diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 2ee64d85..404f42f8 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -1,9 +1,10 @@ name: Release on: - push: - tags: - - "v*.*.*" + # push: + # tags: + # - "v*.*.*" + workflow_dispatch: jobs: build: diff --git a/.gitignore b/.gitignore index d7387cd4..a7a8e187 100644 --- a/.gitignore +++ b/.gitignore @@ -163,3 +163,5 @@ data/transformed/uniprot_genome_features/*.tsv kg_microbe/transform_utils/uniprot/tmp/relevant_file_content.txt kg_microbe/transform_utils/uniprot/tmp/nodes_and_edges/* data/transformed/uniprot_genome_features/uniprot_kgx.zip +data_merged.** +*.tar.gz diff --git a/Makefile b/Makefile index 513bf8d1..eefa3739 100644 --- a/Makefile +++ b/Makefile @@ -80,3 +80,4 @@ feba-schema-diagram: --output-file notebooks/schema.pdf +include kg-microbe.Makefile \ No newline at end of file diff --git a/README.md b/README.md index 329cabbb..015e49a4 100644 --- a/README.md +++ b/README.md @@ -31,6 +31,19 @@ ## Merge - `poetry run kg merge`: This merges all transformed graphs above. +## Release + ### Requirements + In order to be able to make KG releases on this repository, you'll need: + - Appropriate permissions to this repository. + - A Github token that has permissions on this repository. [This is how you set it in GitHub](https://docs.github.com/en/organizations/managing-programmatic-access-to-your-organization/setting-a-personal-access-token-policy-for-your-organization#restricting-access-by-personal-access-tokens-classic). Make sure your token has access to this project. + - Save this token locally assigned to the environemnt variable `GH_TOKEN` + ```shell + export GH_TOKEN = XXXX + ``` + or add it to your `~/.bash_profile` or `~/.bashrc` file. + + + # Contributors Please remember to run `poetry run tox` before every commit to make sure the code you commit is error-free. diff --git a/kg-microbe.Makefile b/kg-microbe.Makefile new file mode 100644 index 00000000..494a4412 --- /dev/null +++ b/kg-microbe.Makefile @@ -0,0 +1,99 @@ +# Define variables +RUNNER_VERSION := 2.317.0 +RUNNER_URL := https://github.com/actions/runner/releases/download/v$(RUNNER_VERSION)/actions-runner-linux-x64-$(RUNNER_VERSION).tar.gz +RUNNER_DIR := actions-runner +REPO_OWNER := Knowledge-Graph-Hub +REPO_NAME := kg-microbe +REPO_URL := https://github.com/$(REPO_OWNER)/$(REPO_NAME) +TOKEN := $(GH_TOKEN) +MERGED_TARBALL := data_merged.tar.gz +PART_SIZE := 2000M # Size of each part (less than 2GB) + +.PHONY: release pre-release tag generate-tarballs check-and-split + +release: generate-tarballs + @$(call create_release,release) + +pre-release: generate-tarballs + @$(call create_release,pre-release) + +tag: generate-tarballs + @$(call create_tag) + +generate-tarballs: + @echo "Generating tarballs of the specified directories..." + @for dir in data/transformed/*; do \ + if [ -d "$$dir" ]; then \ + if [ $$(find $$dir -type f | wc -l) -gt 0 ]; then \ + tarball_name=$$(basename $$dir).tar.gz; \ + tar -czvf $$tarball_name -C $$dir .; \ + echo "Tarball generated successfully as $$tarball_name."; \ + $(MAKE) check-and-split TARFILE=$$tarball_name; \ + else \ + echo "Directory $$dir is empty. Skipping tarball generation."; \ + fi \ + fi \ + done + @if [ -f data/merged/merged-kg.tar.gz ]; then \ + cp data/merged/merged-kg.tar.gz $(MERGED_TARBALL); \ + echo "Merged tarball copied successfully."; \ + $(MAKE) check-and-split TARFILE=$(MERGED_TARBALL); \ + else \ + echo "Merged tarball does not exist. Skipping."; \ + fi + @echo "Tarballs generated successfully." + +check-and-split: + @echo "Checking if $(TARFILE) needs to be split..." + @if [ $$(stat -f%z "$(TARFILE)") -gt 2147483648 ]; then \ + echo "$(TARFILE) is larger than 2GB. Splitting..."; \ + split -b $(PART_SIZE) -d -a 3 $(TARFILE) $(TARFILE).part-; \ + for part in $(TARFILE).part-*; do \ + mv $$part $${part}.tar.gz; \ + done; \ + rm -f $(TARFILE); \ + echo "$(TARFILE) split into smaller parts successfully."; \ + else \ + echo "$(TARFILE) is less than 2GB. No need to split."; \ + fi + +define create_release + @echo "Creating a $(1) on GitHub..." + @read -p "Enter $(1) tag (e.g., $(shell date +%Y-%m-%d)): " TAG_NAME; \ + read -p "Enter $(1) title: " RELEASE_TITLE; \ + read -p "Enter $(1) notes: " RELEASE_NOTES; \ + if git rev-parse "$$TAG_NAME" >/dev/null 2>&1; then \ + echo "Error: Tag '$$TAG_NAME' already exists. Please choose a different tag."; \ + exit 1; \ + fi; \ + git tag -a $$TAG_NAME -m "$$RELEASE_TITLE"; \ + git push origin $$TAG_NAME; \ + gh release create $$TAG_NAME --title "$$RELEASE_TITLE" --notes "$$RELEASE_NOTES" $(if $(filter $(1),pre-release),--prerelease) --repo $(REPO_OWNER)/$(REPO_NAME); \ + for tarball in *.tar.gz; do \ + gh release upload $$TAG_NAME $$tarball --repo $(REPO_OWNER)/$(REPO_NAME); \ + done; \ + for part in *.part-*.tar.gz; do \ + gh release upload $$TAG_NAME $$part --repo $(REPO_OWNER)/$(REPO_NAME); \ + done; \ + rm -f *.tar.gz *.part-*.tar.gz; \ + echo "$(capitalize $(1)) $$TAG_NAME created successfully." +endef + +define create_tag + @echo "Creating a release on GitHub..." + @read -p "Enter release tag (e.g., $(shell date +%Y-%m-%d)): " TAG; \ + read -p "Enter release title: " RELEASE_TITLE; \ + read -p "Enter release notes: " RELEASE_NOTES; \ + git tag -a $$TAG -m "$$RELEASE_TITLE"; \ + git push origin $$TAG; \ + for tarball in *.tar.gz; do \ + gh release upload $$TAG $$tarball --repo $(REPO_OWNER)/$(REPO_NAME); \ + done; \ + for part in *.part-*.tar.gz; do \ + gh release upload $$TAG $$part --repo $(REPO_OWNER)/$(REPO_NAME); \ + done; \ + rm -f *.tar.gz *.part-*.tar.gz; \ + echo "Release $$TAG created successfully." +endef + +capitalize = $(subst $(1),$(shell echo $(1) | tr '[:lower:]' '[:upper:]'),$(1)) diff --git a/merged_graph_stats.yaml b/merged_graph_stats.yaml index e793997e..1005d107 100644 --- a/merged_graph_stats.yaml +++ b/merged_graph_stats.yaml @@ -1,13 +1,13 @@ edge_stats: count_by_predicates: biolink:assesses: - count: 79179 + count: 79192 provided_by: unknown: - count: 79179 + count: 79192 source: unknown: - count: 79179 + count: 79192 biolink:associated_with: count: 7 provided_by: @@ -17,85 +17,85 @@ edge_stats: unknown: count: 7 biolink:capable_of: - count: 131378 + count: 131562 provided_by: unknown: - count: 131378 + count: 131562 source: unknown: - count: 131378 + count: 131562 biolink:consumes: - count: 254333 + count: 253744 provided_by: unknown: - count: 254333 + count: 253744 source: unknown: - count: 254333 + count: 253744 biolink:enabled_by: - count: 8139 + count: 8182 provided_by: unknown: - count: 8139 + count: 8182 source: unknown: - count: 8139 + count: 8182 biolink:enables: - count: 4478 + count: 4490 provided_by: unknown: - count: 4478 + count: 4490 source: unknown: - count: 4478 + count: 4490 biolink:has_chemical_role: - count: 1069 + count: 1068 provided_by: unknown: - count: 1069 + count: 1068 source: unknown: - count: 1069 + count: 1068 biolink:has_input: - count: 80725 + count: 81511 provided_by: unknown: - count: 80725 + count: 81511 source: unknown: - count: 80725 + count: 81511 biolink:has_output: - count: 80725 + count: 81511 provided_by: unknown: - count: 80725 + count: 81511 source: unknown: - count: 80725 + count: 81511 biolink:has_part: - count: 123247 + count: 123884 provided_by: unknown: - count: 123247 + count: 123884 source: unknown: - count: 123247 + count: 123884 biolink:has_participant: - count: 156336 + count: 157846 provided_by: unknown: - count: 156336 + count: 157846 source: unknown: - count: 156336 + count: 157846 biolink:has_phenotype: - count: 163501 + count: 163636 provided_by: unknown: - count: 163501 + count: 163636 source: unknown: - count: 163501 + count: 163636 biolink:is_assessed_by: count: 112 provided_by: @@ -105,21 +105,21 @@ edge_stats: unknown: count: 112 biolink:location_of: - count: 98918 + count: 98937 provided_by: unknown: - count: 98918 + count: 98937 source: unknown: - count: 98918 + count: 98937 biolink:occurs_in: - count: 53585 + count: 53599 provided_by: unknown: - count: 53585 + count: 53599 source: unknown: - count: 53585 + count: 53599 biolink:part_of: count: 509 provided_by: @@ -129,21 +129,21 @@ edge_stats: unknown: count: 509 biolink:produces: - count: 6538 + count: 6541 provided_by: unknown: - count: 6538 + count: 6541 source: unknown: - count: 6538 + count: 6541 biolink:related_to: - count: 116135 + count: 118253 provided_by: unknown: - count: 116135 + count: 118253 source: unknown: - count: 116135 + count: 118253 biolink:same_as: count: 3238 provided_by: @@ -153,21 +153,21 @@ edge_stats: unknown: count: 3238 biolink:subclass_of: - count: 1370902 + count: 1426976 provided_by: unknown: - count: 1370902 + count: 1426976 source: unknown: - count: 1370902 + count: 1426976 biolink:type: - count: 45 + count: 46 provided_by: unknown: - count: 45 + count: 46 source: unknown: - count: 45 + count: 46 unknown: count: 0 count_by_spo: @@ -211,22 +211,14 @@ edge_stats: source: unknown: count: 9 - biolink:AnatomicalEntity-biolink:subclass_of-biolink:NamedThing: - count: 32 - provided_by: - unknown: - count: 32 - source: - unknown: - count: 32 biolink:AnatomicalEntity-biolink:subclass_of-biolink:OntologyClass: - count: 2 + count: 34 provided_by: unknown: - count: 2 + count: 34 source: unknown: - count: 2 + count: 34 biolink:BiologicalProcess-biolink:associated_with-biolink:BiologicalProcess: count: 1 provided_by: @@ -252,85 +244,85 @@ edge_stats: unknown: count: 436 biolink:BiologicalProcess-biolink:related_to-biolink:BiologicalProcess: - count: 14663 + count: 14391 provided_by: unknown: - count: 14663 + count: 14391 source: unknown: - count: 14663 + count: 14391 biolink:BiologicalProcess-biolink:related_to-biolink:CellularComponent: - count: 148 + count: 150 provided_by: unknown: - count: 148 + count: 150 source: unknown: - count: 148 + count: 150 