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Datasets:
anz2
/
NASA_OSDR

License:
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1
anz2 commited on
Commit
c3f9048
•
1 Parent(s): 7ca8ff6

add full assays data.

Browse files
Files changed (3) hide show
  1. NASA_OSDR.py +420 -19
  2. tests/test_dataset_files.py +1 -2
  3. tests/test_nasa_osdr.py +2 -1
NASA_OSDR.py CHANGED
@@ -57,14 +57,417 @@ class NasaOsdr(datasets.GeneratorBasedBuilder):
57
  DEFAULT_CONFIG_NAME = "NASA_OSDR"
58
 
59
  def _info(self):
60
- ASSAY_COLUMNS = ['Sample Name', 'Protocol REF', 'Parameter Value: DNA Fragmentation',
61
- 'Parameter Value: DNA Fragment Size', 'Extract Name', 'Protocol REF.1',
62
- 'Parameter Value: Library Strategy',
63
- 'Parameter Value: Library Selection', 'Parameter Value: Library Layout',
64
- 'Protocol REF.2', 'Parameter Value: Sequencing Instrument',
65
- 'Assay Name', 'Parameter Value: Read Length', 'Raw Data File',
66
- 'Protocol REF.3', 'Parameter Value: Read Depth',
67
- 'Parameter Value: MultiQC File Names']
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
68
 
69
  # SAMPLE_COLUMNS = ['Source Name', 'Sample Name', 'Characteristics: Organism',
70
  # 'Characteristics: Strain', 'Characteristics: Genotype',
@@ -98,15 +501,15 @@ class NasaOsdr(datasets.GeneratorBasedBuilder):
98
  )
99
 
100
  _URL = "https://raw.githubusercontent.com/AnzorGozalishvili/NASA_ODSR_DATA/main"
101
- _ASSAYS_FILE = "assays.csv"
102
- _SAMPLES_FILE = "samples.csv"
103
 
104
  def _split_generators(self, dl_manager):
105
  downloaded_files = dl_manager.download_and_extract(
106
  {
107
  "train": {
108
  "assays": os.path.join(self._URL, self._ASSAYS_FILE),
109
- "samples": os.path.join(self._URL, self._ASSAYS_FILE)
110
  },
111
  }
112
  )
@@ -116,20 +519,18 @@ class NasaOsdr(datasets.GeneratorBasedBuilder):
116
  name=datasets.Split.TRAIN,
117
  gen_kwargs={
118
  "assays_file": downloaded_files['train']['assays'],
119
- "samples_file": downloaded_files['train']['samples'],
120
  },
121
  ),
122
  ]
123
 
124
- def _generate_examples(self, assays_file: str, samples_file):
125
- # assays = os.path.join(dataset_root, "assays.csv")
126
- # samples = os.path.join(dataset_root, "samples.csv")
127
- # there can be other metadata tables merged
128
-
129
  assays_df = pd.read_csv(assays_file)
130
- samples_df = pd.read_csv(samples_file)
131
 
132
- for (idx, assay_row), (_, sample_row) in zip(assays_df.iterrows(), samples_df.iterrows()):
 
133
  _item = {**assay_row.to_dict()}
134
  # _item = {**assay_row.to_dict(), **sample_row.to_dict()}
135
 
