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Configuration organized by ES index; note that this will not parse correctly! It's for purely pedagogical purposes.
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| # [invalid-]evidence-data | |
| evidences: | |
| gs_output_dir: evidence-files | |
| downloads: | |
| - bucket: otar000-evidence_input/CRISPR/json | |
| output_filename: crispr-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar006-reactome | |
| output_filename: reactome-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/uniprot/ | |
| - bucket: otar007-cosmic | |
| output_filename: cosmic-{suffix}.json.gz | |
| excludes: hallmarks | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar008-chembl | |
| output_filename: chembl-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/uniprot/ | |
| - bucket: otar009-gwas | |
| output_filename: gwas-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar010-atlas | |
| output_filename: atlas-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar011-uniprot | |
| output_filename: uniprot-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/uniprot/ | |
| - bucket: otar012-eva | |
| output_filename: eva-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar025-epmc | |
| output_filename: epmc-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/uniprot/ | |
| - bucket: otar000-evidence_input/Gene2Phenotype/json | |
| output_filename: gene2phenotype-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar000-evidence_input/GenomicsEngland/json | |
| output_filename: genomics_england-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar000-evidence_input/IntOgen/json | |
| output_filename: intogen-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar000-evidence_input/PhenoDigm/json | |
| output_filename: phenodigm-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar000-evidence_input/PheWAS/json | |
| output_filename: phewas_catalog-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar000-evidence_input/PROGENy/json | |
| output_filename: progeny-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar000-evidence_input/SLAPEnrich/json | |
| output_filename: slapenrich-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| - bucket: otar000-evidence_input/SysBio/json | |
| output_filename: sysbio-{suffix}.json.gz | |
| resource: input-file | |
| subset_key: | |
| - target | |
| - id | |
| subset_prefix: http://identifiers.org/ensembl/ | |
| annotations: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| - uri: https://raw.githubusercontent.com/opentargets/data_pipeline/master/mrtarget/resources/eco_scores.tsv | |
| output_filename: eco_scores-{suffix}.tsv | |
| resource: eco-scores | |
| # expression-data | |
| - uri: https://raw.githubusercontent.com/opentargets/expression_hierarchy/master/process/map_with_efos.json | |
| output_filename: map_with_efos-{suffix}.json | |
| resource: tissue-translation-map | |
| - uri: https://raw.githubusercontent.com/opentargets/expression_hierarchy/master/process/curation.tsv | |
| output_filename: expression_hierarchy_curation-{suffix}.tsv | |
| resource: tissue-curation-map | |
| - uri: https://www.proteinatlas.org/download/normal_tissue.tsv.zip | |
| output_filename: normal_tissue-{suffix}.tsv.zip | |
| resource: hpa-normal-tissue | |
| - uri: https://storage.googleapis.com/atlas_baseline_expression/expatlas.blueprint2.baseline.binned_v2.tsv | |
| output_filename: expatlas.blueprint2.baseline.binned_v2-{suffix}.tsv | |
| resource: hpa-rna-level | |
| - uri: https://storage.googleapis.com/atlas_baseline_expression/exp_summary_NormCounts_genes_all_Blueprint2_v2.txt | |
| output_filename: exp_summary_NormCounts_genes_all_Blueprint2_v2-{suffix}.txt | |