biolink:BiologicalProcess-biolink:related_to-biolink:MolecularActivity: - count: 956 + count: 935 provided_by: unknown: - count: 956 + count: 935 source: unknown: - count: 956 + count: 935 biolink:BiologicalProcess-biolink:related_to-biolink:OntologyClass: - count: 61 + count: 64 provided_by: unknown: - count: 61 + count: 64 source: unknown: - count: 61 + count: 64 biolink:BiologicalProcess-biolink:subclass_of-biolink:BiologicalProcess: - count: 51807 + count: 49879 provided_by: unknown: - count: 51807 + count: 49879 source: unknown: - count: 51807 + count: 49879 biolink:BiologicalProcess-biolink:subclass_of-biolink:MolecularActivity: - count: 6059 + count: 6016 provided_by: unknown: - count: 6059 + count: 6016 source: unknown: - count: 6059 + count: 6016 biolink:BiologicalProcess-biolink:subclass_of-biolink:NamedThing: - count: 4569 + count: 4587 provided_by: unknown: - count: 4569 + count: 4587 source: unknown: - count: 4569 + count: 4587 biolink:BiologicalProcess-biolink:subclass_of-biolink:OntologyClass: - count: 549 + count: 594 provided_by: unknown: - count: 549 + count: 594 source: unknown: - count: 549 + count: 594 biolink:CellularComponent-biolink:related_to-biolink:CellularComponent: - count: 2022 + count: 1997 provided_by: unknown: - count: 2022 + count: 1997 source: unknown: - count: 2022 + count: 1997 biolink:CellularComponent-biolink:subclass_of-biolink:CellularComponent: - count: 4687 + count: 4664 provided_by: unknown: - count: 4687 + count: 4664 source: unknown: - count: 4687 + count: 4664 biolink:ChemicalEntity-biolink:has_chemical_role-biolink:ChemicalRole: count: 1051 provided_by: @@ -340,29 +332,29 @@ edge_stats: unknown: count: 1051 biolink:ChemicalEntity-biolink:has_chemical_role-biolink:ChemicalSubstance: - count: 1048 + count: 1051 provided_by: unknown: - count: 1048 + count: 1051 source: unknown: - count: 1048 + count: 1051 biolink:ChemicalEntity-biolink:has_part-biolink:ChemicalEntity: - count: 123247 + count: 123884 provided_by: unknown: - count: 123247 + count: 123884 source: unknown: - count: 123247 + count: 123884 biolink:ChemicalEntity-biolink:has_part-biolink:ChemicalSubstance: - count: 82214 + count: 82667 provided_by: unknown: - count: 82214 + count: 82667 source: unknown: - count: 82214 + count: 82667 biolink:ChemicalEntity-biolink:occurs_in-biolink:PhenotypicQuality: count: 282 provided_by: @@ -388,21 +380,21 @@ edge_stats: unknown: count: 335 biolink:ChemicalEntity-biolink:related_to-biolink:ChemicalRole: - count: 1809 + count: 1831 provided_by: unknown: - count: 1809 + count: 1831 source: unknown: - count: 1809 + count: 1831 biolink:ChemicalEntity-biolink:related_to-biolink:ChemicalSubstance: - count: 2954 + count: 2978 provided_by: unknown: - count: 2954 + count: 2978 source: unknown: - count: 2954 + count: 2978 biolink:ChemicalEntity-biolink:subclass_of-biolink:ChemicalEntity: count: 163 provided_by: @@ -412,13 +404,13 @@ edge_stats: unknown: count: 163 biolink:ChemicalEntity-biolink:subclass_of-biolink:ChemicalMixture: - count: 3290 + count: 3307 provided_by: unknown: - count: 3290 + count: 3307 source: unknown: - count: 3290 + count: 3307 biolink:ChemicalEntity-biolink:subclass_of-biolink:ChemicalRole: count: 1 provided_by: @@ -428,13 +420,13 @@ edge_stats: unknown: count: 1 biolink:ChemicalEntity-biolink:subclass_of-biolink:ChemicalSubstance: - count: 2094 + count: 2095 provided_by: unknown: - count: 2094 + count: 2095 source: unknown: - count: 2094 + count: 2095 biolink:ChemicalRole-biolink:subclass_of-biolink:ChemicalRole: count: 72 provided_by: @@ -444,29 +436,29 @@ edge_stats: unknown: count: 72 biolink:ChemicalRole-biolink:subclass_of-biolink:ChemicalSubstance: - count: 269 + count: 271 provided_by: unknown: - count: 269 + count: 271 source: unknown: - count: 269 + count: 271 biolink:ChemicalSubstance-biolink:has_chemical_role-biolink:ChemicalRole: - count: 1069 + count: 1068 provided_by: unknown: - count: 1069 + count: 1068 source: unknown: - count: 1069 + count: 1068 biolink:ChemicalSubstance-biolink:has_chemical_role-biolink:ChemicalSubstance: - count: 1066 + count: 1068 provided_by: unknown: - count: 1066 + count: 1068 source: unknown: - count: 1066 + count: 1068 biolink:ChemicalSubstance-biolink:location_of-biolink:OrganismTaxon: count: 59 provided_by: @@ -492,29 +484,29 @@ edge_stats: unknown: count: 57 biolink:ChemicalSubstance-biolink:related_to-biolink:ChemicalEntity: - count: 6125 + count: 6182 provided_by: unknown: - count: 6125 + count: 6182 source: unknown: - count: 6125 + count: 6182 biolink:ChemicalSubstance-biolink:related_to-biolink:ChemicalRole: - count: 31577 + count: 32225 provided_by: unknown: - count: 31577 + count: 32225 source: unknown: - count: 31577 + count: 32225 biolink:ChemicalSubstance-biolink:related_to-biolink:ChemicalSubstance: - count: 90277 + count: 92692 provided_by: unknown: - count: 90277 + count: 92692 source: unknown: - count: 90277 + count: 