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merge_jenkins.yaml
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merge_jenkins.yaml
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---
configuration:
output_directory: data/merged
checkpoint: false
merged_graph:
name: KG-COVID-19 Graph
source:
drug-central:
input:
format: tsv
filename:
- data/transformed/drug_central/nodes.tsv
- data/transformed/drug_central/edges.tsv
pharmgkb:
input:
format: tsv
filename:
- data/transformed/pharmgkb/nodes.tsv
- data/transformed/pharmgkb/edges.tsv
STRING:
input:
format: tsv
filename:
- data/transformed/STRING/nodes.tsv
- data/transformed/STRING/edges.tsv
filters:
node_filters:
category:
- biolink:Gene
- biolink:Protein
edge_filters:
subject_category:
- biolink:Gene
- biolink:Protein
object_category:
- biolink:Gene
- biolink:Protein
edge_label:
- biolink:interacts_with
- biolink:has_gene_product
operations:
- name: kgx.utils.graph_utils.remap_node_identifier
args:
category: biolink:Protein
alternative_property: xrefs
prefix: UniProtKB
ttd:
input:
format: tsv
filename:
- data/transformed/ttd/nodes.tsv
- data/transformed/ttd/edges.tsv
zhou-host-proteins:
input:
format: tsv
filename:
- data/transformed/zhou_host_proteins/nodes.tsv
- data/transformed/zhou_host_proteins/edges.tsv
SciBite-CORD-19:
input:
format: tsv
filename:
- data/transformed/SciBite-CORD-19/nodes.tsv
- data/transformed/SciBite-CORD-19/edges.tsv
sars-cov-2-gene-annot:
input:
format: tsv
filename:
- data/transformed/sars_cov_2_gene_annot/nodes.tsv
- data/transformed/sars_cov_2_gene_annot/edges.tsv
intact:
input:
format: tsv
filename:
- data/transformed/intact/nodes.tsv
- data/transformed/intact/edges.tsv
chembl:
input:
format: tsv
filename:
- data/transformed/ChEMBL/nodes.tsv
- data/transformed/ChEMBL/edges.tsv
gene-ontology:
input:
format: tsv
filename:
- data/transformed/ontologies/go-plus_nodes.tsv
- data/transformed/ontologies/go-plus_edges.tsv
mondo-ontology:
input:
format: tsv
filename:
- data/transformed/ontologies/mondo_nodes.tsv
- data/transformed/ontologies/mondo_edges.tsv
chebi:
input:
format: tsv
filename:
- data/transformed/ontologies/chebi_nodes.tsv
- data/transformed/ontologies/chebi_edges.tsv
hp-ontology:
input:
format: tsv
filename:
- data/transformed/ontologies/hp_nodes.tsv
- data/transformed/ontologies/hp_edges.tsv
go-cams:
input:
format: tsv
filename:
- data/transformed/GOCAMs/GOCAMs_nodes.tsv
- data/transformed/GOCAMs/GOCAMs_edges.tsv
operations:
- name: kgx.graph_operations.summarize_graph.generate_graph_stats
args:
graph_name: KG-COVID-19 Graph
filename: merged_graph_stats.yaml
node_facet_properties:
- provided_by
edge_facet_properties:
- provided_by
destination:
merged-kg-tsv:
format: tsv
compression: tar.gz
filename: merged-kg
property_types:
# define the type for non-canonical node/edge properties
combined_score: 'xsd:float'
confidence_score: 'xsd:float'
neighborhood: 'xsd:float'
neighborhood_transferred: 'xsd:float'
fusion: 'xsd:float'
cooccurence: 'xsd:float'
homology: 'xsd:float'
coexpression: 'xsd:float'
coexpression_transferred: 'xsd:float'
experiments: 'xsd:float'
experiments_transferred: 'xsd:float'
database: 'xsd:float'
database_transferred: 'xsd:float'
textmining: 'xsd:float'
textmining_transferred: 'xsd:float'
merged-kg-nt:
format: nt
compression: gz
filename: merged-kg.nt.gz
property_types:
# define the type for non-canonical node/edge properties
combined_score: 'xsd:float'
confidence_score: 'xsd:float'
neighborhood: 'xsd:float'
neighborhood_transferred: 'xsd:float'
fusion: 'xsd:float'
cooccurence: 'xsd:float'
homology: 'xsd:float'
coexpression: 'xsd:float'
coexpression_transferred: 'xsd:float'
experiments: 'xsd:float'
experiments_transferred: 'xsd:float'
database: 'xsd:float'
database_transferred: 'xsd:float'
textmining: 'xsd:float'
textmining_transferred: 'xsd:float'
# merged-kg-neo4j:
# format: neo4j
# uri: http://localhost:8484
# username: neo4j
# password: admin