Update Migration Guide #420

uhbrar · 2023-04-04T14:02:40Z

This adds a guide dedicated more to KP's as opposed to ARA's. This also includes an example for source retrieval provenance refactoring.

edeutsch · 2023-04-04T15:01:23Z

You can more easily read the new formatted guide here: https://github.com/uhbrar/ReasonerAPI/blob/update_guide/MigrationAndImplementationGuide1-4.md

Added subclass example

edeutsch

There seemed to be some substantial push-back against implementing this policy when we brought this up, so I think this will need some more discussion before merging.

edeutsch · 2023-04-07T15:47:00Z

MigrationAndImplementationGuide1-4.md

+                    }
+                ]
+            },
+            "edge_bindings": {


I don't think results have edge_bindings any more?

I think it was decided that KP's should not use result.edge_bindings and should instead construct an analysis object.

uhbrar · 2023-04-07T18:58:31Z

I thought that it was pretty well accepted that subclasses could be represented this way when discussed at architecture. There was definitely discussion about this use case being added to the guide.

edeutsch · 2023-04-07T19:19:09Z

My recollection from the TRAPI call is that this was discussed and there was substantial push-back, perhaps from Vlado and others, I don't recall now exactly. The notes say:

There was mention of KPs potentially using AuxiliaryGraph for subclass encoding? Do we want to pursue that? Come up with a recommendation/example on how to encode a subclass reasoning response from a KP? Point people: Chris, Abrar, Matt, Andrew?
For now, the policy is to just keep doing it the current way, and we will consider a change in the future
[Eric] will start a thread to discuss if it is sensible to create a subclass example. DONE

I started the issue here: #414
There is some discussion, but I suspect others will want to contribute.

I think this change will need formal approvals before merging.
There are multiple revisions in this PR so it is hard to see the specific proposed changed, but this link may be more helpful:
e9c41d5

I suggest conversion continue in the issue.
And the topic could be revisited in the Architecture and/or TRAPI calls next week.

uhbrar · 2023-04-11T17:02:11Z

MigrationAndImplementationGuide1-4.md

@@ -1,10 +1,12 @@
-# TRAPI 1.4 Migration and Implementation Guide
+This guide is split into two major sections. The first section focusses on ARA's. The second section focusses on KP's.


colleenXu · 2023-04-11T07:37:19Z

MigrationAndImplementationGuide1-4.md

@@ -225,7 +334,7 @@ Most of the knowledge graph will remain the same in this example. Only one of th
    "predicate": "treats",
    "attributes": [
        {
-            "attribute_type_id": "support graph",
+            "attribute_type_id": "infores:support_graphs",


is this supposed to be "biolink:support_graphs", from here?

And is the value for this attribute_type_id always an array (vs a string key for one auxiliary graph)?

Fixed. Thank you.

There's noting in the specification that necessarily says that it has to be a list, but I think expected practice is a list as opposed to a single value. Unless this was further specified in the biolink model.

uhbrar · 2023-04-11T17:07:02Z

MigrationAndImplementationGuide1-4.md

@@ -452,7 +569,7 @@ Finally, we can put all of it back together, to show the full message.
                "predicate": "treats",
                "attributes": [
                    {
-                        "attribute_type_id": "support graph",
+                        "attribute_type_id": "infores:support_graphs",


uhbrar · 2023-04-11T17:07:16Z

MigrationAndImplementationGuide1-4.md

+    "query_graph": {
+        "nodes": {
+            "query_node_0": {
+                "ids": ["MONDO:0005148"]


Fixed. Thank you.

colleenXu · 2023-04-11T08:35:30Z

Also does the description for Result need editing since it discusses edges and edge-bindings? https://github.com/uhbrar/ReasonerAPI/blob/1.4/TranslatorReasonerAPI.yaml#L564

uhbrar · 2023-04-11T17:08:40Z

I didn't notice that. I thought I'd already fixed the description for Result. I'll put in a separate pull request in for that.

colleenXu · 2023-04-12T04:08:44Z

MigrationAndImplementationGuide1-4.md

@@ -1,10 +1,12 @@
-# TRAPI 1.4 Migration and Implementation Guide
+This guide is split into two major sections. The first section focuses on ARAs. The second section focusses on KPs.


still has a "focusses" typo

edeutsch · 2023-05-18T19:45:08Z

The number of approvals is very meagre, but I'm going to merge this anyway, because if we actually wait for approvals we'll never merge it.

add KP guide

2d173da

edeutsch approved these changes Apr 4, 2023

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uhbrar and others added 3 commits April 4, 2023 15:01

remove creative edge

88827ef

Added subclass example

e9c41d5

Merge pull request #1 from cbizon/update_guide

d2e2155

Added subclass example

edeutsch reviewed Apr 7, 2023

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edeutsch requested changes Apr 7, 2023

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fix edge_bindings

a282fd5

uhbrar added 2 commits April 7, 2023 15:00

fix resource_id

b041ebe

typo

4e78e82

fix errors

370777d

colleenXu reviewed Apr 11, 2023

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uhbrar added 2 commits April 11, 2023 13:01

fix errors

de3db2a

fix value_type_id

9ebf192

colleenXu mentioned this pull request Apr 11, 2023

phase 1: aux-graph/result.analyses refactor for basic querying biothings/biothings_explorer#603

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colleenXu reviewed Apr 12, 2023

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edeutsch added this to the v1.4 milestone Apr 27, 2023

"remove subclass guide"

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uhbrar requested a review from edeutsch May 1, 2023 20:12

edeutsch approved these changes May 2, 2023

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capasfield requested review from RichardBruskiewich and kennethmorton May 3, 2023 22:13

capasfield requested review from andrewsu, vemonet, brettasmi, MarkDWilliams, edeutsch, marcdubybroad, vdancik, gprice1129, yakaboskic, tziomics and edgargaticaCU May 3, 2023 22:13

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edeutsch approved these changes May 4, 2023

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edgargaticaCU approved these changes May 4, 2023

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fix knowledgw_source

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RichardBruskiewich approved these changes May 18, 2023

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edeutsch merged commit c4d2f24 into NCATSTranslator:1.4 May 18, 2023

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Update Migration Guide #420

Update Migration Guide #420

uhbrar commented Apr 4, 2023

edeutsch commented Apr 4, 2023

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edeutsch Apr 7, 2023

uhbrar Apr 7, 2023

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uhbrar Apr 11, 2023

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uhbrar Apr 11, 2023

colleenXu Apr 11, 2023 •

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uhbrar Apr 11, 2023

colleenXu commented Apr 11, 2023

uhbrar commented Apr 11, 2023

colleenXu Apr 12, 2023

edeutsch commented May 18, 2023

		@@ -1,10 +1,12 @@
		# TRAPI 1.4 Migration and Implementation Guide
		This guide is split into two major sections. The first section focusses on ARA's. The second section focusses on KP's.

Update Migration Guide #420

Update Migration Guide #420

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uhbrar commented Apr 7, 2023

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colleenXu Apr 11, 2023 • edited Loading

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colleenXu commented Apr 11, 2023

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edeutsch commented May 18, 2023

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