Initial data upload (#1)

- Add metadata (746dd684a46448d33244b2df335ec75a94c44733)
- Add full data (3bc230efdb4297b3fad259c379e8cb3355a29f48)
- Add species splits (fe882423ff86a72221d6e0bc9b282945ba130143)
- Update configs and README (6696f8aae2e197d239dc57ba8975bb722b59b089)

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README.md

@@ -10,6 +10,91 @@ tags:
 pretty_name: SPARK dataset of human-curated and standardized MICs
 size_categories:
 - 10K<n<100K
+configs:
+  - config_name: full
+    data_files:
+      - split: train
+        path: spark-accumulation-wt.csv.gz
+  - config_name: Acinetobacter-baumannii
+    data_files:
+      - split: train
+        path: Acinetobacter-baumannii/scaffold-split-train.csv.gz
+      - split: validation
+        path: Acinetobacter-baumannii/scaffold-split-validation.csv.gz
+      - split: test
+        path: Acinetobacter-baumannii/scaffold-split-test.csv.gz
+  - config_name: Brucella-abortus
+    data_files:
+      - split: train
+        path: Brucella-abortus/scaffold-split-train.csv.gz
+      - split: validation
+        path: Brucella-abortus/scaffold-split-validation.csv.gz
+      - split: test
+        path: Brucella-abortus/scaffold-split-test.csv.gz
+  - config_name: Escherichia-coli
+    data_files:
+      - split: train
+        path: Escherichia-coli/scaffold-split-train.csv.gz
+      - split: validation
+        path: Escherichia-coli/scaffold-split-validation.csv.gz
+      - split: test
+        path: Escherichia-coli/scaffold-split-test.csv.gz
+  - config_name: Francisella-tularensis
+    data_files:
+      - split: train
+        path: Francisella-tularensis/scaffold-split-train.csv.gz
+      - split: validation
+        path: Francisella-tularensis/scaffold-split-validation.csv.gz
+      - split: test
+        path: Francisella-tularensis/scaffold-split-test.csv.gz
+  - config_name: Klebsiella-pneumoniae
+    data_files:
+      - split: train
+        path: Klebsiella-pneumoniae/scaffold-split-train.csv.gz
+      - split: validation
+        path: Klebsiella-pneumoniae/scaffold-split-validation.csv.gz
+      - split: test
+        path: Klebsiella-pneumoniae/scaffold-split-test.csv.gz
+  - config_name: Pseudomonas-aeruginosa
+    data_files:
+      - split: train
+        path: Pseudomonas-aeruginosa/scaffold-split-train.csv.gz
+      - split: validation
+        path: Pseudomonas-aeruginosa/scaffold-split-validation.csv.gz
+      - split: test
+        path: Pseudomonas-aeruginosa/scaffold-split-test.csv.gz
+  - config_name: Staphylococcus-aureus
+    data_files:
+      - split: train
+        path: Staphylococcus-aureus/scaffold-split-train.csv.gz
+      - split: validation
+        path: Staphylococcus-aureus/scaffold-split-validation.csv.gz
+      - split: test
+        path: Staphylococcus-aureus/scaffold-split-test.csv.gz
+  - config_name: Streptococcus-pneumoniae
+    data_files:
+      - split: train
+        path: Streptococcus-pneumoniae/scaffold-split-train.csv.gz
+      - split: validation
+        path: Streptococcus-pneumoniae/scaffold-split-validation.csv.gz
+      - split: test
+        path: Streptococcus-pneumoniae/scaffold-split-test.csv.gz
+  - config_name: Yersinia-enterocolitica
+    data_files:
+      - split: train
+        path: Yersinia-enterocolitica/scaffold-split-train.csv.gz
+      - split: validation
+        path: Yersinia-enterocolitica/scaffold-split-validation.csv.gz
+      - split: test
+        path: Yersinia-enterocolitica/scaffold-split-test.csv.gz
+  - config_name: Yersinia-pestis
+    data_files:
+      - split: train
+        path: Yersinia-pestis/scaffold-split-train.csv.gz
+      - split: validation
+        path: Yersinia-pestis/scaffold-split-validation.csv.gz
+      - split: test
+        path: Yersinia-pestis/scaffold-split-test.csv.gz
 ---
 
 # SPARK (wild-type accumulator phenotype): Human-curated and standardized MICs
@@ -25,12 +110,33 @@ These data were collated by the authors of:
 We cleaned the original SPARK dataset to subset the most relevant columns, remove empty values, 
 give succint column titles, and split by species.
 
