3 Aug 2021 PAINT Conference Call: Difference between revisions

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===Taxon constraint family review===
===Taxon constraint family review===
The validation program removed certain IBDs due to TCV. Each of us was assigned to review a few of these families. Let's have a report back.
The validation program removed certain IBDs due to TCV. Each of us was assigned to review a few of these families (Huaiyu's email on June 7th, 2021).


A file has been generated for each book in http://data.pantherdb.org/Paint/taxon_check/ with possible node that can be annotated for given term with IBD code
Huaiyu's review - The IBD removals due to TCV seem to be correct in the cases reviewed. However, most of TCs should have "only_in" relations to the ancestors, meaning they would gain the function in a more recent species. Therefore, there should be a mechanism in the PAINT tool to check it. For example, in PTHR10161, the GO term "ossification (GO:0001503)" was annotated to PTN000017834 (Deuterostomia) with IBD. It is correct to remove it. However, the terms should be correct to a child node of Euteleostomi. We have many cases like this. 
 
A file has been generated for each book in http://data.pantherdb.org/Paint/taxon_check/ with possible node that can be annotated for given term with IBD code.


===PAINT software updates===
===PAINT software updates===

Revision as of 17:57, 2 August 2021

Present

Agenda

Taxon constraint family review

The validation program removed certain IBDs due to TCV. Each of us was assigned to review a few of these families (Huaiyu's email on June 7th, 2021).

Huaiyu's review - The IBD removals due to TCV seem to be correct in the cases reviewed. However, most of TCs should have "only_in" relations to the ancestors, meaning they would gain the function in a more recent species. Therefore, there should be a mechanism in the PAINT tool to check it. For example, in PTHR10161, the GO term "ossification (GO:0001503)" was annotated to PTN000017834 (Deuterostomia) with IBD. It is correct to remove it. However, the terms should be correct to a child node of Euteleostomi. We have many cases like this.

A file has been generated for each book in http://data.pantherdb.org/Paint/taxon_check/ with possible node that can be annotated for given term with IBD code.

PAINT software updates

Disabled functionality that prevents creation of IBD and TCV annotations due to taxonomy violation

Added functionality via drop down menu to view taxonomy violations for existing annotations in book

Future update - Upgrade Java version to 11