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Collapse two cerebellum subgroups to one for GTEX, update blood #106
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This is the original table comparing GTEx Descriptions, UBERON codes, and UBERON descriptions. |
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I have done this in #85 , so it remains to be done in the histologies file. |
jharenza
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# 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
5 tasks
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closing with PR 61 |
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What data file(s) does this issue pertain to?
histologies.tsvWhat release are you using?
v6
Put your question or report your issue here.
Since GTEX Uberon codes for cerebellum and cerebellum hemisphere are both for "cerebellum", we will Merge cerebellum hemisphere and cerebellum to
CerebellumChange
Whole BloodtoBloodannotation for alphabetizationcc @afarrel @kgaonkar6 @sangeetashukla
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