Item.md

Item

Properties

Name	Type	Description	Notes
schema_version	str	The version of the JSON schema that the server uses to validate the object.	[optional]
uuid	str	The unique identifier associated with every object.	[optional]
notes	str	DACC internal notes.	[optional]
aliases	List[str]	Lab specific identifiers to reference an object.	[optional]
creation_timestamp	str	The date the object was created.	[optional]
submitted_by	str	The user who submitted the object.	[optional]
submitter_comment	str	Additional information specified by the submitter to be displayed as a comment on the portal.	[optional]
description	str	A plain text description of the object.	[optional]
status	str	The status of the metadata object.	[optional]
user	str	The user that is assigned to this access key.	[optional]
access_key_id	str	An access key.	[optional]
secret_access_key_hash	str	A secret access key.	[optional]
id	str		[optional]
type	List[str]		[optional]
summary	str		[optional]
preview_timestamp	str	The date the object was previewed.	[optional]
release_timestamp	str	The date the object was released.	[optional]
lab	str	Lab associated with the submission.	[optional]
award	str	Grant associated with the submission.	[optional]
analysis_step_types	List[str]	The classification of the software.	[optional]
step_label	str	Unique lowercased label of the analysis step that includes the relevant assays, the software used, and the purpose of the step, e.g. rampage-grit-peak-calling-step	[optional]
title	str	The full name of the user.	[optional]
parents	List[str]	The precursor steps.	[optional]
input_content_types	List[str]	The content types used as input for the analysis step.	[optional]
output_content_types	List[str]	The content types produced as output by the analysis step.	[optional]
analysis_step_versions	List[str]	The available versions of the analysis steps linked to this workflow.	[optional]
analysis_step	str	The analysis step which this version belongs to.	[optional]
software_versions	List[str]	The software versions associated with this publication.	[optional]
workflows	List[str]	The workflows associated with this publication.	[optional]
url	str	An external resource with additional information.	[optional]
name	str	The preferred viewable name of the workflow.	[optional]
start_date	str	The date when the award begins.	[optional]
end_date	str	The date when the award concludes.	[optional]
pis	List[str]	Principal Investigator(s) of the grant.	[optional]
contact_pi	str	The contact Principal Investigator of the grant.	[optional]
project	str	The collection of biological data related to a single initiative, originating from a consortium.	[optional]
viewing_group	str	The group that determines which set of data the user has permission to view.	[optional]
component	str	The project component the award is associated with.	[optional]
classification	str	Sample specific biomarker.	[optional]
quantification	str	The biomarker association to the biosample, disease or other condition. This can be the absence of the biomarker or the presence of the biomarker in some low, intermediate or high quantity.	[optional]
synonyms	List[str]	Synonyms for the term that have been recorded in an ontology.	[optional]
gene	str	Biomarker gene.	[optional]
name_quantification	str	A concatenation of the name and quantification of the biomarker.	[optional]
biomarker_for	List[str]	The samples which have been confirmed to have this biomarker.	[optional]
attachment	Attachment		[optional]
document_type	str	The category that best describes the document.	[optional]
characterization_method	str	The method used for the characterization.	[optional]
urls	List[str]	Link to the institutional certification form.	[optional]
standardized_file_format	bool	Specifies whether this format is an IGVF-standardized file format defined by Focus Groups or produced by a uniform pipeline.	[optional]
is_on_anvil	bool	Indicates whether the data object has been submitted to AnVIL.	[optional]
taxa	str	The species of the organism.	[optional]
publications	List[str]	The publications associated with this object.	[optional]
documents	List[str]	Documents that provide additional information (not data file).	[optional]
accession	str	A unique identifier to be used to reference the object prefixed with IGVF.	[optional]
alternate_accessions	List[str]	Accessions previously assigned to objects that have been merged with this object.	[optional]
collections	List[str]	Some samples are part of particular data collections.	[optional]
revoke_detail	str	Explanation of why an object was transitioned to the revoked status.	[optional]
dbxrefs	List[str]	Biosample identifiers from external resources, such as Biosample database or Cellosaurus.	[optional]
sex	str		[optional]
phenotypic_features	List[str]	A list of associated phenotypic features of the sample.	[optional]
