clone another repo.

.gitattributes

@@ -53,3 +53,7 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.jpg filter=lfs diff=lfs merge=lfs -text
 *.jpeg filter=lfs diff=lfs merge=lfs -text
 *.webp filter=lfs diff=lfs merge=lfs -text
+data/train/experiment_columns.json filter=lfs diff=lfs merge=lfs -text
+data/train/samples_columns.json filter=lfs diff=lfs merge=lfs -text
+data/train/experiments.csv filter=lfs diff=lfs merge=lfs -text
+data/train/samples.csv filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,11 @@
+---
+license: apache-2.0
+configs:
+- config_name: experiments
+  data_files: "data/train/experiments.csv"
+  sep: ","
+  default: true
+- config_name: samples
+  data_files: "data/train/samples.csv"
+  sep: ","
+---

data/train/experiment_columns.json

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+size 187

data/train/experiments.csv

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+size 195199

data/train/samples.csv

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+version https://git-lfs.github.com/spec/v1
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data/train/samples_columns.json

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+version https://git-lfs.github.com/spec/v1
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+size 31127

nasa-osdr.py

@@ -0,0 +1,548 @@
+# 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 - Open Science Data Repository"""
+
+import os
+
+import datasets
+import pandas as pd
+
+_CITATION = """
+NASA Space Biology Open Science Data Repository (OSDR) was accessed on 11.10.2023 from https://registry.opendata.aws/nasa-osdr.
+"""
+
+_DESCRIPTION = """
+This contains aggregated data from nasa-osdr s3 bucket. 
+It contains up to 451 experiments and tables of samples from those experiments. 
+Dataset curation is done in another github repo: https://github.com/AnzorGozalishvili/nasa_osdr_data_curation
+"""
+
+_HOMEPAGE = "https://huggingface.co/datasets/anz2/nasa-osdr"
+
+_DATA_URL = "https://huggingface.co/datasets/anz2/nasa-osdr/resolve/main/data"
+
+_LICENSE = "Apache 2.0"
+
+_SPLITS = ["train"]
+
+class NasaOsdrConfig(datasets.BuilderConfig):
+    """BuilderConfig for nasa-osdr dataset."""
+
+    def __init__(self, features, data_url, citation, license, url, **kwargs):
+        """BuilderConfig for SuperGLUE.
+
+        Args:
+        features: *list[string]*, list of the features that will appear in the
+            feature dict. Should not include "label".
+        data_url: *string*, url to download the zip file from.
+        citation: *string*, citation for the data set.
+        url: *string*, url for information about the data set.
+        label_classes: *list[string]*, the list of classes for the label if the
+            label is present as a string. Non-string labels will be cast to either
+            'False' or 'True'.
+        **kwargs: keyword arguments forwarded to super.
+        """
+        super().__init__(**kwargs)
+        self.features = features
+        self.data_url = data_url
+        self.citation = citation
+        self.license = license
+        self.url = url
+
+
+class NasaOsdr(datasets.GeneratorBasedBuilder):
+    """NASA OSDR dataset."""
+
+    BUILDER_CONFIGS = [
+        NasaOsdrConfig(
+            name="experiments",
+            version=datasets.Version("1.0.0"),
+            description=_DESCRIPTION,
+            citation=_CITATION,
+            features=["experiment_id", "version", "all_studies", "metadata_file_extensions", "metadata_filename",
+                      "metadata_path", "metadata_filenames", "study_metadata_filenames", "metadata_sample_filename"],
+            data_url=_DATA_URL,
+            license=_LICENSE,
+            url=_HOMEPAGE,
+        ),
+        NasaOsdrConfig(
+            name="samples",
+            version=datasets.Version("1.0.0"),
+            description=_DESCRIPTION,
+            citation=_CITATION,
+            features=["source name", "sample name", "characteristics[organism]", "term source ref",
+                      "term accession number", "characteristics[strain]", "term source ref.1",
+                      "term accession number.1", "characteristics[sex]", "term source ref.2", "term accession number.2",
+                      "characteristics[developmental stage]", "term source ref.3", "term accession number.3",
+                      "characteristics[material type]", "term source ref.4", "term accession number.4",
+                      "factor value[spaceflight]", "term source ref.5", "term accession number.5",
+                      "factor value[infection]", "term source ref.6", "term accession number.6",
+                      "characteristics[experiment start date (dd/mm/yyyy)]",
+                      "characteristics[experiment end date (dd/mm/yyyy)]", "protocol ref", "protocol ref.1",
+                      "parameter value[vehicle]", "term source ref.7", "term accession number.7",
+                      "parameter value[absorbed radiation dose]", "unit", "term source ref.8",
+                      "term accession number.8", "parameter value[absorbed radiation dose rate]", "unit.1",
+                      "term source ref.9", "term accession number.9", "parameter value[exposure duration]", "unit.2",
+                      "term source ref.10", "term accession number.10",
+                      "parameter value[ionizing radiation categorized by source]", "term source ref.11",
+                      "term accession number.11", "parameter value[ionizing radiation]", "term source ref.12",
+                      "term accession number.12", "comment [sample_description]", "comment [sample_source_name]",
+                      "comment [sample_title]", "experiment_id", "version", "metadata_filename", "metadata_path",
+                      "metadata_sample_filename", "characteristics[animal source]", "characteristics[age at launch]",