 
57
  DEFAULT_CONFIG_NAME = "NASA_OSDR"
58
 
59
  def _info(self):
60
+ ASSAY_COLUMNS = ["source name", "sample name", "characteristics[organism]", "term source ref",
61
+ "term accession number", "characteristics[strain]", "term source ref.1",
62
+ "term accession number.1", "characteristics[sex]", "term source ref.2",
63
+ "term accession number.2", "characteristics[developmental stage]", "term source ref.3",
64
+ "term accession number.3", "characteristics[material type]", "term source ref.4",
65
+ "term accession number.4", "factor value[spaceflight]", "term source ref.5",
66
+ "term accession number.5", "factor value[infection]", "term source ref.6",
67
+ "term accession number.6", "characteristics[experiment start date (dd/mm/yyyy)]",
68
+ "characteristics[experiment end date (dd/mm/yyyy)]", "protocol ref", "protocol ref.1",
69
+ "parameter value[vehicle]", "term source ref.7", "term accession number.7",
70
+ "parameter value[absorbed radiation dose]", "unit", "term source ref.8",
71
+ "term accession number.8", "parameter value[absorbed radiation dose rate]", "unit.1",
72
+ "term source ref.9", "term accession number.9", "parameter value[exposure duration]", "unit.2",
73
+ "term source ref.10", "term accession number.10",
74
+ "parameter value[ionizing radiation categorized by source]", "term source ref.11",
75
+ "term accession number.11", "parameter value[ionizing radiation]", "term source ref.12",
76
+ "term accession number.12", "comment [sample_description]", "comment [sample_source_name]",
77
+ "comment [sample_title]", "osdr_experiment_id", "characteristics[animal source]",
78
+ "characteristics[age at launch]", "characteristics[diet]", "comment[feeding schedule]",
79
+ "parameter value[light cycle]", "parameter value[habitat]", "parameter value[duration]",
80
+ "parameter value[euthanasia method]", "parameter value[carcass preservation method]",
81
+ "parameter value[sample preservation method]", "parameter value[sample storage temperature]",
82
+ "term source ref.13", "term accession number.13", "comment[source description]",
83
+ "comment[original submitted sample name]", "comment[alsda biospecimen id]",
84
+ "comment[alsda biospecimen subject id]", "comment[sample name description]",
85
+ "comment[animal source]", "parameter value[euthanasia chemical]",
86
+ "comment[lsda biospecimen id]", "comment[lsda biospecimen subject id]", "protocol ref.2",
87
+ "unit.3", "term source ref.14", "term accession number.14", "unit.4", "term source ref.15",
88
+ "term accession number.15", "unit.5", "term source ref.16", "term accession number.16",
89
+ "term source ref.17", "term accession number.17", "term source ref.18",
90
+ "term accession number.18", "parameter value[carcass storage method]",
91
+ "characteristics[strain,http://www.ebi.ac.uk/efo/efo_0005135,efo]",
92
+ "parameter value[light cycle,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c90419,ncit]",
93
+ "parameter value[habitat,http://purl.obolibrary.org/obo/envo_01000739,envo]", "material type",
94
+ "characteristics[sex,http://purl.obolibrary.org/obo/pato_0000047,efo]",
95
+ "parameter value[source storage method]",
96
+ "characteristics[growth,http://purl.obolibrary.org/obo/go_0040007,go]",
97
+ "factor value[weightlessness simulation]", "characteristics [age]",
98
+ "characteristics [genotype]", "characteristics [organism part]", "characteristics [protocol]",
99
+ "characteristics [strain]", "factor value[genotype]", "factor value[treatment]",
100
+ "comment[initiation date]", "comment[completion date]",
101
+ "parameter value[storage temperature setting]", "comment[maximum total absorbed dose ]",
102
+ "comment[minimum total absorbed dose ]", "factor value[absorbed radiation dose]",
103
+ "characteristics[exposure duration,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c83280,ncit]",
104
+ "characteristics[age]", "factor value[ionizing radiation]",
105
+ "parameter value[dose,http://purl.obolibrary.org/obo/exo_0000076,exo]", "factor value[time]",
106
+ "comment[sample_source_name]", "characteristics[genotype]", "characteristics[subspecies]",
107
+ "characteristics[flight name]", "characteristics[duration]", "parameter value[hardware]",
108
+ "parameter value[growth environment]", "parameter value[growth medium]",
109
+ "comment[sample characteristic]",
110
+ "factor value[weightlessness simulation,http://purl.bioontology.org/ontology/mesh/d018474,mesh]",
111
+ "factor value[tissue]", "comment[enclosure]",
112
+ "characteristics[diet,http://www.ebi.ac.uk/efo/efo_0002755,efo]",
113
+ "parameter value[exposure duration,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c83280,ncit]",
114
+ "parameter value[low let average abs. dose (spds only)]",
115
+ "parameter value[high let average abs. dose (all detectors)]",
116
+ "parameter value[abs. dose (gcr) rd3-b3]", "unit.6", "parameter value[abs. dose (orb) rd3-b3]",
117
+ "unit.7", "parameter value[abs. dose (total) rd3-b3]", "unit.8",
118
+ "parameter value[low let average abs. dose (all detectors)]", "unit.9",
119
+ "parameter value[low let max. abs. dose (all detectors)]", "unit.10",
120
+ "parameter value[high let min. abs. dose (all detectors)]", "unit.11",
121
+ "parameter value[high let max. abs. dose (all detectors)]", "unit.12",
122
+ "parameter value[low let min. abs. dose (all detectors)]", "unit.13", "term source ref.19",
123
+ "term accession number.19", "parameter value[abs. dose (irb/saa) rd3-b3]", "unit.14",
124
+ "term source ref.20", "term accession number.20",
125
