From 57cd4e18a5b068895eebaa68f5eb5b1167d9af7b Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 17 Sep 2024 11:19:28 -0500 Subject: [PATCH] The keys were not aligned to the column names --- data/transformed/BactoTraits/edges.tsv | 95299 +++++++++------- data/transformed/BactoTraits/nodes.tsv | 13 + kg_microbe/transform_utils/custom_curies.yaml | 26 +- 3 files changed, 52092 insertions(+), 43246 deletions(-) diff --git a/data/transformed/BactoTraits/edges.tsv b/data/transformed/BactoTraits/edges.tsv index 050627c..a13c7ac 100644 --- a/data/transformed/BactoTraits/edges.tsv +++ b/data/transformed/BactoTraits/edges.tsv @@ -2,405 +2,459 @@ subject predicate object relation primary_knowledge_source NCBITaxon:100 biolink:has_phenotype gc:high RO:0002200 BactoTraits.csv NCBITaxon:100053 biolink:has_phenotype gc:low RO:0002200 BactoTraits.csv NCBITaxon:1000566 biolink:has_phenotype gc:high RO:0002200 BactoTraits.csv -NCBITaxon:1001240 biolink:has_phenotype gram_stain:positive RO:0002200 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-NCBITaxon:999611 biolink:has_phenotype temp_range:mid4 RO:0002200 BactoTraits.csv -NCBITaxon:999611 biolink:has_phenotype temp_delta:high RO:0002200 BactoTraits.csv -NCBITaxon:999611 biolink:has_phenotype gram_stain:negative RO:0002200 BactoTraits.csv -NCBITaxon:999611 biolink:capable_of sporulation:non_spore_forming RO:0002215 BactoTraits.csv -NCBITaxon:999611 biolink:has_phenotype gc:mid2 RO:0002200 BactoTraits.csv -NCBITaxon:999611 biolink:has_phenotype cell_width:high RO:0002200 BactoTraits.csv -NCBITaxon:999611 biolink:has_phenotype temp_range:mid3 RO:0002200 BactoTraits.csv -NCBITaxon:999611 biolink:has_phenotype cell_shape:ovoid RO:0002200 BactoTraits.csv -NCBITaxon:999611 biolink:has_phenotype pH_opt:mid2 RO:0002200 BactoTraits.csv -NCBITaxon:999611 biolink:has_phenotype pH_range:mid4 RO:0002200 BactoTraits.csv -NCBITaxon:999611 biolink:has_phenotype pH_range:mid3 RO:0002200 BactoTraits.csv -NCBITaxon:999611 biolink:has_phenotype pH_range:mid2 RO:0002200 BactoTraits.csv -NCBITaxon:999611 biolink:has_phenotype NaCl_opt:mid RO:0002200 BactoTraits.csv -NCBITaxon:999894 biolink:has_phenotype gc:mid1 RO:0002200 BactoTraits.csv +NCBITaxon:999894 biolink:has_phenotype cell_shape:ovoid RO:0002200 BactoTraits.csv NCBITaxon:999894 biolink:has_phenotype cell_length:very_low RO:0002200 BactoTraits.csv +NCBITaxon:999894 biolink:has_phenotype pH_range:mid1 RO:0002200 BactoTraits.csv +NCBITaxon:999894 biolink:has_phenotype pH_opt:mid1 RO:0002200 BactoTraits.csv +NCBITaxon:999894 biolink:has_phenotype gc:mid1 RO:0002200 BactoTraits.csv NCBITaxon:999894 biolink:capable_of sporulation:non_spore_forming RO:0002215 BactoTraits.csv NCBITaxon:999894 biolink:has_phenotype gram_stain:negative RO:0002200 BactoTraits.csv NCBITaxon:999894 biolink:has_phenotype temp_delta:high RO:0002200 BactoTraits.csv NCBITaxon:999894 biolink:has_phenotype temp_range:high RO:0002200 BactoTraits.csv +NCBITaxon:999894 biolink:has_phenotype cell_width:low RO:0002200 BactoTraits.csv NCBITaxon:999894 biolink:has_phenotype NaCl_delta:low RO:0002200 BactoTraits.csv NCBITaxon:999894 biolink:has_phenotype NaCl_range:mid RO:0002200 BactoTraits.csv NCBITaxon:999894 biolink:has_phenotype NaCl_range:low