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ingests.yaml
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ingests.yaml
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## Pass-through modular ingests
alliance_genotype:
url:
- 'https://github.com/monarch-initiative/alliance-genotype-ingest/releases/latest/download/alliance_genotype_nodes.tsv'
alliance_phenotype:
url:
- 'https://github.com/monarch-initiative/alliance-phenotype-association-ingest/releases/latest/download/alliance_phenotype_edges.tsv'
alliance_disease_association:
url:
- 'https://github.com/monarch-initiative/alliance-disease-association-ingest/releases/latest/download/alliance_disease_edges.tsv'
zfin_genotype_to_phenotype:
url:
- 'https://github.com/monarch-initiative/zfin-genotype-to-phenotype-ingest/releases/latest/download/zfin_genotype_to_phenotype_edges.tsv'
clingen_variant:
url:
- 'https://github.com/monarch-initiative/clingen-ingest/releases/latest/download/clingen_variant_nodes.tsv'
- 'https://github.com/monarch-initiative/clingen-ingest/releases/latest/download/clingen_variant_edges.tsv'
clinvar_variant:
url:
- 'https://github.com/monarch-initiative/clinvar-ingest/releases/latest/download/clinvar_variant_nodes.tsv'
- 'https://github.com/monarch-initiative/clinvar-ingest/releases/latest/download/clinvar_variant_edges.tsv'
## Ingests within this repository
alliance_gene:
config: 'ingests/alliance/gene.yaml'
alliance_gene_to_expression:
config: 'ingests/alliance/gene_to_expression.yaml'
# alliance_publication:
# config: 'ingests/alliance/publication.yaml'
bgee_gene_to_expression:
config: 'ingests/bgee/gene_to_expression.yaml'
biogrid:
config: 'ingests/biogrid/biogrid.yaml'
ctd_chemical_to_disease:
config: 'ingests/ctd/chemical_to_disease.yaml'
# flybase_publication_to_gene::
# config: 'ingests/flybase/publication_to_gene.yaml'
dictybase_gene:
config: 'ingests/dictybase/gene.yaml'
dictybase_gene_to_phenotype:
config: 'ingests/dictybase/gene_to_phenotype.yaml'
go_annotation:
config: 'ingests/go/annotation.yaml'
hgnc_gene:
config: 'ingests/hgnc/gene.yaml'
hpoa_disease_to_phenotype:
config: 'ingests/hpoa/disease_to_phenotype.yaml'
hpoa_gene_to_disease:
config: 'ingests/hpoa/gene_to_disease.yaml'
hpoa_disease_mode_of_inheritance:
config: 'ingests/hpoa/disease_mode_of_inheritance.yaml'
hpoa_gene_to_phenotype:
config: 'ingests/hpoa/gene_to_phenotype.yaml'
# mgi_publication_to_gene:
# config: 'ingests/mgi/publication_to_gene.yaml'
ncbi_gene:
config: 'ingests/ncbi/gene.yaml'
panther_genome_orthologs:
config: 'ingests/panther/genome_orthologs.yaml'
pombase_gene:
config: 'ingests/pombase/gene.yaml'
pombase_gene_to_phenotype:
config: 'ingests/pombase/gene_to_phenotype.yaml'
reactome_chemical_to_pathway:
config: 'ingests/reactome/chemical_to_pathway.yaml'
reactome_gene_to_pathway:
config: 'ingests/reactome/gene_to_pathway.yaml'
reactome_pathway:
config: 'ingests/reactome/pathway.yaml'
# rgd_publication_to_gene:
# config: 'ingests/rgd/publication_to_gene.yaml'
# sgd_publication_to_gene:
# config: 'ingests/sgd/publication_to_gene.yaml'
string_protein_links:
config: 'ingests/string/protein_links.yaml'
xenbase_gene_to_phenotype:
config: 'ingests/xenbase/gene_to_phenotype.yaml'
xenbase_orthologs:
config: 'ingests/xenbase/orthologs.yaml'
xenbase_non_entrez_orthologs:
config: 'ingests/xenbase/non_entrez_orthologs.yaml'
# xenbase_publication_to_gene:
# config: 'ingests/xenbase/publication_to_gene.yaml'
zfin_gene_to_phenotype:
config: 'ingests/zfin/gene_to_phenotype.yaml'
# zfin_publication_to_gene:
# config: 'ingests/zfin/publication_to_gene.yaml'