+ "parameter value[average absorbed dose (spds only)]", "unit.15", "term source ref.21",
126
+ "term accession number.21", "parameter value[high let average abs. dose (spds only)]",
127
+ "unit.16", "term source ref.22", "term accession number.22", "characteristics[stage]",
128
+ "parameter value[sampling time,http://www.ebi.ac.uk/efo/efo_0000689,efo]",
129
+ "parameter value[temperature,http://www.ebi.ac.uk/efo/efo_0001702,efo]",
130
+ "factor value[microgravity]", "parameter value[housing temperature]", "comment[sample title]",
131
+ "comment[sanple description]", "factor value[bleomycin treatment]",
132
+ "characteristics[treatment duration]", "comment[sample source name]",
133
+ "factor value[irradiation]", "factor value[timepoint]",
134
+ "characteristics[cell line,http://purl.bioontology.org/ontology/mesh/d002460,mesh]",
135
+ "characteristics[cell type,http://purl.obolibrary.org/obo/cl_0000000,clo]",
136
+ "comment[source name description]", "characteristics[secondary organism]",
137
+ "characteristics[symbiosis,http://purl.bioontology.org/ontology/mesh/d013559,mesh]",
138
+ "factor value[simulated microgravity]", "characteristics [strainorline]",
139
+ "characteristics [biosourceprovider]", "characteristics [generation]",
140
+ "factor value[generation]", "factor value[environmentalstress]", "factor value[ecotype]",
141
+ "characteristics[organism part]", "characteristics[seed source]",
142
+ "characteristics[stratification exposure]", "parameter value[light source]",
143
+ "parameter value[growth time]",
144
+ "characteristics[ecotype,http://www.ebi.ac.uk/efo/efo_0000434,efo]",
145
+ "parameter value[maximum total absorbed dose]", "parameter value[minimum total absorbed dose]",
146
+ "factor value[hypergravity]", "characteristics [cell type]", "characteristics [passage]",
147
+ "factor value[electromagnetic fields]", "parameter value[growth termperature]",
148
+ "characteristics[cell source]", "factor value[cell line]",
149
+ "parameter value[sample media information]", "parameter value[growth temperature]",
150
+ "factor value[microgravity simulation]", "comment[sample description]",
151
+ "comment[iss expedition]", "factor value[sample location]", "comment [ena_sample]",
152
+ "characteristics [developmental stage]", "factor value[ionzing radiation]",
153
+ "characteristics[cell type]",
154
+ "characteristics[cell type,http://www.ebi.ac.uk/efo/efo_0000324,efo]",
155
+ "factor value[time of sample collection after treatment]", "comment[nih geo sample name]",
156
+ "factor value[age]", "characteristics[collection date]", "characteristics[isolation source]",
157
+ "characteristics[ecotype]", "factor value[atmospheric pressure]",
158
+ "factor value[organism part]", "parameter value[light regimen]",
159
+ "parameter value[mean growth temperature]", "parameter value[container]",
160
+ "parameter value[light intensity]", "parameter value[ph of growth medium]",
161
+ "comment[original submitted sample]",
162
+ "parameter value[absorbed radiation dose,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c95181,ncit]",
163
+ "comment[enclosure/habitat]",
164
+ "characteristics[ecotype,http://mged.sourceforge.net/ontologies/mgedontology.owl#ecotype,mo]",
165
+ "characteristics[age,http://mged.sourceforge.net/ontologies/mgedontology.owl#age,mo]",
166
+ "parameter value[growth condition,http://www.ebi.ac.uk/efo/efo_0000523,efo]",
167
+ "parameter value[duration,http://www.ebi.ac.uk/efo/efo_0000433,efo]",
168
+ "parameter value[treatment]", "parameter value[carcass weight]",
169
+ "parameter value[source storage temperature]", "comment[dissection date]",
170
+ "comment[alsda biospecimen source id]", "parameter value[canister and position]",
171
+ "factor value[freezing]", "parameter value[total cfu count]",
172
+ "parameter value[sample storage method]", "factor value[muscle, skeletal]",
173
+ "factor value[weightlessness,http://purl.bioontology.org/ontology/mesh/d014893,mesh]",
174
+ "characteristics[age,http://purl.obolibrary.org/obo/pato_0000011,pato]",
175
+ "comment[average absorbed dose (mgy) (spds only)]",
176
+ "comment[low let average abs. dose (spds only - mgy)]",
177
+ "comment[high let average abs. dose (spds only - mgy)]", "comment[abs. dose (gcr mgy) rd3-b3]",
178
+ "comment[abs. dose (irb/saa mgy) rd3-b3]", "comment[abs. dose (orb mgy) rd3-b3]",
179
+ "comment[abs. dose (total mgy) rd3-b3]",
180
+ "comment[low let average abs. dose (all detectors - mgy)]",
181
+ "comment[high let average abs. dose (all detectors - mgy)]",
182
+ "comment[low let min. abs. dose (all detectors - mgy)]",
183
+ "comment[low let max. abs. dose (all detectors - mgy)]",
184
+ "comment[high let min. abs. dose (all detectors - mgy)]",
185
+ "comment[high let max. abs. dose (all detectors - mgy)]",
186
+ "parameter value[media,http://www.ebi.ac.uk/efo/efo_0000579,ccont]",
187
+ "characteristics [individual identifier]", "characteristics [sex]",
188
+ "factor value[sample collection protocol]",
189
+ "characteristics[cell line,http://purl.obolibrary.org/obo/clo_0000031,obi]",
190
+ "characteristics[age,http://purl.obolibrary.org/obo/pato_0000011,obi]",
191
+ "characteristics[cell cycle phase]", "factor value[cell cycle phase]", "comment[sample_title]",
192
+ "comment[sample_description]", "characteristics[host organism]", "factor value[dose]",
193
+ "characteristics[cultivar]", "parameter value[environment]", "factor value[sex]",
194
+ "characteristics[culture condition]", "factor value[culture condition]",
195
+ "characteristics[biosourceprovider]", "parameter value[ccont:media]",
196
