Bill Duncan

ChEBI drug is confusing

3

The `ChEBI` class `drug` has been imported into `CIDO`.  But the definitions don't make sense: - `role (CHEBI:50906)`: A role is particular behaviour which a material entity may exhibit....

drug product vs drug substance

7

`drug product` is a subclass of `drug substance`, but the reason for the distinction is not clear. The definition for `drug substance` is: ``` A drug is a material entity...

merge disease (OGMS_0000031) and disease (DOID:4)

4

The definitions for disease (OGMS_0000031) and disease (DOID:4) are the same. We should only use one of the classes. cc @yongqunh @sivaramarabandi @linikujp

add strains of COVID-19

1

The new strains (i.e., genetic variants) of COVID-19 need to be added to the ontology.

The following classes seem like they should be subclasses of `biological process`: - `immune response` - `host response to coronavirus infection` - `host-coronavirus interaction` There are possibly more. cc @yongqunh...

The class `COVID-19 treatment` has the axiom: ``` 'has participant' some 'COVID-19 disease process' ``` The range of `'has participant'` is `continuant`, but in this axiom the range is an...

Problems running band example

2

I installed swi-prolog using Homebrew. Version install is ` 8.0.3`. Sparqlprog version is `0.2.9`. I tried to run the example described here: ``` https://www.swi-prolog.org/pack/file_details/sparqlprog/prolog/sparqlprog.pl ``` This runs fine: `[library(sparqlprog)].` This...

Use biolink Named Thing as root node

2

The current root node is [Entity](https://cancerdhc.github.io/ccdhmodel/v1.1/Entity/). I think it would be advantageous to use Biolinks [Named Thing](https://biolink.github.io/biolink-model/docs/NamedThing) as the root. This allows for easier integration with Biolink and consistency across...

Create observation abstract class

5

The model has many types of observation classes. E.g.: - AlcoholExposureObservation - CancerGradeObservation - HistologicalCompositionObservation etc. In scenarios like this, there is often an abstract parent class that the children...

In [Biolink](https://biolink.github.io/biolink-model/docs/QuantityValue) and [NMDC](https://microbiomedata.github.io/nmdc-schema/QuantityValue/#class-quantity-value) we use a `quantity value` class to represent quantitative information. In NMDC we have a general [attribute value](https://microbiomedata.github.io/nmdc-schema/AttributeValue/) class from which quantity values, text values, images...