virtual	bool	Virtual samples do not represent actual physical entities from experiments, but instead capture metadata about hypothetical or inferred samples relevant to reported analysis results, including those derived through demultiplexing.	[optional]
supersedes	List[str]	The sample(s) that this sample supersedes by virtue of being newer, better, or a fixed version of etc. than the one(s) it supersedes.	[optional]
related_donors	List[RelatedDonor]	Familial relations of this donor.	[optional]
ethnicities	List[str]	Ethnicity of the donor.	[optional]
human_donor_identifiers	List[str]	Identifiers of this human donor.	[optional]
superseded_by	List[str]	Sample(s) this sample is superseded by virtue of those sample(s) being newer, better, or a fixed version of etc. than this one.	[optional]
sources	List[str]	The originating lab(s) or vendor(s).	[optional]
lot_id	str	The lot identifier provided by the originating lab or vendor.	[optional]
product_id	str	The product identifier provided by the originating lab or vendor.	[optional]
strain_background	str	The specific parent strain designation of a non-human donor.	[optional]
strain	str	The specific strain designation of a non-human donor.	[optional]
genotype	str	The genotype of the strain according to accepted nomenclature conventions.	[optional]
individual_rodent	bool	This rodent donor represents an individual rodent.	[optional]
rodent_identifier	str	The identifier for this individual rodent donor.	[optional]
anvil_url	str	URL linking to the controlled access file that has been deposited at AnVIL workspace.	[optional]
base_modifications	List[str]	The chemical modifications to bases in a DNA sequence that are detected in this file.	[optional]
controlled_access	bool	Indicator of whether the samples are under controlled access.	[optional]
reference_files	List[str]	Link to the reference files used to generate this file.	[optional]
filtered	bool	Indicates whether the file has gone through some filtering step, for example, removal of PCR duplicates or filtering based on significance calling.	[optional]
analysis_step_version	str	The analysis step version of the quality metric.	[optional]
content_md5sum	str	The MD5sum of the uncompressed file.	[optional]
content_type	str	The type of content in the file.	[optional]
derived_from	List[str]	The files participating as inputs into software to produce this output file.	[optional]
derived_manually	bool	A boolean indicating whether the file has been dervided manually without automated computational methods.	[optional]
file_format	str	The file format or extension of the file.	[optional]
file_format_specifications	List[str]	Documents that describe the file format and fields of this file.	[optional]
file_set	str	The file set that this file belongs to.	[optional]
file_size	int	File size specified in bytes.	[optional]
md5sum	str	The md5sum of the file being transferred.	[optional]
submitted_file_name	str	Original name of the file.	[optional]
upload_status	str	The upload/validation status of the file.	[optional]
validation_error_detail	str	Explanation of why the file failed the automated content checks.	[optional]
checkfiles_version	str	The Checkfiles GitHub version release the file was validated with.	[optional]
checkfiles_timestamp	str	The date and time the file object was last checked by the Checkfiles script.	[optional]
read_count	int	Number of reads in a fastq file.	[optional]
redacted	bool	Indicates whether the alignments data have been sanitized (redacted) to prevent leakage of private and potentially identifying genomic information.	[optional]
integrated_in	List[str]	Construct library set(s) that this file was used for in insert design.	[optional]
input_file_for	List[str]	The files which are derived from this file.	[optional]
gene_list_for	List[str]	File Set(s) that this file is a gene list for.	[optional]
loci_list_for	List[str]	File Set(s) that this file is a loci list for.	[optional]
quality_metrics	List[str]	The quality metrics that are associated with this file.	[optional]
assay_titles	List[str]	Ontology term names from Ontology of Biomedical Investigations (OBI) for assays.	[optional]
preferred_assay_titles	List[str]	The custom lab preferred label for the experiment performed.	[optional]
href	str	The download path to obtain file.	[optional]
s3_uri	str	The S3 URI of public file object.	[optional]
upload_credentials	object	The upload credentials for S3 to submit the file content.	[optional]
content_summary	str	A summary of the data in the signal file.	[optional]
transcriptome_annotation	str	The annotation and version of the reference resource.	[optional]
assembly	str	Genome assembly applicable for the tabular data.	[optional]
catalog_collections	List[str]	The collections in the IGVF catalog that contain the data in this file.	[optional]