+                      "characteristics[diet]", "comment[feeding schedule]", "parameter value[light cycle]",
+                      "parameter value[habitat]", "parameter value[duration]", "parameter value[euthanasia method]",
+                      "parameter value[carcass preservation method]", "parameter value[sample preservation method]",
+                      "parameter value[sample storage temperature]", "term source ref.13", "term accession number.13",
+                      "comment[source description]", "comment[original submitted sample name]",
+                      "comment[alsda biospecimen id]", "comment[alsda biospecimen subject id]",
+                      "comment[sample name description]", "comment[animal source]",
+                      "parameter value[euthanasia chemical]", "comment[lsda biospecimen id]",
+                      "comment[lsda biospecimen subject id]", "protocol ref.2", "unit.3", "term source ref.14",
+                      "term accession number.14", "unit.4", "term source ref.15", "term accession number.15", "unit.5",
+                      "term source ref.16", "term accession number.16", "term source ref.17",
+                      "term accession number.17", "term source ref.18", "term accession number.18",
+                      "parameter value[carcass storage method]",
+                      "characteristics[strain,http://www.ebi.ac.uk/efo/efo_0005135,efo]",
+                      "parameter value[light cycle,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c90419,ncit]",
+                      "parameter value[habitat,http://purl.obolibrary.org/obo/envo_01000739,envo]", "material type",
+                      "characteristics[sex,http://purl.obolibrary.org/obo/pato_0000047,efo]",
+                      "parameter value[source storage method]",
+                      "characteristics[growth,http://purl.obolibrary.org/obo/go_0040007,go]",
+                      "factor value[weightlessness simulation]", "characteristics [age]", "characteristics [genotype]",
+                      "characteristics [organism part]", "characteristics [protocol]", "characteristics [strain]",
+                      "factor value[genotype]", "factor value[treatment]", "comment[initiation date]",
+                      "comment[completion date]", "parameter value[storage temperature setting]",
+                      "comment[maximum total absorbed dose ]", "comment[minimum total absorbed dose ]",
+                      "factor value[absorbed radiation dose]",
+                      "characteristics[exposure duration,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c83280,ncit]",
+                      "characteristics[age]", "factor value[ionizing radiation]",
+                      "parameter value[dose,http://purl.obolibrary.org/obo/exo_0000076,exo]", "factor value[time]",
+                      "comment[sample_source_name]", "characteristics[genotype]", "characteristics[subspecies]",
+                      "characteristics[flight name]", "characteristics[duration]", "parameter value[hardware]",
+                      "parameter value[growth environment]", "parameter value[growth medium]",
+                      "comment[sample characteristic]",
+                      "factor value[weightlessness simulation,http://purl.bioontology.org/ontology/mesh/d018474,mesh]",
+                      "factor value[tissue]", "comment[enclosure]",
+                      "characteristics[diet,http://www.ebi.ac.uk/efo/efo_0002755,efo]",
+                      "parameter value[exposure duration,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c83280,ncit]",
+                      "parameter value[low let average abs. dose (spds only)]",
+                      "parameter value[high let average abs. dose (all detectors)]",
+                      "parameter value[abs. dose (gcr) rd3-b3]", "unit.6", "parameter value[abs. dose (orb) rd3-b3]",
+                      "unit.7", "parameter value[abs. dose (total) rd3-b3]", "unit.8",
+                      "parameter value[low let average abs. dose (all detectors)]", "unit.9",
+                      "parameter value[low let max. abs. dose (all detectors)]", "unit.10",
+                      "parameter value[high let min. abs. dose (all detectors)]", "unit.11",
+                      "parameter value[high let max. abs. dose (all detectors)]", "unit.12",
+                      "parameter value[low let min. abs. dose (all detectors)]", "unit.13", "term source ref.19",
+                      "term accession number.19", "parameter value[abs. dose (irb/saa) rd3-b3]", "unit.14",
+                      "term source ref.20", "term accession number.20",
+                      "parameter value[average absorbed dose (spds only)]", "unit.15", "term source ref.21",
+                      "term accession number.21", "parameter value[high let average abs. dose (spds only)]", "unit.16",
+                      "term source ref.22", "term accession number.22", "characteristics[stage]",
+                      "parameter value[sampling time,http://www.ebi.ac.uk/efo/efo_0000689,efo]",
+                      "parameter value[temperature,http://www.ebi.ac.uk/efo/efo_0001702,efo]",
+                      "factor value[microgravity]", "parameter value[housing temperature]", "comment[sample title]",
+                      "comment[sanple description]", "factor value[bleomycin treatment]",
+                      "characteristics[treatment duration]", "comment[sample source name]", "factor value[irradiation]",
+                      "factor value[timepoint]",
+                      "characteristics[cell line,http://purl.bioontology.org/ontology/mesh/d002460,mesh]",
+                      "characteristics[cell type,http://purl.obolibrary.org/obo/cl_0000000,clo]",
+                      "comment[source name description]", "characteristics[secondary organism]",
+                      "characteristics[symbiosis,http://purl.bioontology.org/ontology/mesh/d013559,mesh]",