92692 biolink:ChemicalSubstance-biolink:related_to-biolink:EnvironmentalFeature: count: 5 provided_by: @@ -524,45 +516,45 @@ edge_stats: unknown: count: 5 biolink:ChemicalSubstance-biolink:subclass_of-biolink:ChemicalEntity: - count: 1774 + count: 2036 provided_by: unknown: - count: 1774 + count: 2036 source: unknown: - count: 1774 + count: 2036 biolink:ChemicalSubstance-biolink:subclass_of-biolink:ChemicalRole: - count: 342 + count: 350 provided_by: unknown: - count: 342 + count: 350 source: unknown: - count: 342 + count: 350 biolink:ChemicalSubstance-biolink:subclass_of-biolink:ChemicalSubstance: - count: 240712 + count: 278860 provided_by: unknown: - count: 240712 + count: 278860 source: unknown: - count: 240712 + count: 278860 biolink:ChemicalSubstance-biolink:subclass_of-biolink:EnvironmentalFeature: - count: 58 + count: 107 provided_by: unknown: - count: 58 + count: 107 source: unknown: - count: 58 + count: 107 biolink:ChemicalSubstance-biolink:subclass_of-biolink:OntologyClass: - count: 6 + count: 7 provided_by: unknown: - count: 6 + count: 7 source: unknown: - count: 6 + count: 7 biolink:EnvironmentalFeature-biolink:location_of-biolink:OrganismTaxon: count: 63 provided_by: @@ -644,29 +636,29 @@ edge_stats: unknown: count: 14 biolink:Enzyme-biolink:related_to-biolink:BiologicalProcess: - count: 4720 + count: 4728 provided_by: unknown: - count: 4720 + count: 4728 source: unknown: - count: 4720 + count: 4728 biolink:Enzyme-biolink:related_to-biolink:MolecularActivity: - count: 4720 + count: 4728 provided_by: unknown: - count: 4720 + count: 4728 source: unknown: - count: 4720 + count: 4728 biolink:Enzyme-biolink:subclass_of-biolink:Enzyme: - count: 7163 + count: 7166 provided_by: unknown: - count: 7163 + count: 7166 source: unknown: - count: 7163 + count: 7166 biolink:Enzyme-biolink:subclass_of-biolink:NamedThing: count: 7 provided_by: @@ -684,13 +676,13 @@ edge_stats: unknown: count: 454 biolink:MolecularActivity-biolink:enabled_by-biolink:Enzyme: - count: 7683 + count: 7726 provided_by: unknown: - count: 7683 + count: 7726 source: unknown: - count: 7683 + count: 7726 biolink:MolecularActivity-biolink:enabled_by-biolink:PhenotypicQuality: count: 35 provided_by: @@ -700,93 +692,69 @@ edge_stats: unknown: count: 35 biolink:MolecularActivity-biolink:enables-biolink:BiologicalProcess: - count: 4478 + count: 4490 provided_by: unknown: - count: 4478 + count: 4490 source: unknown: - count: 4478 + count: 4490 biolink:MolecularActivity-biolink:enables-biolink:MolecularActivity: - count: 4453 + count: 4489 provided_by: unknown: - count: 4453 + count: 4489 source: unknown: - count: 4453 + count: 4489 biolink:MolecularActivity-biolink:has_input-biolink:ChemicalEntity: - count: 15525 + count: 15658 provided_by: unknown: - count: 15525 + count: 15658 source: unknown: - count: 15525 + count: 15658 biolink:MolecularActivity-biolink:has_input-biolink:ChemicalSubstance: - count: 80482 + count: 81511 provided_by: unknown: - count: 80482 + count: 81511 source: unknown: - count: 80482 - biolink:MolecularActivity-biolink:has_input-unknown: - count: 243 - provided_by: - unknown: - count: 243 - source: - unknown: - count: 243 + count: 81511 biolink:MolecularActivity-biolink:has_output-biolink:ChemicalEntity: - count: 15525 + count: 15658 provided_by: unknown: - count: 15525 + count: 15658 source: unknown: - count: 15525 + count: 15658 biolink:MolecularActivity-biolink:has_output-biolink:ChemicalSubstance: - count: 80482 + count: 81511 provided_by: unknown: - count: 80482 + count: 81511 source: unknown: - count: 80482 - biolink:MolecularActivity-biolink:has_output-unknown: - count: 243 - provided_by: - unknown: - count: 243 - source: - unknown: - count: 243 + count: 81511 biolink:MolecularActivity-biolink:has_participant-biolink:ChemicalEntity: - count: 30170 + count: 30408 provided_by: unknown: - count: 30170 + count: 30408 source: unknown: - count: 30170 + count: 30408 biolink:MolecularActivity-biolink:has_participant-biolink:ChemicalSubstance: - count: 155856 + count: 157846 provided_by: unknown: - count: 155856 + count: 157846 source: unknown: - count: 155856 - biolink:MolecularActivity-biolink:has_participant-unknown: - count: 480 - provided_by: - unknown: - count: 480 - source: - unknown: - count: 480 + count: 157846 biolink:MolecularActivity-biolink:part_of-biolink:BiologicalProcess: count: 500 provided_by: @@ -796,13 +764,13 @@ edge_stats: unknown: count: 500 biolink:MolecularActivity-biolink:related_to-biolink:BiologicalProcess: - count: 881 + count: 860 provided_by: unknown: - count: 881 + count: 860 source: unknown: - count: 881 + count: 860 biolink:MolecularActivity-biolink:related_to-biolink:CellularComponent: count: 48 provided_by: @@ -812,53 +780,77 @@ edge_stats: unknown: count: 48 biolink:MolecularActivity-biolink:related_to-biolink:MolecularActivity: - count: 240 + count: 243 provided_by: unknown: - count: 240 + count: 