in a cell by virtue of it ability to take on two or more different shapes during its life cycle pulvinate - shaped like a cushion or has a marked convex cushion-like form umbonate - having a knob or knoblike protuberance rugose - having many wrinkles or creases on the surface glistening - emitting or reflecting lots of light dull - emitting or reflecting little or no light viscid- covered with a sticky or clammy coating mucoid - consistency of mucus spiral - plane curve traced by a point circling about the center but at increasing distances from the center rhizoidal - having root like extensions radiating from its center spiny - having spines, thorns or similar stiff projections on its surface warty - having a hard rough surface; not smooth curled - having parallel chains in undulate fashion on the border fragile - easily damaged or disrupted; brittle butyraceous - resembling butter in appearance and consistency undulate - having a wavy, shallow edge punctiform - small and resembling a point lobate - a morphological quality in which the bearer has deeply undulated edges forming lobes erose - having an irregularly toothed edge raised - is a thick colony that appear above the medium surface with terraced edges convex- a shape that obtains by virtue of having inward facing edges; having a surface or boundary that curves or bulges outward, as the exterior of a sphere

42. Proportions “amylose to amylopectin ratio”TO:0000372 Def: a compositionality which is directed towards amylose relative_to amylopectin [ inheres_in organism ]