+ "characteristics[sample type]", "characteristics[tissue]", "characteristics[study subject]",
197
+ "parameter value[ionizing radiation energy]", "parameter value[ionizing radiation device]",
198
+ "characteristics[sex,http://purl.bioontology.org/ontology/mesh/d012723,mesh]",
199
+ "characteristics[diet,http://purl.bioontology.org/ontology/mesh/d004032,mesh]",
200
+ "unit[time unit]", "characteristics[culture type]", "factor value[donor]",
201
+ "factor value[gender]", "factor value[radiation dose]", "factor value[smoking status]",
202
+ "characteristics[strain or line]", "characteristics[launch mission]",
203
+ "comment[lsda subject id]", "comment[sample name in raw and processed data]",
204
+ "factor value[weightlessness]", "factor value[altered gravity]", "factor value[space mission]",
205
+ "characteristics[genotype,http://purl.bioontology.org/ontology/mesh/d005838,mesh]",
206
+ "characteristics[ecotype,http://purl.bioontology.org/ontology/mesh/d060146,mesh]",
207
+ "unit[timeunit]", "parameter value[sample description]",
208
+ "characteristics[collection date,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c81286,ncit]",
209
+ "factor value[altitude]", "characteristics[cell line]", "parameter value[preservation method]",
210
+ "factor value[exposure duration]", "comment [sample_characteristics]",
211
+ "comment[location of afflicted plants]", "characteristics [treatment group]",
212
+ "characteristics [cellline]", "factor value[treatment group]",
213
+ "characteristics[cell line origin]", "characteristics[treatment]",
214
+ "characteristics[treatment time]", "factor value[mitochondrial status]",
215
+ "factor value[rad9 status]", "comment[sample_name]", "characteristics [rad9 status]",
216
+ "parameter value[time]", "comment[bric canister]",
217
+ "parameter value[sample storage temeperature]", "parameter value[time in microgravity]",
218
+ "parameter value[time in hypergravity]", "factor value[hindlimb unloading]",
219
+ "factor value[gravity, altered]", "characteristics [culture]", "characteristics [organism]",
220
+ "parameter value[group]", "factor value[light cycle]", "factor value[animal housing]",
221
+ "factor value[food deprivation]", "factor value[water deprivation]",
222
+ "parameter value[sample storage temperature setting]", "parameter value[light amount]",
223
+ "unnamed: 72", "factor value[bed rest]", "factor value[sampling time]",
224
+ "factor value[experimental campaign]",
225
+ "parameter value[tissue preservation,http://purl.bioontology.org/ontology/mesh/d014021,mesh]",
226
+ "parameter value[particle charge]", "parameter value[linear energy transfer]",
227
+ "comment[nsrl run]", "characteristics [growth condition]",
228
+ "comment[maximum total absorbed dose]", "comment[minimum total absorbed dose]",
229
+ "parameter value[sequencing blank]", "factor value[sieve size]",
230
+ "parameter value[sex,http://purl.obolibrary.org/obo/pato_0000047,efo]",
231
+ "parameter value[age,http://purl.obolibrary.org/obo/pato_0000011,obcs]",
232
+ "factor value[tetanus toxoid]", "factor value[vaccine adjuvant]",
233
+ "parameter value[starting body mass]", "parameter value[final body mass]",
234
+ "parameter value[thymus mass]", "parameter value[injection date]",
235
+ "parameter value[ncorticosterone]", "parameter value[sac date]",
236
+ "parameter value[preservatin method]", "comment[genotype info]", "parameter value[ph]",
237
+ "parameter value[age at sample harvest]", "factor value[dissection timeline]",
238
+ "comment[average absorbed dose (spds only - mgy)]", "comment[duration]",
239
+ "characteristics[age at harvest]", "parameter value[mesh: cosmic radiation]",
240
+ "parameter value[time of sample collection after treatment]",
241
+ "parameter value[quantity of growth medium]", "parameter value[culture media]",
242
+ "protocol ref.3", "parameter value[sacrifice date]", "parameter value[age at harvest]",
243
+ "comment[seed source]", "comment[sample name notes]", "factor value[cultivar]",
244
+ "parameter value[light quality]",
245
+ "parameter value[environment,http://purl.bioontology.org/ontology/mesh/d004777,mesh]",
246
+ "factor value[soil environment exposure]", "parameter value[watering method]",
247
+ "parameter value[number of plants per sample (pooled)]", "parameter value[light time]",
248
+ "parameter value[light exposure]", "factor value[clinical treatment]",
249
+ "parameter value[body weight]",
250
+ "characteristics[age,http://www.ebi.ac.uk/efo/efo_0000246,efo]",
251
+ "characteristics[tissue,http://purl.obolibrary.org/obo/uberon_0000479,envo]",
252
+ "parameter value[temperature,http://purl.obolibrary.org/obo/pato_0000146,envo]",
253
+ "parameter value[light,http://www.ebi.ac.uk/efo/efo_0000568,efo]",
254
+ "parameter value[euthanasia time after hs]", "factor value[growth time]",
255
+ "factor value[euthanasia method]", "factor value[carcass preservation method]",
256
+ "factor value[dissection condition]", "factor value[tissue preservation method]",
257
+ "factor value[diet]", "parameter value[sample weight]", "comment[launch date]",
258
+ "comment[euthanasia date]", "parameter value[enrichment material]",
259
+ "comment[date of ucla arrival]", "comment[alsda source name]", "comment[lsda source name]",
260
+ "factor value[duration]", "factor value[euthanasia location]", "comment[lsda sample name]",
261
+ "comment[alsda sample name]",
262
+ "characteristics[organism,http://purl.bioontology.org/ontology/sty/t001,mesh]",
263
+ "characteristics[mission duration (between launch and landing)]",
264
+ "characteristics[time between launch and sample harvest]",
