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"""NASA OSDR - Open Science Data Repository""" |
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import os |
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import datasets |
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import pandas as pd |
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_CITATION = """ |
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NASA Space Biology Open Science Data Repository (OSDR) was accessed on 11.10.2023 from https://registry.opendata.aws/nasa-osdr. |
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""" |
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_DESCRIPTION = """ |
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This contains aggregated data from nasa-osdr s3 bucket. |
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It contains up to 451 experiments and tables of samples from those experiments. |
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Dataset curation is done in another github repo: https://github.com/AnzorGozalishvili/nasa_osdr_data_curation |
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""" |
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_HOMEPAGE = "https://huggingface.co/datasets/anz2/nasa-osdr" |
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_DATA_URL = "https://huggingface.co/datasets/anz2/nasa-osdr/resolve/main/data" |
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_LICENSE = "Apache 2.0" |
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_SPLITS = ["train"] |
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class NasaOsdrConfig(datasets.BuilderConfig): |
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"""BuilderConfig for nasa-osdr dataset.""" |
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def __init__(self, features, data_url, citation, license, url, **kwargs): |
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"""BuilderConfig for SuperGLUE. |
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Args: |
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features: *list[string]*, list of the features that will appear in the |
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feature dict. Should not include "label". |
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data_url: *string*, url to download the zip file from. |
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citation: *string*, citation for the data set. |
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url: *string*, url for information about the data set. |
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label_classes: *list[string]*, the list of classes for the label if the |
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label is present as a string. Non-string labels will be cast to either |
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'False' or 'True'. |
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**kwargs: keyword arguments forwarded to super. |
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""" |
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super().__init__(**kwargs) |
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self.features = features |
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self.data_url = data_url |
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self.citation = citation |
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self.license = license |
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self.url = url |
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class NasaOsdr(datasets.GeneratorBasedBuilder): |
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"""NASA OSDR dataset.""" |
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BUILDER_CONFIGS = [ |
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NasaOsdrConfig( |
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name="experiments", |
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version=datasets.Version("1.0.0"), |
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description=_DESCRIPTION, |
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citation=_CITATION, |
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features=["experiment_id", "version", "all_studies", "metadata_file_extensions", "metadata_filename", |
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"metadata_path", "metadata_filenames", "study_metadata_filenames", "metadata_sample_filename"], |
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data_url=_DATA_URL, |
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license=_LICENSE, |
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url=_HOMEPAGE, |
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), |
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NasaOsdrConfig( |
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name="samples", |
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version=datasets.Version("1.0.0"), |
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description=_DESCRIPTION, |
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citation=_CITATION, |
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features=["source name", "sample name", "characteristics[organism]", "term source ref", |
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"term accession number", "characteristics[strain]", "term source ref.1", |
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"term accession number.1", "characteristics[sex]", "term source ref.2", "term accession number.2", |
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"characteristics[developmental stage]", "term source ref.3", "term accession number.3", |
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"characteristics[material type]", "term source ref.4", "term accession number.4", |
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"factor value[spaceflight]", "term source ref.5", "term accession number.5", |
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"factor value[infection]", "term source ref.6", "term accession number.6", |
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"characteristics[experiment start date (dd/mm/yyyy)]", |
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"characteristics[experiment end date (dd/mm/yyyy)]", "protocol ref", "protocol ref.1", |
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"parameter value[vehicle]", "term source ref.7", "term accession number.7", |
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"parameter value[absorbed radiation dose]", "unit", "term source ref.8", |
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"term accession number.8", "parameter value[absorbed radiation dose rate]", "unit.1", |
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"term source ref.9", "term accession number.9", "parameter value[exposure duration]", "unit.2", |
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"term source ref.10", "term accession number.10", |
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"parameter value[ionizing radiation categorized by source]", "term source ref.11", |
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"term accession number.11", "parameter value[ionizing radiation]", "term source ref.12", |
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"term accession number.12", "comment [sample_description]", "comment [sample_source_name]", |
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"comment [sample_title]", "experiment_id", "version", "metadata_filename", "metadata_path", |
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"metadata_sample_filename", "characteristics[animal source]", "characteristics[age at launch]", |