catalog_class	str	The class curated in the IGVF catalog that the data in this file belongs to.	[optional]
catalog_notes	str	DACC notes for data loading in the IGVF catalog	[optional]
seqspec_of	List[str]	Sequence files this file is a seqspec of.	[optional]
validate_onlist_files	bool	Whether checkfiles will validate the onlist files.	[optional]
imaging_platform	str	The measurement device used to produce imaging data.	[optional]
principal_dimension	str	The principal dimension of the matrix.	[optional]
secondary_dimensions	List[str]	The secondary, tertiary....n levels of dimensions of the matrix.	[optional]
externally_hosted	bool		[optional]
external_host_url	str	A link to the resource where the file is externally hosted.	[optional]
catalog_adapters	List[str]	IGVF Catalog Adapters that ingests this file	[optional]
source_url	str	An external resource to the code base of the workflow in github.	[optional]
file_format_type	str	The subtype of bed files.	[optional]
catalog_method	str	The method curated in the IGVF catalog that the non-IGVF data in this file processed with	[optional]
flowcell_id	str	The alphanumeric identifier for the flowcell of a sequencing machine.	[optional]
lane	int	An integer identifying the lane of a sequencing machine.	[optional]
tile	Tile		[optional]
minimum_read_length	int	For high-throughput sequencing, the minimum number of contiguous nucleotides determined by sequencing.	[optional]
maximum_read_length	int	For high-throughput sequencing, the maximum number of contiguous nucleotides determined by sequencing.	[optional]
mean_read_length	float	For high-throughput sequencing, the mean number of contiguous nucleotides determined by sequencing.	[optional]
seqspec_document	str	A seqspec document describing the library and read structure.	[optional]
sequencing_platform	str	The measurement device used to produce sequencing data.	[optional]
sequencing_kit	str	A reagent kit used with a library to prepare it for sequencing.	[optional]
sequencing_run	int	An ordinal number indicating which sequencing run of the associated library that the file belongs to.	[optional]
illumina_read_type	str	The read type of the file. Relevant only for files produced using an Illumina sequencing platform.	[optional]
index	str	An Illumina index associated with the file.	[optional]
read_names	List[str]	The read names of a sequence file based on how it will be used by uniform pipelines.	[optional]
seqspecs	List[str]	Link(s) to the associated seqspec YAML configuration file(s).	[optional]
strand_specificity	str	Indicates whether a transcriptomic library is forward, reverse, or unstranded based on the strand-specific protocol used.	[optional]
normalized	bool	Indicates if the signal file is normalized.	[optional]
start_view_position	str	The 0-based coordinate for the default starting position when viewing the signal in a genome browser.	[optional]
barcode_map_for	List[str]	Link(s) to the Multiplexed samples using this file as barcode map.	[optional]
enrichment_design_for	List[str]	Link(s) to the measurement sets using this file as a enrichment design.	[optional]
doi	str	The Digital Object Identifier (DOI) associated with this object.	[optional]
input_file_sets	List[str]	The file set(s) required for this pseudobulking analysis.	[optional]
samples	List[str]	The samples associated with this publication.	[optional]
donors	List[str]	Donor(s) the sample was derived from.	[optional]
file_set_type	str	The level of this analysis set.	[optional]
external_image_data_url	str	Links to the external site where images and related data produced by this analysis are stored.	[optional]
demultiplexed_samples	List[str]	The sample(s) associated with this analysis set inferred through demultiplexing.	[optional]
uniform_pipeline_status	str	The status of the single cell or Perturb-seq uniform pipeline processing for this analysis set, if applicable.	[optional]
pipeline_parameters	List[str]	The document(s) or file(s) providing necessary configurations for reproducing the analysis.	[optional]
files	List[str]	The files associated with this file set.	[optional]
control_for	List[str]	The file sets for which this file set is a control.	[optional]
submitted_files_timestamp	str	The timestamp the first file object in the file_set or associated auxiliary sets was created.	[optional]
input_for	List[str]	The file sets that use this file set as an input.	[optional]
construct_library_sets	List[str]	The construct library sets of vectors introduced to this sample prior to performing an assay.	[optional]
data_use_limitation_summaries	List[str]	The data use limitation summaries of institutional certificates covering the sample associated with this file set which are signed by the same lab (or their partner lab) as the lab that submitted this file set.	[optional]
protocols	List[str]	Links to the protocol(s) for preparing the samples on Protocols.io.	[optional]