| resource: hpa-rna-value | |
| - uri: https://storage.googleapis.com/atlas_baseline_expression/expatlas.blueprint2.baseline.z-score.binned_v2.tsv | |
| output_filename: expatlas.blueprint2.baseline.z-score.binned_v2-{suffix}.tsv | |
| resource: hpa-rna-zscore | |
| # efo-data | |
| annotations: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/ibd_2_pheno_associations.owl?format=raw | |
| output_filename: ibd_2_pheno_associations-{suffix}.owl | |
| resource: disease-phenotype | |
| - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/immune_disease_2_pheno.owl?format=raw | |
| output_filename: immune_disease_2_pheno-{suffix}.owl | |
| resource: disease-phenotype | |
| - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/rareAlbuminuria_associations_03Jun15.owl?format=raw | |
| output_filename: rareAlbuminuria_associations_03Jun15-{suffix}.owl | |
| resource: disease-phenotype | |
| - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/rareIBDpheno.owl?format=raw | |
| output_filename: rareIBDpheno-{suffix}.owl | |
| resource: disease-phenotype | |
| - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/ordo_hpo_mappings.owl?format=raw | |
| output_filename: ordo_hpo_mappings-{suffix}.owl | |
| resource: disease-phenotype | |
| - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/charite_HP_ORDO_07Oct15.owl?format=raw | |
| output_filename: charite_HP_ORDO_07Oct15-{suffix}.owl | |
| resource: disease-phenotype | |
| # gene-data Plugin: Safety | |
| known_target_safety: | |
| output_filename: known_target_safety-{suffix}.json | |
| resource: safety | |
| gs_output_dir: annotation-files | |
| spreadsheets: | |
| - gkey: 1EvpcnUkDASUNoBU5PzQPGD5YtZxh7cgotr2MqClJ7t0 | |
| gid: 1760619926 | |
| output_filename: adverse_effects.tsv | |
| s_type: adr | |
| - gkey: 1EvpcnUkDASUNoBU5PzQPGD5YtZxh7cgotr2MqClJ7t0 | |
| gid: 650742396 | |
| output_filename: safety_risk_information.tsv | |
| s_type: sri | |
| - gkey: 1EvpcnUkDASUNoBU5PzQPGD5YtZxh7cgotr2MqClJ7t0 | |
| gid: 1774810192 | |
| output_filename: UBERON_mapping.tsv | |
| s_type: ubr | |
| - gkey: 1EvpcnUkDASUNoBU5PzQPGD5YtZxh7cgotr2MqClJ7t0 | |
| gid: 1717378859 | |
| output_filename: EFO_mapping.tsv | |
| s_type: efo | |
| - gkey: 1EvpcnUkDASUNoBU5PzQPGD5YtZxh7cgotr2MqClJ7t0 | |
| gid: 1223815020 | |
| output_filename: references.tsv | |
| s_type: ref | |
| # gene-data Plugin: Tractability | |
| annotations_from_buckets: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| - bucket: otar001-core/Tractability | |
| output_filename: tractability_buckets-{suffix}.tsv | |
| resource: tractability | |
| # gene-data Plugin: ChemicalProbes | |
| chemical_probes: | |
| output_filename: chemicalprobes_portalprobes-{suffix}.tsv | |
| resource: chemical-probes-1 | |
| gs_output_dir: annotation-files | |
| spreadsheets: | |
| - gkey: 1VL3eHGpvJMaQ7LYp0Kp1plEo-NueP3CT7FUCrW0p2dg | |
| gid: 1686598114 | |
| output_filename: chemical_probes_SGC.tsv | |
| cp_type: sgc | |
| - gkey: 1VL3eHGpvJMaQ7LYp0Kp1plEo-NueP3CT7FUCrW0p2dg | |
| gid: 1636863333 | |
| output_filename: chemical_probes_portal.tsv | |
| cp_type: cpp | |
| - gkey: 1VL3eHGpvJMaQ7LYp0Kp1plEo-NueP3CT7FUCrW0p2dg | |
| gid: 349856989 | |
| output_filename: open_science_probes.tsv | |
| cp_type: osp | |
| annotations_from_buckets: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| - bucket: otar001-core/ProbeMiner/annotation | |
| output_filename: chemicalprobes_probeminer-{suffix}.tsv | |
| resource: chemical-probes-2 | |
| # gene-data Plugin: CancerBiomarkers | |
| annotations_from_buckets: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| - bucket: otar001-core/CancerBiomarkers/annotation | |
| output_filename: cancerbiomarkers-{suffix}.tsv | |
| resource: biomarker | |
