add the ability to declare "prefixmaps" contexts (including bioregistry contexts) in default_curie_maps. fixes #604

[sierra-moxon]

use case here is:

• project needs a new prefix to be added to Biolink
• create prefix in bioregistry
  • not available in prefixcommons without secondary curation in prefixcommons
  • prefix isn't accessible via default_curie_maps in LinkML
  • dual annotation required in Biolink

Incorporate prefixmaps context lookup functionality to linkml-runtime.utils.namespaces.add_prefixmap so that we can use bioregistry contexts as a fallback when none of obo_context, idot_contex, monarch_context, semweb_context, etc. contain the prefix.

somewhat related to https://github.com/linkml/linkml/issues/852 - this doesn't deprecate default_prefix_maps, it just adds to the available maps that folks can use (incl. bioregistry maps).

The next step here is to allow this changed method to read a prefix map directly without the requirement that it be in prefixcommons or prefixmaps.

Hard-coding the map names here is not the best approach; I see a TODO in prefixmaps repo that those at least should be introspected from a config file (👍 ).

[codecov-commenter]

Codecov Report

Merging #231 (0dba73b) into main (badf9b3) will increase coverage by 0.33%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #231      +/-   ##
==========================================
+ Coverage   63.28%   63.61%   +0.33%     
==========================================
  Files          52       53       +1     
  Lines        6076     6126      +50     
  Branches     1642     1652      +10     
==========================================
+ Hits         3845     3897      +52     
  Misses       1774     1774              
+ Partials      457      455       -2     

Impacted Files	Coverage Δ
linkml_runtime/utils/namespaces.py	73.05% <100.00%> (+2.16%)	:arrow_up:
linkml_runtime/linkml_model/meta.py	52.79% <0.00%> (ø)
linkml_runtime/loaders/rdf_loader.py	28.20% <0.00%> (ø)
linkml_runtime/__init__.py	100.00% <0.00%> (ø)
linkml_runtime/utils/schemaview.py	86.40% <0.00%> (+0.38%)	:arrow_up:
linkml_runtime/utils/yamlutils.py	78.15% <0.00%> (+0.42%)	:arrow_up:

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[caufieldjh]

Taking a look - is the plan to use a list of prioritized prefix contexts as fallbacks or just one context?

[sierra-moxon]

in biolink-model, I want to use merged alone from prefixmaps.