Update README.md

README.md

@@ -14,9 +14,18 @@ size_categories:
 - 1M<n<10M
 dataset_info:
   features:
+    - name: regulator_locus_tag
+      dtype: string
+      description: induced transcriptional regulator systematic ID. See hf/BrentLab/yeast_genome_resources
+    - name: regulator_symbol
+      dtype: string
+      description: induced transcriptional regulator common name. If no common name exists, then the `regulator_locus_tag` is used.
     - name: target_locus_tag
       dtype: string
-      description: The feature to which the effect/pvalue is assigned. See hf/BrentLab/yeast_genome_resources
+      description: The systematic ID of the feature to which the effect/pvalue is assigned. See hf/BrentLab/yeast_genome_resources
+    - name: target_symbol
+      dtype: string
+      description: The common name of the feature to which the effect/pvalue is assigned. If there is no common name, the `target_locus_tag` is used.
     - name: green_median
       dtype: float
       description: median of green (reference) channel fluorescence
@@ -41,493 +50,6 @@ dataset_info:
     - name: log2_shrunken_timecourses
       dtype: float
       description: selected timecourses with observation-level shrinkage based on local FDR (false discovery rate). Most users of the data will want to use this column.
-  partitioning:
-    keys:
-      - name: regulator_locus_tag
-        dtype: string
-        levels:
-          - YER045C
-          - YLR131C
-          - YDR448W
-          - YDR216W
-          - YGL071W
-          - YPL202C
-          - YMR042W
-          - YML099C
-          - YDR421W
-          - YPR199C
-          - YKL185W
-          - YOR113W
-          - YKR099W
-          - YDL070W
-          - YER177W
-          - YDR423C
-          - YPL048W
-          - YMR280C
-          - YJR060W
-          - YLR418C
-          - YLR098C
-          - YOR028C
-          - YDR223W
-          - YNL027W
-          - YNR010W
-          - YIL036W
-          - YPL181W
-          - YOL145C
-          - YGL166W
-          - YPL177C
-          - YKR034W
-          - YIR023W
-          - YNL314W
-          - YPL049C
-          - YDR480W
-          - YGL043W
-          - YLR228C
-          - YBR239C
-          - YNL023C
-          - YPR104C
-          - YIL131C
-          - YNL068C
-          - YER109C
-          - YGL254W
-          - YOL051W
-          - YPL248C
-          - YML051W
-          - YMR136W
-          - YLR013W
-          - YIR013C
-          - YEL009C
-          - YGR252W
-          - YPL075W
-          - YNL199C
-          - GEV
-          - YDR096W
-          - YER040W
-          - YDR098C
-          - YER174C
-          - YJL103C
-          - YGL181W
-          - YJL110C
-          - YPR008W
-          - YFL031W
-          - YLR256W
-          - YGL237C
-          - YBL021C
-          - YKL109W
-          - YOR358W
-          - YCR065W
-          - YPL254W
-          - YBL008W
-          - YOR038C
-          - YJR140C
-          - YCR097W
-          - YOR032C
-          - YMR172W
-          - YJR094C
-          - YOL108C
-          - YCL055W
-          - YGR040W
-          - YOR123C
-          - YLR451W
-          - YLR011W
-          - YDR034C
-          - YMR021C
-          - YDL056W
-          - YDL005C
-          - YIR017C
-          - YPL038W
-          - YDR253C
-          - YNL103W
-          - YGR249W
-          - YGL035C
-          - YGL209W
-          - YER028C
-          - YMR070W
-          - YMR037C
-          - YKL062W
-          - YMR164C
-          - YMR228W
-          - YHR124W
-          - YDR043C
-          - YNR009W
-          - YAL051W
-          - YKR064W
-          - YHL020C
-          - YBR279W
-          - YGL013C
-          - YBL005W
-          - YLR266C
-          - YGL025C
-          - YKL043W
