add first version of dataset files.

data/assays.csv

@@ -0,0 +1,26 @@
+Sample Name,Protocol REF,Parameter Value: DNA Fragmentation,Parameter Value: DNA Fragment Size,Extract Name,Protocol REF,Parameter Value: Library Strategy,Parameter Value: Library Selection,Parameter Value: Library Layout,Protocol REF,Parameter Value: Sequencing Instrument,Assay Name,Parameter Value: Read Length,Raw Data File,Protocol REF,Parameter Value: Read Depth,Parameter Value: MultiQC File Names
+GSM2684058,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684058,Library Construction,Bisulfite-Seq,RANDOM-PCR,PAIRED,Nucleic Acid Sequencing,Illumina HiSeq 4000,Bisulfite-Seq,150 base pair,"GLDS-524_wgbs_GSM2684058_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684058_R2_raw.fastq.gz",GeneLab raw data processing protocol,121705532 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684059,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684059,Library Construction,Bisulfite-Seq,RANDOM-PCR,PAIRED,Nucleic Acid Sequencing,Illumina HiSeq 4000,Bisulfite-Seq,150 base pair,"GLDS-524_wgbs_GSM2684059_R2_raw.fastq.gz, GLDS-524_wgbs_GSM2684059_R1_raw.fastq.gz",GeneLab raw data processing protocol,125506087 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684060,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684060,Library Construction,Bisulfite-Seq,RANDOM-PCR,PAIRED,Nucleic Acid Sequencing,Illumina HiSeq 4000,Bisulfite-Seq,150 base pair,"GLDS-524_wgbs_GSM2684060_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684060_R2_raw.fastq.gz",GeneLab raw data processing protocol,124250067 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684061,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684061,Library Construction,Bisulfite-Seq,RANDOM-PCR,PAIRED,Nucleic Acid Sequencing,Illumina HiSeq 4000,Bisulfite-Seq,150 base pair,"GLDS-524_wgbs_GSM2684061_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684061_R2_raw.fastq.gz",GeneLab raw data processing protocol,127659454 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684062,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684062,Library Construction,Bisulfite-Seq,RANDOM-PCR,PAIRED,Nucleic Acid Sequencing,Illumina HiSeq 4000,Bisulfite-Seq,150 base pair,"GLDS-524_wgbs_GSM2684062_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684062_R2_raw.fastq.gz",GeneLab raw data processing protocol,126360478 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684063,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684063,Library Construction,Bisulfite-Seq,RANDOM-PCR,PAIRED,Nucleic Acid Sequencing,Illumina HiSeq 4000,Bisulfite-Seq,150 base pair,"GLDS-524_wgbs_GSM2684063_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684063_R2_raw.fastq.gz",GeneLab raw data processing protocol,138417466 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684064,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684064,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684064_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684064_R2_raw.fastq.gz",GeneLab raw data processing protocol,252983 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684065,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684065,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684065_R2_raw.fastq.gz, GLDS-524_wgbs_GSM2684065_R1_raw.fastq.gz",GeneLab raw data processing protocol,219059 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684066,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684066,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684066_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684066_R2_raw.fastq.gz",GeneLab raw data processing protocol,212458 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684067,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684067,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684067_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684067_R2_raw.fastq.gz",GeneLab raw data processing protocol,168361 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684068,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684068,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684068_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684068_R2_raw.fastq.gz",GeneLab raw data processing protocol,199027 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684069,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684069,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684069_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684069_R2_raw.fastq.gz",GeneLab raw data processing protocol,202776 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684070,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684070,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684070_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684070_R2_raw.fastq.gz",GeneLab raw data processing protocol,234908 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684071,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684071,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684071_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684071_R2_raw.fastq.gz",GeneLab raw data processing protocol,213334 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684072,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684072,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684072_R2_raw.fastq.gz, GLDS-524_wgbs_GSM2684072_R1_raw.fastq.gz",GeneLab raw data processing protocol,217558 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684073,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684073,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684073_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684073_R2_raw.fastq.gz",GeneLab raw data processing protocol,212746 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684074,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684074,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684074_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684074_R2_raw.fastq.gz",GeneLab raw data processing protocol,219767 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684075,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684075,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684075_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684075_R2_raw.fastq.gz",GeneLab raw data processing protocol,199327 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684076,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684076,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684076_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684076_R2_raw.fastq.gz",GeneLab raw data processing protocol,214269 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684077,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684077,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684077_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684077_R2_raw.fastq.gz",GeneLab raw data processing protocol,193869 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684078,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684078,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684078_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684078_R2_raw.fastq.gz",GeneLab raw data processing protocol,90942 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684079,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684079,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684079_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684079_R2_raw.fastq.gz",GeneLab raw data processing protocol,187559 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684080,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684080,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684080_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684080_R2_raw.fastq.gz",GeneLab raw data processing protocol,189166 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684081,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684081,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684081_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684081_R2_raw.fastq.gz",GeneLab raw data processing protocol,182152 read,GLDS-524_Gwgbs_raw_multiqc_report.zip
+GSM2684082,Nucleic Acid Extraction,sonication,200-300 base pair,GSM2684082,Library Construction,BisPCR2,other,PAIRED,Nucleic Acid Sequencing,Illumina MiSeq,BisPCR2,150 base pair,"GLDS-524_wgbs_GSM2684082_R1_raw.fastq.gz, GLDS-524_wgbs_GSM2684082_R2_raw.fastq.gz",GeneLab raw data processing protocol,183590 read,GLDS-524_Gwgbs_raw_multiqc_report.zip