+                      "factor value[simulated microgravity]", "characteristics [strainorline]",
+                      "characteristics [biosourceprovider]", "characteristics [generation]", "factor value[generation]",
+                      "factor value[environmentalstress]", "factor value[ecotype]", "characteristics[organism part]",
+                      "characteristics[seed source]", "characteristics[stratification exposure]",
+                      "parameter value[light source]", "parameter value[growth time]",
+                      "characteristics[ecotype,http://www.ebi.ac.uk/efo/efo_0000434,efo]",
+                      "parameter value[maximum total absorbed dose]", "parameter value[minimum total absorbed dose]",
+                      "factor value[hypergravity]", "characteristics [cell type]", "characteristics [passage]",
+                      "factor value[electromagnetic fields]", "parameter value[growth termperature]",
+                      "characteristics[cell source]", "factor value[cell line]",
+                      "parameter value[sample media information]", "parameter value[growth temperature]",
+                      "factor value[microgravity simulation]", "comment[sample description]", "comment[iss expedition]",
+                      "factor value[sample location]", "comment [ena_sample]", "characteristics [developmental stage]",
+                      "factor value[ionzing radiation]", "characteristics[cell type]",
+                      "characteristics[cell type,http://www.ebi.ac.uk/efo/efo_0000324,efo]",
+                      "factor value[time of sample collection after treatment]", "comment[nih geo sample name]",
+                      "factor value[age]", "characteristics[collection date]", "characteristics[isolation source]",
+                      "characteristics[ecotype]", "factor value[atmospheric pressure]", "factor value[organism part]",
+                      "parameter value[light regimen]", "parameter value[mean growth temperature]",
+                      "parameter value[container]", "parameter value[light intensity]",
+                      "parameter value[ph of growth medium]", "comment[original submitted sample]",
+                      "parameter value[absorbed radiation dose,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c95181,ncit]",
+                      "comment[enclosure/habitat]",
+                      "characteristics[ecotype,http://mged.sourceforge.net/ontologies/mgedontology.owl#ecotype,mo]",
+                      "characteristics[age,http://mged.sourceforge.net/ontologies/mgedontology.owl#age,mo]",
+                      "parameter value[growth condition,http://www.ebi.ac.uk/efo/efo_0000523,efo]",
+                      "parameter value[duration,http://www.ebi.ac.uk/efo/efo_0000433,efo]",
+                      "parameter value[treatment]", "parameter value[carcass weight]",
+                      "parameter value[source storage temperature]", "comment[dissection date]",
+                      "comment[alsda biospecimen source id]", "parameter value[canister and position]",
+                      "factor value[freezing]", "parameter value[total cfu count]",
+                      "parameter value[sample storage method]", "factor value[muscle, skeletal]",
+                      "factor value[weightlessness,http://purl.bioontology.org/ontology/mesh/d014893,mesh]",
+                      "characteristics[age,http://purl.obolibrary.org/obo/pato_0000011,pato]",
+                      "comment[average absorbed dose (mgy) (spds only)]",
+                      "comment[low let average abs. dose (spds only - mgy)]",
+                      "comment[high let average abs. dose (spds only - mgy)]", "comment[abs. dose (gcr mgy) rd3-b3]",
+                      "comment[abs. dose (irb/saa mgy) rd3-b3]", "comment[abs. dose (orb mgy) rd3-b3]",
+                      "comment[abs. dose (total mgy) rd3-b3]",
+                      "comment[low let average abs. dose (all detectors - mgy)]",
+                      "comment[high let average abs. dose (all detectors - mgy)]",
+                      "comment[low let min. abs. dose (all detectors - mgy)]",
+                      "comment[low let max. abs. dose (all detectors - mgy)]",
+                      "comment[high let min. abs. dose (all detectors - mgy)]",
+                      "comment[high let max. abs. dose (all detectors - mgy)]",
+                      "parameter value[media,http://www.ebi.ac.uk/efo/efo_0000579,ccont]",
+                      "characteristics [individual identifier]", "characteristics [sex]",
+                      "factor value[sample collection protocol]",
+                      "characteristics[cell line,http://purl.obolibrary.org/obo/clo_0000031,obi]",
+                      "characteristics[age,http://purl.obolibrary.org/obo/pato_0000011,obi]",
+                      "characteristics[cell cycle phase]", "factor value[cell cycle phase]", "comment[sample_title]",
+                      "comment[sample_description]", "characteristics[host organism]", "factor value[dose]",
+                      "characteristics[cultivar]", "parameter value[environment]", "factor value[sex]",
+                      "characteristics[culture condition]", "factor value[culture condition]",
+                      "characteristics[biosourceprovider]", "parameter value[ccont:media]",
+                      "characteristics[sample type]", "characteristics[tissue]", "characteristics[study subject]",
+                      "parameter value[ionizing radiation energy]", "parameter value[ionizing radiation device]",
+                      "characteristics[sex,http://purl.bioontology.org/ontology/mesh/d012723,mesh]",
+                      "characteristics[diet,http://purl.bioontology.org/ontology/mesh/d004032,mesh]", "unit[time unit]",
+                      "characteristics[culture type]", "factor value[donor]", "factor value[gender]",
