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config.yaml
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config.yaml
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destination: &dest syn12177492
staging_path: ./staging
gx_folder: syn52948668
gx_table: syn60527066
sources:
- genes_biodomains:
genes_biodomains_files: &genes_biodomains_files
- name: genes_biodomains
id: syn44151254.5
format: csv
genes_biodomains_provenance: &genes_biodomains_provenance
- syn44151254.5
- overall_scores:
overall_scores_files: &overall_scores_files
- name: overall_scores
id: syn25575156.13
format: table
overall_scores_provenance: &overall_scores_provenance
- syn25575156.13
- agora_proteomics:
agora_proteomics_files: &agora_proteomics_files
- name: proteomics
id: syn18689335.4
format: csv
agora_proteomics_provenance: &agora_proteomics_provenance
- syn18689335.4
- agora_proteomics_tmt:
agora_proteomics_tmt_files: &agora_proteomics_tmt_files
- name: proteomics_tmt
id: syn35221005.2
format: csv
agora_proteomics_tmt_provenance: &agora_proteomics_tmt_provenance
- syn35221005.2
- agora_proteomics_srm:
agora_proteomics_srm_files: &agora_proteomics_srm_files
- name: proteomics_srm
id: syn52579640.4
format: csv
agora_proteomics_srm_provenance: &agora_proteomics_srm_provenance
- syn52579640.4
- rna_diff_expr_data:
rna_diff_expr_data_files: &rna_diff_expr_data_files
- name: diff_exp_data
id: syn27211942.1
format: tsv
rna_diff_expr_data_provenance: &rna_diff_expr_data_provenance
- syn27211942.1
datasets:
- biodomain_info:
files: *genes_biodomains_files
final_format: json
custom_transformations: 1
provenance: *genes_biodomains_provenance
column_rename:
biodomain: name
destination: *dest
gx_enabled: true
- genes_biodomains:
files: *genes_biodomains_files
final_format: json
custom_transformations: 1
provenance: *genes_biodomains_provenance
column_rename:
ensembl_id: ensembl_gene_id
goterm_name: go_terms
destination: *dest
gx_enabled: true
gx_nested_columns:
- gene_biodomains
- neuropath_corr:
files:
- name: neuropath_regression_results
id: syn22017882.5
format: csv
final_format: json
provenance:
- syn22017882.5
column_rename:
ensg: ensembl_gene_id
gname: hgnc_gene_id
agora_rename:
ensembl_gene_id: ensg
hgnc_gene_id: gname
destination: *dest
gx_enabled: true
- proteomics:
files: *agora_proteomics_files
final_format: json
custom_transformations: 1
provenance: *agora_proteomics_provenance
column_rename:
genename: hgnc_symbol
ensg: ensembl_gene_id
destination: *dest
gx_enabled: true
- proteomics_tmt:
files: *agora_proteomics_tmt_files
final_format: json
custom_transformations: 1
provenance: *agora_proteomics_tmt_provenance
column_rename:
genename: hgnc_symbol
ensg: ensembl_gene_id
destination: *dest
gx_enabled: true
- proteomics_srm:
files: *agora_proteomics_srm_files
final_format: json
custom_transformations: 1
provenance: *agora_proteomics_srm_provenance
column_rename:
genename: hgnc_symbol
ensg: ensembl_gene_id
destination: *dest
gx_enabled: true
- target_exp_validation_harmonized:
files:
- name: target_exp_validation_harmonized
id: syn24184512.9
format: csv
final_format: json
provenance:
- syn24184512.9
destination: *dest
gx_enabled: true
- metabolomics:
files:
- name: metabolomics
id: syn26064497.1
format: feather
final_format: json
provenance:
- syn26064497.1
destination: *dest
gx_enabled: true
- gene_info:
files:
- name: gene_metadata
id: syn25953363.13
format: feather
- name: igap
id: syn12514826.5
format: csv
- name: eqtl
id: syn12514912.3
format: csv
- <<: *agora_proteomics_files