-          - YDL106C
-          - YFR034C
-          - YOR363C
-          - YLR014C
-          - YOR380W
-          - YPL133C
-          - YLR176C
-          - YMR182C
-          - YLR071C
-          - YKL038W
-          - YHL027W
-          - YPL089C
-          - YGR044C
-          - YPR065W
-          - YBL093C
-          - YNL330C
-          - YER169W
-          - YDL020C
-          - YBL025W
-          - YJR127C
-          - YGL244W
-          - YOL067C
-          - YGL252C
-          - YBL103C
-          - YOR140W
-          - YLR403W
-          - YCL010C
-          - YOL004W
-          - YNL236W
-          - YNL257C
-          - YJL089W
-          - YDL042C
-          - YHR206W
-          - YNL167C
-          - YBR182C
-          - YOR290C
-          - YBR289W
-          - YMR016C
-          - YOL148C
-          - YDR392W
-          - YGR063C
-          - YLR055C
-          - YHR041C
-          - YGR104C
-          - YCR081W
-          - YDR443C
-          - YNL309W
-          - YHR178W
-          - YHR084W
-          - YDR463W
-          - YHR006W
-          - YMR039C
-          - YDR310C
-          - YGL162W
-          - YPR009W
-          - YPL016W
-          - YDR146C
-          - YLR182W
-          - YCR042C
-          - YOR337W
-          - YBR083W
-          - YDR079C-A
-          - YDL080C
-          - YER184C
-          - YOR344C
-          - YOR295W
-          - YDL170W
-          - YPL139C
-          - YDR207C
-          - YDR213W
-          - YNL229C
-          - YPL230W
-          - YIL056W
-          - YML076C
-          - YOR083W
-          - YOR230W
-          - YOR229W
-          - YIL101C
-          - YML007W
-          - YHL009C
-          - YIR018W
-          - YDR259C
-          - YDR451C
-          - YLL054C
-          - YML027W
-          - YOR172W
-          - YOR162C
-          - Z3EV
-          - YJL056C
-          - YFL052W
-      - name: time
-        dtype: string
-        levels:
-          - 0
-          - 2
-          - 5
-          - 7
-          - 8
-          - 10
-          - 12
-          - 15
-          - 18
-          - 20
-          - 30
-          - 45
-          - 60
-          - 90
-          - 100
-          - 120
-          - 180
-          - 290
-      - name: mechanism
-        dtype: string
-        levels:
-          - GEV
-          - ZEV
-      - name: restriction
-        dtype: string
-        levels:
-          - M
-          - N
-          - P
-      - name: date
-        dtype: string
-        levels:
-          - 20150101
-          - 20150616
-          - 20150903
-          - 20151006
-          - 20151026
-          - 20151210
-          - 20151216
-          - 20160209
-          - 20160229
-          - 20160303
-          - 20160321
-          - 20160421
-          - 20160504
-          - 20160524
-          - 20160606
-          - 20160628
-          - 20160801
-          - 20160823
-          - 20160921
-          - 20161006
-          - 20161101
-          - 20161103
-          - 20161117
-      - name: strain
-        dtype: string
-        levels:
-          - SMY10
-          - SMY104
-          - SMY108
-          - SMY108n
-          - SMY110
-          - SMY113
-          - SMY117
-          - SMY117n
-          - SMY124
-          - SMY125
-          - SMY128
-          - SMY141
-          - SMY143
-          - SMY146
-          - SMY153
-          - SMY155
-          - SMY156
-          - SMY156n
-          - SMY159
-          - SMY170
-          - SMY179
-          - SMY181
-          - SMY19
-          - SMY196
-          - SMY2035
-          - SMY2049
-          - SMY2052
-          - SMY2055
-          - SMY2056
-          - SMY2057
-          - SMY2058
-          - SMY2059
-          - SMY2060
-          - SMY2061
-          - SMY2062
-          - SMY2063