+                      "factor value[radiation dose]", "factor value[smoking status]", "characteristics[strain or line]",
+                      "characteristics[launch mission]", "comment[lsda subject id]",
+                      "comment[sample name in raw and processed data]", "factor value[weightlessness]",
+                      "factor value[altered gravity]", "factor value[space mission]",
+                      "characteristics[genotype,http://purl.bioontology.org/ontology/mesh/d005838,mesh]",
+                      "characteristics[ecotype,http://purl.bioontology.org/ontology/mesh/d060146,mesh]",
+                      "unit[timeunit]", "parameter value[sample description]",
+                      "characteristics[collection date,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c81286,ncit]",
+                      "factor value[altitude]", "characteristics[cell line]", "parameter value[preservation method]",
+                      "factor value[exposure duration]", "comment [sample_characteristics]",
+                      "comment[location of afflicted plants]", "characteristics [treatment group]",
+                      "characteristics [cellline]", "factor value[treatment group]",
+                      "characteristics[cell line origin]", "characteristics[treatment]",
+                      "characteristics[treatment time]", "factor value[mitochondrial status]",
+                      "factor value[rad9 status]", "comment[sample_name]", "characteristics [rad9 status]",
+                      "parameter value[time]", "comment[bric canister]", "parameter value[sample storage temeperature]",
+                      "parameter value[time in microgravity]", "parameter value[time in hypergravity]",
+                      "factor value[hindlimb unloading]", "factor value[gravity, altered]", "characteristics [culture]",
+                      "characteristics [organism]", "characteristics[subject]", "parameter value[group]",
+                      "factor value[light cycle]", "factor value[animal housing]", "factor value[food deprivation]",
+                      "factor value[water deprivation]", "parameter value[sample storage temperature setting]",
+                      "parameter value[light amount]", "unnamed: 72", "factor value[bed rest]",
+                      "factor value[sampling time]", "factor value[experimental campaign]",
+                      "parameter value[tissue preservation,http://purl.bioontology.org/ontology/mesh/d014021,mesh]",
+                      "parameter value[particle charge]", "parameter value[linear energy transfer]",
+                      "comment[nsrl run]", "characteristics [growth condition]", "comment[maximum total absorbed dose]",
+                      "comment[minimum total absorbed dose]", "parameter value[sequencing blank]",
+                      "factor value[sieve size]", "factor value[tetanus toxoid]", "factor value[vaccine adjuvant]",
+                      "parameter value[housing condition]", "parameter value[starting body mass]",
+                      "parameter value[final body mass]", "parameter value[final body mass].1",
+                      "parameter value[sample preservatin method]", "parameter value[thymus mass]",
+                      "comment[injection date]", "comment[sacrifice date]", "comment[ncorticosterone]",
+                      "comment[genotype info]", "parameter value[ph]", "parameter value[age at sample harvest]",
+                      "parameter value[sex,http://purl.obolibrary.org/obo/pato_0000047,efo]",
+                      "factor value[dissection timeline]", "comment[average absorbed dose (spds only - mgy)]",
+                      "comment[duration]", "characteristics[age at harvest]", "parameter value[mesh: cosmic radiation]",
+                      "parameter value[time of sample collection after treatment]",
+                      "parameter value[quantity of growth medium]", "parameter value[culture media]", "protocol ref.3",
+                      "parameter value[injection date]", "parameter value[sacrifice date]",
+                      "parameter value[ncorticosterone]", "parameter value[age at harvest]", "comment[seed source]",
+                      "comment[sample name notes]", "factor value[cultivar]", "parameter value[light quality]",
+                      "parameter value[environment,http://purl.bioontology.org/ontology/mesh/d004777,mesh]",
+                      "factor value[soil environment exposure]", "parameter value[watering method]",
+                      "parameter value[number of plants per sample (pooled)]", "parameter value[light time]",
+                      "parameter value[light exposure]", "factor value[clinical treatment]",
+                      "parameter value[body weight]", "characteristics[age,http://www.ebi.ac.uk/efo/efo_0000246,efo]",
+                      "characteristics[tissue,http://purl.obolibrary.org/obo/uberon_0000479,envo]",
+                      "parameter value[temperature,http://purl.obolibrary.org/obo/pato_0000146,envo]",
+                      "parameter value[light,http://www.ebi.ac.uk/efo/efo_0000568,efo]",
+                      "parameter value[euthanasia time after hs]", "factor value[growth time]",
+                      "factor value[euthanasia method]", "factor value[carcass preservation method]",
+                      "factor value[dissection condition]", "factor value[tissue preservation method]",
+                      "factor value[diet]", "parameter value[sample weight]", "comment[launch date]",
+                      "comment[euthanasia date]", "parameter value[enrichment material]",
+                      "comment[date of ucla arrival]", "comment[alsda source name]", "comment[lsda source name]",
+                      "factor value[duration]", "factor value[euthanasia location]", "comment[lsda sample name]",
