Skip to content

Commit

Permalink
Add info for 21.09 (#208)
Browse files Browse the repository at this point in the history
  • Loading branch information
@cmalangone
cmalangone authored Sep 20, 2021
1 parent dc9864b commit 0916875
Showing 1 changed file with 22 additions and 22 deletions.
44 changes: 22 additions & 22 deletions src/main/resources/reference.conf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,23 +28,23 @@ common {
"fda"
]
output-format = "parquet"
output = "gs://open-targets-pre-data-releases/21.08.preview/output/etl/parquet"
output = "gs://open-targets-pre-data-releases/21.09.1/output/etl/parquet"
output = ${?OT_ETL_OUTPUT}

metadata {
format = "json"
path = ${common.output}"/metadata/"
}

input = "gs://open-targets-pre-data-releases/21.08.preview/input"
input = "gs://open-targets-pre-data-releases/21.09.1/input"

}

reactome {
inputs {
pathways {
format = "csv"
path = ${common.input}"/annotation-files/ReactomePathways-2021-06-18.txt"
path = ${common.input}"/annotation-files/ReactomePathways-2021-09-16.txt"
options = [
{k: "sep", v: "\\t"},
{k: "header", v: "false"}
Expand All @@ -53,7 +53,7 @@ reactome {
}
relations {
format = "csv"
path = ${common.input}"/annotation-files/ReactomePathwaysRelation-2021-06-18.txt"
path = ${common.input}"/annotation-files/ReactomePathwaysRelation-2021-09-16.txt"
options = [
{k: "sep", v: "\\t"},
{k: "header", v: "false"}
Expand Down Expand Up @@ -97,7 +97,7 @@ expression {
}
exprhierarchy {
format = "csv"
path = ${common.input}"/annotation-files/hpa/expression_hierarchy_curation-2021-08-09.tsv"
path = ${common.input}"/annotation-files/hpa/expression_hierarchy_curation-2021-09-15.tsv"
options = [
{k: "sep", v: "\\t"},
{k: "header", v: "false"}
Expand All @@ -106,11 +106,11 @@ expression {
}
efomap {
format = "json"
path = ${common.input}"/annotation-files/hpa/map_with_efos-2021-08-09.json"
path = ${common.input}"/annotation-files/hpa/map_with_efos-2021-09-15.json"
}
tissues {
format = "csv"
path = ${common.input}"/annotation-files/hpa/normal_tissue-2021-08-09.tsv"
path = ${common.input}"/annotation-files/hpa/normal_tissue-2021-09-15.tsv"
options = [
{k: "sep", v: "\\t"},
{k: "header", v: "true"}
Expand Down Expand Up @@ -156,7 +156,7 @@ interactions {
}
intact {
format = "json"
path = ${common.input}"/annotation-files/interactions/intact-interactors-2021-06-07.json"
path = ${common.input}"/annotation-files/interactions/intact-interactors-2021-09-15.json"
}
strings {
format = "csv"
Expand Down Expand Up @@ -324,12 +324,12 @@ target {
]
}
safety-adverse-event {
format = "json"
path = ${common.input}"/target-inputs/safety/ae.json"
format = "parquet"
path = ${common.input}"/target-inputs/safety/ae_safety/*.parquet"
}
safety-safety-risk {
format = "json"
path = ${common.input}"/target-inputs/safety/sr.json"
format = "parquet"
path = ${common.input}"/target-inputs/safety/sr_safety/*.parquet"
}
tep {
format = "json"
Expand Down Expand Up @@ -374,7 +374,7 @@ target {
disease {
efo-ontology {
format = "json"
path = ${common.input}"/annotation-files/ontology/efo_json/ontology-efo-v3.31.0.jsonl"
path = ${common.input}"/annotation-files/ontology/efo_json/ontology-efo-v3.34.0.jsonl"
}
hpo-ontology {
format = "json"
Expand All @@ -386,7 +386,7 @@ disease {
}
hpo-phenotype {
format = "json"
path = ${common.input}"/annotation-files/ontology/efo_json/hpo-phenotypes-2021-06-18.jsonl"
path = ${common.input}"/annotation-files/ontology/efo_json/hpo-phenotypes-2021-09-15.jsonl"
}
outputs = {
diseases {
Expand All @@ -407,23 +407,23 @@ disease {
drug {
chembl-molecule {
format = "json"
path = ${common.input}"/annotation-files/chembl/chembl_29_molecule-2021-08-20.jsonl"
path = ${common.input}"/annotation-files/chembl/chembl_29_molecule-2021-09-16.jsonl"
}
chembl-indication {
format = "json"
path = ${common.input}"/annotation-files/chembl/chembl_29_drug_indication-2021-08-20.jsonl"
path = ${common.input}"/annotation-files/chembl/chembl_29_drug_indication-2021-09-16.jsonl"
}
chembl-mechanism {
format = "json"
path = ${common.input}"/annotation-files/chembl/chembl_29_mechanism-2021-08-20.jsonl"
path = ${common.input}"/annotation-files/chembl/chembl_29_mechanism-2021-09-16.jsonl"
}
chembl-target {
format = "json"
path = ${common.input}"/annotation-files/chembl/chembl_28_target-2021-03-02.jsonl"
path = ${common.input}"/annotation-files/chembl/chembl_29_target-2021-09-16.jsonl"
}
chembl-warning {
format = "json"
path = ${common.input}"/annotation-files/chembl/chembl_29_drug_warning-2021-08-20.jsonl"
path = ${common.input}"/annotation-files/chembl/chembl_29_drug_warning-2021-09-16.jsonl"
}
disease-etl = ${disease.outputs.diseases}
target-etl {
Expand All @@ -433,7 +433,7 @@ drug {
evidence-etl = ${evidences.outputs.succeeded}
drugbank-to-chembl {
format = "csv"
path = ${common.input}"/annotation-files/chembl/drugbank/db.csv.gz"
path = ${common.input}"/annotation-files/chembl/db.csv.gz"
options = [
{k: "sep", v: "\\t"},
{k: "header", v: "true"}
Expand Down Expand Up @@ -1002,12 +1002,12 @@ openfda {
meddra-preferred-terms {
format = "csv"
// Change this to whatever location the data is sitting on
path = ${openfda.step-root-input-path}"/meddra/MedAscii/pt.asc"
path = "gs://open-targets-data-releases-private/meddra/meddra23.1/MedAscii/pt.asc"
}
meddra-low-level-terms {
format = "csv"
// Change this to whatever location the data is sitting on
path = ${openfda.step-root-input-path}"/meddra/MedAscii/llt.asc"
path = "gs://open-targets-data-releases-private/meddra/meddra23.1/MedAscii/llt.asc"
}
}
meddra-preferred-terms-cols = ["pt_code", "pt_name"]
Expand Down

0 comments on commit 0916875

Please sign in to comment.