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# 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 |