- <<: *agora_proteomics_tmt_files
- <<: *agora_proteomics_srm_files
- <<: *rna_diff_expr_data_files
- name: target_list
id: syn12540368.51
format: csv
- name: median_expression
id: syn27211878.2
format: csv
- name: druggability
id: syn13363443.11
format: csv
- <<: *genes_biodomains_files
- name: tep_adi_info
id: syn51942280.3
format: csv
- name: ensg_to_uniprot_mapping
id: syn54113663.3
format: tsv
final_format: json
custom_transformations:
adjusted_p_value_threshold: 0.05
protein_level_threshold: 0.05
column_rename:
ensg: ensembl_gene_id
ensembl_id: ensembl_gene_id
geneid: ensembl_gene_id
has_eqtl: is_eqtl
minimumlogcpm: min
quartile1logcpm: first_quartile
medianlogcpm: median
meanlogcpm: mean
quartile3logcpm: third_quartile
maximumlogcpm: max
possible_replacement: ensembl_possible_replacements
permalink: ensembl_permalink
uniprotkb_accession: uniprotkb_accessions
resource_identifier: ensembl_gene_id
provenance:
- syn25953363.13
- syn12514826.5
- syn12514912.3
- *agora_proteomics_provenance
- *agora_proteomics_tmt_provenance
- *agora_proteomics_srm_provenance
- *rna_diff_expr_data_provenance
- syn12540368.51
- syn27211878.2
- syn13363443.11
- *genes_biodomains_provenance
- syn51942280.3
- syn54113663.3
agora_rename:
symbol: hgnc_symbol
destination: *dest
gx_enabled: true
gx_nested_columns:
- target_nominations
- median_expression
- druggability
- ensembl_info
- team_info:
files:
- name: team_info
id: syn12615624.18
format: csv
- name: team_member_info
id: syn12615633.19
format: csv
final_format: json
custom_transformations: 1
provenance:
- syn12615624.18
- syn12615633.19
destination: *dest
gx_enabled: true
gx_nested_columns:
- members
- overall_scores:
files: *overall_scores_files
final_format: json
custom_transformations: 1
column_rename:
genename: hgnc_gene_id
provenance: *overall_scores_provenance
agora_rename:
ensg: ensembl_gene_id
hgnc_gene_id: hgnc_symbol
geneticsscore: genetics_score
overall: target_risk_score
omicsscore: multi_omics_score
destination: *dest
gx_enabled: true
- network:
files:
- name: networks
id: syn11685347.1
format: csv
final_format: json
provenance:
- syn11685347.1
- syn27211942.1
agora_rename:
genea_ensembl_gene_id: geneA_ensembl_gene_id
genea_external_gene_name: geneA_external_gene_name
geneb_ensembl_gene_id: geneB_ensembl_gene_id
geneb_external_gene_name: geneB_external_gene_name
brainregion: brainRegion
destination: *dest
gx_enabled: true
- rnaseq_differential_expression:
files: *rna_diff_expr_data_files
final_format: json
custom_transformations: 1
provenance: *rna_diff_expr_data_provenance
destination: *dest
gx_enabled: true
- distribution_data:
files: *overall_scores_files
final_format: json
custom_transformations:
overall_max_score: 5
genetics_max_score: 3
omics_max_score: 2
provenance: *overall_scores_provenance
column_rename:
overall: target_risk_score
geneticsscore: genetics_score
omicsscore: multi_omics_score
destination: *dest
gx_enabled: true
gx_nested_columns:
- target_risk_score
- genetics_score
- multi_omics_score
- rna_distribution_data:
files: *rna_diff_expr_data_files
final_format: json
custom_transformations: 1
provenance: *rna_diff_expr_data_provenance
destination: *dest
gx_enabled: true
- proteomics_distribution_data:
files:
- <<: *agora_proteomics_files
- <<: *agora_proteomics_tmt_files
- <<: *agora_proteomics_srm_files
final_format: json
custom_transformations: 1
provenance:
- *agora_proteomics_provenance
- *agora_proteomics_tmt_provenance
- *agora_proteomics_srm_provenance
destination: *dest
gx_enabled: true