243 source: unknown: - count: 240 + count: 243 biolink:MolecularActivity-biolink:related_to-biolink:OntologyClass: - count: 2 + count: 1 provided_by: unknown: - count: 2 + count: 1 source: unknown: - count: 2 + count: 1 biolink:MolecularActivity-biolink:subclass_of-biolink:BiologicalProcess: - count: 908 + count: 898 provided_by: unknown: - count: 908 + count: 898 source: unknown: - count: 908 + count: 898 biolink:MolecularActivity-biolink:subclass_of-biolink:MolecularActivity: - count: 81401 + count: 82080 provided_by: unknown: - count: 81401 + count: 82080 source: unknown: - count: 81401 + count: 82080 biolink:MolecularActivity-biolink:subclass_of-biolink:NamedThing: - count: 4569 + count: 4587 provided_by: unknown: - count: 4569 + count: 4587 + source: + unknown: + count: 4587 + biolink:MolecularActivity-biolink:subclass_of-biolink:OntologyClass: + count: 151 + provided_by: + unknown: + count: 151 + source: + unknown: + count: 151 + biolink:NamedThing-None-biolink:OntologyClass: + count: 2 + provided_by: + unknown: + count: 2 + source: + unknown: + count: 2 + biolink:OntologyClass-None-biolink:NamedThing: + count: 1 + provided_by: + unknown: + count: 1 source: unknown: - count: 4569 + count: 1 biolink:OntologyClass-None-biolink:OntologyClass: - count: 259 + count: 260 provided_by: unknown: - count: 259 + count: 260 source: unknown: - count: 259 + count: 260 biolink:OntologyClass-biolink:enabled_by-biolink:BiologicalProcess: count: 2 provided_by: @@ -892,13 +884,13 @@ edge_stats: unknown: count: 20 biolink:OntologyClass-biolink:related_to-biolink:ChemicalEntity: - count: 77 + count: 79 provided_by: unknown: - count: 77 + count: 79 source: unknown: - count: 77 + count: 79 biolink:OntologyClass-biolink:related_to-biolink:ChemicalRole: count: 4 provided_by: @@ -908,13 +900,13 @@ edge_stats: unknown: count: 4 biolink:OntologyClass-biolink:related_to-biolink:ChemicalSubstance: - count: 182 + count: 184 provided_by: unknown: - count: 182 + count: 184 source: unknown: - count: 182 + count: 184 biolink:OntologyClass-biolink:related_to-biolink:EnvironmentalFeature: count: 3 provided_by: @@ -924,21 +916,21 @@ edge_stats: unknown: count: 3 biolink:OntologyClass-biolink:related_to-biolink:OntologyClass: - count: 1930 + count: 1942 provided_by: unknown: - count: 1930 + count: 1942 source: unknown: - count: 1930 + count: 1942 biolink:OntologyClass-biolink:related_to-biolink:OrganismTaxon: - count: 18 + count: 17 provided_by: unknown: - count: 18 + count: 17 source: unknown: - count: 18 + count: 17 biolink:OntologyClass-biolink:subclass_of-biolink:AnatomicalEntity: count: 3 provided_by: @@ -948,13 +940,13 @@ edge_stats: unknown: count: 3 biolink:OntologyClass-biolink:subclass_of-biolink:BiologicalProcess: - count: 73 + count: 75 provided_by: unknown: - count: 73 + count: 75 source: unknown: - count: 73 + count: 75 biolink:OntologyClass-biolink:subclass_of-biolink:ChemicalEntity: count: 1 provided_by: @@ -972,45 +964,37 @@ edge_stats: unknown: count: 1 biolink:OntologyClass-biolink:subclass_of-biolink:ChemicalSubstance: - count: 11 + count: 10 provided_by: unknown: - count: 11 + count: 10 source: unknown: - count: 11 - biolink:OntologyClass-biolink:subclass_of-biolink:NamedThing: - count: 13 + count: 10 + biolink:OntologyClass-biolink:subclass_of-biolink:MolecularActivity: + count: 1 provided_by: unknown: - count: 13 + count: 1 source: unknown: - count: 13 + count: 1 biolink:OntologyClass-biolink:subclass_of-biolink:OntologyClass: - count: 5435 + count: 5646 provided_by: unknown: - count: 5435 + count: 5646 source: unknown: - count: 5435 - biolink:OntologyClass-biolink:subclass_of-biolink:OrganismTaxon: - count: 1 - provided_by: - unknown: - count: 1 - source: - unknown: - count: 1 + count: 5646 biolink:OntologyClass-biolink:type-biolink:OntologyClass: - count: 45 + count: 46 provided_by: unknown: - count: 45 + count: 46 source: unknown: - count: 45 + count: 46 biolink:OrganismTaxon-biolink:capable_of-biolink:ActivityAndBehavior: count: 24353 provided_by: @@ -1020,53 +1004,53 @@ edge_stats: unknown: count: 24353 biolink:OrganismTaxon-biolink:capable_of-biolink:BiologicalProcess: - count: 8939 + count: 9030 provided_by: unknown: - count: 8939 + count: 9030 source: unknown: - count: 8939 + count: 9030 biolink:OrganismTaxon-biolink:capable_of-biolink:Enzyme: - count: 75273 + count: 75352 provided_by: unknown: - count: 75273 + count: 75352 source: unknown: - count: 75273 - biolink:OrganismTaxon-biolink:capable_of-biolink:OntologyClass: - count: 258 + count: 75352 + biolink:OrganismTaxon-biolink:capable_of-biolink:PhenotypicQuality: + count: 122532 provided_by: unknown: - count: 258 + count: 122532 source: unknown: - count: 258 - biolink:OrganismTaxon-biolink:capable_of-biolink:PhenotypicQuality: - count: 122439 + count: 122532 + biolink:OrganismTaxon-biolink:consumes-biolink:ChemicalEntity: + count: 253696 provided_by: unknown: - count: 