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‎datapackage.json‎

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@@ -69,4 +69,4 @@
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"path": "https://zenodo.org/records/7055715"
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}
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]
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}
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}

‎scripts/convert-meta.py‎

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# More than one measure in metadata_maternal_bl?
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"""
173173
11 - Metadata_Maternal_placenta.csv
174-
* Variables
174+
* Variables
175175
o Exp: Samples IDs. The same “Exp” represent the same sample in Concentration_Maternal.placenta.csv file.
176-
o Mother_ID: IDs of mothers.
176+
o Mother_ID: IDs of mothers.
177177
o Batch: The experiment was conducted over two batches (Batch1 or Batch2)
178178
o Group: Lean or Obese.
179179
o GD: Exact gestational day (GD) when samples were collected.
180-
o Target_GD: Target GD for sample collection.
181-
o Dilution_factor: Dilution factor used to prepare NMR samples.
182-
o BCS: Body Condition Score (BCS)
183-
o Tissue_weight: Weight of placental tissue sample.
180+
o Target_GD: Target GD for sample collection.
181+
o Dilution_factor: Dilution factor used to prepare NMR samples.
182+
o BCS: Body Condition Score (BCS)
183+
o Tissue_weight: Weight of placental tissue sample.
184184
o V1: Volume of solvent used to extract (uL). Used to correct the metabolite concentration.
185185
o V2: Volume of polar layer (methanol + water) collected (uL). Used to correct the metabolite concentration.
186-
o V3: Buffer added to reconstitute the sample after freeze drying (uL). Used to correct the metabolite concentration.
186+
o V3: Buffer added to reconstitute the sample after freeze drying (uL). Used to correct the metabolite concentration.
187187
* Missing data codes: Indicated by NAs.
188188
"""

‎scripts/download-data.py‎

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@@ -36,17 +36,17 @@
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1 - Concentration_Infant.blood.csv
3737
* Columns: Samples. The same “Exp” represent the same sample in Metadata_Infant.blood.csv & Cytokine_Infant.blood.csv files.
3838
* Rows: Metabolites
39-
* The unit is uM.
39+
* The unit is uM.
4040
4141
2 - Concentration_Infant.urine.csv
4242
* Columns: Samples. The same “Exp” represent the same sample in Metadata_Infant.urine.csv file.
4343
* Rows: Metabolites
44-
* The unit is uM.
44+
* The unit is uM.
4545
4646
3 - Concentration_Maternal.blood.csv
47-
* Columns: Sample IDs. The same “Exp” represent the same sample in Concentration_Maternal.blood.csv, Cytokine_Infant.blood.csv, and Metadata_Maternal.blood.csv files.
47+
* Columns: Sample IDs. The same “Exp” represent the same sample in Concentration_Maternal.blood.csv, Cytokine_Infant.blood.csv, and Metadata_Maternal.blood.csv files.
4848
* Rows: Metabolites
49-
* The unit is uM.
49+
* The unit is uM.
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5151
4 - Concentration_Maternal.placenta.csv
5252
* Columns: Samples. The same “Exp” represent the same sample in Metadata_Maternal.placenta.csv file.
@@ -56,154 +56,154 @@
5656
5 - Concentration_Maternal.urine.csv
5757
* Columns: Samples. The same “Exp” represent the same sample in Metadata_Maternal.urine.csv file.
5858
* Rows: Metabolites
59-
* The unit is uM.
59+
* The unit is uM.
6060
6161
6 - Cortisol_Infant.blood.csv
62-
* Variables
63-
o Infant_ID: IDs of infants.
62+
* Variables
63+
o Infant_ID: IDs of infants.
6464
o Group: Lean or Obese.
6565
o PD: Exact postnatal day (PD) when samples were collected.
66-
o Mother_ID: IDs of mothers.
67-
o Foster_ID: IDs of foster mothers.
68-
o Infant_weight: Infant weights (kg) recorded at samples collection.
69-
o samp1: Cortisol level from the 1st blood samples collected from infants at 11am, after being separated from mothers at 9am.
70-
o samp2: Cortisol level from the 2nd blood samples collected 4 pm. After the blood collection, 500 ?g/kg dexamethasone was injected intramuscularly.
66+
o Mother_ID: IDs of mothers.
67+
o Foster_ID: IDs of foster mothers.
68+
o Infant_weight: Infant weights (kg) recorded at samples collection.
69+
o samp1: Cortisol level from the 1st blood samples collected from infants at 11am, after being separated from mothers at 9am.
