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| # relation-data | |
| ddr: | |
| evidence-count: 3 | |
| score-threshold: 0.1 | |
| # association-data | |
| scoring_weights: | |
| crisp: 1 | |
| europepmc: 0.2 | |
| expression_atlas: 0.2 | |
| phenodigm: 0.2 | |
| progeny: 0.5 | |
| slapenrich: 0.5 | |
| sysbio: 0.5 | |
| is_direct_do_not_propagate: | |
| - expression_atlas | |
| #datasources_to_datatypes: | |
| # drug-data | |
| chembl-drug-indication: | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/chembl_drug_indication_rest_api-2019-06-03.json.gz | |
| #chembl-component: | |
| #chembl-mechanism: | |
| #chembl-molecule: | |
| #chembl-protein: | |
| #chembl-target: | |
| # [invalid-]evidence-data | |
| input-file: | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/eva-2019-06-03.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/phenodigm-2019-05-31.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/cosmic-2019-05-15.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/genomics_england-2018-10-02.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/crispr-2019-04-08.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/intogen-2018-07-23.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/gene2phenotype-2019-05-30.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/phewas_catalog-2018-11-28.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/atlas-2019-06-04.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/reactome-2019-05-29.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/sysbio-2019-01-31.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/chembl-2019-03-25.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/epmc-2019-05-24.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/uniprot-2019-05-20.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/gwas-2019-05-29.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/progeny-2018-07-23.json.gz | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/evidence-files/slapenrich-2018-11-29.json.gz | |
| eco-scores: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/eco_scores-2019-06-04.tsv | |
| schema: https://raw.githubusercontent.com/opentargets/json_schema/1.6.0/opentargets.json | |
| excluded-biotypes: | |
| expression_atlas: | |
| - 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 | |
| datasources_to_datatypes: | |
| cancer_gene_census: somatic_mutation | |
| chembl: known_drug | |
| crispr: affected_pathway | |
| europepmc: literature | |
| eva: genetic_association | |
| eva_somatic: somatic_mutation | |
| expression_atlas: rna_expression | |
| gene2phenotype: genetic_association | |
| genomics_england: genetic_association | |
| gwas_catalog: genetic_association | |
| intogen: somatic_mutation | |
| phenodigm: animal_model | |
| phewas_catalog: genetic_association | |
| postgap: genetic_association | |
| progeny: affected_pathway | |
| reactome: affected_pathway | |
| slapenrich: affected_pathway | |
| sysbio: affected_pathway | |
| uniprot: genetic_association | |
| uniprot_literature: genetic_association | |
| uniprot_somatic: somatic_mutation | |
| # expression-data | |
| tissue-curation-map: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/expression_hierarchy_curation-2019-06-04.tsv | |
| tissue-translation-map: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/map_with_efos-2019-06-04.json | |
| hpa-normal-tissue: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/normal_tissue-2019-06-04.tsv.zip | |
| hpa-rna-level: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/expatlas.blueprint2.baseline.binned_v2-2019-06-04.tsv | |
| hpa-rna-value: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/exp_summary_NormCounts_genes_all_Blueprint2_v2-2019-06-04.txt | |
| hpa-rna-zscore: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/expatlas.blueprint2.baseline.z-score.binned_v2-2019-06-04.tsv | |
| # eco-data | |
| ontology-eco: https://raw.githubusercontent.com/evidenceontology/evidenceontology/v2018-11-10/eco.owl | |
| ontology-so: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/v3.1/releases/so-xp.owl/so.owl | |
| # efo-data | |
| ontology-efo: https://raw.githubusercontent.com/EBISPOT/efo/v2019-03-18/efo_inferred.owl | |
| ontology-hpo: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/v2018-10-09/hp.owl | |
| #ontology-mp: | |
| disease-phenotype: | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/rareAlbuminuria_associations_03Jun15-2019-06-04.owl | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/charite_HP_ORDO_07Oct15-2019-06-04.owl | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/ibd_2_pheno_associations-2019-06-04.owl | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/immune_disease_2_pheno-2019-06-04.owl | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/ordo_hpo_mappings-2019-06-04.owl | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/rareIBDpheno-2019-06-04.owl | |
| # Plugin: Safety | |
| safety: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/known_target_safety-2019-06-04.json | |
| # Plugin: Tractability | |
| tractability: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/tractability_buckets-2019-04-16.tsv | |
| # Plugin: ChemicalProbes | |
| chemical-probes-1: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/chemicalprobes_portalprobes-2019-06-04.tsv | |
| chemical-probes-2: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/chemicalprobes_probeminer-2018-10-15.tsv | |
| # Plugin: CancerBiomarkers | |
| biomarker: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/cancerbiomarkers-2018-05-01.tsv | |
| # Plugin: Hallmarks | |
| hallmark: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/cosmic-hallmarks-2019-05-15.tsv.gz | |
| # Plugin: MousePhenotypes | |
| ontology-mp: http://www.informatics.jax.org/downloads/reports/mp.owl | |
| mouse-phenotypes-orthology: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/HMD_HumanPhenotype-2019-06-04.rpt | |
| mouse-phenotypes-report: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/MGI_PhenoGenoMP-2019-06-04.rpt | |
| # Plugin: ChEMBL | |
| chembl-component: | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/chembl_target_component_rest_api-2019-06-03.json.gz | |
| chembl-mechanism: | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/chembl_mechanism_rest_api-2019-06-03.json.gz | |
| chembl-molecule: | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/chembl_molecule_rest_api-2019-06-03.json.gz | |
| chembl-protein: | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/chembl_protein_class_rest_api-2019-06-03.json.gz | |
| chembl-target: | |
| - https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/chembl_target_rest_api-2019-06-03.json.gz | |
| # Plugin: Orthologs | |
| hgnc-orthologs: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/human_all_hcop_sixteen_column-2019-06-04.txt.gz | |
| hgnc-orthologs-species: | |
| - 9606-human | |
| - 9598-chimpanzee | |
| - 9544-macaque | |
| - 10090-mouse | |
| - 10116-rat | |
| - 9615-dog | |
| - 9823-pig | |
| - 8364-frog | |
| - 7955-zebrafish | |
| - 7227-fly | |
| - 6239-worm | |
| - 4932-yeast | |
| # Plugin: HGNC | |
| hgnc-complete-set: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/hgnc_complete_set-2019-06-04.json | |
| # gene-data | |
| gene-data-plugin-names: | |
| - HGNC | |
| - Orthologs | |
| - Ensembl | |
| - Uniprot | |
| - ChEMBL | |
| - MousePhenotypes | |
| - Hallmarks | |
| - CancerBiomarkers | |
| - ChemicalProbes | |
| - Tractability | |
| - Safety | |
| # reactome-data | |
| reactome-pathway-data: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/ReactomePathways-2019-06-04.txt | |
| reactome-pathway-relation: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/ReactomePathwaysRelation-2019-06-04.txt | |
| # uniprot-data | |
| uniprot-uri: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/uniprot-2019-06-04.xml.gz | |
| # ensembl-data | |
| ensembl-filename: https://storage.googleapis.com/open-targets-data-releases/19.06/input/annotation-files/homo_sapiens_core_96_38_genes.json.gz |
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