265
+ "parameter value[growth light color]", "parameter value[growth time start date (mm/dd/yy)]",
266
+ "parameter value[actual gravity level]", "parameter value[light treatment duration]",
267
+ "parameter value[treatment light intensity]", "parameter value[treatment light color]",
268
+ "parameter value[treatment light source]", "parameter value[gravity treatment duration]",
269
+ "parameter value[mission launch]", "parameter value[mission return]",
270
+ "parameter value[launch date (mm/dd/yy)]", "term source ref.23", "term accession number.23",
271
+ "parameter value[absorbed radiation dose (from launch to sample harvest)]",
272
+ "term source ref.24", "term accession number.24", "term source ref.25",
273
+ "term accession number.25", "term source ref.26", "term accession number.26",
274
+ "parameter value[sample harvest date (mm/dd/yy)]", "term source ref.27",
275
+ "term accession number.27", "comment[run]", "comment[mission]",
276
+ "parameter value[sampling material]", "comment[collection date]", "factor value[strain]",
277
+ "parameter value[carcass storage temperature]", "comment[bsp dissection date]",
278
+ "comment[lsda biospecimen source id]",
279
+ "characteristics[filter,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c41199,ncit]",
280
+ "parameter value[carbon dioxide,http://purl.obolibrary.org/obo/chebi_16526,efo]",
281
+ "parameter value[sample preservation temperature]",
282
+ "parameter value[location,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c25341,ncit]",
283
+ "parameter value[sample location]", "factor value[uv mutagenesis]",
284
+ "factor value[growth cycle]", "factor value[sample storage]", "characteristics[strain source]",
285
+ "parameter value[minimum growth temperature]", "parameter value[maximum growth temperature]",
286
+ "parameter value[uv light exposure]", "characteristics[host strain]",
287
+ "characteristics[host genotype]", "characteristics[host age (at irradiation)]",
288
+ "characteristics[donor strain]", "characteristics[donor genotype]",
289
+ "characteristics[donor age (at mammary gland collection)]", "parameter value[light color]",
290
+ "parameter value[harvest date (dd/mm/yyyy)]", "parameter value[experiment start date]",
291
+ "parameter value[harvest date]", "parameter value[number of seeds per container]",
292
+ "characteristics[developmental stage,http://www.ebi.ac.uk/efo/efo_0000399,efo]",
293
+ "factor value[altered gravity simulator]", "factor value[temperature]",
294
+ "characteristics[return mission]", "comment[source description].1",
295
+ "parameter value[whole tissue weight]", "parameter value[tissue section level]",
296
+ "comment[slide quadrant]", "comment[technical replicate #]",
297
+ "comment[initiation date (dd-mmm-yy)]", "comment[completion date (dd-mmm-yy)]",
298
+ "comment[dissection date (dd-mmm-yy)]", "factor value[preservation method]",
299
+ "factor value[order of preservation]", "comment[spleen collection date]",
300
+ "comment[liver collection date]", "comment[carcass weight (g)]",
301
+ "comment[soleus collection date]", "parameter value[tissue]",
302
+ "parameter value[host sample media information]", "parameter value[host growth time]",
303
+ "parameter value[co2 level]", "characteristics[title]", "characteristics[biosample]",
304
+ "characteristics[host,http://www.ebi.ac.uk/efo/efo_0000532,efo]",
305
+ "parameter value[subject id]", "parameter value[sample collection timepoint]",
306
+ "characteristics[age at onset of treatment]", "parameter value[anoxia treatment duration]",
307
+ "parameter value[heat treatment duration]", "parameter value[treatment light regimen]",
308
+ "comment[original submittted sample name]", "comment[sample name in raw data file]",
309
+ "characteristics[identification,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c25737,ncit]",
310
+ "parameter value[growth media information]",
311
+ "characteristics[tissue,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c12801,ncit]",
312
+ "parameter value[experiment batch]", "characteristics[age(at launch)]",
313
+ "characteristics[growth time]", "parameter value[flight no.]",
314
+ "parameter value[sampling matrial]", "factor value[light]",
315
+ "factor value[developmental stage]",
316
+ "characteristics[organism,http://mged.sourceforge.net/ontologies/mgedontology.owl#organism,mo]",
317
+ "comment[description]", "characteristics[cultivar,http://www.ebi.ac.uk/efo/efo_0005136,efo]",
318
+ "comment[seed lot]", "parameter value[broad-scale environmental context]",
319
+ "parameter value[environmental medium]", "parameter value[isolation and growth condition]",
320
+ "comment[biosample]", "comment[accession]", "comment[wgs accession no.]",
321
+ "factor value[atmospheric composition]", "comment[biosample accession]",
322
+ "parameter value[light type]", "parameter value[air temperature]",
323
+ "parameter value[relative air humidity]", "parameter value[relative humidity]",
324
+ "characteristics[maternal age]", "characteristics[paternal age]", "comment[ncbi accession]",
325
+ "parameter value[ovariectomy]", "parameter value[euthanasia timing]",
326
+ "parameter value[growth light cycle]", "parameter value[growth light source]",
327
+ "parameter value[growth light intensity]", "parameter value[treatment light cycle]",
328
+ "parameter value[gravity, altered]", "parameter value[mission]",
329
+ "parameter value[developmental stage at onset of gravity treatment]",
330
+ "parameter value[developmental stage at onset of light treatment]",
331