+                      "comment[alsda sample name]", "characteristics[host strain]", "characteristics[feeding schedule]",
+                      "parameter value[nurfb lot number used during acclimation]",
+                      "parameter value[nurfb lot number used in the habitat]",
+                      "parameter value[nurfb nutrition values]", "term source ref.23", "term accession number.23",
+                      "term source ref.24", "term accession number.24", "parameter value[ionizing radiation source]",
+                      "term source ref.25", "term accession number.25",
+                      "characteristics[organism,http://purl.bioontology.org/ontology/sty/t001,mesh]",
+                      "comment[euthanasia and dissection date]",
+                      "characteristics[mission duration (between launch and landing)]",
+                      "characteristics[time between launch and sample harvest]", "parameter value[growth light color]",
+                      "parameter value[growth time start date (mm/dd/yy)]", "parameter value[actual gravity level]",
+                      "parameter value[light treatment duration]", "parameter value[treatment light intensity]",
+                      "parameter value[treatment light color]", "parameter value[treatment light source]",
+                      "parameter value[gravity treatment duration]", "parameter value[mission launch]",
+                      "parameter value[mission return]", "parameter value[launch date (mm/dd/yy)]",
+                      "parameter value[absorbed radiation dose (from launch to sample harvest)]", "term source ref.26",
+                      "term accession number.26", "parameter value[sample harvest date (mm/dd/yy)]",
+                      "term source ref.27", "term accession number.27", "comment[run]", "comment[mission]",
+                      "parameter value[sampling material]", "comment[collection date]", "factor value[strain]",
+                      "parameter value[carcass storage temperature]", "comment[bsp dissection date]",
+                      "comment[lsda biospecimen source id]",
+                      "characteristics[filter,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c41199,ncit]",
+                      "parameter value[carbon dioxide,http://purl.obolibrary.org/obo/chebi_16526,efo]",
+                      "parameter value[sample preservation temperature]",
+                      "parameter value[location,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c25341,ncit]",
+                      "parameter value[sample location]", "factor value[uv mutagenesis]", "factor value[growth cycle]",
+                      "factor value[sample storage]", "characteristics[strain source]",
+                      "parameter value[minimum growth temperature]", "parameter value[maximum growth temperature]",
+                      "parameter value[uv light exposure]", "characteristics[host genotype]",
+                      "characteristics[host age (at irradiation)]", "characteristics[donor strain]",
+                      "characteristics[donor genotype]", "characteristics[donor age (at mammary gland collection)]",
+                      "parameter value[light color]", "parameter value[harvest date (dd/mm/yyyy)]",
+                      "parameter value[experiment start date]", "parameter value[harvest date]",
+                      "parameter value[number of seeds per container]",
+                      "characteristics[developmental stage,http://www.ebi.ac.uk/efo/efo_0000399,efo]",
+                      "factor value[altered gravity simulator]", "factor value[temperature]",
+                      "characteristics[return mission]", "comment[source description].1",
+                      "parameter value[whole tissue weight]", "parameter value[tissue section level]",
+                      "comment[slide quadrant]", "comment[technical replicate #]",
+                      "comment[initiation date (dd-mmm-yy)]", "comment[completion date (dd-mmm-yy)]",
+                      "comment[dissection date (dd-mmm-yy)]", "factor value[preservation method]",
+                      "factor value[order of preservation]", "comment[spleen collection date]",
+                      "comment[liver collection date]", "comment[carcass weight (g)]",
+                      "comment[soleus collection date]", "parameter value[tissue]",
+                      "parameter value[host sample media information]", "parameter value[host growth time]",
+                      "parameter value[co2 level]", "characteristics[title]", "characteristics[biosample]",
+                      "characteristics[host,http://www.ebi.ac.uk/efo/efo_0000532,efo]", "parameter value[subject id]",
+                      "parameter value[sample collection timepoint]", "characteristics[age at onset of treatment]",
+                      "parameter value[anoxia treatment duration]", "parameter value[heat treatment duration]",
+                      "parameter value[treatment light regimen]", "comment[original submittted sample name]",
+                      "comment[sample name in raw data file]",
+                      "characteristics[identification,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c25737,ncit]",
+                      "parameter value[growth media information]",
+                      "characteristics[tissue,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c12801,ncit]",
+                      "parameter value[experiment batch]", "characteristics[age(at launch)]",
+                      "characteristics[growth time]", "parameter value[flight no.]",
+                      "parameter value[sampling matrial]", "factor value[light]", "factor value[developmental stage]",
+                      "characteristics[organism,http://mged.sourceforge.net/ontologies/mgedontology.owl#organism,mo]",
+                      "comment[description]", "characteristics[cultivar,http://www.ebi.ac.uk/efo/efo_0005136,efo]",