70+
o samp2: Cortisol level from the 2nd blood samples collected 4 pm. After the blood collection, 500 ?g/kg dexamethasone was injected intramuscularly.
7171
o samp3: Cortisol level from the 3rd blood samples collected at 8:30 am of the following day. After the blood collection, 2.5 IU of adrenocorticotropic hormone (ACTH) was injected intramuscularly.
72-
o samp4: Cortisol level from the 4th blood samples collected 30 min after ACTH injection.
72+
o samp4: Cortisol level from the 4th blood samples collected 30 min after ACTH injection.
7373
o pctsuppression: Values obtained by dividing samp3 by samp2.
7474
* Missing data codes: Indicated by NAs.
7575
7676
7 - Metadata_Infant.blood.csv
77-
* Variables
77+
* Variables
7878
o Exp: Samples IDs. The same “Exp” represent the same sample in Concentration_Infant.blood.csv & Cytokine_Infant.blood.csv files.
79-
o Infant_ID: IDs of infants.
79+
o Infant_ID: IDs of infants.
8080
o Batch: The experiment was conducted over two batches (Batch1 or Batch2)
8181
o Group: Lean or Obese.
8282
o PD: Exact postnatal day (PD) when samples were collected.
83-
o Target_PD: Target PD for sample collection.
84-
o Dilution_factor: Dilution factor used to prepare NMR samples.
85-
o Mother_ID: IDs of mothers.
86-
o GD_Delivery: Gestational day at delivery.
83+
o Target_PD: Target PD for sample collection.
84+
o Dilution_factor: Dilution factor used to prepare NMR samples.
85+
o Mother_ID: IDs of mothers.
86+
o GD_Delivery: Gestational day at delivery.
8787
o Mode_birth: Mode of delivery.
8888
o Fostered: Yes (fostered) or No (was not fostered).
89-
o Foster_ID: IDs of foster mothers.
89+
o Foster_ID: IDs of foster mothers.
9090
o Weight_PD7: Infant weights recorded at around PD7.
91-
o ActualDay_PD7: Actual day for “Weight_PD7”.
92-
o Infant_weight: Infant weights (kg) recorded at samples collection.
91+
o ActualDay_PD7: Actual day for “Weight_PD7”.
92+
o Infant_weight: Infant weights (kg) recorded at samples collection.
9393
* Missing data codes: Indicated by NAs.
9494
9595
8 - Metadata_Infant.urine.csv
96-
* Variables
96+
* Variables
9797
o Exp: Samples IDs. The same “Exp” represent the same sample in Concentration_Infant.urine.csv file.
98-
o Infant_ID: IDs of infants.
98+
o Infant_ID: IDs of infants.
9999
o Batch: The experiment was conducted over two batches (Batch1 or Batch2)
100100
o Group: Lean or Obese.
101101
o PD: Exact postnatal day (PD) when samples were collected.
102-
o Target_PD: Target PD for sample collection.
103-
o Dilution_factor: Dilution factor used to prepare NMR samples.
104-
o Mother_ID: IDs of mothers.
105-
o GD_Delivery: Gestational day at delivery.
102+
o Target_PD: Target PD for sample collection.
103+
o Dilution_factor: Dilution factor used to prepare NMR samples.
104+
o Mother_ID: IDs of mothers.
105+
o GD_Delivery: Gestational day at delivery.
106106
o Mode_birth: Mode of delivery.
107107
o Fostered: Yes (fostered) or No (was not fostered).
108-
o Foster_ID: IDs of foster mothers.
109-
o Infant_weight: Infant weights (kg) recorded at samples collection.
108+
o Foster_ID: IDs of foster mothers.
109+
o Infant_weight: Infant weights (kg) recorded at samples collection.
110110
* Missing data codes: Indicated by NAs.
111111
112112
9 - Metadata_Maternal.blood.csv
113-
* Variables
113+
* Variables
114114
o Exp: Samples IDs. The same “Exp” represent the same sample in Concentration_Maternal.blood.csv, Cytokine_Infant.blood.csv, and Metadata_Maternal.blood.csv files.
115-
o Mother_ID: IDs of mothers.
115+
o Mother_ID: IDs of mothers.
116116
o Batch: The experiment was conducted over two batches (Batch1 or Batch2)
117117
o Group: Lean or Obese.
118118
o GD: Exact gestational day (GD) when samples were collected.
119-
o Target_GD: Target GD for sample collection.
120-
o Dilution_factor: Dilution factor used to prepare NMR samples.