+ "parameter value[developmental stage at time of sample collection]", "factor value[tiime]",
332
+ "parameter value[sex]", "parameter value[growth temprature]", "factor value[study subject]",
333
+ "parameter value[dose rate]", "comment[animal source (host)]",
334
+ "characteristics[age (at irradiation)]", "characteristics[strain (donor strain)]",
335
+ "comment[animal source (donor)]", "characteristics[genotype (donor genotype)]",
336
+ "characteristics[control diet]", "parameter value[housing temperature(pre hibernation)]",
337
+ "parameter value[light cycle (pre-hibernation)]",
338
+ "parameter value[housing temperature (hibernation)]",
339
+ "parameter value[light cycle (hibernation)]", "parameter value[energy]",
340
+ "parameter value[radiation dose rate]", "parameter value[age at time of sampling]",
341
+ "parameter value[treatment duration]", "comment[sampling time]",
342
+ "parameter value[growth time].1",
343
+ "parameter value[euthanasia method,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c90336,ncit]",
344
+ "parameter value[age at euthanasia]",
345
+ "characteristics[developmental stage at onset of treatment]",
346
+ "characteristics[genetic modification]", "characteristics [cage]",
347
+ "characteristics [location]", "characteristics [strain or line]", "factor value[cage]",
348
+ "factor value[location]", "parameter value[time,http://www.ebi.ac.uk/efo/efo_0000721,efo]",
349
+ "parameter value[outer frame rotation]", "parameter value[inner frame rotation]",
350
+ "factor value[particle charge]",
351
+ "parameter value[time of sample collection after irradiation]",
352
+ "characteristics[drosophila developmental stage,http://www.ebi.ac.uk/efo/efo_0005651,efo]",
353
+ "factor value[ground based facilities]", "parameter value[radiation]",
354
+ "parameter value[radiation source]",
355
+ "characteristics[sex,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c28421,ncit]",
356
+ "comment[animal id]",
357
+ "parameter value[diet,http://purl.bioontology.org/ontology/mesh/d004032,mesh]",
358
+ "parameter value[age at launch]",
359
+ "parameter value[euthanasia,http://purl.bioontology.org/ontology/mesh/d005065,mesh]",
360
+ "characteristics[mission return]", "parameter value[growth time start date (mm/dd/yyyy)]",
361
+ "comment[light treatment description]", "parameter value[sample harvest date (mm/dd/yyyy)]",
362
+ "characteristics[growth condition,http://www.ebi.ac.uk/efo/efo_0000523,efo]",
363
+ "comment[technical replicate]", "comment[sacrifice date (dd-mmm-yy)]",
364
+ "factor value[dry immersion]", "characteristics [biosourcetype]", "factor value[hze]",
365
+ "comment[biosample no.]", "characteristics[height]", "characteristics[weight]",
366
+ "factor value[intracranial pressure]", "parameter value[average icp]", "comment[plate]",
367
+ "comment[plate well]", "parameter value[average fractionated dose rate]",
368
+ "parameter value[ionizing radiation source]", "parameter value[ionizing radiation facility]",
369
+ "parameter value[sample media informtion]", "factor value[radiation distance]",
370
+ "parameter value[hze]", "parameter value[sample media informtio]",
371
+ "parameter value[container diameter]", "parameter value[age at sample collection]",
372
+ "characteristics[nasa isolate identifier]", "characteristics[mission collected]",
373
+ "factor value[collection date]", "factor value[accession]",
374
+ "parameter value[parental treatment light cycle]",
375
+ "parameter value[parental treatment growth medium]",
376
+ "parameter value[parental treatment light intensity]",
377
+ "parameter value[parental treatment growth temperature]",
378
+ "comment[lar animal receipt date at scrippts]", "comment[euthanasia dates]",
379
+ "comment[dissection dates]", "characteristics[variety]",
380
+ "factor value[sample preservation method]", "factor value[seed sanitization]",
381
+ "characteristics[escherichia coli strain]", "parameter value[quantity of fertilizer]",
382
+ "parameter value[collection date]", "comment[biosample accession ]",
383
+ "comment[original sample id]", "comment[wgs accession no]", "comment[biosample no]",
384
+ "parameter value[recovery duration on earth]", "comment[rfid]", "comment[date of birth]",
385
+ "comment[lar animal receipt data at scripps]", "factor value[spacecraft]",
386
+ "factor value[gravity]", "parameter value[quantity growth medium]",
387
+ "parameter value[average percent humidity]", "parameter value[temperature range]",
388
+ "parameter value[mean light intensity]", "comment[data file note]",
389
+ "parameter value[mouse cage id]", "comment[rfid(last 4 digit)]",
390
+ "comment[rfid(complete or last 4 digit)]", "factor value[partial weight bearing]",
391
+ "comment[euthanasia and dissection date]", "comment[bsp dissection date (final dissection)]",
392
+ "characteristics[experiment]", "characteristics[age when exposed to x-ray]",
393
+ "characteristics[age when exposed to rapamycin/placebo]",
394
+ "characteristics[age at irradiation]", "parameter value[diet]",
395
+ "parameter value[number of particle types]", "parameter value[time between exposures]",
396
+ "parameter value[nsrl run]", "comment[did samples remain in the beamline between exposures?]",
397
+ "characteristics[sampling time,http://www.ebi.ac.uk/efo/efo_0000689,efo]",
398
+ "comment[original submitter sample name]", "factor value[time after treatment]",
399
+ "comment[alsda subject id]", "parameter value[body weight upon euthanasia]",
400
+ "characteristics[age at euthanasia]",
401
+ "parameter value[number of leaves at onset of treatment]",
402
