Refactor CellularLocation Searches to be dataset-specific and cleanup unused searches#147
Open
Refactor CellularLocation Searches to be dataset-specific and cleanup unused searches#147
Conversation
1. Make GenesByGoTermCL dataset-specific: - Add cellularLocImageDataset parameter (geneParams.xml) - Create shared GenesByGoTermCLDataset query with external database joins - Add templates for dataset-specific questions and ontology entries - Update GeneImage.java injector to use templates - Remove old shared GenesByGoTermCL question and query - Remove redundant GenesByGoTermCLTriTryp query 2. Remove unused GenesByLOPIT search: - Remove GenesByLOPIT question from geneQuestions.xml - Remove GenesByLopit query from geneQueries.xml - Remove ontology entry from individuals.txt - Git remove obsolete Lopit.java injectors (ToxoDB and TriTrypDB) 3. Remove extra phenotype attributes from transcriptRecord.xml: - Remove P.falciparum 3D7 piggyBac mutagenesis attributes - Remove P.knowlesi strain AIHI piggyBac mutagenesis attributes - Remove P.knowlesi strain H piggyBac mutagenesis attributes 4. Add missing TEMPLATE_ANCHOR for cellularLocalizationEdaAttributeCategory in individuals.txt to support EDA cellular localization attribute categorization Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Make GenesByGoTermCL dataset-specific:
Remove unused GenesByLOPIT search:
Remove extra phenotype attributes from transcriptRecord.xml:
Add missing TEMPLATE_ANCHOR for cellularLocalizationEdaAttributeCategory in individuals.txt to support EDA cellular localization attribute categorization