122439 + count: 253696 source: unknown: - count: 122439 - biolink:OrganismTaxon-biolink:consumes-biolink:ChemicalEntity: - count: 254286 + count: 253696 + biolink:OrganismTaxon-biolink:consumes-biolink:ChemicalSubstance: + count: 253696 provided_by: unknown: - count: 254286 + count: 253696 source: unknown: - count: 254286 - biolink:OrganismTaxon-biolink:consumes-biolink:ChemicalSubstance: - count: 254286 + count: 253696 + biolink:OrganismTaxon-biolink:consumes-unknown: + count: 1 provided_by: unknown: - count: 254286 + count: 1 source: unknown: - count: 254286 + count: 1 biolink:OrganismTaxon-biolink:has_phenotype-biolink:AbstractEntity: count: 21000 provided_by: @@ -1076,21 +1060,21 @@ edge_stats: unknown: count: 21000 biolink:OrganismTaxon-biolink:has_phenotype-biolink:ActivityAndBehavior: - count: 21267 + count: 21282 provided_by: unknown: - count: 21267 + count: 21282 source: unknown: - count: 21267 + count: 21282 biolink:OrganismTaxon-biolink:has_phenotype-biolink:PhenotypicQuality: - count: 151218 + count: 151353 provided_by: unknown: - count: 151218 + count: 151353 source: unknown: - count: 151218 + count: 151353 biolink:OrganismTaxon-biolink:location_of-biolink:AnatomicalEntity: count: 1759 provided_by: @@ -1132,37 +1116,37 @@ edge_stats: unknown: count: 624 biolink:OrganismTaxon-biolink:location_of-unknown: - count: 78938 + count: 78957 provided_by: unknown: - count: 78938 + count: 78957 source: unknown: - count: 78938 + count: 78957 biolink:OrganismTaxon-biolink:occurs_in-biolink:ChemicalEntity: - count: 53242 + count: 53256 provided_by: unknown: - count: 53242 + count: 53256 source: unknown: - count: 53242 + count: 53256 biolink:OrganismTaxon-biolink:produces-biolink:ChemicalEntity: - count: 5541 + count: 5544 provided_by: unknown: - count: 5541 + count: 5544 source: unknown: - count: 5541 + count: 5544 biolink:OrganismTaxon-biolink:produces-biolink:ChemicalSubstance: - count: 6536 + count: 6539 provided_by: unknown: - count: 6536 + count: 6539 source: unknown: - count: 6536 + count: 6539 biolink:OrganismTaxon-biolink:same_as-biolink:OrganismTaxon: count: 1258 provided_by: @@ -1188,37 +1172,37 @@ edge_stats: unknown: count: 3 biolink:OrganismTaxon-biolink:subclass_of-biolink:OntologyClass: - count: 36 + count: 46 provided_by: unknown: - count: 36 + count: 46 source: unknown: - count: 36 + count: 46 biolink:OrganismTaxon-biolink:subclass_of-biolink:OrganismTaxon: - count: 971182 + count: 990119 provided_by: unknown: - count: 971182 + count: 990119 source: unknown: - count: 971182 + count: 990119 biolink:OrganismTaxon-biolink:subclass_of-unknown: - count: 9 + count: 22 provided_by: unknown: - count: 9 + count: 22 source: unknown: - count: 9 + count: 22 biolink:PhenotypicQuality-biolink:assesses-biolink:OrganismTaxon: - count: 79179 + count: 79192 provided_by: unknown: - count: 79179 + count: 79192 source: unknown: - count: 79179 + count: 79192 biolink:PhenotypicQuality-biolink:associated_with-biolink:AbstractEntity: count: 2 provided_by: @@ -1324,13 +1308,13 @@ edge_stats: unknown: count: 9 unknown-biolink:subclass_of-biolink:ChemicalMixture: - count: 5 + count: 9 provided_by: unknown: - count: 5 + count: 9 source: unknown: - count: 5 + count: 9 unknown-biolink:subclass_of-unknown: count: 317 provided_by: @@ -1365,7 +1349,7 @@ edge_stats: - unknown source: - unknown - total_edges: 2733358 + total_edges: 2795104 graph_name: kg-microbe graph node_stats: count_by_category: @@ -1387,32 +1371,37 @@ node_stats: nodes.tsv: count: 4 biolink:BiologicalProcess: - count: 36986 + count: 37130 provided_by: ec_nodes.tsv: - count: 4569 + count: 4587 envo.json: count: 42 go.json: - count: 35802 + count: 35951 nodes.tsv: - count: 4588 + count: 4600 upa.json: count: 1053 + biolink:Cell: + count: 1 + provided_by: + envo.json: + count: 1 biolink:CellularComponent: - count: 4494 + count: 4519 provided_by: go.json: - count: 4494 + count: 4519 biolink:ChemicalEntity: - count: 10337 + count: 10385 provided_by: chebi.json: count: 1133 envo.json: count: 60 nodes.tsv: - count: 10337 + count: 10385 biolink:ChemicalMixture: count: 2 provided_by: @@ -1422,20 +1411,20 @@ node_stats: count: 235 provided_by: chebi.json: - count: 234 + count: 235 envo.json: count: 55 nodes.tsv: count: 235 biolink:ChemicalSubstance: - count: 185303 + count: 219498 provided_by: chebi.json: - count: 185295 + count: 219490 envo.json: count: 930 nodes.tsv: - count: 1377 + count: 1378 biolink:EnvironmentalFeature: count: 412 provided_by: @@ -1448,7 +1437,7 @@ node_stats: nodes.tsv: count: 412 biolink:Enzyme: - count: 7209 + count: 7249 provided_by: http://purl.obolibrary.org/obo/EC_1: count: 1 @@ -1932,8 +1921,6 @@ node_stats: count: 1 http://purl.obolibrary.org/obo/EC_1.1.1.329: count: 1 - http://purl.obolibrary.org/obo/EC_1.1.1.33: - count: 1 http://purl.obolibrary.org/obo/EC_1.1.1.330: count: 1 http://purl.obolibrary.org/obo/EC_1.1.1.331: @@ -3434,8 +3421,6 @@ node_stats: count: 1 http://purl.obolibrary.org/obo/EC_1.14.14.14: count: 1 - http://purl.obolibrary.org/obo/EC_1.14.14.140: - count: 1 http://purl.obolibrary.org/obo/EC_1.14.14.141: count: 1 http://purl.obolibrary.org/obo/EC_1.14.14.142: @@ -6402,6 +6387,10 @@ node_stats: count: 1 http://purl.obolibrary.org/obo/EC_2.1.1.387: count: 1 + http://purl.obolibrary.org/obo/EC_2.1.1.388: + count: 1 + http://purl.obolibrary.org/obo/EC_2.1.1.389: + count: 1 http://purl.obolibrary.org/obo/EC_2.1.1.39: count: 1 http://purl.obolibrary.org/obo/EC_2.1.1.4: @@ -7094,6 +7083,10 @@ node_stats: count: 1 http://purl.obolibrary.org/obo/EC_2.3.1.311: count: 1 + http://purl.obolibrary.org/obo/EC_2.3.1.312: + count: 1 + http://purl.obolibrary.org/obo/EC_2.3.1.313: + count: 1 http://purl.obolibrary.org/obo/EC_2.3.1.32: count: 1 http://purl.obolibrary.org/obo/EC_2.3.1.33: @@ -7308,6 +7301,8 @@ node_stats: count: 1 http://purl.obolibrary.org/obo/EC_2.3.2.36: count: 1 + http://purl.obolibrary.org/obo/EC_2.3.2.37: + count: 1 http://purl.obolibrary.org/obo/EC_2.3.2.5: count: 1 http://purl.obolibrary.org/obo/EC_2.3.2.6: @@ -7982,6 +7977,8 @@ node_stats: count: 1 http://purl.obolibrary.org/obo/EC_2.4.1.392: count: 1 + http://purl.obolibrary.org/obo/EC_2.4.1.393: + count: 1 http://purl.obolibrary.org/obo/EC_2.4.1.4: count: 1 http://purl.obolibrary.org/obo/EC_2.4.1.40: @@ -9264,8 +9261,6 @@ node_stats: count: 1 http://purl.obolibrary.org/obo/EC_2.7.11.26: count: 1 - http://purl.obolibrary.org/obo/EC_2.7.11.27: - count: 1 http://purl.obolibrary.org/obo/EC_2.7.11.28: count: 1 http://purl.obolibrary.org/obo/EC_2.7.11.29: @@ -15791,36 +15786,40 @@ node_stats: http://purl.obolibrary.org/obo/EC_7.6.2.9: count: 1 nodes.tsv: - count: 6075 + count: 6114 biolink:MolecularActivity: - count: 80187 + count: 81028 provided_by: ec_nodes.tsv: - count: 4569 + count: 4587 + envo.json: + count: 2 go.json: - count: 12535 + count: 12614 nodes.tsv: - count: 72058 + count: 72854 upa.json: count: 33 upa_nodes.tsv: count: 942 biolink:NamedThing: - count: 4 + count: 2 provided_by: - Graph: - count: 3 ec_nodes.tsv: + count: 2 + envo.json: count: 1 biolink:OntologyClass: - count: 9256 + count: 9380 provided_by: chebi.json: count: 25 + ec_nodes.tsv: + count: 1 envo.json: - count: 5541 + count: 5667 go.json: - count: 3797 + count: 3800 http://purl.obolibrary.org/obo/RO_0002327: count: 1 http://purl.obolibrary.org/obo/RO_0002351: @@ -15831,17 +15830,15 @@ node_stats: count: 1 ncbitaxon_removed_subset.json: count: 30 - nodes.tsv: - count: 3 biolink:OrganismTaxon: - count: 978148 + count: 997303 provided_by: envo.json: count: 204 ncbitaxon_removed_subset.json: - count: 815343 + count: 834303 nodes.tsv: - count: 216263 + count: 216414 biolink:PhenotypicQuality: count: 543 provided_by: @@ -15976,71 +15973,78 @@ node_stats: nodes.tsv: count: 543 unknown: - count: 1547 + count: 1400 provided_by: nodes.tsv: count: 5 unknown: - count: 1521 + count: 1374 upa_nodes.tsv: count: 21 count_by_id_prefixes: BFO: 34 - CARO: 3 - CAS-RN: 232 - CHEBI: 186838 - EC: 7281 - ENVO: 4340 + CARO: 4 + CAS-RN: 233 + CHEBI: 220877 + CL: 1 + EC: 7321 + ENVO: 4385 FAO: 1 FOODON: 421 - GO: 56543 - IAO: 28 + GO: 56774 + IAO: 34 KEGG: 2 - NCBITaxon: 815979 + NCBITaxon: 834987 NaCl_delta: 4 NaCl_opt: 4 NaCl_range: 4 OBI: 6 - OBO: 40 - OIO: 15 + OBO: 62 + OIO: 27 PATO: 402 PCO: 8 PO: 48 PubChem: 20 - RHEA: 67640 - RO: 222 + RHEA: 68402 + RO: 231 UBERON: 602 UPA: 1086 WD_Entity: 4 assay: 354 bacdive: 8454 + carbon_substrates: 2 cell_length: 2 cell_shape: 38 cell_width: 2 + dc: 6 + dcterms: 6 envo: 43 + foaf: 1 foodon: 1 gc: 4 gram_stain: 3 - ingredient: 258 + ingredient: 260 isolation_source: 702 - medium: 3299 + medium: 3320 medium-type: 2 motility: 2 - owl: 1 + owl: 2 oxygen: 15 pH_delta: 1 pH_opt: 4 pH_range: 5 pathogen: 3 - pathways: 82 + pathways: 101 pato: 6 pigment: 10 po: 1 production: 8 + rdfs: 2 salinity: 7 - solution: 5381 + skos: 1 + solution: 5408 sporulation: 2 - strain: 154094 + strain: 154245 temp_delta: 1 temp_opt: 7 temp_range: 7 @@ -16054,26 +16058,29 @@ node_stats: biolink:AnatomicalEntity: UBERON: 596 biolink:BiologicalProcess: - GO: 35826 + GO: 35951 UPA: 1053 - pathways: 81 + pathways: 100 trophic_type: 26 + biolink:Cell: + CL: 1 biolink:CellularComponent: - GO: 4494 + GO: 4519 biolink:ChemicalEntity: - CAS-RN: 232 + CAS-RN: 233 CHEBI: 1150 KEGG: 2 PubChem: 20 - ingredient: 258 - medium: 3294 - solution: 5381 + carbon_substrates: 1 + ingredient: 260 + medium: 3311 + solution: 5408 biolink:ChemicalMixture: medium-type: 2 biolink:ChemicalRole: CHEBI: 235 biolink:ChemicalSubstance: - CHEBI: 185295 + CHEBI: 219490 production: 8 biolink:EnvironmentalFeature: CHEBI: 2 @@ -16085,33 +16092,40 @@ node_stats: pato: 6 po: 1 biolink:Enzyme: - EC: 7209 + EC: 7249 biolink:MolecularActivity: - GO: 12535 - RHEA: 67619 + GO: 12614 + RHEA: 68381 UPA: 33 biolink:NamedThing: - CARO: 3 + RO: 1 owl: 1 biolink:OntologyClass: BFO: 34 - ENVO: 4340 + CARO: 4 + ENVO: 4385 FAO: 1 FOODON: 420 - GO: 3688 - IAO: 28 + GO: 3690 + IAO: 34 OBI: 6 - OBO: 40 - OIO: 15 + OBO: 62 + OIO: 27 PATO: 402 PCO: 8 PO: 48 - RO: 222 + RO: 230 WD_Entity: 4 + dc: 6 + dcterms: 6 + foaf: 1 + owl: 1 + rdfs: 2 + skos: 1 biolink:OrganismTaxon: - NCBITaxon: 815975 + NCBITaxon: 834979 bacdive: 7515 - strain: 154094 + strain: 154245 biolink:PhenotypicQuality: EC: 72 NaCl_delta: 4 @@ -16138,21 +16152,22 @@ node_stats: temp_range: 7 temperature: 4 unknown: - CHEBI: 156 FOODON: 1 - NCBITaxon: 3 + NCBITaxon: 7 RHEA: 21 assay: 50 bacdive: 939 + carbon_substrates: 1 cell_shape: 1 isolation_source: 354 - medium: 5 + medium: 9 trophic_type: 1 node_categories: - biolink:AbstractEntity - biolink:ActivityAndBehavior - biolink:AnatomicalEntity - biolink:BiologicalProcess + - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:ChemicalMixture @@ -16170,6 +16185,7 @@ node_stats: - CARO - CAS-RN - CHEBI + - CL - EC - ENVO - FAO @@ -16195,10 +16211,14 @@ node_stats: - WD_Entity - assay - bacdive + - carbon_substrates - cell_length - cell_shape - cell_width + - dc + - dcterms - envo + - foaf - foodon - gc - gram_stain @@ -16218,7 +16238,9 @@ node_stats: - pigment - po - production + - rdfs - salinity + - skos - solution - sporulation - strain @@ -16239,6 +16261,8 @@ node_stats: - trophic_type - UPA - pathways + biolink:Cell: + - CL biolink:CellularComponent: - GO biolink:ChemicalEntity: @@ -16249,6 +16273,7 @@ node_stats: - solution - ingredient - PubChem + - carbon_substrates biolink:ChemicalMixture: - medium-type biolink:ChemicalRole: @@ -16272,7 +16297,7 @@ node_stats: - RHEA - UPA biolink:NamedThing: - - CARO + - RO - owl biolink:OntologyClass: - IAO @@ -16280,8 +16305,8 @@ node_stats: - OIO - BFO - RO + - CARO - ENVO - - WD_Entity - FAO - FOODON - GO @@ -16289,6 +16314,13 @@ node_stats: - PATO - PCO - PO + - WD_Entity + - dc + - dcterms + - rdfs + - owl + - skos + - foaf biolink:OrganismTaxon: - NCBITaxon - strain @@ -16324,13 +16356,12 @@ node_stats: - bacdive - NCBITaxon - medium - - CHEBI - RHEA - FOODON + - carbon_substrates - cell_shape - trophic_type provided_by: - - Graph - chebi.json - ec_nodes.tsv - envo.json @@ -16576,7 +16607,6 @@ node_stats: - http://purl.obolibrary.org/obo/EC_1.1.1.327 - http://purl.obolibrary.org/obo/EC_1.1.1.328 - http://purl.obolibrary.org/obo/EC_1.1.1.329 - - http://purl.obolibrary.org/obo/EC_1.1.1.33 - http://purl.obolibrary.org/obo/EC_1.1.1.330 - http://purl.obolibrary.org/obo/EC_1.1.1.331 - http://purl.obolibrary.org/obo/EC_1.1.1.332 @@ -17327,7 +17357,6 @@ node_stats: - http://purl.obolibrary.org/obo/EC_1.14.14.138 - http://purl.obolibrary.org/obo/EC_1.14.14.139 - http://purl.obolibrary.org/obo/EC_1.14.14.14 - - http://purl.obolibrary.org/obo/EC_1.14.14.140 - http://purl.obolibrary.org/obo/EC_1.14.14.141 - http://purl.obolibrary.org/obo/EC_1.14.14.142 - http://purl.obolibrary.org/obo/EC_1.14.14.143 @@ -18811,6 +18840,8 @@ node_stats: - http://purl.obolibrary.org/obo/EC_2.1.1.385 - http://purl.obolibrary.org/obo/EC_2.1.1.386 - http://purl.obolibrary.org/obo/EC_2.1.1.387 + - http://purl.obolibrary.org/obo/EC_2.1.1.388 + - http://purl.obolibrary.org/obo/EC_2.1.1.389 - http://purl.obolibrary.org/obo/EC_2.1.1.39 - http://purl.obolibrary.org/obo/EC_2.1.1.4 - http://purl.obolibrary.org/obo/EC_2.1.1.40 @@ -19157,6 +19188,8 @@ node_stats: - http://purl.obolibrary.org/obo/EC_2.3.1.31 - http://purl.obolibrary.org/obo/EC_2.3.1.310 - http://purl.obolibrary.org/obo/EC_2.3.1.311 + - http://purl.obolibrary.org/obo/EC_2.3.1.312 + - http://purl.obolibrary.org/obo/EC_2.3.1.313 - http://purl.obolibrary.org/obo/EC_2.3.1.32 - http://purl.obolibrary.org/obo/EC_2.3.1.33 - http://purl.obolibrary.org/obo/EC_2.3.1.34 @@ -19264,6 +19297,7 @@ node_stats: - http://purl.obolibrary.org/obo/EC_2.3.2.34 - http://purl.obolibrary.org/obo/EC_2.3.2.35 - http://purl.obolibrary.org/obo/EC_2.3.2.36 + - http://purl.obolibrary.org/obo/EC_2.3.2.37 - http://purl.obolibrary.org/obo/EC_2.3.2.5 - http://purl.obolibrary.org/obo/EC_2.3.2.6 - http://purl.obolibrary.org/obo/EC_2.3.2.7 @@ -19601,6 +19635,7 @@ node_stats: - http://purl.obolibrary.org/obo/EC_2.4.1.390 - http://purl.obolibrary.org/obo/EC_2.4.1.391 - http://purl.obolibrary.org/obo/EC_2.4.1.392 + - http://purl.obolibrary.org/obo/EC_2.4.1.393 - http://purl.obolibrary.org/obo/EC_2.4.1.4 - http://purl.obolibrary.org/obo/EC_2.4.1.40 - http://purl.obolibrary.org/obo/EC_2.4.1.41 @@ -20242,7 +20277,6 @@ node_stats: - http://purl.obolibrary.org/obo/EC_2.7.11.24 - http://purl.obolibrary.org/obo/EC_2.7.11.25 - http://purl.obolibrary.org/obo/EC_2.7.11.26 - - http://purl.obolibrary.org/obo/EC_2.7.11.27 - http://purl.obolibrary.org/obo/EC_2.7.11.28 - http://purl.obolibrary.org/obo/EC_2.7.11.29 - http://purl.obolibrary.org/obo/EC_2.7.11.3 @@ -23514,4 +23548,4 @@ node_stats: - unknown - upa.json - upa_nodes.tsv - total_nodes: 1308597 + total_nodes: 1362983