+ "parameter value[maximum growth protocol]",
403
+ "parameter value[developmental stage at onset of treatment]",
404
+ "parameter value[number of leaves at time of sample collection]",
405
+ "parameter value[number of open flowers at time of sample collection]",
406
+ "characteristics[feeding schedule]", "characteristics[variant]",
407
+ "parameter value[number of seeds sown per well]", "characteristics[final body weight]",
408
+ "characteristics[run number]", "factor value[parabola]", "factor value[sample condition]",
409
+ "comment[sample type]", "parameter value[collection condition]",
410
+ "factor value[sample storage time]", "characteristics [celltype]",
411
+ "factor value[space flight,http://purl.bioontology.org/ontology/mesh/d013026,mesh]",
412
+ "characteristics[age before irradiation]", "characteristics [tissue]",
413
+ "comment[lar animal receipt date at scripps]", "characteristics[generation]",
414
+ "parameter value[age of f0 at launch]", "comment[experiment start date (dd/mm/yyyy)]",
415
+ "comment[experiment end date (dd/mm/yyyy)]", "parameter value[mean treatment temperature]",
416
+ "parameter value[age at time of sample collection]", "comment[parental treatment]",
417
+ "characteristics[sample collection phase]", "factor value[tissue segment]",
418
+ "parameter value[duration on iss]", "characteristics[donor id]",
419
+ "comment[maximum total absorbed dose]", "characteristics [cell line]",
420
+ "characteristics [sample type]", "characteristics [treatment duration]",
421
+ "factor value[treatment duration]", "characteristics[subject]", "parameter value[experiment]",
422
+ "characteristics [individual]", "characteristics [sample name]", "factor value[individual]",
423
+ "factor value[growth environment]", "parameter value[euthanasia date]",
424
+ "comment[euthanasia date (dd/mm/yyyy)]", "parameter value[growth hardware]",
425
+ "parameter value[treatment hardware]", "comment[other sample source name]",
426
+ "factor value[tissue model]",
427
+ "factor value[culture media,http://purl.bioontology.org/ontology/mesh/d003470,mesh]",
428
+ "factor value[zygosity,http://semanticscience.org/resource/sio_001263,sio]",
429
+ "factor value[generation number,http://semanticscience.org/resource/sio_010061,sio]",
430
+ "parameter value[age at onset of treatment]",
431
+ "comment[intensity of best extracted proteins by beatbox homogenizer]",
432
+ "parameter value[tonometry window]",
433
+ "parameter value[sample preservation method histology and immunohistochemistry]",
434
+ "parameter value[sample preservation method immunoblotting]", "comment[set]",
435
+ "characteristics[seed source (host)]", "characteristics[pathogen strain source]",
436
+ "parameter value[irrigation]", "parameter value[treatment mean growth temperature]",
437
+ "parameter value[culture medium]", "comment[pathosystem]",
438
+ "characteristics[age at start of assay]", "characteristics[stimulus]", "performer",
439
+ "parameter value[anesthesia method]", "comment[euthanasia date (dd-mm-year)]",
440
+ "comment[euthanasia time (hh:mm:ss)]", "comment[body weight at euthanasia]",
441
+ "comment[bsp dissection date (dd-mm-year)]",
442
+ "comment[partial body weight on bsp dissection date]", "factor value[housing condition]",
443
+ "parameter value[number of cagemates]", "parameter value[feeding schedule]",
444
+ "parameter value[age at time of assay]", "characteristics[growth temperature]",
445
+ "characteristics[growth condition]", "comment[sample_characteristics]",
446
+ "factor value[tissue type]", "factor value[developmental condition]",
447
+ "comment[iss module type]", "parameter value[sample collection method]",
448
+ "characteristics[age at experiment start]", "comment[sample location]",
449
+ "comment[flight number]", "comment[location]", "comment[sample id]",
450
+ "comment[sample collection date]", "comment[growthcondition]", "factor value[oxygen gas]",
451
+ "characteristics[volunteers,http://purl.bioontology.org/ontology/mesh/d014838,mesh]",
452
+ "characteristics[age at launch or beginning of treatment]",
453
+ "characteristics [biological replicate]", "characteristics [dose gray]",
454
+ "characteristics [post radiation time hour]", "characteristics [radiation]",
455
+ "characteristics [technical replicate]", "factor value[post radiation timepoint]",
456
+ "factor value[radiation type]", "parameter value[highly charged energetic nuclei]",
457
+ "factor value[stress]",
458
+ "characteristics[passage number,http://www.ebi.ac.uk/efo/efo_0007061,efo]",
459
+ "characteristics[sample media information]", "factor value[variation]",
460
+ "factor value[magnetic field]", "comment[sample type description]",
461
+ "characteristics [exposure]", "characteristics [exposure time]", "factor value[pressure]",
462
+ "factor value[collection set]", "characteristics[organism 2]", "characteristics[strain 2]",
463
+ "characteristics[organism 3]", "parameter value[euthanasia time after landing]",
464
+ "characteristics[sample_type]", "characteristics[organism_part]",
465
+ "characteristics[sample_title]", "characteristics[irradation]", "characteristics[cell model]",
466
+ "factor value[radiation]", "characteristics [mouse strain]", "factor value[mouse strain]",
467
+ "characteristics[dose,http://www.ebi.ac.uk/efo/efo_0000428,efo]",
468
+ "characteristics[radiation quality]", "characteristics [pathology]", "factor value[neoplasm]",
469
+ "characteristics[antibiotic]", "factor value[antibiotic concentration]",
470
+ "comment[source name- channel 2]", "factor value[radiation, ionzing]", "Unnamed: 0"]
471
 