data/samples.csv

@@ -0,0 +1,26 @@
+Source Name,Sample Name,Characteristics: Organism,Characteristics: Strain,Characteristics: Genotype,Characteristics: Material Type,Factor Value: Ionizing Radiation,Factor Value: Generation,Protocol REF,Protocol REF,Parameter Value: ionizing radiation energy,Parameter Value: exposure duration,Parameter Value: absorbed radiation dose,Parameter Value: absorbed radiation dose rate,Parameter Value: ionizing radiation categorized by source,Protocol REF,Parameter Value: Sample Preservation Method,Parameter Value: Sample Storage Temperature,Parameter Value: Age at time of sample collection,Comment: Animal Source,Comment: Parental Treatment
+WGBS_control_1,GSM2684058,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F1,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+WGBS_control_2,GSM2684059,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F1,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+WGBS_control_3,GSM2684060,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F1,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+WGBS_exposed_1,GSM2684061,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F1,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed
+WGBS_exposed_2,GSM2684062,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F1,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed
+WGBS_exposed_3,GSM2684063,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F1,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed
+BisPCR2_F1_control_1,GSM2684064,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F1,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+BisPCR2_F1_control_2,GSM2684065,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F1,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+BisPCR2_F1_control_3,GSM2684066,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F1,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+BisPCR2_F1_control_4,GSM2684067,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F1,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+BisPCR2_F1_control_5,GSM2684068,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F1,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+BisPCR2_F1_exposed_1,GSM2684069,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F1,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed
+BisPCR2_F1_exposed_2,GSM2684070,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F1,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed
+BisPCR2_F1_exposed_3,GSM2684071,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F1,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed
+BisPCR2_F1_exposed_4,GSM2684072,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F1,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed
+BisPCR2_F1_exposed_5,GSM2684073,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F1,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed
+BisPCR2_F2_control_1,GSM2684074,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F2,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+BisPCR2_F2_control_2,GSM2684075,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F2,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+BisPCR2_F2_control_3,GSM2684076,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F2,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+BisPCR2_F2_control_4,GSM2684077,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F2,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+BisPCR2_F2_control_5,GSM2684078,Danio rerio,AB Zebrafish,Wild Type,whole embryos,non-irradiated,F2,Animal husbandry,irradiation protocol,Not Applicable,Not Applicable,Not Applicable,Not Applicable,Not Applicable,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,control
+BisPCR2_F2_exposed_1,GSM2684079,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F2,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed
+BisPCR2_F2_exposed_2,GSM2684080,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F2,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed
+BisPCR2_F2_exposed_3,GSM2684081,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F2,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed
+BisPCR2_F2_exposed_4,GSM2684082,Danio rerio,AB Zebrafish,Wild Type,whole embryos,Cobalt-60 gamma radiation,F2,Animal husbandry,irradiation protocol,1.173:1.332 Megaelectronvolt,27 day,5.2 gray,8.7 milligray per hour,gamma irradiator,sample collection,Liquid Nitrogen,-80 degree Celsius,5.5 hours post-fertilization,Norwegian University of Life Sciences zebrafish facility,exposed