121-
o BCS: Body Condition Score (BCS)
122-
o Mother_Weight: Maternal weight in kg at sample collection.
123-
o Mother_age: Maternal age at conception.
124-
o GD_Delivery: Gestational day at delivery.
119+
o Target_GD: Target GD for sample collection.
120+
o Dilution_factor: Dilution factor used to prepare NMR samples.
121+
o BCS: Body Condition Score (BCS)
122+
o Mother_Weight: Maternal weight in kg at sample collection.
123+
o Mother_age: Maternal age at conception.
124+
o GD_Delivery: Gestational day at delivery.
125125
o Infant_sex: Infant sex.
126126
o Mode_birth: Mode of delivery.
127-
o Reject: Whether mothers rejected infants or not.
127+
o Reject: Whether mothers rejected infants or not.
128128
o Placenta_Width: Width of placenta at sample collection.
129129
o Placenta_Height: Height of placenta at sample collection.
130130
o Placenta_Thickness: Thickness of placenta at sample collection.
131-
o EPV: Estimated placental volume.
131+
o EPV: Estimated placental volume.
132132
* Missing data codes: Indicated by NAs.
133133
134134
10 - Metadata_Maternal.urine.csv
135-
* Variables
135+
* Variables
136136
o Exp: Samples IDs. The same “Exp” represent the same sample in Concentration_Maternal.urine.csv file.
137-
o Mother_ID: IDs of mothers.
137+
o Mother_ID: IDs of mothers.
138138
o Batch: The experiment was conducted over two batches (Batch1 or Batch2)
139139
o Group: Lean or Obese.
140140
o GD: Exact gestational day (GD) when samples were collected.
141-
o Target_GD: Target GD for sample collection.
142-
o Dilution_factor: Dilution factor used to prepare NMR samples.
143-
o BCS: Body Condition Score (BCS)
144-
o Mother_Weight: Maternal weight in kg at sample collection.
145-
o Mother_age: Maternal age at conception.
146-
o GD_Delivery: Gestational day at delivery.
141+
o Target_GD: Target GD for sample collection.
142+
o Dilution_factor: Dilution factor used to prepare NMR samples.
143+
o BCS: Body Condition Score (BCS)
144+
o Mother_Weight: Maternal weight in kg at sample collection.
145+
o Mother_age: Maternal age at conception.
146+
o GD_Delivery: Gestational day at delivery.
147147
o Infant_sex: Infant sex.
148148
o Mode_birth: Mode of delivery.
149149
* Missing data codes: Indicated by NAs.
150150
151151
11 - Metadata_Maternal.placenta.csv
152-
* Variables
152+
* Variables
153153
o Exp: Samples IDs. The same “Exp” represent the same sample in Concentration_Maternal.placenta.csv file.
154-
o Mother_ID: IDs of mothers.
154+
o Mother_ID: IDs of mothers.
155155
o Batch: The experiment was conducted over two batches (Batch1 or Batch2)
156156
o Group: Lean or Obese.
157157
o GD: Exact gestational day (GD) when samples were collected.
158-
o Target_GD: Target GD for sample collection.
159-
o Dilution_factor: Dilution factor used to prepare NMR samples.
160-
o BCS: Body Condition Score (BCS)
161-
o Tissue_weight: Weight of placental tissue sample.
158+
o Target_GD: Target GD for sample collection.
159+
o Dilution_factor: Dilution factor used to prepare NMR samples.
160+
o BCS: Body Condition Score (BCS)
161+
o Tissue_weight: Weight of placental tissue sample.
162162
o V1: Volume of solvent used to extract (uL). Used to correct the metabolite concentration.
163163
o V2: Volume of polar layer (methanol + water) collected (uL). Used to correct the metabolite concentration.
164-
o V3: Buffer added to reconstitute the sample after freeze drying (uL). Used to correct the metabolite concentration.
164+
o V3: Buffer added to reconstitute the sample after freeze drying (uL). Used to correct the metabolite concentration.
165165
* Missing data codes: Indicated by NAs.
166166
167167
12 - Cytokine_Infant.blood
168-
* Variables:
168+
* Variables:
169169
o Exp: Samples IDs. The same “Exp” represent the same sample in Concentration_Infant.blood.csv & Metadata_Infant.blood.csv files.
170-
o Infant_ID: IDs of infants.
170+
o Infant_ID: IDs of infants.
171171
o Batch: The experiment was conducted over two batches (Batch1 or Batch2)
172172
o Group: Lean or Obese.