-          - SMY2066
-          - SMY2067
-          - SMY2069
-          - SMY2071
-          - SMY2073
-          - SMY2074
-          - SMY2075
-          - SMY2076
-          - SMY2077
-          - SMY2078
-          - SMY2081
-          - SMY2082
-          - SMY2083
-          - SMY2085
-          - SMY2086
-          - SMY2087
-          - SMY2088
-          - SMY2092
-          - SMY2094
-          - SMY2096
-          - SMY2099
-          - SMY2100
-          - SMY2101
-          - SMY2103
-          - SMY2104
-          - SMY2105
-          - SMY2106
-          - SMY2107
-          - SMY2108
-          - SMY2109
-          - SMY2110
-          - SMY2111
-          - SMY2112
-          - SMY2113
-          - SMY2114
-          - SMY2115
-          - SMY2116
-          - SMY2118
-          - SMY2119
-          - SMY2120
-          - SMY2121
-          - SMY2123
-          - SMY2124
-          - SMY2125
-          - SMY2126
-          - SMY2127
-          - SMY2129
-          - SMY2132
-          - SMY2141
-          - SMY2143
-          - SMY2145
-          - SMY2146
-          - SMY2147
-          - SMY2148
-          - SMY2149
-          - SMY2150
-          - SMY2151
-          - SMY2152
-          - SMY2153
-          - SMY2154
-          - SMY2155
-          - SMY2156
-          - SMY2157
-          - SMY2159
-          - SMY2160
-          - SMY2161
-          - SMY2162
-          - SMY2163
-          - SMY2164
-          - SMY2165
-          - SMY2166
-          - SMY2167
-          - SMY2168
-          - SMY2169
-          - SMY2170
-          - SMY2171
-          - SMY2173
-          - SMY2174
-          - SMY2175
-          - SMY2176
-          - SMY2177
-          - SMY2178
-          - SMY2179
-          - SMY2180
-          - SMY2181
-          - SMY2182
-          - SMY2183
-          - SMY2184
-          - SMY2185
-          - SMY2186
-          - SMY2187
-          - SMY2188
-          - SMY2189
-          - SMY2190
-          - SMY2191
-          - SMY2192
-          - SMY2193
-          - SMY2194
-          - SMY2195
-          - SMY2196
-          - SMY2197
-          - SMY22
-          - SMY2202
-          - SMY2203
-          - SMY2204
-          - SMY2205
-          - SMY2206
-          - SMY2207
-          - SMY2208
-          - SMY2209
-          - SMY2210
-          - SMY2211
-          - SMY2212
-          - SMY2213
-          - SMY2214
-          - SMY2215
-          - SMY2216
-          - SMY2217
-          - SMY2219
-          - SMY2220
-          - SMY2221
-          - SMY2222
-          - SMY2223
-          - SMY2224
-          - SMY2225
-          - SMY2226
-          - SMY2227
-          - SMY2228
-          - SMY2229
-          - SMY2230
-          - SMY2232
-          - SMY2233
-          - SMY2234
-          - SMY2235
-          - SMY2236
-          - SMY2237
-          - SMY2238
-          - SMY2239
-          - SMY2240
-          - SMY2241
-          - SMY2242
-          - SMY2243
-          - SMY2244
-          - SMY2245
-          - SMY2263
-          - SMY2264
-          - SMY2266a
-          - SMY2266b
-          - SMY2266c
-          - SMY2270
-          - SMY2273
-          - SMY254a
-          - SMY254c
-          - SMY257
-          - SMY26
-          - SMY27
-          - SMY39
-          - SMY40
-          - SMY41
-          - SMY42
-          - SMY44
-          - SMY54
-          - SMY55
-          - SMY57
-          - SMY58
-          - SMY59
-          - SMY62
-          - SMY64
-          - SMY69
-          - yRSM164
-          - yRSM170
-          - yRSM175
-          - yRSM204
-          - yRSM206
-          - yRSM209
-          - yRSM84
-          - yRSM86
-          - yRSM92
-          - YukoSMY2047
-configs:
-  - config_name: data
-    default: true
 ---
 # Hackett 2020
 