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"characteristics[diet]", "comment[feeding schedule]", "parameter value[light cycle]", |
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"parameter value[habitat]", "parameter value[duration]", "parameter value[euthanasia method]", |
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"parameter value[carcass preservation method]", "parameter value[sample preservation method]", |
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"parameter value[sample storage temperature]", "term source ref.13", "term accession number.13", |
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"comment[source description]", "comment[original submitted sample name]", |
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"comment[alsda biospecimen id]", "comment[alsda biospecimen subject id]", |
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"comment[sample name description]", "comment[animal source]", |
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"parameter value[euthanasia chemical]", "comment[lsda biospecimen id]", |
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"comment[lsda biospecimen subject id]", "protocol ref.2", "unit.3", "term source ref.14", |
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"term accession number.14", "unit.4", "term source ref.15", "term accession number.15", "unit.5", |
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"term source ref.16", "term accession number.16", "term source ref.17", |
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"term accession number.17", "term source ref.18", "term accession number.18", |
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"parameter value[carcass storage method]", |
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"characteristics[strain,http://www.ebi.ac.uk/efo/efo_0005135,efo]", |
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"parameter value[light cycle,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c90419,ncit]", |
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"parameter value[habitat,http://purl.obolibrary.org/obo/envo_01000739,envo]", "material type", |
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"characteristics[sex,http://purl.obolibrary.org/obo/pato_0000047,efo]", |
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"parameter value[source storage method]", |
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"characteristics[growth,http://purl.obolibrary.org/obo/go_0040007,go]", |
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"factor value[weightlessness simulation]", "characteristics [age]", "characteristics [genotype]", |
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"characteristics [organism part]", "characteristics [protocol]", "characteristics [strain]", |
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"factor value[genotype]", "factor value[treatment]", "comment[initiation date]", |
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"comment[completion date]", "parameter value[storage temperature setting]", |
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"comment[maximum total absorbed dose ]", "comment[minimum total absorbed dose ]", |
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"factor value[absorbed radiation dose]", |
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"characteristics[exposure duration,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c83280,ncit]", |
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"characteristics[age]", "factor value[ionizing radiation]", |
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"parameter value[dose,http://purl.obolibrary.org/obo/exo_0000076,exo]", "factor value[time]", |
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"comment[sample_source_name]", "characteristics[genotype]", "characteristics[subspecies]", |
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"characteristics[flight name]", "characteristics[duration]", "parameter value[hardware]", |
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"parameter value[growth environment]", "parameter value[growth medium]", |
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"comment[sample characteristic]", |
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"factor value[weightlessness simulation,http://purl.bioontology.org/ontology/mesh/d018474,mesh]", |
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"factor value[tissue]", "comment[enclosure]", |
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"characteristics[diet,http://www.ebi.ac.uk/efo/efo_0002755,efo]", |
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"parameter value[exposure duration,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c83280,ncit]", |
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"parameter value[low let average abs. dose (spds only)]", |
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"parameter value[high let average abs. dose (all detectors)]", |
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"parameter value[abs. dose (gcr) rd3-b3]", "unit.6", "parameter value[abs. dose (orb) rd3-b3]", |
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"unit.7", "parameter value[abs. dose (total) rd3-b3]", "unit.8", |
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"parameter value[low let average abs. dose (all detectors)]", "unit.9", |
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"parameter value[low let max. abs. dose (all detectors)]", "unit.10", |
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"parameter value[high let min. abs. dose (all detectors)]", "unit.11", |
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"parameter value[high let max. abs. dose (all detectors)]", "unit.12", |
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"parameter value[low let min. abs. dose (all detectors)]", "unit.13", "term source ref.19", |
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"term accession number.19", "parameter value[abs. dose (irb/saa) rd3-b3]", "unit.14", |
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"term source ref.20", "term accession number.20", |
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"parameter value[average absorbed dose (spds only)]", "unit.15", "term source ref.21", |
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"term accession number.21", "parameter value[high let average abs. dose (spds only)]", "unit.16", |
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"term source ref.22", "term accession number.22", "characteristics[stage]", |
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"parameter value[sampling time,http://www.ebi.ac.uk/efo/efo_0000689,efo]", |
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"parameter value[temperature,http://www.ebi.ac.uk/efo/efo_0001702,efo]", |
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"factor value[microgravity]", "parameter value[housing temperature]", "comment[sample title]", |
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"comment[sanple description]", "factor value[bleomycin treatment]", |
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"characteristics[treatment duration]", "comment[sample source name]", "factor value[irradiation]", |
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"factor value[timepoint]", |
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"characteristics[cell line,http://purl.bioontology.org/ontology/mesh/d002460,mesh]", |
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"characteristics[cell type,http://purl.obolibrary.org/obo/cl_0000000,clo]", |
