first pass at howto for ontologies as values #1585
Conversation
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
| GenePhenotypeAssociation: | ||
| attributes: | ||
| gene: | ||
| range: Gene |
There was a problem hiding this comment.
Where did the pattern go? Shouldnt it be reflected somewhere?
| GenePhenotypeAssociation: | ||
| attributes: | ||
| gene: | ||
| range: Gene |
There was a problem hiding this comment.
See below, its unclear why this pattern match constraint suddenly disappeared.
There was a problem hiding this comment.
Conversely, as a naive reader, I would expect to be able to add the constraint on the Gene class (I guess through a mapping of some kind?). Maybe keep the example isomorphic here, and when you extract a class, make sure the model does still validate the same kinds of associations as before.
docs/howtos/ontologies-as-values.md
Outdated
| is_a: NamedThing | ||
| ``` | ||
|
|
||
| Let's add a container class: |
There was a problem hiding this comment.
Maybe add a sentece why we would want to do that at this point, since we are still expecting to model a simple g2p association
| ``` | ||
| Container: | ||
| attributes: | ||
| genes: |
There was a problem hiding this comment.
I can see why we need an associations container now, but not so much a genes container, at least not for the running example (EDIT I see it becomes clearer a bit later)
docs/howtos/ontologies-as-values.md
Outdated
| ``` | ||
|
|
||
| We can go one step further, and represent the ontology | ||
| hierarchy in the data, by adding a `parents` slot in the schema: |
There was a problem hiding this comment.
Why would we want that if the hierarchy is already in the ontology (add a remark explaining why one would want to do that, given that the hierarchy already exists in the ontology)
|
|
||
| This is very practical - consumers of the data can consume the | ||
| associations and the ontology hierarchy together to perform rollup | ||
| operations, etc. |
There was a problem hiding this comment.
Needs 1 sentence more to be convincing
|
|
||
| The fact that we have two classification systems co-existing (LinkML | ||
| is_a hierarchy and ontology hierarchy as data) should not be a cause | ||
| for concern. |
docs/howtos/ontologies-as-values.md
Outdated
| In fact this is quite straightforward - ontology classes (typically | ||
| formalized in OWL) and classes in LinkML are not the same thing, | ||
| despite the name "class". And instances in LinkML and instances in | ||
| realist OBO ontologies are not the same thing. |
There was a problem hiding this comment.
Why realist? are instances in OBO ontologies that are not realist (in the sense of, BFO aligned), the same as instances in LinkML? Maybe drop that word - most people would not even know what it means.
There was a problem hiding this comment.
It's tricky. This part of the guide is aimed primarily at people who may be coming from an OBO/Realist viewpoint. Those that haven't been exposed to this way of thinking generally have no issues thinking of ontologies as data.
docs/howtos/ontologies-as-values.md
Outdated
| despite the name "class". And instances in LinkML and instances in | ||
| realist OBO ontologies are not the same thing. | ||
|
|
||
| So long as we realize this, there isn't any issue. Again, this is |
There was a problem hiding this comment.
You say: the two are different. If this is the realisation you are looking for, then I agree, its clear! But I don't understand the exact point of this whole paragraph here.. (Row 272-275)
Addressing @matentzn's comments
Co-authored-by: Nomi Harris <nlharris@users.noreply.github.com>
|
Can this be merged or is it waiting for Chris to address Nico's comments? |
No description provided.