173173
o PD: Exact postnatal day (PD) when samples were collected.
174-
o Target_PD: Target PD for sample collection.
174+
o Target_PD: Target PD for sample collection.
175175
o Mother_ID: IDs of mothers.
176-
o GD_Delivery: Gestational day at delivery.
176+
o GD_Delivery: Gestational day at delivery.
177177
o Mode_birth: Mode of delivery.
178178
o Fostered: Yes (fostered) or No (was not fostered).
179-
o Foster_ID: IDs of foster mothers.
179+
o Foster_ID: IDs of foster mothers.
180180
o Weight_PD7: Infant weights recorded at around PD7.
181-
o hsCPP, GM_CSF, IFN_g, IL_1b, IL_ra, IL_2, IL_4, IL_5, IL_6, IL_8, IL_10, IL_12.23_p40, IL_13, IL_15,
182-
IL_17a, MCP_1, MIP_1b, sCD40L_38, TGFa, TNFa, VEGF, C_Peptide, GIP, Inflammatory markers.
181+
o hsCPP, GM_CSF, IFN_g, IL_1b, IL_ra, IL_2, IL_4, IL_5, IL_6, IL_8, IL_10, IL_12.23_p40, IL_13, IL_15,
182+
IL_17a, MCP_1, MIP_1b, sCD40L_38, TGFa, TNFa, VEGF, C_Peptide, GIP, Inflammatory markers.
183183
o Insulin: Insulin level (pg/mL).
184184
* Missing data codes: Indicated by NAs.
185-
* Specialized formats or other abbreviations used: GD, gestational day; BCS, Body Condition Score;
186-
GM-CSF, granulocyte-macrophage colony-stimulating factor; IFN- ?, interferon ?; TNF-?, tumor necrosis factor-?;
187-
TGF-?, transforming growth factor-?; MCP-1, monocyte chemoattractant protein-1; MIP-1?, macrophage inflammatory protein-1?;
185+
* Specialized formats or other abbreviations used: GD, gestational day; BCS, Body Condition Score;
186+
GM-CSF, granulocyte-macrophage colony-stimulating factor; IFN- ?, interferon ?; TNF-?, tumor necrosis factor-?;
187+
TGF-?, transforming growth factor-?; MCP-1, monocyte chemoattractant protein-1; MIP-1?, macrophage inflammatory protein-1?;
188188
hs-CRP, high-sensitivity C-reactive protein; IL, interleukin.
189189
190190
13 - Cytokine_Maternal.blood
191-
* Variables:
191+
* Variables:
192192
o Exp: Samples IDs. The same “Exp” represent the same sample in Concentration_Maternal.blood.csv, Cytokine_Infant.blood.csv, and Metadata_Maternal.blood.csv files.
193-
o Mother_ID: IDs of mothers.
193+
o Mother_ID: IDs of mothers.
194194
o Batch: The experiment was conducted over two batches (Batch1 or Batch2)
195195
o Group: Lean or Obese.
196196
o GD: Exact gestational day (GD) when samples were collected.
197-
o Target_GD: Target GD for sample collection.
198-
o BCS: Body Condition Score (BCS)
199-
o hsCPP, GM_CSF, IFN_g, IL_1b, IL_ra, IL_2, IL_6, IL_8, IL_10, IL_12/23_p40, IL_13, IL_15,
200-
IL_17a, MCP_1, MIP_1b, sCD40L, TGFa, VEGF, C_Peptide, GIP, PP_53, PYY_54: Inflammatory markers.
197+
o Target_GD: Target GD for sample collection.
198+
o BCS: Body Condition Score (BCS)
199+
o hsCPP, GM_CSF, IFN_g, IL_1b, IL_ra, IL_2, IL_6, IL_8, IL_10, IL_12/23_p40, IL_13, IL_15,
200+
IL_17a, MCP_1, MIP_1b, sCD40L, TGFa, VEGF, C_Peptide, GIP, PP_53, PYY_54: Inflammatory markers.
201201
o Insulin: Insulin level (uU/mL)
202202
* Missing data codes: Indicated by NAs.
