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Filter evidences by a list of enabled target biotypes #369

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mkarmona opened this issue Dec 11, 2018 · 1 comment
Closed

Filter evidences by a list of enabled target biotypes #369

mkarmona opened this issue Dec 11, 2018 · 1 comment
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Bug Something isn't working Enhancement Update to existing feature

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@mkarmona
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The list of current biotypes Ensembl returns

"3prime_overlapping_ncRNA"
"antisense"
"bidirectional_promoter_lncRNA"
"IG_C_gene"
"IG_C_pseudogene"
"IG_D_gene"
"IG_J_gene"
"IG_J_pseudogene"
"IG_pseudogene"
"IG_V_gene"
"IG_V_pseudogene"
"lincRNA"
"macro_lncRNA"
"miRNA"
"misc_RNA"
"Mt_rRNA"
"Mt_tRNA"
"non_coding"
"polymorphic_pseudogene"
"processed_pseudogene"
"processed_transcript"
"protein_coding"
"pseudogene"
"ribozyme"
"rRNA"
"rRNA_pseudogene"
"scaRNA"
"scRNA"
"sense_intronic"
"sense_overlapping"
"snoRNA"
"snRNA"
"sRNA"
"TEC"
"transcribed_processed_pseudogene"
"transcribed_unitary_pseudogene"
"transcribed_unprocessed_pseudogene"
"translated_processed_pseudogene"
"TR_C_gene"
"TR_D_gene"
"TR_J_gene"
"TR_J_pseudogene"
"TR_V_gene"
"TR_V_pseudogene"
"unitary_pseudogene"
"unprocessed_pseudogene"
"vaultRNA"

This feature has to be

  1. Setting a dictionary of data-sources as keys with a list of excluded bio-types as values on the Settings.py
  2. If not passing fixing process in Validation step then it has to be reported as failed evidence with the reason (excluded bio-type)
@mkarmona mkarmona added Bug Something isn't working Enhancement Update to existing feature Priority: Critical labels Dec 11, 2018
@mkarmona mkarmona self-assigned this Dec 11, 2018
@mkarmona
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the curated list of biotypes to exclude for expression_atlas evidences

"IG_C_pseudogene"
"IG_J_pseudogene"
"IG_pseudogene"
"IG_V_pseudogene"
"polymorphic_pseudogene"
"processed_pseudogene"
"pseudogene"
"rRNA"
"rRNA_pseudogene"
"snoRNA"
"snRNA"
"transcribed_processed_pseudogene"
"transcribed_unitary_pseudogene"
"transcribed_unprocessed_pseudogene"
"TR_J_pseudogene"
"TR_V_pseudogene"
"unitary_pseudogene"
"unprocessed_pseudogene"

mkarmona added a commit to opentargets-archive/data_pipeline that referenced this issue Dec 11, 2018
mkarmona added a commit to opentargets-archive/data_pipeline that referenced this issue Dec 11, 2018
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