1. Lawrence Hunter, Ph.D. Director, Computational Bioscience Program University of Colorado School of Medicine Larry.Hunter@uchsc.edu http://compbio.uchsc.edu/Hunter Epistemic relations

2. Epistemology Epistemology: how do we know things? (cf ontology: what exists?) Epistemic relations link: – Propositions (statements that can be true or false, AKA “asserted sentences”) –with evidence (something that bears on their truth or falsity). Probably all instance-level relations

3. Consensus (of RO list) Instance-level epistemic relations: –Supports Evidence E RO:supports proposition P iff E can be linked by inference to establishing that P is true. –Is_supported_by is the OWL:inverse-of supports –Contradics Evidence E RO:contradicts proposition P iff E can be linked by inference to establishing that P is false. –Is_contradicted_by is the OWL:inverse-of contradicts Not clear if class-level relation is necessary

4. Domain and Range The range of supports is clear: propositions The domain is more complicated: what can (or can’t) count as evidence? Large literature, mostly related to law, e.g. –Schum, Thoughts about a science of evidence http://www.evidencescience.org/content/Science.doc http://www.evidencescience.org/content/Science.doc –Anderson,Schum & Twining, Analysis of Evidence, 2nd ed. Cambridge U. Press 2005 In the legal world, evidence is either testimony or a physical entity (exhibit) under the supervision of a court.

5. Scientific evidence Not the same as legal evidence (no courts!) Definitional help from scientific culture: –Peer review is an essential aspect of science. –Scientific evidence must be capable of being communicated to other scientists –Secret information can’t be scientific evidence Ontologically, information entities are what can be communicated, hence the domain of supports, least in a scientific context.

6. What is an information entity? OBI uses DENRIE (“Digital Entity and Non- Realizable Information Entity”) –Tentative definition: "An information entity is a generically dependent continuant that always originates with a sentient - either by a person perceiving, thinking, and communicating, or by a machine that was designed to have a function to produce and/or communicate information." –Subsumes, e.g. instrument readouts and publications. Information Entity Ontology meeting next month is to address this (and generalize, e.g. to software) Can wait for an exact definition; whatever the result, it (or a subclass) is clearly the domain of supports.

7. GAF use case GO annotation files (GAF) contain all asserted links between gene (products) and GO terms Currently a database format, with three epistemic columns DB:reference, qualifier & evidence code –DB:Reference is a pointer to a database entry in a model organism database or a publication (identified by PMID) that supports the annotation –Evidence code is a term that describes the relation of the assertion to the reference (e.g. “Inferred by direct assay” or “inferred through electronic analysis”) –Quantifier is overloaded, but includes “NOT”

8. Modeling GAF DB:Reference is the evidence for the assertion – is_supported_by NOT quantifier flips evidence, not assertion – is_contradicted_by What about evidence codes?

9. Evidence can play multiple roles A single piece of evidence can support two (or more) assertions in different ways. –Example: PMID-X provides inferred by direct assay evidence that GeneY has-function “RNA polymerase II transcription factor activity” and the same information entity also provides inferred by curator evidence the gene has-location nucleus. Two choices: –Subclass binary supports, e.g. supports_by_direct_assay –Make supports ternary relation, e.g. (supports ) –[PMID-X as an instance of evidence type doesn’t work since we have to match the support to the evidence type.]

10. I like the subclass version Evidence type (as defined in the ECO) is realist only through cognitive states, e.g. whose inference? Potential subclasses taken from current GO evidence class use, e.g. –is_supported_by_(evidence_from)_direct_ass ay –is_supported_by_inference_of_curator Works with possible revision of GO evidence codes (projecting out manually review)