+                      "comment[seed lot]", "parameter value[broad-scale environmental context]",
+                      "parameter value[environmental medium]", "parameter value[isolation and growth condition]",
+                      "comment[biosample]", "comment[accession]", "comment[wgs accession no.]",
+                      "factor value[atmospheric composition]", "comment[biosample accession]",
+                      "parameter value[light type]", "parameter value[air temperature]",
+                      "parameter value[relative air humidity]", "parameter value[relative humidity]",
+                      "characteristics[maternal age]", "characteristics[paternal age]", "comment[ncbi accession]",
+                      "parameter value[ovariectomy]", "parameter value[euthanasia timing]",
+                      "parameter value[growth light cycle]", "parameter value[growth light source]",
+                      "parameter value[growth light intensity]", "parameter value[treatment light cycle]",
+                      "parameter value[gravity, altered]", "parameter value[mission]",
+                      "parameter value[developmental stage at onset of gravity treatment]",
+                      "parameter value[developmental stage at onset of light treatment]",
+                      "parameter value[developmental stage at time of sample collection]", "factor value[tiime]",
+                      "parameter value[sex]", "parameter value[growth temprature]", "factor value[study subject]",
+                      "parameter value[dose rate]", "comment[animal source (host)]",
+                      "characteristics[age (at irradiation)]", "characteristics[strain (donor strain)]",
+                      "comment[animal source (donor)]", "characteristics[genotype (donor genotype)]",
+                      "characteristics[control diet]", "parameter value[housing temperature(pre hibernation)]",
+                      "parameter value[light cycle (pre-hibernation)]",
+                      "parameter value[housing temperature (hibernation)]",
+                      "parameter value[light cycle (hibernation)]", "comment[sampling time]",
+                      "parameter value[growth time].1",
+                      "parameter value[euthanasia method,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c90336,ncit]",
+                      "parameter value[age at euthanasia]",
+                      "characteristics[developmental stage at onset of treatment]",
+                      "characteristics[genetic modification]", "characteristics [cage]", "characteristics [location]",
+                      "characteristics [strain or line]", "factor value[cage]", "factor value[location]",
+                      "parameter value[time,http://www.ebi.ac.uk/efo/efo_0000721,efo]",
+                      "parameter value[outer frame rotation]", "parameter value[inner frame rotation]",
+                      "factor value[particle charge]", "parameter value[time of sample collection after irradiation]",
+                      "characteristics[drosophila developmental stage,http://www.ebi.ac.uk/efo/efo_0005651,efo]",
+                      "factor value[ground based facilities]", "parameter value[radiation]", "parameter value[energy]",
+                      "parameter value[radiation source]",
+                      "characteristics[sex,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c28421,ncit]",
+                      "comment[animal id]",
+                      "parameter value[diet,http://purl.bioontology.org/ontology/mesh/d004032,mesh]",
+                      "parameter value[age at launch]",
+                      "parameter value[euthanasia,http://purl.bioontology.org/ontology/mesh/d005065,mesh]",
+                      "characteristics[mission return]", "parameter value[growth time start date (mm/dd/yyyy)]",
+                      "comment[light treatment description]", "parameter value[sample harvest date (mm/dd/yyyy)]",
+                      "characteristics[growth condition,http://www.ebi.ac.uk/efo/efo_0000523,efo]",
+                      "comment[technical replicate]", "comment[sacrifice date (dd-mmm-yy)]",
+                      "factor value[dry immersion]", "characteristics [biosourcetype]", "factor value[hze]",
+                      "comment[biosample no.]", "characteristics[height]", "characteristics[weight]",
+                      "factor value[intracranial pressure]", "parameter value[average icp]", "comment[plate]",
+                      "comment[plate well]", "parameter value[average fractionated dose rate]",
+                      "parameter value[ionizing radiation facility]", "parameter value[sample media informtion]",
+                      "factor value[radiation distance]", "parameter value[hze]",
+                      "parameter value[sample media informtio]", "parameter value[container diameter]",
+                      "parameter value[age at sample collection]", "characteristics[nasa isolate identifier]",
+                      "characteristics[mission collected]", "factor value[collection date]", "factor value[accession]",
+                      "parameter value[parental treatment light cycle]",
+                      "parameter value[parental treatment growth medium]",
+                      "parameter value[parental treatment light intensity]",
+                      "parameter value[parental treatment growth temperature]",
+                      "comment[lar animal receipt date at scrippts]", "comment[euthanasia dates]",
+                      "comment[dissection dates]", "characteristics[variety]",
+                      "factor value[sample preservation method]", "factor value[seed sanitization]",
+                      "characteristics[escherichia coli strain]", "parameter value[quantity of fertilizer]",
+                      "parameter value[collection date]", "comment[biosample accession ]",