RO:0002200 BactoTraits.csv +NCBITaxon:999894 biolink:has_phenotype pH_delta:mid1 RO:0002200 BactoTraits.csv NCBITaxon:999894 biolink:has_phenotype pH_range:mid3 RO:0002200 BactoTraits.csv NCBITaxon:999894 biolink:has_phenotype pH_range:mid2 RO:0002200 BactoTraits.csv -NCBITaxon:999894 biolink:has_phenotype pH_range:mid1 RO:0002200 BactoTraits.csv -NCBITaxon:999894 biolink:has_phenotype pH_opt:mid1 RO:0002200 BactoTraits.csv NCBITaxon:999894 biolink:has_phenotype temp_opt:high RO:0002200 BactoTraits.csv -NCBITaxon:999894 biolink:has_phenotype cell_shape:ovoid RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype temp_range:mid3 RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype temp_range:mid4 RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype temp_delta:mid2 RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype gram_stain:positive RO:0002200 BactoTraits.csv NCBITaxon:999931 biolink:has_phenotype gc:high RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:capable_of sporulation:non_spore_forming RO:0002215 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype cell_width:high RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype cell_length:very_low RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype cell_shape:sphere RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype temp_range:mid2 RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:capable_of motility:non_motile RO:0002215 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype temp_range:mid1 RO:0002200 BactoTraits.csv NCBITaxon:999931 biolink:has_phenotype NaCl_range:low RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype NaCl_delta:high RO:0002200 BactoTraits.csv NCBITaxon:999931 biolink:has_phenotype pH_opt:mid2 RO:0002200 BactoTraits.csv -NCBITaxon:999931 biolink:has_phenotype pH_range:mid1 RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype temp_opt:mid3 RO:0002200 BactoTraits.csv NCBITaxon:999931 biolink:has_phenotype pH_range:mid2 RO:0002200 BactoTraits.csv NCBITaxon:999931 biolink:has_phenotype pH_range:mid3 RO:0002200 BactoTraits.csv NCBITaxon:999931 biolink:has_phenotype pH_range:mid4 RO:0002200 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype pH_range:mid1 RO:0002200 BactoTraits.csv NCBITaxon:999931 biolink:has_phenotype NaCl_opt:low RO:0002200 BactoTraits.csv NCBITaxon:999931 biolink:has_phenotype NaCl_range:very_low RO:0002200 BactoTraits.csv -NCBITaxon:999931 biolink:has_phenotype cell_shape:sphere RO:0002200 BactoTraits.csv NCBITaxon:999931 biolink:has_phenotype NaCl_range:mid RO:0002200 BactoTraits.csv -NCBITaxon:999931 biolink:has_phenotype NaCl_delta:high RO:0002200 BactoTraits.csv NCBITaxon:999931 biolink:has_phenotype NaCl_range:high RO:0002200 BactoTraits.csv -NCBITaxon:999931 biolink:has_phenotype temp_range:mid1 RO:0002200 BactoTraits.csv -NCBITaxon:999931 biolink:has_phenotype temp_range:mid2 RO:0002200 BactoTraits.csv -NCBITaxon:999931 biolink:has_phenotype temp_range:mid3 RO:0002200 BactoTraits.csv -NCBITaxon:999931 biolink:has_phenotype temp_range:mid4 RO:0002200 BactoTraits.csv -NCBITaxon:999931 biolink:has_phenotype gram_stain:positive RO:0002200 BactoTraits.csv -NCBITaxon:999931 biolink:capable_of motility:non_motile RO:0002215 BactoTraits.csv -NCBITaxon:999931 biolink:capable_of sporulation:non_spore_forming RO:0002215 BactoTraits.csv -NCBITaxon:999931 biolink:has_phenotype cell_width:high RO:0002200 BactoTraits.csv -NCBITaxon:999931 biolink:has_phenotype cell_length:very_low RO:0002200 BactoTraits.csv -NCBITaxon:999931 biolink:has_phenotype temp_opt:mid3 RO:0002200 BactoTraits.csv -cell_shape:curved_spiral biolink:capable_of cell_shape:spiral PATO:0001668 BactoTraits.csv +NCBITaxon:999931 biolink:has_phenotype pH_delta:mid2 RO:0002200 BactoTraits.csv cell_shape:curved_spiral biolink:capable_of cell_shape:curved PATO:0001668 BactoTraits.csv -cell_shape:star_dumbbell_pleomorphic biolink:capable_of cell_shape:star PATO:0001668 BactoTraits.csv +cell_shape:curved_spiral biolink:capable_of cell_shape:spiral PATO:0001668 BactoTraits.csv cell_shape:star_dumbbell_pleomorphic biolink:capable_of cell_shape:dumbbell PATO:0001668 BactoTraits.csv +cell_shape:star_dumbbell_pleomorphic biolink:capable_of cell_shape:star PATO:0001668 BactoTraits.csv cell_shape:star_dumbbell_pleomorphic biolink:capable_of cell_shape:pleomorphic PATO:0001668 BactoTraits.csv trophic_type:copiotroph_diazotrophy biolink:capable_of trophic_type:copiotrophy PATO:0001668 BactoTraits.csv trophic_type:copiotroph_diazotrophy biolink:capable_of trophic_type:diazotrophy PATO:0001668 BactoTraits.csv diff --git a/data/transformed/BactoTraits/nodes.tsv b/data/transformed/BactoTraits/nodes.tsv index d72a72d..9d2cbf1 100644 --- a/data/transformed/BactoTraits/nodes.tsv +++ b/data/transformed/BactoTraits/nodes.tsv @@ -8,6 +8,7 @@ NCBITaxon:438 biolink:OrganismTaxon Acetobacter pasteurianus NCBITaxon:940265 biolink:OrganismTaxon Acetobacter pasteurianus subsp. pasteurianus LMG 1262 = NBRC 106471 temp_range:mid1 biolink:PhenotypicQuality temperature range 22 deg C to 27 deg C temp_range:mid2 biolink:PhenotypicQuality temperature range 27 deg C to 30 deg C +temp_delta:low biolink:PhenotypicQuality temperature delta 1 deg C to 5 deg C NCBITaxon:1231342 biolink:OrganismTaxon Acetobacter orleanensis JCM 7639 motility:non_motile biolink:PhenotypicQuality non-motile cell_width:high biolink:PhenotypicQuality cell width > 0.9um @@ -15,18 +16,22 @@ cell_length:very_low biolink:PhenotypicQuality cell length <= 1.3um NCBITaxon:1307917 biolink:OrganismTaxon Acetobacter pomorum DSM 11825 gram_stain:negative biolink:PhenotypicQuality gram negative sporulation:non_spore_forming biolink:PhenotypicQuality non spore forming +cell_length:mid biolink:PhenotypicQuality cell length 2um to 3um cell_shape:rod biolink:PhenotypicQuality rod shaped cell NCBITaxon:1307903 biolink:OrganismTaxon Acetobacter cerevisiae DSM 14362 NCBITaxon:1307910 biolink:OrganismTaxon Acetobacter malorum DSM 14337 temp_opt:mid2 biolink:PhenotypicQuality optimal temperature 27 deg C to 30 deg C motility:motile biolink:PhenotypicQuality motile +cell_width:mid biolink:PhenotypicQuality cell width 0.65um to 0.9um cell_length:high biolink:PhenotypicQuality cell length > 3um NCBITaxon:1307912 biolink:OrganismTaxon Acetobacter oeni LMG 21952 cell_width:very_low biolink:PhenotypicQuality cell width <= 0.5um +cell_length:low biolink:PhenotypicQuality cell length 1.3um to 2um NCBITaxon:1120919 biolink:OrganismTaxon Acetobacter