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Create Table with Uberon codes for GTEx Subgroups #85

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Tracked by #92
afarrel opened this issue Jun 30, 2021 · 6 comments
Closed
Tracked by #92

Create Table with Uberon codes for GTEx Subgroups #85

afarrel opened this issue Jun 30, 2021 · 6 comments
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@afarrel
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afarrel commented Jun 30, 2021

What data file(s) does this issue pertain to?

GTEx data that will be used in Differential expression tables, etc

What release are you using?

This will be included in v6

Put your question or report your issue here.

Please create a table that match UBERON code to the GTEx subgroup tissues.

When should this be done.

~ 1 Week.
@kgaonkar6 kgaonkar6 mentioned this issue Jun 30, 2021
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@sangeetashukla
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@afarrel @jharenza
I have updated the excel below with the Uberon codes for the tissues and subgroups listed, as best as I could find via this link

In cases where I am not sure of the most suitable code, I have added potential options in the Notes column which need to be reviewed. Would one of you please take a look?

Uberon_codes_for_GTEX.xlsx

@jharenza jharenza mentioned this issue Jul 14, 2021
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afarrel commented Jul 14, 2021

Uberon-map.xlsx

Here is a table comparing GTEX descriptions with UBERON codes and UBERON descriptions.

@jharenza jharenza mentioned this issue Jul 15, 2021
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@kgaonkar6 kgaonkar6 mentioned this issue Jul 15, 2021
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Since v8 gtex lists "whole blood" subgroup and "whole blood" group as UBERON_0013756, which is mapped to venous blood, we are changing this nomenclature to "blood". "Whole blood" maps to UBERON_0000178. I will submit an issue on their portal.

Also collapsing the cerebellums here as noted in #106

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these are now in s3 v7 folder cc @kgaonkar6

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Update from GTEX portal:

If you look at this link definition, in the Term Relations Box, you'll note that they are equivalent terms.
https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0013756
Thanks,
Kristin

jharenza pushed a commit to d3b-center/OpenPedCan-analysis that referenced this issue Jul 23, 2021
release v7
1b84598 
# release notes
## curremt release
- release date: 2021-07-23
- status: available
- changes:
   - Updated EFO/MONDO mapping file per [ticket 88](d3b-center/ticket-tracker-OPC#88)
   - Added GTEX UBERON mapping files for subgroup and group per [ticket 85](d3b-center/ticket-tracker-OPC#85)
     - Collapsed `Cerebellum hemisphere` and `Cerebellum` to `Cerebellum` since GTEX has the same UBERON code listed for both per [ticket 106](d3b-center/ticket-tracker-OPC#106)
     - Renamed `Whole Blood` to `Blood` per John Maris's suggestion to alphabetize and [ticket 106](d3b-center/ticket-tracker-OPC#106).
       - Note: v8 gtex lists "whole blood" subgroup and "whole blood" group as UBERON_0013756, which is mapped to venous blood and "Whole blood" maps to UBERON_0000178.
       - After inquiry at GTEx, we were told they are equivalent terms as seen in [this link](https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0013756)
    - Updated `ensg-hugo-rmtl-v1-mapping.tsv` with minor updates according to [ticket 125](d3b-center/ticket-tracker-OPC#125) and changed filename to `ensg-hugo-rmtl-mapping.tsv`
    - Histology file updates:
      - Collapsed `Cerebellum hemisphere` and `Cerebellum` to `Cerebellum` since GTEX has the same UBERON code listed for both per [ticket 106](d3b-center/ticket-tracker-OPC#106)
      - Renamed `Whole Blood` to `Blood` per John Maris's suggestion to alphabetize and [ticket 106](d3b-center/ticket-tracker-OPC#106).
      - Added inferred strandedness to RNA-Seq samples per [ticket 104](d3b-center/ticket-tracker-OPC#104)
      - Added `broad_tumor_descriptor` to designate grouped `Diagnosis` and `Relapse` samples used in SNV, CNV, Fusion tables as well as for grouping on pedcbio per [ticket 109](d3b-center/ticket-tracker-OPC#109)
      - Added ploidy information for TARGET AML and NBL WXS samples per [ticket 121](d3b-center/ticket-tracker-OPC#121)
      - Collapsed TARGET ids containing suffixes to match the BAM file sample IDs from GDC and match the RDS processed files per [comment here](https://github.com/d3b-center/D3b-codes/pull/41#issuecomment-885809293)
    - Added TARGET NBL and AML WXS, PBTA WXS CNV calls to `cnv-cnvkit.seg.gz` and `cnv-controlfreec.tsv.gz` per [ticket 80](d3b-center/ticket-tracker-OPC#80)
    - Added `consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz` (removed WGS only file `consensus_seg_annotated_cn_autosomes.tsv.gz`) and `consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz` (removed WGS only file `consensus_seg_annotated_cn_x_and_y.tsv.gz`) containing consensus WGS and CNVkit WXS data per [ticket 102](d3b-center/ticket-tracker-OPC#102)
    - Updated RNA-Seq files to include TARGET RNA (N = 1329) samples:
      - fusion-arriba.tsv.gz
      - fusion-starfusion.tsv.gz
      - fusion-putative-oncogenic.tsv
      - gene-counts-rsem-expected_count-collapsed.rds
      - gene-expression-rsem-tpm-collapsed.rds
@jharenza jharenza mentioned this issue Jul 23, 2021
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closing with PR 61

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