cmungall
commented
9 years ago Commented by mchibuco on 2011-06-10 14:20 UTC Hello Anne.
Thank you for taking the time to contact ECO. Unfortunately, I do not think we can create the terms you have proposed for the following reason. It seems that you are asking for terms that indicate quality or confidence in the evidence and that is not within the scope of ECO. ECO does not capture quality of evidence, but rather types of evidence and types of assertions. We suggest that you consider an alternative mechanism for coding quality of evidence or confidence in the evidence into your annotation system.
We are in the process of creating better documentation, which includes explaining the scope of ECO, as well as clarifying "assertion method" and how it should be used. For example, regarding your last item (4), one can not "infer a manual assertion" because an assertion method is a means by which a statement is made about an entity (an assertion method is a fact).
As we have attempted to improve and clarify ECO, one of the major changes is to separate out evidence from how evidence is applied (e.g. making an annotation), and from the inferences that evidence is used to support (e.g. "inferred from..."). ECO now has two root classes: evidence is "a type of information that is used to support an assertion" and assertion method is "a means by which a statement is made about an entity". A third thing is the inference/assertion/statement itself, which is implied in making an annotation.
Please feel free to follow up with questions, and if you need other terms in the future, please do not hesitate to contact us. I will email you once our improved ECO documentation goes live, as well.
Best regards, Marcus Chibucos
Reported by anneniknejad on 2011-06-10 13:10 UTC Hello, I propose to have new items in the Evidence code ontology, such as:
1.- 'debated traceable author statement used in manual assertion' (would be child of 'traceable author statement used in manual assertion') in case of a debated assertion proposed definition: A traceable author statement used in manual assertion that is used to define a debated assertion.
2.- 'uncertain traceable author statement used in manual assertion' (would be child of 'traceable author statement used in manual assertion') proposed definition: A traceable author statement used in manual assertion that is used if uncertainty is claimed explicitly in the reference or if the curator judges that the reference has not enough value.
3.- 'uncertain inference from background scientific knowledge used in manual assertion' (would be child of 'inference from background scientific knowledge used in manual assertion') to describe uncertainty of the assertion in case no reference is found. proposed definition: A type of inference from background scientific knowledge used in a manual assertion that is used to define the uncertainty of the assertion for example if no reference was found.
4.- 'infered by similarity in manual assertion' (would be child of 'similarity used in manual assertion') when a similarity evidence is used to infer a manual assertion proposed definition: Similarity evidence that is used to infer a manual assertion.
Please let me know your comments, thank you in advance.
Best regards,
Anne Niknejad Biocurator Bgee database http://bgee.unil.ch/bgee