472
  # SAMPLE_COLUMNS = ['Source Name', 'Sample Name', 'Characteristics: Organism',
473
  # 'Characteristics: Strain', 'Characteristics: Genotype',
 
501
  )
502
 
503
  _URL = "https://raw.githubusercontent.com/AnzorGozalishvili/NASA_ODSR_DATA/main"
504
+ _ASSAYS_FILE = "assays_all.csv"
505
+ # _SAMPLES_FILE = "samples.csv"
506
 
507
  def _split_generators(self, dl_manager):
508
  downloaded_files = dl_manager.download_and_extract(
509
  {
510
  "train": {
511
  "assays": os.path.join(self._URL, self._ASSAYS_FILE),
512
+ # "samples": os.path.join(self._URL, self._SAMPLES_FILE)
513
  },
514
  }
515
  )
 
519
  name=datasets.Split.TRAIN,
520
  gen_kwargs={
521
  "assays_file": downloaded_files['train']['assays'],
522
+ # "samples_file": downloaded_files['train']['samples'],
523
  },
524
  ),
525
  ]
526
 
527
+ # def _generate_examples(self, assays_file: str, samples_file):
528
+ def _generate_examples(self, assays_file: str):
 
 
 
529
  assays_df = pd.read_csv(assays_file)
530
+ # samples_df = pd.read_csv(samples_file)
531
 
532
+ # for (idx, assay_row), (_, sample_row) in zip(assays_df.iterrows(), samples_df.iterrows()):
533
+ for (idx, assay_row) in assays_df.iterrows():
534
  _item = {**assay_row.to_dict()}
535
  # _item = {**assay_row.to_dict(), **sample_row.to_dict()}
536
 
tests/test_dataset_files.py CHANGED
@@ -2,5 +2,4 @@ import os
2
 
3
 
4
  def test_dataset_files():
5
- assert os.path.exists('data/assays.csv')
6
- assert os.path.exists('data/samples.csv')
 
2
 
3
 
4
  def test_dataset_files():
5
+ assert os.path.exists('data/assays_all.csv')
 
tests/test_nasa_osdr.py CHANGED
@@ -33,7 +33,8 @@ def test_inherit_generator_base_builder_works():
33
 
34
  def test_generate_examples():
35
  dataset = NasaOsdr()
36
- train_data = dataset._generate_examples(assays_file='data/assays.csv', samples_file='data/samples.csv')
 
37
  idx, sample = next(iter(train_data))
38
  print(idx, sample.keys())
39
 
 
33
 
34
  def test_generate_examples():
35
  dataset = NasaOsdr()
36
+ # train_data = dataset._generate_examples(assays_file='data/assays_all.csv', samples_file='data/samples.csv')
37
+ train_data = dataset._generate_examples(assays_file='data/assays_all.csv')
38
  idx, sample = next(iter(train_data))
39
  print(idx, sample.keys())
40