+                      "comment[original sample id]", "comment[wgs accession no]", "comment[biosample no]",
+                      "parameter value[recovery duration on earth]", "comment[rfid]", "comment[date of birth]",
+                      "comment[lar animal receipt data at scripps]", "factor value[spacecraft]",
+                      "factor value[gravity]", "parameter value[quantity growth medium]",
+                      "parameter value[average percent humidity]", "parameter value[temperature range]",
+                      "parameter value[mean light intensity]", "comment[data file note]",
+                      "parameter value[mouse cage id]", "comment[rfid(last 4 digit)]",
+                      "comment[rfid(complete or last 4 digit)]", "factor value[partial weight bearing]",
+                      "comment[bsp dissection date (final dissection)]",
+                      "comment[euthanasia and dissection date (mm/dd/yyyy)]", "characteristics[experiment]",
+                      "characteristics[age when exposed to x-ray]",
+                      "characteristics[age when exposed to rapamycin/placebo]", "characteristics[age at irradiation]",
+                      "parameter value[diet]", "parameter value[number of particle types]",
+                      "parameter value[time between exposures]", "parameter value[nsrl run]",
+                      "comment[did samples remain in the beamline between exposures?]",
+                      "characteristics[sampling time,http://www.ebi.ac.uk/efo/efo_0000689,efo]",
+                      "comment[original submitter sample name]", "factor value[time after treatment]",
+                      "comment[alsda subject id]", "parameter value[body weight upon euthanasia]",
+                      "characteristics[age at euthanasia]", "parameter value[number of leaves at onset of treatment]",
+                      "parameter value[maximum growth protocol]",
+                      "parameter value[developmental stage at onset of treatment]",
+                      "parameter value[number of leaves at time of sample collection]",
+                      "parameter value[number of open flowers at time of sample collection]",
+                      "characteristics[variant]", "parameter value[number of seeds sown per well]",
+                      "characteristics[final body weight]", "characteristics[run number]",
+                      "parameter value[study subject]", "factor value[parabola]", "factor value[sample condition]",
+                      "comment[sample type]", "parameter value[collection condition]",
+                      "factor value[sample storage time]", "characteristics [celltype]",
+                      "factor value[space flight,http://purl.bioontology.org/ontology/mesh/d013026,mesh]",
+                      "characteristics[age before irradiation]", "characteristics [tissue]",
+                      "comment[lar animal receipt date at scripps]", "characteristics[generation]",
+                      "parameter value[age of f0 at launch]", "comment[experiment start date (dd/mm/yyyy)]",
+                      "comment[experiment end date (dd/mm/yyyy)]", "parameter value[mean treatment temperature]",
+                      "parameter value[age at time of sample collection]", "comment[parental treatment]",
+                      "characteristics[sample collection phase]", "factor value[tissue segment]",
+                      "parameter value[duration on iss]", "characteristics[donor id]",
+                      "comment[maximum total absorbed  dose]", "characteristics [cell line]",
+                      "characteristics [sample type]", "characteristics [treatment duration]",
+                      "factor value[treatment duration]", "parameter value[experiment]", "characteristics [individual]",
+                      "characteristics [sample name]", "factor value[individual]", "factor value[growth environment]",
+                      "parameter value[euthanasia date]", "comment[euthanasia date (dd/mm/yyyy)]",
+                      "comment[euthanasia date (dd-mmm-yyyy)]", "comment[bsp dissection date (dd-mmm-yyyy)]",
+                      "parameter value[growth hardware]", "parameter value[treatment hardware]",
+                      "comment[other sample source name]", "factor value[tissue model]",
+                      "factor value[culture media,http://purl.bioontology.org/ontology/mesh/d003470,mesh]",
+                      "factor value[zygosity,http://semanticscience.org/resource/sio_001263,sio]",
+                      "factor value[generation number,http://semanticscience.org/resource/sio_010061,sio]",
+                      "parameter value[age at onset of treatment]",
+                      "comment[intensity of best extracted proteins by beatbox homogenizer]",
+                      "parameter value[tonometry window]",
+                      "parameter value[sample preservation method histology and immunohistochemistry]",
+                      "parameter value[sample preservation method immunoblotting]", "comment[set]",
+                      "characteristics[seed source (host)]", "characteristics[pathogen strain source]",
+                      "parameter value[irrigation]", "parameter value[treatment mean growth temperature]",
+                      "parameter value[culture medium]", "comment[pathosystem]",
+                      "characteristics[age at start of assay]", "characteristics[stimulus]", "performer",
+                      "parameter value[anesthesia method]", "comment[euthanasia date (dd-mm-year)]",
+                      "comment[euthanasia time (hh:mm:ss)]", "comment[body weight at euthanasia]",
+                      "comment[bsp dissection date (dd-mm-year)]",
+                      "comment[partial body weight on bsp dissection date]", "factor value[housing condition]",
