Questions from RFI participants and answers

This page lists questions raised by RFI participants and the Project Team's best effort to provide answers

Visualisation of Ontological space

Q1.      What is meant by a two-dimensional matrix? Does it involve only the ontologies or actually involve an alignment?

A1.      This is matrix with classes from each of two ontologies running along each side. Potential overlap between the the two can be displayed as intersections in the matrix. This display will be based on an alignment between two ontologies.

Q2.      What is expected to be viewed in the “areas of overlap between ontologies”?

A2.      This is a high level view of areas of most overlap based on an alignment between two ontologies.

Mapping Alignment Editor

Q3.      Can you clarify or give an example about the “definition of context”?

A3.      The equivalence between two concepts, or otherwise their relation, may depend on a context. Is "Person" the same as "Employee"? Probably yes in the context of payroll, but not otherwise. Especially in an iterative environment, it would be good to have some way to specify assumptions (or limits of validity) for a mapping.   

Import equivalence mappings

Q4.      To clarify, does this request indicate the need for partial mappings to be provided externally rather than being automatically calculated by the alignment algorithm?

A4.      Ref 3.1.1, this indicates the need for the tool to be able to consume reference mappings that can be sourced externally. This is in contrast with a tool that can only generate mappings, but not make use of mapping already existing. For instance, the tool could be used to visualise overlap or edit/annotate externally provided mappings.

Evaluation of mapping quality

Q5.      Do you want a table every mapping we can compute for all terms from both HP ->MP and DOID > ORDO? Or should we just pick a subset of interesting ones?

A5.       A table for all terms would show that your tool can operate at scale which would be useful. Please ensure that you include the specific areas of disease or phenotype which we specify in the RFI process document, in section 3.3 Evaluation of mapping quality. I will include this Q & A on the public wiki page.