From f87f87fbb31822a2aee26849a6224836ae815e73 Mon Sep 17 00:00:00 2001 From: James McLaughlin Date: Wed, 25 Sep 2024 21:24:27 +0100 Subject: [PATCH] add ROBOKOP --- 00_fetch_data/robokop/Makefile | 96 +++++++++++++++++++ README.md | 3 +- .../datasource_configs/robokop_alliance.json | 21 ++++ .../datasource_configs/robokop_binding.json | 21 ++++ configs/datasource_configs/robokop_cam.json | 21 ++++ configs/datasource_configs/robokop_ctd.json | 21 ++++ .../robokop_drugcentral.json | 21 ++++ configs/datasource_configs/robokop_gtex.json | 21 ++++ .../datasource_configs/robokop_gtopdb.json | 21 ++++ .../datasource_configs/robokop_hetionet.json | 21 ++++ configs/datasource_configs/robokop_hgoa.json | 21 ++++ configs/datasource_configs/robokop_hmdb.json | 21 ++++ configs/datasource_configs/robokop_icees.json | 21 ++++ .../datasource_configs/robokop_intact.json | 21 ++++ .../datasource_configs/robokop_panther.json | 21 ++++ .../datasource_configs/robokop_pharos.json | 21 ++++ .../datasource_configs/robokop_string.json | 21 ++++ .../robokop_textmining.json | 21 ++++ .../robokop_viralproteome.json | 21 ++++ .../subgraph_configs/ebi_full_monarch.json | 19 +++- 20 files changed, 473 insertions(+), 2 deletions(-) create mode 100644 00_fetch_data/robokop/Makefile create mode 100644 configs/datasource_configs/robokop_alliance.json create mode 100644 configs/datasource_configs/robokop_binding.json create mode 100644 configs/datasource_configs/robokop_cam.json create mode 100644 configs/datasource_configs/robokop_ctd.json create mode 100644 configs/datasource_configs/robokop_drugcentral.json create mode 100644 configs/datasource_configs/robokop_gtex.json create mode 100644 configs/datasource_configs/robokop_gtopdb.json create mode 100644 configs/datasource_configs/robokop_hetionet.json create mode 100644 configs/datasource_configs/robokop_hgoa.json create mode 100644 configs/datasource_configs/robokop_hmdb.json create mode 100644 configs/datasource_configs/robokop_icees.json create mode 100644 configs/datasource_configs/robokop_intact.json create mode 100644 configs/datasource_configs/robokop_panther.json create mode 100644 configs/datasource_configs/robokop_pharos.json create mode 100644 configs/datasource_configs/robokop_string.json create mode 100644 configs/datasource_configs/robokop_textmining.json create mode 100644 configs/datasource_configs/robokop_viralproteome.json diff --git a/00_fetch_data/robokop/Makefile b/00_fetch_data/robokop/Makefile new file mode 100644 index 0000000..f40699f --- /dev/null +++ b/00_fetch_data/robokop/Makefile @@ -0,0 +1,96 @@ + +all: binding_nodes.jsonl.gz binding_edges.jsonl.gz cam_nodes.jsonl.gz cam_edges.jsonl.gz ctd_nodes.jsonl.gz ctd_edges.jsonl.gz drugcentral_nodes.jsonl.gz drugcentral_edges.jsonl.gz alliance_nodes.jsonl.gz alliance_edges.jsonl.gz gtex_nodes.jsonl.gz gtex_edges.jsonl.gz gtopdb_nodes.jsonl.gz gtopdb_edges.jsonl.gz hetionet_nodes.jsonl.gz hetionet_edges.jsonl.gz hgnc_nodes.jsonl.gz hgnc_edges.jsonl.gz hmdb_nodes.jsonl.gz hmdb_edges.jsonl.gz hgoa_nodes.jsonl.gz hgoa_edges.jsonl.gz icees_nodes.jsonl.gz icees_edges.jsonl.gz intact_nodes.jsonl.gz intact_edges.jsonl.gz panther_nodes.jsonl.gz panther_edges.jsonl.gz pharos_nodes.jsonl.gz pharos_edges.jsonl.gz string_nodes.jsonl.gz string_edges.jsonl.gz textmining_nodes.jsonl.gz textmining_edges.jsonl.gz viralproteome_nodes.jsonl.gz viralproteome_edges.jsonl.gz + +binding_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/BINDING_Automat/9164067231dc9b8c/nodes.jsonl.gz > $@ +binding_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/BINDING_Automat/9164067231dc9b8c/edges.jsonl.gz > $@ + +cam_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/CAMKP_Automat/e92bd7b217535f2d/nodes.jsonl.gz > $@ +cam_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/CAMKP_Automat/e92bd7b217535f2d/edges.jsonl.gz > $@ + +ctd_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/CTD_Automat/f92c663160ec5e36/nodes.jsonl.gz > $@ +ctd_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/CTD_Automat/f92c663160ec5e36/edges.jsonl.gz > $@ + +drugcentral_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/DrugCentral_Automat/dec0617490b49c7a/nodes.jsonl.gz > $@ +drugcentral_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/DrugCentral_Automat/dec0617490b49c7a/edges.jsonl.gz > $@ + +alliance_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/GenomeAllianceOrthologs_Automat/06e2a3c1eeea5251/nodes.jsonl.gz > $@ +alliance_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/GenomeAllianceOrthologs_Automat/06e2a3c1eeea5251/edges.jsonl.gz > $@ + +gtex_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/GTEx_Automat/a6448b9092bb81a1/nodes.jsonl.gz > $@ +gtex_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/GTEx_Automat/a6448b9092bb81a1/edges.jsonl.gz > $@ + +gtopdb_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/GtoPdb_Automat/0ea6074c824c2236/nodes.jsonl.gz > $@ +gtopdb_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/GtoPdb_Automat/0ea6074c824c2236/edges.jsonl.gz > $@ + +hetionet_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/Hetio_Automat/85a5f53e63150e1e/nodes.jsonl.gz > $@ +hetionet_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/Hetio_Automat/85a5f53e63150e1e/edges.jsonl.gz > $@ + +hgnc_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/HGNC_Automat/dee31cfce74e5944/nodes.jsonl.gz > $@ +hgnc_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/HGNC_Automat/dee31cfce74e5944/edges.jsonl.gz > $@ + +hmdb_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/HMDB_Automat/6715124699b6dbf0/nodes.jsonl.gz > $@ +hmdb_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/HMDB_Automat/6715124699b6dbf0/edges.jsonl.gz > $@ + +hgoa_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/HumanGOA_Automat/06f107a4e9e8e547/nodes.jsonl.gz > $@ +hgoa_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/HumanGOA_Automat/06f107a4e9e8e547/edges.jsonl.gz > $@ + +icees_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/nodes.jsonl.gz > $@ +icees_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/edges.jsonl.gz > $@ + +intact_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/IntAct_Automat/e5b936f966a02c2c/nodes.jsonl.gz > $@ +intact_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/IntAct_Automat/e5b936f966a02c2c/edges.jsonl.gz > $@ + +panther_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/PANTHER_Automat/c0189f14ba41da6c/nodes.jsonl.gz > $@ +panther_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/PANTHER_Automat/c0189f14ba41da6c/edges.jsonl.gz > $@ + +pharos_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/PHAROS_Automat/d3068b509bf17ff3/nodes.jsonl.gz > $@ +pharos_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/PHAROS_Automat/d3068b509bf17ff3/edges.jsonl.gz > $@ + +string_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/STRING-DB_Automat/4ca5a0ce557e2c18/nodes.jsonl.gz > $@ +string_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/STRING-DB_Automat/4ca5a0ce557e2c18/edges.jsonl.gz > $@ + +textmining_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/TMKP_Automat/2ae17047aa1b5f3c/nodes.jsonl.gz > $@ +textmining_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/TMKP_Automat/2ae17047aa1b5f3c/edges.jsonl.gz > $@ + +viralproteome_nodes.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/ViralProteome_Automat/8ca116ae0bba6945/nodes.jsonl.gz > $@ +viralproteome_edges.jsonl.gz: + curl -L https://stars.renci.org/var/plater/bl-4.2.1/ViralProteome_Automat/8ca116ae0bba6945/edges.jsonl.gz > $@ + +.PHONY: all + + diff --git a/README.md b/README.md index e055e86..602962c 100644 --- a/README.md +++ b/README.md @@ -10,10 +10,11 @@ EBI Codon HPC pipeline for building integrated knowledge graphs from [EMBL-EBI r * [Metabolights](https://www.ebi.ac.uk/metabolights) * [ChEMBL](https://www.ebi.ac.uk/chembl/) -GrEBI also imports complementary datasets, so far: +In addition to loading from EBI databases GrEBI also imports other knowledge graphs, so far: * [MONARCH Initiative KG](https://monarch-initiative.github.io/monarch-ingest/Sources/) * [Ubergraph](https://github.com/INCATools/ubergraph) +* [ROBOKOP](https://robokop.renci.org/) * [Human Reference Atlas KG](https://humanatlas.io/) * [AOPWiki](https://aopwiki.org/) (via [AOPWikiRDF](https://github.com/marvinm2/AOPWikiRDF)) diff --git a/configs/datasource_configs/robokop_alliance.json b/configs/datasource_configs/robokop_alliance.json new file mode 100644 index 0000000..10cb55d --- /dev/null +++ b/configs/datasource_configs/robokop_alliance.