nasa_osdr.py

@@ -0,0 +1,125 @@
+# coding=utf-8
+# Copyright 2020 The HuggingFace Datasets Authors and the current dataset script contributor.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""NASA_OSDR dataset"""
+
+import json
+import os
+
+import datasets
+import pandas as pd
+
+_CITATION = """
+@inproceedings{singh2019towards,
+    title={},
+    author={},
+    booktitle={},
+    pages={},
+    year={}
+}
+"""
+
+_DESCRIPTION = """
+TODO: write description
+"""
+
+_HOMEPAGE = "https://"
+
+_LICENSE = ""
+
+_SPLITS = ["train"]
+
+_FIFTYONE_DATASET_URL = ""
+
+
+class NasaOsdr(datasets.GeneratorBasedBuilder):
+    """NASA OSDR dataset."""
+
+    BUILDER_CONFIGS = [
+        datasets.BuilderConfig(
+            name="NASA_OSDR",
+            version=datasets.Version("1.0.0"),
+            description=_DESCRIPTION,
+        )
+    ]
+
+    DEFAULT_CONFIG_NAME = "NASA_OSDR"
+
+    def _info(self):
+        ASSAY_COLUMNS = ['Sample Name', 'Protocol REF', 'Parameter Value: DNA Fragmentation',
+                         'Parameter Value: DNA Fragment Size', 'Extract Name', 'Protocol REF.1',
+                         'Parameter Value: Library Strategy',
+                         'Parameter Value: Library Selection', 'Parameter Value: Library Layout',
+                         'Protocol REF.2', 'Parameter Value: Sequencing Instrument',
+                         'Assay Name', 'Parameter Value: Read Length', 'Raw Data File',
+                         'Protocol REF.3', 'Parameter Value: Read Depth',
+                         'Parameter Value: MultiQC File Names']
+
+        # SAMPLE_COLUMNS = ['Source Name', 'Sample Name', 'Characteristics: Organism',
+        #                   'Characteristics: Strain', 'Characteristics: Genotype',
+        #                   'Characteristics: Material Type', 'Factor Value: Ionizing Radiation',
+        #                   'Factor Value: Generation', 'Protocol REF', 'Protocol REF.1',
+        #                   'Parameter Value: ionizing radiation energy',
+        #                   'Parameter Value: exposure duration',
+        #                   'Parameter Value: absorbed radiation dose',
+        #                   'Parameter Value: absorbed radiation dose rate',
+        #                   'Parameter Value: ionizing radiation categorized by source',
+        #                   'Protocol REF.2', 'Parameter Value: Sample Preservation Method',
+        #                   'Parameter Value: Sample Storage Temperature',
+        #                   'Parameter Value: Age at time of sample collection',
+        #                   'Comment: Animal Source', 'Comment: Parental Treatment']
+
+        features = datasets.Features(
+            {
+                column_name: datasets.Value("string")
+                for column_name in ASSAY_COLUMNS
+                # for column_name in sorted(list(set(ASSAY_COLUMNS + SAMPLE_COLUMNS)))
+            }
+        )
+
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=features,
+            supervised_keys=None,
+            homepage=_HOMEPAGE,
+            license=_LICENSE,
+            citation=_CITATION,
+        )
+
+    def _split_generators(self, dl_manager):
+        # no need to download, dataset is there!
+        # dataset_root = dl_manager.download_and_extract(_FIFTYONE_DATASET_URL)
+        return [
+            datasets.SplitGenerator(
+                name=datasets.Split.TRAIN,
+                gen_kwargs={
+                    "split": "train",
+                    "dataset_root": "/Users/anz2/PycharmProjects/NASA/NASA_OSDR/data",
+                },
+            ),
+        ]
+
+    def _generate_examples(self, split: str, dataset_root: str):
+        assays = os.path.join(dataset_root, "assays.csv")
+        samples = os.path.join(dataset_root, "samples.csv")
+        # there can be other metadata tables merged
+
+        assays_df = pd.read_csv(assays)
+        samples_df = pd.read_csv(samples)
+
+        for (idx, assay_row), (_, sample_row) in zip(assays_df.iterrows(), samples_df.iterrows()):
+            _item = {**assay_row.to_dict()}
+            # _item = {**assay_row.to_dict(), **sample_row.to_dict()}
+
+            yield idx, _item

tests/test_dataset_files.py

@@ -0,0 +1,6 @@
+import os
+
+
+def test_dataset_files():
+    assert os.path.exists('data/assays.csv')
+    assert os.path.exists('data/samples.csv')

tests/test_iliauni_icc_georgian_ocr.py

@@ -0,0 +1,50 @@
+import datasets
+from datasets import DatasetInfo, DownloadManager
+
+from nasa_osdr import NasaOsdr
+
+
+def test_inherit_generator_base_builder_works():
+    class Child(datasets.GeneratorBasedBuilder):
+        BUILDER_CONFIGS = [
+            datasets.BuilderConfig(
+                name="some dataset",
+                version=datasets.Version("1.0.0"),
+                description="some description",
+            )
+        ]
+
+        DEFAULT_CONFIG_NAME = "some dataset"
+
+        def _info(self) -> DatasetInfo:
+            return datasets.DatasetInfo(
+                description="""dadada """,
+                features=None,
+                supervised_keys=None,
+                homepage="dada",
+                license="dada",
+                citation="dsada",
+            )
+
+    child = Child()
+
+    assert child
+
+
+def test_generate_examples():
+    dataset = NasaOsdr()
+    train_data = dataset._generate_examples(dataset_root='data', split='train')
+    idx, sample = next(iter(train_data))
+    print(idx, sample.keys())
+
+
+def test_load_dataset():
+    from datasets import load_dataset
+    dataset = load_dataset("nasa_osdr.py")
+    print(len(dataset["train"]))
+
+
+# def test_load_dataset2():
+#     from datasets import load_dataset
+#     dataset = load_dataset("anz2/NASA_OSDR", use_auth_token="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")
+#     print(len(dataset["test"]))