Robert Allaway

Use case from cancer biologist

3

Issue #3 was getting cluttered so I started a new one for a new use case at @gwaygenomics recommendation. I'm following the format from the first couple of posts there....

Difficult to understand documentation with regard to sqlite databases

2

I am trying to annotate some variants using the `exac_03` database. I retrieved it using `download.database()`, but it retrieved the following database: `hg19_exac03.sqlite.sql`. It's now in my "annovar/humandb" directory. When...

Revise NF2 to NF2-related schwannomatosis

1

**Mondo term (ID and Label):** MONDO:0007039 neurofibromatosis type 2 **Suggested new label:** NF2-related schwannomatosis **Your nano-attribution (ORCID)** 0000-0003-3573-3565 **_Optional_: Any additional information (like supporting evidence, PubMed ID, etc.)** Renamed in...

split term: schwannomatosis

2

**Term to split:** Schwannomatosis **Name for new terms:** SMARCB1-related schwannomatosis LZTR1-related schwannomatosis 22q-related schwannomatosis Schwannomatosis-NOS Schwannomatosis-NEC **List properties that should be moved to new term:** Note- ORDO tends to represent...

Add a suggested replacement in validation

4

**Is your feature request related to a problem? Please describe.** Sometimes, our investigators submit a slightly wrong version of a correct term. Eg. the correct term for a particular mouse...

Feature request: provide way to autopopulate Valid Values from children

14

For example, we have attributes defined for a parent `tissue` with children: `medial dorsal nucleus of thalamus, posterior inferior parietal cortex, midbrain, cerebral cortex, frontal lobe, hippocampus, nerve tissue, dorsolateral...

Reproduce issue: schematic CLI submit does not respect -dl parameter

1

**Describe the bug** Annotations are being uploaded using the SchemaLabel instead of the displayLabel: **To Reproduce** Steps to reproduce the behavior: 1. `schematic model --config ./schematic_config.yml submit -mp NF_Genomics_Assay_Reh_final.csv -vc...

Hello, Is there any documentation available describing the best practices for harmonizing external data to the Pharmacodb datasets? Is the solution simply to run all of our data through PharmacoGx,...

please add back synSetAnnotations or similar

3

## Operating system Mac OS X ## Description of the problem as described in #331, synSetAnnotations has been removed. Our nfportalutils package (github.com/nf-osi/nfportalutils) depends on this function in several places....