203-
* Specialized formats or other abbreviations used: GD, gestational day; BCS, Body Condition Score;
204-
hs-CRP, high-sensitivity C-reactive protein; GM_CSF, granulocyte-macrophage colony-stimulating factor;
205-
IFN- ?, interferon-?; TNF-?, tumor necrosis factor-?; TGF-?, transforming growth factor-?;
206-
MCP-1, monocyte chemoattractant protein-1; MIP-1?, macrophage inflammatory protein-1?; IL, interleukin;
203+
* Specialized formats or other abbreviations used: GD, gestational day; BCS, Body Condition Score;
204+
hs-CRP, high-sensitivity C-reactive protein; GM_CSF, granulocyte-macrophage colony-stimulating factor;
205+
IFN- ?, interferon-?; TNF-?, tumor necrosis factor-?; TGF-?, transforming growth factor-?;
206+
MCP-1, monocyte chemoattractant protein-1; MIP-1?, macrophage inflammatory protein-1?; IL, interleukin;
207207
IL-1ra, IL-1 receptor antagonist.
208208
209209
14 - WB.infant.brain
@@ -214,42 +214,42 @@
214214
o Akt, p.Akt, AMPK, p.AMPK, S6K, p.S6K: Normalized relative intensity levels.
215215
216216
15 - HI_infant.behavior
217-
* Variables
218-
o Infant_ID: IDs of infants.
217+
* Variables
218+
o Infant_ID: IDs of infants.
219219
o Group: Lean or Obese.
220220
o PD: Exact postnatal day (PD) when samples were collected.
221-
o Mother_ID: IDs of mothers.
222-
o Foster_ID: IDs of foster mothers.
223-
o Infant_weight: Infant weights (kg) recorded at samples collection.
221+
o Mother_ID: IDs of mothers.
222+
o Foster_ID: IDs of foster mothers.
223+
o Infant_weight: Infant weights (kg) recorded at samples collection.
224224
o pfscratch: Profile-Far (technician presented the left profile from ~1 m away from an infant in a cage)
225225
o pnscratch: Profile-Near (presented left profile from ~0.3 m)
226226
o sfscratch: Stare-Far (made direct eye contact with the animal from far)
227227
o snscratch: Stare-Near (direct eye contact from near position)
228228
* Missing data codes: Indicated by NAs.
229229
230230
16 - VPC_infant_cognitive
231-
* Variables
232-
o Infant_ID: IDs of infants.
233-
o Mother_ID: IDs of mothers.
234-
o Foster_ID: IDs of foster mothers.
231+
* Variables
232+
o Infant_ID: IDs of infants.
233+
o Mother_ID: IDs of mothers.
234+
o Foster_ID: IDs of foster mothers.
235235
o Batch: The experiment was conducted over two batches (Batch1 or Batch2)
236236
o Group: Lean or Obese.
237-
o GD_Delivery: Gestational day at delivery.
237+
o GD_Delivery: Gestational day at delivery.
238238
o PCD: post-conception day.
239-
o PxTx Total number Look RIGHT/LEFT FAM: Total number of looks at a familiar object that was placed right or left side. P stands for the number of problem (1 to 4) and T stands for the number of Trial (1 or 2).
239+
o PxTx Total number Look RIGHT/LEFT FAM: Total number of looks at a familiar object that was placed right or left side. P stands for the number of problem (1 to 4) and T stands for the number of Trial (1 or 2).
240240
o PxTx Total number Look RIGHT/LEFT NOVEL: Total number of looks at a novel object that was placed right or left side. P stands for the number of problem (1 to 4) and T stands for the number of Trial (1 or 2).
241241
o PxTx Total number Look Away: Total number of looks away from either of the object. P stands for the number of problem (1 to 4) and T stands for the number of Trial (1 or 2).
242-
o no.looks_N: Total number of looks at novel object throughout the problems and trials.
242+
o no.looks_N: Total number of looks at novel object throughout the problems and trials.
243243
o no.looks_F: Total number of looks at familiar object throughout the problems and trials.
244244
o no.looks_N+F: Total number of looks at novel and familiar object throughout the problems and trials.
245245
o no.looks_N/N+F: Novelty preference calculated as: number of fixations at the novel stimulus (no.looks_N)/number of fixations at both the novel and familiar stimulus (no.looks_N+F).
246246
247247
17 - Gestational.weight.gain.rate
248-
* Variables
249-
o Mother_ID: IDs of mothers.
248+
* Variables
249+
o Mother_ID: IDs of mothers.
250250
o Batch: The experiment was conducted over two batches (Batch1 or Batch2)
251251
o Group: Lean or Obese.
252-
o Infant_ID: IDs of infants.
253-
o Foster_ID: IDs of foster mothers.
254-
o GWG: Gestational weight gain rate.
252+
o Infant_ID: IDs of infants.
253+
o Foster_ID: IDs of foster mothers.
254+
o GWG: Gestational weight gain rate.
255255
"""

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