Richard Bruskiewich

doc bug

1

https://flask-session.readthedocs.io/en/latest/ flask.ext.session => flask_session?

Behave runner.py bug, "recovered safely" but seems a bit strange

12

``` Traceback (most recent call last): File "C:\Program Files\JetBrains\PyCharm 2019.2\plugins\python\helpers\pydev\_pydevd_bundle\pydevd_xml.py", line 282, in frame_vars_to_xml xml += var_to_xml(v, str(k), evaluate_full_value=eval_full_val) File "C:\Program Files\JetBrains\PyCharm 2019.2\plugins\python\helpers\pydev\_pydevd_bundle\pydevd_xml.py", line 369, in var_to_xml elif hasattr(v, "__len__")...

Resolves issue #943

Modelling sets in Biolink

4

**Is your feature request related to a problem? Please describe.** The best practices for modelling sets of things in Biolink remains somewhat undefined or, at best, heterogeneously defined. **What working...

Modelling Gene to Gene Family relationships (are additional Biolink Association and predicates needed?)

4

Gene orthology knowledge curation (i.e. from the [Panther database]()) relates gene instances to gene families. It's relatively easy to infer guess what concept nodes need to be captured, i.e. `biolink:Gene`...

Review and curate Biolink Model prefix/URI namespaces for internet resolvability

3

Need to review status of prefix/URI namespaces in the BIolink Model for internet resolvability. A related issue is to use the "correct" URI mapping (e.g. see issue #648)

Biolink QC audit script

3

Continuing evolution and design decisions suggest various quality assurance measures which could be computationally assessed (using a Biolink Model-specific script). This is a placeholder for this objective. Some of the...

Realign Biolink Model `Attribute` to final TRAPI standard

2

See https://github.com/NCATSTranslator/ReasonerAPI/issues/192 and associated PR https://github.com/NCATSTranslator/ReasonerAPI/pull/186. The final TRAPI schema nomenclature and content of their Attribute schema should be closely reflected in the Biolink Model

Confounding semantics of the 'attribute' tag - entity

2

**_Note: See PR https://github.com/biolink/biolink-model/pull/539 for a significant resolution of this issue..._** The current definition of the 'attribute' class (and its parent) in the Biolink Model is the following: ```yaml abstract...

Provide additional(?) formally documented guidelines for curating mappings, etc. of edges (and nodes?) in the Biolink Model

3

Among other tasks (there may be other), the task of assigning third party `relation` ("predicate") mappings to a biolink model edge slot, in particular with respect to the partitioning of...