+This particular dataset retains only measurements on bacteria with wild-type accumulation phenotypes.
+
 The SMILES strings have been canonicalized, and split into training (70%), validation (15%), and test (15%) sets 
 by Murcko scaffold for each species with more than 1000 entries. Additional features like molecular weight and 
 topological polar surface area have also been calculated.
 
 ## Dataset Details
 
+### Configurations
+
+The config `full` gives the entire cleaned wild-type accumulator dataset. Species specific configurations can be accessed:
+
+```
+configuration            n_rows
+--------------------------------
+Acinetobacter-baumannii    2148
+Brucella-abortus           9946
+Escherichia-coli          20451
+Francisella-tularensis     9671
+Klebsiella-pneumoniae      3920
+Pseudomonas-aeruginosa    15677
+Staphylococcus-aureus      2115
+Streptococcus-pneumoniae   1254
+Yersinia-enterocolitica    1405
+Yersinia-pestis           10002
+```
+
 ### Dataset Description
 
 - Curated by: @eachanjohnson

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species-with-dataset.tsv

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+species_name	n_rows

species-with-dataset.txt

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+Acinetobacter baumannii
+Brucella abortus
+Escherichia coli
+Francisella tularensis
+Klebsiella pneumoniae
+Pseudomonas aeruginosa
+Staphylococcus aureus
+Streptococcus pneumoniae
+Yersinia enterocolitica
+Yersinia pestis
+Acinetobacter baumannii	2148
+Brucella abortus	9946
+Escherichia coli	20451
+Francisella tularensis	9671
+Klebsiella pneumoniae	3920
+Pseudomonas aeruginosa	15677
+Staphylococcus aureus	2115
+Streptococcus pneumoniae	1254
+Yersinia enterocolitica	1405
+Yersinia pestis	10002
+Acinetobacter baumannii	2148
+Brucella abortus	9946
+Escherichia coli	20451
+Francisella tularensis	9671
+Klebsiella pneumoniae	3920
+Pseudomonas aeruginosa	15677
+Staphylococcus aureus	2115
+Streptococcus pneumoniae	1254
+Yersinia enterocolitica	1405
+Yersinia pestis	10002
+Acinetobacter baumannii	2148
+Brucella abortus	9946
+Escherichia coli	20451
+Francisella tularensis	9671
+Klebsiella pneumoniae	3920
+Pseudomonas aeruginosa	15677
+Staphylococcus aureus	2115
+Streptococcus pneumoniae	1254
+Yersinia enterocolitica	1405
+Yersinia pestis	10002
+Acinetobacter baumannii	2148
+Acinetobacter baumannii	2148
+Brucella abortus	9946
+Escherichia coli	20451
+Francisella tularensis	9671
+Klebsiella pneumoniae	3920
+Pseudomonas aeruginosa	15677
+Staphylococcus aureus	2115
+Streptococcus pneumoniae	1254
+Yersinia enterocolitica	1405
+Yersinia pestis	10002

species.txt

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+Acinetobacter baumannii
+Bacillus subtilis
+Brucella abortus
+Burkholderia thailandensis
+Caulobacter crescentus
+Enterobacter cloacae
+Enterococcus faecalis
+Escherichia coli
+Francisella novicida
+Francisella tularensis
+Haemophilus influenzae
+Klebsiella pneumoniae
+Moraxella catarrhalis
+Mycobacterium vaccae
+Proteus hauseri
+Proteus mirabilis
+Pseudomonas aeruginosa
+Pseudomonas fluorescens
+Pseudomonas syringae
+Salmonella enterica serovar Typhimurium
+Staphylococcus aureus
+Stenotrophomonas maltophilia
+Streptococcus pneumoniae
+Vibrio cholerae
+Yersinia enterocolitica
+Yersinia pestis
+Yersinia pseudotuberculosis

unique-species.txt

@@ -0,0 +1,27 @@
+Acinetobacter baumannii
+Bacillus subtilis
+Brucella abortus
+Burkholderia thailandensis
+Caulobacter crescentus
+Enterobacter cloacae
+Enterococcus faecalis
+Escherichia coli
+Francisella novicida
+Francisella tularensis
+Haemophilus influenzae
+Klebsiella pneumoniae
+Moraxella catarrhalis
+Mycobacterium vaccae
+Proteus hauseri
+Proteus mirabilis
+Pseudomonas aeruginosa
+Pseudomonas fluorescens
+Pseudomonas syringae
+Salmonella enterica serovar Typhimurium
+Staphylococcus aureus
+Stenotrophomonas maltophilia
+Streptococcus pneumoniae
+Vibrio cholerae
+Yersinia enterocolitica
+Yersinia pestis
+Yersinia pseudotuberculosis