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"comment[source name description]", "characteristics[secondary organism]", |
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"characteristics[symbiosis,http://purl.bioontology.org/ontology/mesh/d013559,mesh]", |
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"factor value[simulated microgravity]", "characteristics [strainorline]", |
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"characteristics [biosourceprovider]", "characteristics [generation]", "factor value[generation]", |
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"factor value[environmentalstress]", "factor value[ecotype]", "characteristics[organism part]", |
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"characteristics[seed source]", "characteristics[stratification exposure]", |
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"parameter value[light source]", "parameter value[growth time]", |
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"characteristics[ecotype,http://www.ebi.ac.uk/efo/efo_0000434,efo]", |
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"parameter value[maximum total absorbed dose]", "parameter value[minimum total absorbed dose]", |
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"factor value[hypergravity]", "characteristics [cell type]", "characteristics [passage]", |
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"factor value[electromagnetic fields]", "parameter value[growth termperature]", |
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"characteristics[cell source]", "factor value[cell line]", |
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"parameter value[sample media information]", "parameter value[growth temperature]", |
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"factor value[microgravity simulation]", "comment[sample description]", "comment[iss expedition]", |
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"factor value[sample location]", "comment [ena_sample]", "characteristics [developmental stage]", |
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"factor value[ionzing radiation]", "characteristics[cell type]", |
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"characteristics[cell type,http://www.ebi.ac.uk/efo/efo_0000324,efo]", |
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"factor value[time of sample collection after treatment]", "comment[nih geo sample name]", |
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"factor value[age]", "characteristics[collection date]", "characteristics[isolation source]", |
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"characteristics[ecotype]", "factor value[atmospheric pressure]", "factor value[organism part]", |
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"parameter value[light regimen]", "parameter value[mean growth temperature]", |
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"parameter value[container]", "parameter value[light intensity]", |
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"parameter value[ph of growth medium]", "comment[original submitted sample]", |
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"parameter value[absorbed radiation dose,http://ncicb.nci.nih.gov/xml/owl/evs/thesaurus.owl#c95181,ncit]", |
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"comment[enclosure/habitat]", |
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"characteristics[ecotype,http://mged.sourceforge.net/ontologies/mgedontology.owl#ecotype,mo]", |
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"characteristics[age,http://mged.sourceforge.net/ontologies/mgedontology.owl#age,mo]", |
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"parameter value[growth condition,http://www.ebi.ac.uk/efo/efo_0000523,efo]", |
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"parameter value[duration,http://www.ebi.ac.uk/efo/efo_0000433,efo]", |
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"parameter value[treatment]", "parameter value[carcass weight]", |
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"parameter value[source storage temperature]", "comment[dissection date]", |
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"comment[alsda biospecimen source id]", "parameter value[canister and position]", |
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"factor value[freezing]", "parameter value[total cfu count]", |
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"parameter value[sample storage method]", "factor value[muscle, skeletal]", |
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"factor value[weightlessness,http://purl.bioontology.org/ontology/mesh/d014893,mesh]", |
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"characteristics[age,http://purl.obolibrary.org/obo/pato_0000011,pato]", |
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"comment[average absorbed dose (mgy) (spds only)]", |
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"comment[low let average abs. dose (spds only - mgy)]", |
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"comment[high let average abs. dose (spds only - mgy)]", "comment[abs. dose (gcr mgy) rd3-b3]", |
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"comment[abs. dose (irb/saa mgy) rd3-b3]", "comment[abs. dose (orb mgy) rd3-b3]", |
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"comment[abs. dose (total mgy) rd3-b3]", |
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"comment[low let average abs. dose (all detectors - mgy)]", |
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"comment[high let average abs. dose (all detectors - mgy)]", |
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"comment[low let min. abs. dose (all detectors - mgy)]", |
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"comment[low let max. abs. dose (all detectors - mgy)]", |
|
"comment[high let min. abs. dose (all detectors - mgy)]", |
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"comment[high let max. abs. dose (all detectors - mgy)]", |
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"parameter value[media,http://www.ebi.ac.uk/efo/efo_0000579,ccont]", |
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"characteristics [individual identifier]", "characteristics [sex]", |
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"factor value[sample collection protocol]", |
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"characteristics[cell line,http://purl.obolibrary.org/obo/clo_0000031,obi]", |
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"characteristics[age,http://purl.obolibrary.org/obo/pato_0000011,obi]", |
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"characteristics[cell cycle phase]", "factor value[cell cycle phase]", "comment[sample_title]", |
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"comment[sample_description]", "characteristics[host organism]", "factor value[dose]", |
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"characteristics[cultivar]", "parameter value[environment]", "factor value[sex]", |
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"characteristics[culture condition]", "factor value[culture condition]", |
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"characteristics[biosourceprovider]", "parameter value[ccont:media]", |
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"characteristics[sample type]", "characteristics[tissue]", "characteristics[study subject]", |
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"parameter value[ionizing radiation energy]", "parameter value[ionizing radiation device]", |