nitrogenifigens DSM 23921 = NBRC 105050 temp_opt:mid4 biolink:PhenotypicQuality optimal temperature 34 deg C to 40 deg C temp_range:mid3 biolink:PhenotypicQuality temperature range 30 deg C to 34 deg C temp_range:mid4 biolink:PhenotypicQuality temperature range 34 deg C to 40 deg C +temp_delta:mid2 biolink:PhenotypicQuality temperature delta 10 deg C to 20 deg C cell_shape:sphere biolink:PhenotypicQuality sphere shaped cell NCBITaxon:1307918 biolink:OrganismTaxon Acetobacter senegalensis DSM 18889 NCBITaxon:1307907 biolink:OrganismTaxon Acetobacter ghanensis DSM 18895 @@ -34,6 +39,7 @@ NCBITaxon:1307906 biolink:OrganismTaxon Acetobacter fabarum DSM 19596 NCBITaxon:104098 biolink:OrganismTaxon Acetobacter peroxydans pH_range:low biolink:PhenotypicQuality pH range 0 to 4 pH_range:mid1 biolink:PhenotypicQuality pH range 4 to 6 +pH_delta:mid2 biolink:PhenotypicQuality pH delta 3 to 4 gc:high biolink:PhenotypicQuality GC content > 66.3% NCBITaxon:524 biolink:OrganismTaxon Acidiphilium cryptum NCBITaxon:1307921 biolink:OrganismTaxon Acidiphilium acidophilum DSM 700 @@ -46,18 +52,22 @@ NCBITaxon:1236502 biolink:OrganismTaxon Asaia prunellae JCM 25354 pH_opt:mid1 biolink:PhenotypicQuality optimal pH 6 to 7 pH_range:mid2 biolink:PhenotypicQuality pH range 6 to 7 pH_range:mid3 biolink:PhenotypicQuality pH range 7 to 8 +pH_delta:low biolink:PhenotypicQuality pH delta 1 to 2 temp_opt:mid1 biolink:PhenotypicQuality optimal temperature 22 deg C to 27 deg C temp_range:low biolink:PhenotypicQuality temperature range 10 deg C to 22 deg C NCBITaxon:1121106 biolink:OrganismTaxon Belnapia moabensis DSM 16746 pH_opt:mid2 biolink:PhenotypicQuality optimal pH 7 to 8 +pH_delta:mid1 biolink:PhenotypicQuality pH delta 2 to 3 NaCl_range:very_low biolink:PhenotypicQuality NaCl range <= 1% NaCl_delta:very_low biolink:PhenotypicQuality NaCl delta <= 1% NCBITaxon:938405 biolink:OrganismTaxon Belnapia rosea NCBITaxon:272568 biolink:OrganismTaxon Gluconacetobacter diazotrophicus PA1 5 NCBITaxon:89584 biolink:OrganismTaxon Gluconacetobacter liquefaciens NCBITaxon:1307940 biolink:OrganismTaxon Gluconacetobacter sacchari DSM 12717 +cell_width:low biolink:PhenotypicQuality cell width 0.5um to 0.65um NCBITaxon:1307932 biolink:OrganismTaxon Gluconacetobacter azotocaptans DSM 13594 NCBITaxon:1307935 biolink:OrganismTaxon Gluconacetobacter johannae DSM 13595 +pH_delta:mid3 biolink:PhenotypicQuality pH delta 4 to 5 NCBITaxon:1234672 biolink:OrganismTaxon Komagataeibacter kakiaceti JCM 25156 NCBITaxon:442 biolink:OrganismTaxon Gluconobacter oxydans NCBITaxon:38308 biolink:OrganismTaxon Gluconobacter frateurii @@ -83,6 +93,7 @@ pH_range:mid4 biolink:PhenotypicQuality pH range 8 to 10 NaCl_range:low biolink:PhenotypicQuality NaCl range 1% to 3% NaCl_range:mid biolink:PhenotypicQuality NaCl range 3% to 8% NaCl_delta:mid biolink:PhenotypicQuality NaCl delta 3% to 8% +temp_delta:mid3 biolink:PhenotypicQuality temperature delta 20 deg C to 30 deg C NCBITaxon:1123061 biolink:OrganismTaxon Neoroseomonas lacus DSM 19439 NCBITaxon:373043 biolink:OrganismTaxon Paeniroseomonas aquatica NaCl_delta:low biolink:PhenotypicQuality NaCl delta 1% to 3% @@ -129,6 +140,7 @@ NCBITaxon:33059 biolink:OrganismTaxon Acidithiobacillus caldus NCBITaxon:119978 