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.Alliance", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/alliance_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/alliance_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_binding.json b/configs/datasource_configs/robokop_binding.json new file mode 100644 index 0000000..7aa509b --- /dev/null +++ b/configs/datasource_configs/robokop_binding.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.BINDING", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/binding_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/binding_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_cam.json b/configs/datasource_configs/robokop_cam.json new file mode 100644 index 0000000..da2020e --- /dev/null +++ b/configs/datasource_configs/robokop_cam.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.CAM", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/cam_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/cam_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_ctd.json b/configs/datasource_configs/robokop_ctd.json new file mode 100644 index 0000000..0e9a34b --- /dev/null +++ b/configs/datasource_configs/robokop_ctd.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.CTD", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/ctd_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/ctd_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_drugcentral.json b/configs/datasource_configs/robokop_drugcentral.json new file mode 100644 index 0000000..7c7558f --- /dev/null +++ b/configs/datasource_configs/robokop_drugcentral.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.DrugCentral", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/drugcentral_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/drugcentral_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_gtex.json b/configs/datasource_configs/robokop_gtex.json new file mode 100644 index 0000000..966bef4 --- /dev/null +++ b/configs/datasource_configs/robokop_gtex.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.GTEx", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/gtex_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/gtex_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_gtopdb.json b/configs/datasource_configs/robokop_gtopdb.json new file mode 100644 index 0000000..7bed99e --- /dev/null +++ b/configs/datasource_configs/robokop_gtopdb.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.GtoPdb", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/gtopdb_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/gtopdb_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_hetionet.json b/configs/datasource_configs/robokop_hetionet.json new file mode 100644 index 0000000..19b6250 --- /dev/null +++ b/configs/datasource_configs/robokop_hetionet.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.Hetionet", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/hetionet_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/hetionet_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_hgoa.json b/configs/datasource_configs/robokop_hgoa.json new file mode 100644 index 0000000..9ab7bac --- /dev/null +++ b/configs/datasource_configs/robokop_hgoa.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.HumanGOA", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/hgoa_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/hgoa_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_hmdb.json b/configs/datasource_configs/robokop_hmdb.json new file mode 100644 index 0000000..2d4f2cb --- /dev/null +++ b/configs/datasource_configs/robokop_hmdb.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.HMDB", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/hmdb_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/hmdb_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_icees.json b/configs/datasource_configs/robokop_icees.json new file mode 100644 index 0000000..f4612d4 --- /dev/null +++ b/configs/datasource_configs/robokop_icees.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.ICEES", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/icees_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/icees_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_intact.json b/configs/datasource_configs/robokop_intact.json new file mode 100644 index 0000000..1dedce6 --- /dev/null +++ b/configs/datasource_configs/robokop_intact.