In vitro versus in vivo evidence

[samuelrosko]

As far as I know, we have not included any in vitro data in our import of the old DIKB to the MP/OA/NP system... However, we probably need a way to distinguish between the types for purposes of developing queries... We were considering adding in vivo/in vitro as subclasses of representation? ie in vitro materials/methods/data

[jodischneider]

Sam will write in vitro evidence with a 'like' matching SPARQL query -- for EV_EX_Met_Enz_ID and EV_EX_Met_Enz_Inhibit and their subclasses.

In the future we will want to formalize the evidence taxonomy. We envision that:

• MP:Material will have subclasses for in vivo and in vitro
• The evidence taxonomy http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html will be used to create MP:Material subclasses (subclassing the in vivo class or in vitro class as appropriate) (and at that point we will revisit the query)

[jodischneider]

What resolution did we come to with this? Did we take some action? Decide not to do anything?

On Tue, Jul 21, 2015 at 11:00 AM, Samuel Rosko notifications@github.com wrote:

Closed #16 https://github.com/dbmi-pitt/DIKB-Micropublication/issues/16.

— Reply to this email directly or view it on GitHub https://github.com/dbmi-pitt/DIKB-Micropublication/issues/16#event-361260029 .

[samuelrosko]

Sorry, I misunderstood what this issue was about. Not resolved yet.

[jodischneider]

The DIKB ontology http://bioportal.bioontology.org/ontologies/DIKB has "in vitro study" and "in vivo study" from EDDA http://bioportal.bioontology.org/ontologies/EDDA

Treat these as a property of the Method class.

[jodischneider]

Queries to updated.