@@ -538,108 +60,29 @@ by Calico to this Dataset.
 
 [Hackett SR, Baltz EA, Coram M, Wranik BJ, Kim G, Baker A, Fan M, Hendrickson DG, Berndl M, McIsaac RS. Learning causal networks using inducible transcription factors and transcriptome-wide time series. Mol Syst Biol. 2020 Mar;16(3):e9174. doi: 10.15252/msb.20199174. PMID: 32181581; PMCID: PMC7076914.](https://doi.org/10.15252/msb.20199174)
 
-## Usage
-
-You may access just the Dataset metadata like this:
-
-```python
-from huggingface_hub import ModelCard
-
-card = ModelCard.load("BrentLab/hackett_2020", repo_type="dataset")
-
-# cast to dict
-card_dict = card.data.to_dict()
-
-# Get partition information
-card_dict.get("dataset_info").get("partitioning").get("keys")
-```
-
-Output:
-
-```raw
-[{'name': 'regulator_locus_tag',
-  'dtype': 'string',
-  'levels': ['YER045C',
-   'YLR131C',
-   'YDR448W',
-   'YDR216W',
-   'YGL071W',
-   'YPL202C',
-   ...]},
- {'name': 'time',
-  'dtype': 'string',
-  'levels': [0,
-   2,
-   5,
-   7,
-   ...]},
- {'name': 'mechanism', 'dtype': 'string', 'levels': ['GEV', 'ZEV']},
- {'name': 'restriction', 'dtype': 'string', 'levels': ['M', 'N', 'P']},
- {'name': 'date',
-  'dtype': 'string',
-  'levels': [20150101,
-   20150616,
-   20150903,
-   ...]},
- {'name': 'strain',
-  'dtype': 'string',
-  'levels': ['SMY10',
-   'SMY104',
-   'SMY108',
-   'SMY108n',
-   ...]}]
-```
-
-You can use this information to pull only the partition(s) you're interested in, eg
-
-```python
-from pathlib import Path
-from huggingface_hub import snapshot_download
-import pyarrow.dataset as ds
-
-# pull all data for regulator `YAL051W`
-root = snapshot_download(
-    repo_id="BrentLab/hackett_2020",
-    repo_type="dataset",
-    allow_patterns=[
-        "data/regulator_locus_tag=YAL051W/*/*/*/*/*/part-0.parquet"
-    ],
-)
-
-base = Path(root) / "data"  # the dataset root directory
-dataset = ds.dataset(base, format="parquet", partitioning="hive")
-print(dataset.schema)
-```
-
-<details>
-<summary><strong>Dataset Details</strong></summary>
+## Dataset Details
 
 The data was extract from the [Calico website](https://idea.research.calicolabs.com/data).
 
 I pulled the 'Raw & processed gene expression data' versions and did some minimal parsing to
 save the data as a partitioned parquet dataset (see `scripts/`)
 
-</details>
+### Dataset Structure
 
-<details>
-<summary><strong>Dataset Structure</strong></summary>
-
-### data/
-
-This is a **Parquet** dataset where the partitions are based on `regulator_locus_tag`, `time`, `mechanism`, `restriction`, `date`, `strain`.
-This means that each individual parquet file represents a single experiment. Each record provides data on the effect of the induction of
-a transcriptional regulator.
+The data is stored in a single parquet file which has the following fields. 
 
 | Field                       | Description                                                                                                                                                                                                 |
 |-----------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| `regulator_locus_tag`       | induced transcriptional regulator                                                                                                                                                         |
+| `regulator_locus_tag`       | induced transcriptional regulator systematic ID                                                                                                                |
+| `regulator_symbol`          | induced transcriptional regulator common name. If no common name exists, then the `regulator_locus_tag` is used.                                               |
+| `target_locus_tag`          | Systmatic ID of the feature to which the induced transcriptional regulator's affect is ascribed                                                                |
+| `target_symbol`             | Common name of feature to which the induced transcriptional regulator's affect is ascribed. If there is no common name, the systematic ID is used.             |                                                                                                                                                       |
 | `time`                      | time point (minutes)                                                                                                                                                          |
 | `mechanism`                 | induction system (GEV or ZEV)                                                                                                                                                           |
 | `restriction`               | nutrient limitation (M, N or P)                                                                                                                                                          |
 | `date`                      | date performed                                                                                                                                                           |
 | `strain`                    | strain name                                                                                                                                                           |
 | `green_median`              | Median of green (reference) channel fluorescence                                                                                                                                                           |
-| `green_median`              | Median of green (reference) channel fluorescence                                                                                                                                                           |
 | `red_median`                | Median of red (experimental) channel fluorescence                                                                                                                                                          |
 | `log2_ratio`                | log2(red / green) subtracting value at time zero                                                                                                                                                           |
 | `log2_cleaned_ratio`        | Non-specific stress response and prominent outliers removed                                                                                                                                                |
@@ -648,6 +91,4 @@ a transcriptional regulator.
 | `log2_selected_timecourses` | Cleaned timecourses hard-thresholded based on single observations passing noise model and impulse evaluation of biological feasibility                                                                     |
 | `log2_shrunken_timecourses` | Selected timecourses with observation-level shrinkage based on local FDR (false discovery rate). **Most users of the data will want to use this column.**                                                       |
 
-</details>
-
 **Dataset Author and Contact**: Chase Mateusiak [@cmatKhan](https://github.com/cmatkhan/)