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.IntAct", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/intact_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/intact_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_panther.json b/configs/datasource_configs/robokop_panther.json new file mode 100644 index 0000000..f7e9118 --- /dev/null +++ b/configs/datasource_configs/robokop_panther.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.PANTHER", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/panther_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/panther_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_pharos.json b/configs/datasource_configs/robokop_pharos.json new file mode 100644 index 0000000..df7e127 --- /dev/null +++ b/configs/datasource_configs/robokop_pharos.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.Pharos", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/pharos_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/pharos_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_string.json b/configs/datasource_configs/robokop_string.json new file mode 100644 index 0000000..6dfedec --- /dev/null +++ b/configs/datasource_configs/robokop_string.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.STRING", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/string_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/string_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_textmining.json b/configs/datasource_configs/robokop_textmining.json new file mode 100644 index 0000000..2a21f80 --- /dev/null +++ b/configs/datasource_configs/robokop_textmining.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.TextMining", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/textmining_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/textmining_nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/datasource_configs/robokop_viralproteome.json b/configs/datasource_configs/robokop_viralproteome.json new file mode 100644 index 0000000..73ca6c9 --- /dev/null +++ b/configs/datasource_configs/robokop_viralproteome.json @@ -0,0 +1,21 @@ +{ + "name": "Robokop.ViralProteome", + "enabled": true, + "ingests": [ + { + "ingest_files": ["./00_fetch_data/robokop/viralproteome_edges.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_kgx_edges", + "ingest_args": [ + { "name": "--kgx-inject-key-prefix", "value": "robokop:" } + ] + }, + { + "ingest_files": ["./00_fetch_data/robokop/viralproteome.nodes.jsonl.gz"], + "ingest_script": "./target/release/grebi_ingest_json", + "ingest_args": [ + { "name": "--json-rename-field", "value": "category:grebi:type" }, + { "name": "--json-inject-key-prefix", "value": "robokop:" } + ] + } + ] +} \ No newline at end of file diff --git a/configs/subgraph_configs/ebi_full_monarch.json b/configs/subgraph_configs/ebi_full_monarch.json index ad40878..fc51093 100644 --- a/configs/subgraph_configs/ebi_full_monarch.json +++ b/configs/subgraph_configs/ebi_full_monarch.json @@ -85,6 +85,23 @@ "./configs/datasource_configs/hett_pesticides_eu.json", "./configs/datasource_configs/hett_pesticides_gb.json", "./configs/datasource_configs/aopwiki.json", - "./configs/datasource_configs/chembl.json" + "./configs/datasource_configs/chembl.json", + "./configs/datasource_configs/robokop_alliance.json", + "./configs/datasource_configs/robokop_binding.json", + "./configs/datasource_configs/robokop_cam.json", + "./configs/datasource_configs/robokop_ctd.json", + "./configs/datasource_configs/robokop_drugcentral.json", + "./configs/datasource_configs/robokop_gtex.json", + "./configs/datasource_configs/robokop_gtopdb.json", + "./configs/datasource_configs/robokop_hetionet.json", + "./configs/datasource_configs/robokop_hgoa.json", + "./configs/datasource_configs/robokop_hmdb.json", + "./configs/datasource_configs/robokop_icees.json", + "./configs/datasource_configs/robokop_intact.json", + "./configs/datasource_configs/robokop_panther.json", + "./configs/datasource_configs/robokop_pharos.json", + "./configs/datasource_configs/robokop_string.json", + "./configs/datasource_configs/robokop_textmining.json", + "./configs/datasource_configs/robokop_viralproteome.json" ] }