biolink:OrganismTaxon Acidithiobacillus albertensis NCBITaxon:240015 biolink:OrganismTaxon Acidobacterium capsulatum ATCC 51196 NCBITaxon:388466 biolink:OrganismTaxon Edaphobacter modestus +temp_delta:mid1 biolink:PhenotypicQuality temperature delta 5 deg C to 10 deg C NCBITaxon:1121860 biolink:OrganismTaxon Edaphobacter aggregans DSM 19364 NCBITaxon:926566 biolink:OrganismTaxon Terriglobus roseus DSM 18391 NCBITaxon:870903 biolink:OrganismTaxon Terriglobus saanensis @@ -296,6 +308,7 @@ NCBITaxon:285091 biolink:OrganismTaxon Alloalcanivorax dieselolei NCBITaxon:413232 biolink:OrganismTaxon Alloalcanivorax balearicus NCBITaxon:523791 biolink:OrganismTaxon Kangiella koreensis DSM 16069 NCBITaxon:1122134 biolink:OrganismTaxon Kangiella aquimarina DSM 16071 +pH_delta:high biolink:PhenotypicQuality pH delta 5 to 9 NCBITaxon:796379 biolink:OrganismTaxon Kangiella spongicola NCBITaxon:1450 biolink:OrganismTaxon Alicyclobacillus acidoterrestris NCBITaxon:1356854 biolink:OrganismTaxon Alicyclobacillus acidoterrestris ATCC 49025 diff --git a/kg_microbe/transform_utils/custom_curies.yaml b/kg_microbe/transform_utils/custom_curies.yaml index 42805aa..007c9dd 100644 --- a/kg_microbe/transform_utils/custom_curies.yaml +++ b/kg_microbe/transform_utils/custom_curies.yaml @@ -580,23 +580,23 @@ pH_delta: curie: "pH_delta:very_low" name: "pH delta <= 1" <<: *phenotypic_quality_block - phd_1_to_2: + phd_1_2: curie: "pH_delta:low" name: "pH delta 1 to 2" <<: *phenotypic_quality_block - phd_2_to_3: + phd_2_3: curie: "pH_delta:mid1" name: "pH delta 2 to 3" <<: *phenotypic_quality_block - phd_3_to_4: + phd_3_4: curie: "pH_delta:mid2" name: "pH delta 3 to 4" <<: *phenotypic_quality_block - phd_4_to_5: + phd_4_5: curie: "pH_delta:mid3" name: "pH delta 4 to 5" <<: *phenotypic_quality_block - phd_5_to_9: + phd_5_9: curie: "pH_delta:high" name: "pH delta 5 to 9" <<: *phenotypic_quality_block @@ -720,19 +720,19 @@ temperature_delta: curie: "temp_delta:very_low" name: "temperature delta <= 1 deg C" <<: *phenotypic_quality_block - td_1_to_5: + td_1_5: curie: "temp_delta:low" name: "temperature delta 1 deg C to 5 deg C" <<: *phenotypic_quality_block - td_5_to_10: + td_5_10: curie: "temp_delta:mid1" name: "temperature delta 5 deg C to 10 deg C" <<: *phenotypic_quality_block - td_10_to_20: + td_10_20: curie: "temp_delta:mid2" name: "temperature delta 10 deg C to 20 deg C" <<: *phenotypic_quality_block - td_20_to_30: + td_20_30: curie: "temp_delta:mid3" name: "temperature delta 20 deg C to 30 deg C" <<: *phenotypic_quality_block @@ -746,11 +746,11 @@ cell_width: curie: "cell_width:very_low" name: "cell width <= 0.5um" <<: *phenotypic_quality_block - w_0.5_to_0.65: + w_0.5_0.65: curie: "cell_width:low" name: "cell width 0.5um to 0.65um" <<: *phenotypic_quality_block - w_0.65_to_0.9: + w_0.65_0.9: curie: "cell_width:mid" name: "cell width 0.65um to 0.9um" <<: *phenotypic_quality_block @@ -764,11 +764,11 @@ cell_length: curie: "cell_length:very_low" name: "cell length <= 1.3um" <<: *phenotypic_quality_block - l_1.3_to_2: + l_1.3_2: curie: "cell_length:low" name: "cell length 1.3um to 2um" <<: *phenotypic_quality_block - l_2_to_3: + l_2_3: curie: "cell_length:mid" name: "cell length 2um to 3um" <<: *phenotypic_quality_block