+                      "parameter value[number of cagemates]", "parameter value[feeding schedule]",
+                      "parameter value[age at time of assay]", "characteristics[growth temperature]",
+                      "characteristics[growth condition]", "comment[sample_characteristics]",
+                      "factor value[tissue type]", "factor value[developmental condition]", "comment[iss module type]",
+                      "parameter value[sample collection method]", "characteristics[age at experiment start]",
+                      "comment[sample location]", "comment[flight number]", "comment[location]", "comment[sample id]",
+                      "comment[sample collection date]", "comment[growthcondition]", "factor value[oxygen gas]",
+                      "characteristics[volunteers,http://purl.bioontology.org/ontology/mesh/d014838,mesh]",
+                      "characteristics[age at launch or beginning of treatment]",
+                      "characteristics [biological replicate]", "characteristics [dose gray]",
+                      "characteristics [post radiation time hour]", "characteristics [radiation]",
+                      "characteristics [technical replicate]", "factor value[post radiation timepoint]",
+                      "factor value[radiation type]", "parameter value[highly charged energetic nuclei]",
+                      "factor value[stress]",
+                      "characteristics[passage number,http://www.ebi.ac.uk/efo/efo_0007061,efo]",
+                      "characteristics[sample media information]", "factor value[variation]",
+                      "factor value[magnetic field]", "comment[sample type description]", "characteristics [exposure]",
+                      "characteristics [exposure time]", "factor value[pressure]", "factor value[collection set]",
+                      "characteristics[organism 2]", "characteristics[strain 2]", "characteristics[organism 3]",
+                      "parameter value[euthanasia time after landing]", "characteristics[sample_type]",
+                      "characteristics[organism_part]", "characteristics[sample_title]", "characteristics[irradation]",
+                      "characteristics[cell model]", "factor value[radiation]", "characteristics [mouse strain]",
+                      "factor value[mouse strain]", "characteristics[dose,http://www.ebi.ac.uk/efo/efo_0000428,efo]",
+                      "characteristics[radiation quality]", "characteristics [pathology]", "factor value[neoplasm]",
+                      "characteristics[antibiotic]", "factor value[antibiotic concentration]",
+                      "comment[source name- channel 2]", "factor value[radiation, ionzing]"],
+            data_url=_DATA_URL,
+            license=_LICENSE,
+            url=_HOMEPAGE,
+        ),
+    ]
+
+    def _info(self):
+        features = datasets.Features(
+            {
+                feature: datasets.Value("string")
+                for feature in self.config.features
+            }
+        )
+
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=features,
+            homepage=self.config.url,
+            license=self.config.license,
+            citation=self.config.citation,
+        )
+
+    def _split_generators(self, dl_manager):
+        if self.config.name == 'experiments':
+            downloaded_files = dl_manager.download_and_extract(
+                {
+                    "train": {
+                        "file": os.path.join(self.config.data_url, 'train/experiments.csv'),
+                    },
+                }
+            )
+
+            return [
+                datasets.SplitGenerator(
+                    name=datasets.Split.TRAIN,
+                    gen_kwargs={
+                        "file": downloaded_files['train']['file'],
+                    },
+                ),
+            ]
+        elif self.config.name == 'samples':
+            downloaded_files = dl_manager.download_and_extract(
+                {
+                    "train": {
+                        "file": os.path.join(self.config.data_url, 'train/samples.csv'),
+                    },
+                }
+            )
+
+            return [
+                datasets.SplitGenerator(
+                    name=datasets.Split.TRAIN,
+                    gen_kwargs={
+                        "file": downloaded_files['train']['file'],
+                    },
+                ),
+            ]
+
+    def _generate_examples(self, file: str):
+        df = pd.read_csv(file, index_col=0, low_memory=False)
+        for idx, row in df.iterrows():
+            _item = {**row.to_dict()}
+            yield idx, _item

tests/test_nasa_osdr.py

@@ -0,0 +1,64 @@
+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(name='experiments')
+    train_data = dataset._generate_examples(file='data/train/experiments.csv')
+    idx, sample = next(iter(train_data))
+    print(idx, sample.keys())
+
+    dataset = NasaOsdr(name='samples')
+    train_data = dataset._generate_examples(file='data/train/samples.csv')
+    idx, sample = next(iter(train_data))
+    print(idx, sample.keys())
+
+
+def test_load_dataset():
+    from datasets import load_dataset
+    experiments_dataset = load_dataset("nasa_osdr.py", "experiments")
+    print(len(experiments_dataset["train"]))
+    print(experiments_dataset['train'][:10])
+
+    samples_dataset = load_dataset("nasa_osdr.py", "samples")
+    print(len(samples_dataset["train"]))
+    print(samples_dataset['train'][:10])
+
+
+# def test_load_dataset2():
+#     from datasets import load_dataset
+#     dataset = load_dataset("anz2/NASA_OSDR", "experiments", use_auth_token="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")
+#     print(len(dataset["train"]))
+
+#     from datasets import load_dataset
+#     dataset = load_dataset("anz2/NASA_OSDR", "samples", use_auth_token="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")
+#     print(len(dataset["train"]))