Rename biological_context to experiment_context within evidence schema.

[nbargnesi]

I'm talking about the schema and API specifically here whose audience is largely made up of integrators, engineers, developers, etc.

We're talking about knowledge representing the existence of biological entities and the relationships between them. The "biological" qualifier on context is implied under most circumstances(see 1️⃣ below).

For example:

"biological_context": [
  { "name": "Cell", "value": "cardiac muscle cell" },
  { "name": "Species", "value": 9606 }
]

That "biological_" prefix is redundant.

1️⃣ The annotations stored in biological_context aren't required to be biological in nature. We have examples like the following:

"biological_context": [
  { "name": "Species", "value": 29062 },
  { "name": "curatedBy", "value": "nlp" },
  { "name": "nlpCurator", "value": "GENIA" }
]

Using "context" here is more to the point.

[nbargnesi]

@wshayes @abargnesi thoughts?

[abargnesi]

If we rename biological_context to context then it might obscure when one would use it over metadata. I think curatedBy and nlpCurator are better suited in metadata, because they are not curated directly from the article.

[nbargnesi]

Concede the point about curatedBy and nlpCurator. I'll put forth foundIn instead. This annotation captures what section of a paper the evidence is found in (i.e., the context). It's values might be abstract, introduction, and results.

"biological_context": [
  { "name": "Species", "value": 29062 },
  { "name": "foundIn", "value": "abstract" }
]

So again, annotations in biological_context aren't required to be biological in nature and there are annotations that are context that have no place in metadata.

[ncatlett]

Can we rename biological_context to experiment_context? My feeling is that the context annotations should reflect the experiment information (which may not be "biological") and the metadata should reflect information about the curation.