| # gene-data Plugin: Hallmarks | |
| annotations_from_buckets: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| - bucket: otar007-cosmic | |
| output_filename: cosmic-hallmarks-{suffix}.tsv.gz | |
| resource: hallmark | |
| includes: hallmarks | |
| # gene-data Plugin: MousePhenotypes | |
| annotations: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| - uri: http://www.informatics.jax.org/downloads/reports/HMD_HumanPhenotype.rpt | |
| output_filename: HMD_HumanPhenotype-{suffix}.rpt | |
| resource: mouse-phenotypes-orthology | |
| - uri: http://www.informatics.jax.org/downloads/reports/MGI_PhenoGenoMP.rpt | |
| output_filename: MGI_PhenoGenoMP-{suffix}.rpt | |
| resource: mouse-phenotypes-report | |
| # drug-data | |
| # gene-data Plugin: ChEMBL | |
| ChEMBL: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| drug: | |
| uri: https://www.ebi.ac.uk/chembl/api/data/drug_indication.json | |
| output_filename: chembl_drug_indication_rest_api-{suffix}.json | |
| resource: chembl-drug-indication | |
| molecule: | |
| uri: https://www.ebi.ac.uk/chembl/api/data/molecule.json | |
| output_filename: chembl_molecule_rest_api-{suffix}.json | |
| resource: chembl-molecule | |
| target: | |
| uri: https://www.ebi.ac.uk/chembl/api/data/target.json | |
| output_filename: chembl_target_rest_api-{suffix}.json | |
| resource: chembl-target | |
| mechanism: | |
| uri: https://www.ebi.ac.uk/chembl/api/data/mechanism.json | |
| output_filename: chembl_mechanism_rest_api-{suffix}.json | |
| resource: chembl-mechanism | |
| target_component: | |
| uri: https://www.ebi.ac.uk/chembl/api/data/target_component.json | |
| output_filename: chembl_target_component_rest_api-{suffix}.json | |
| resource: chembl-component | |
| protein_class: | |
| uri: https://www.ebi.ac.uk/chembl/api/data/protein_class.json | |
| output_filename: chembl_protein_class_rest_api-{suffix}.json | |
| resource: chembl-protein | |
| # gene-data Plugin: Orthologs | |
| annotations: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| - uri: http://ftp.ebi.ac.uk/pub/databases/genenames/hcop/human_all_hcop_sixteen_column.txt.gz | |
| output_filename: human_all_hcop_sixteen_column-{suffix}.txt.gz | |
| resource: hgnc-orthologs | |
| # gene-data Plugin: HGNC | |
| annotations: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| - uri: http://ftp.ebi.ac.uk/pub/databases/genenames/new/json/hgnc_complete_set.json | |
| output_filename: hgnc_complete_set-{suffix}.json | |
| resource: hgnc-complete-set | |
| # reactome-data | |
| annotations: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| - uri: https://www.reactome.org/download/current/ReactomePathways.txt | |
| output_filename: ReactomePathways-{suffix}.txt | |
| resource: reactome-pathway-data | |
| - uri: https://www.reactome.org/download/current/ReactomePathwaysRelation.txt | |
| output_filename: ReactomePathwaysRelation-{suffix}.txt | |
| resource: reactome-pathway-relation | |
| # uniprot-data | |
| annotations: | |
| gs_output_dir: annotation-files | |
| downloads: | |
| - uri: https://www.uniprot.org/uniprot/?query=reviewed%3Ayes%2BAND%2Borganism%3A9606&compress=yes&format=xml | |
| output_filename: uniprot-{suffix}.xml.gz | |
| resource: uniprot-uri | |
| # ensembl-data | |
| ensembl: | |
| resource: ensembl-filename | |
| conda_env: backend-genetics | |
| conda_create: bash -c "~/anaconda2/bin/conda env create -f {root_dir}/scripts/ensembl/environment.yaml" | |
| python_script: python {script_path}/create_genes_dictionary.py -o {ensembl_output_dir}/. | |
| -e -z -n | |
| ensembl_release: homo_sapiens_core_96_38 | |
| extension_file: _genes.json.gz | |
| gs_output_dir: annotation-files |
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