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"characteristics[sex,http://purl.bioontology.org/ontology/mesh/d012723,mesh]", |
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"characteristics[diet,http://purl.bioontology.org/ontology/mesh/d004032,mesh]", "unit[time unit]", |
|
"characteristics[culture type]", "factor value[donor]", "factor value[gender]", |
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"factor value[radiation dose]", "factor value[smoking status]", "characteristics[strain or line]", |
|
"characteristics[launch mission]", "comment[lsda subject id]", |
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"comment[sample name in raw and processed data]", "factor value[weightlessness]", |
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"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]", |
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"factor value[altitude]", "characteristics[cell line]", "parameter value[preservation method]", |
|
"factor value[exposure duration]", "comment [sample_characteristics]", |
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"comment[location of afflicted plants]", "characteristics [treatment group]", |
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"characteristics [cellline]", "factor value[treatment group]", |
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"characteristics[cell line origin]", "characteristics[treatment]", |
|
"characteristics[treatment time]", "factor value[mitochondrial status]", |
|
"factor value[rad9 status]", "comment[sample_name]", "characteristics [rad9 status]", |
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"parameter value[time]", "comment[bric canister]", "parameter value[sample storage temeperature]", |
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"parameter value[time in microgravity]", "parameter value[time in hypergravity]", |
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"factor value[hindlimb unloading]", "factor value[gravity, altered]", "characteristics [culture]", |
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"characteristics [organism]", "characteristics[subject]", "parameter value[group]", |
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"factor value[light cycle]", "factor value[animal housing]", "factor value[food deprivation]", |
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"factor value[water deprivation]", "parameter value[sample storage temperature setting]", |
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"parameter value[light amount]", "unnamed: 72", "factor value[bed rest]", |
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"factor value[sampling time]", "factor value[experimental campaign]", |
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"parameter value[tissue preservation,http://purl.bioontology.org/ontology/mesh/d014021,mesh]", |
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"parameter value[particle charge]", "parameter value[linear energy transfer]", |
|
"comment[nsrl run]", "characteristics [growth condition]", "comment[maximum total absorbed dose]", |
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"comment[minimum total absorbed dose]", "parameter value[sequencing blank]", |
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"factor value[sieve size]", "factor value[tetanus toxoid]", "factor value[vaccine adjuvant]", |
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"parameter value[housing condition]", "parameter value[starting body mass]", |
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"parameter value[final body mass]", "parameter value[final body mass].1", |
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"parameter value[sample preservatin method]", "parameter value[thymus mass]", |
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"comment[injection date]", "comment[sacrifice date]", "comment[ncorticosterone]", |
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"comment[genotype info]", "parameter value[ph]", "parameter value[age at sample harvest]", |
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"parameter value[sex,http://purl.obolibrary.org/obo/pato_0000047,efo]", |
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"factor value[dissection timeline]", "comment[average absorbed dose (spds only - mgy)]", |
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"comment[duration]", "characteristics[age at harvest]", "parameter value[mesh: cosmic radiation]", |
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"parameter value[time of sample collection after treatment]", |
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"parameter value[quantity of growth medium]", "parameter value[culture media]", "protocol ref.3", |
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"parameter value[injection date]", "parameter value[sacrifice date]", |
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"parameter value[ncorticosterone]", "parameter value[age at harvest]", "comment[seed source]", |
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"comment[sample name notes]", "factor value[cultivar]", "parameter value[light quality]", |
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"parameter value[environment,http://purl.bioontology.org/ontology/mesh/d004777,mesh]", |
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"factor value[soil environment exposure]", "parameter value[watering method]", |
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"parameter value[number of plants per sample (pooled)]", "parameter value[light time]", |
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"parameter value[light exposure]", "factor value[clinical treatment]", |
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"parameter value[body weight]", "characteristics[age,http://www.ebi.ac.uk/efo/efo_0000246,efo]", |
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"characteristics[tissue,http://purl.obolibrary.org/obo/uberon_0000479,envo]", |
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"parameter value[temperature,http://purl.obolibrary.org/obo/pato_0000146,envo]", |
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"parameter value[light,http://www.ebi.ac.uk/efo/efo_0000568,efo]", |
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"parameter value[euthanasia time after hs]", "factor value[growth time]", |
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"factor value[euthanasia method]", "factor value[carcass preservation method]", |
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"factor value[dissection condition]", "factor value[tissue preservation method]", |
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"factor value[diet]", "parameter value[sample weight]", "comment[launch date]", |
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"comment[euthanasia date]", "parameter value[enrichment material]", |
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"comment[date of ucla arrival]", "comment[alsda source name]", "comment[lsda source name]", |
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"factor value[duration]", "factor value[euthanasia location]", "comment[lsda sample name]", |
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"comment[alsda sample name]", "characteristics[host strain]", "characteristics[feeding schedule]", |
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"parameter value[nurfb lot number used during acclimation]", |
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"parameter value[nurfb lot number used in the habitat]", |
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"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 |