sample_summary	str	A summary of the samples associated with input file sets of this analysis set.	[optional]
functional_assay_mechanisms	List[str]	The biological processes measured by this functional assay. For example, a VAMP-seq (MultiSTEP) assay measures the effects of variants on protein carboxylation and secretion processes.	[optional]
targeted_genes	List[str]	A list of genes targeted in this assay. For example, TF ChIP-seq attempts to identify binding sites of a protein encoded by a specific gene. In CRISPR FlowFISH, the modified samples are sorted based on expression of a specific gene. This property differs from small_scale_gene_list in Construct Library Set, which describes genes targeted by the content integrated in the constructs (such as guide RNAs.)	[optional]
enrichment_designs	List[str]	Files describing the assay-specific enrichment strategy (e.g., primer designs for PCR-based methods or probe/bait designs for hybrid capture) that define which regions are preferentially sequenced in this measurement set.	[optional]
barcode_map	str	The link to the barcode mapping tabular file.	[optional]
measurement_sets	List[str]	The measurement sets that link to this auxiliary set.	[optional]
control_file_sets	List[str]	File sets that can serve as scientific controls for this file set.	[optional]
small_scale_loci_list	List[Locus1]	A small scale (<=100) list of specific chromosomal region(s) whose functionality is investigated in this prediction set. This property describes the input variables of the prediction set. For example, this list consists of the genetic variants whose functionality is predicted in this prediction set.	[optional]
large_scale_loci_list	str	A large scale list (>100) of specific chromosomal regions whose functionality is investigated in this prediction set. This property describes the input variables of the prediction set. For example, this list consists of the genetic variants whose functionality is predicted in this prediction set.	[optional]
small_scale_gene_list	List[str]	The specific, small scale list of (<=100) gene(s) whose functionality is investigated in this prediction set. This property describes the input variables of the prediction set. For example, this list consists of the genes whose expression level is predicted in this prediction set. It differs from assessed_genes (see more information under assessed_genes).	[optional]
large_scale_gene_list	str	The large scale list of (>100 genes) whose functionality is investigated in this prediction set. This property describes the input variables of the prediction set. For example, this list consists of the genes whose expression level is predicted in this prediction set. It differs from assessed_genes (see more information under assessed_genes).	[optional]
control_types	List[str]	The types of control this measurement set represents.	[optional]
scope	str	The scope or scale that this prediction set is designed to target.	[optional]
selection_criteria	List[str]	The criteria used to select the sequence material cloned into the library.	[optional]
integrated_content_files	List[str]	The files containing sequence material of interest either used for insert design or directly cloned into vectors in this library.	[optional]
associated_phenotypes	List[str]	Ontological terms for diseases or phenotypes associated with this prediction set.	[optional]
orf_list	List[str]	List of Open Reading Frame this construct library was designed to target.	[optional]
exon	str	An identifier in plain text for the specific exon in an expression vector library. The associated gene must be listed in the small_scale_gene_list property.	[optional]
guide_type	str	The design of guides used in a CRISPR library, paired-guide (pgRNA) or single-guide (sgRNA).	[optional]
tiling_modality	str	The tiling modality of guides across elements or loci in a CRISPR library.	[optional]
average_guide_coverage	float	The average number of guides targeting each element of interest in the library.	[optional]
lower_bound_guide_coverage	int	Lower bound of the number of guides targeting each element of interest in the library.	[optional]
upper_bound_guide_coverage	int	Upper bound of the number of guides targeting each element of interest in the library.	[optional]
average_insert_size	float	The average size of the inserts cloned into vectors in the library.	[optional]
lower_bound_insert_size	int	Lower bound of the size of the inserts cloned in vectors in the library.	[optional]
upper_bound_insert_size	int	Upper bound of the size of the inserts cloned in vectors in the library.	[optional]
targeton	str	An identifier in plain text for the specific targeton in an editing template library. The associated gene must be listed in the small_scale_gene_list property.	[optional]
file_sets	List[str]	The file sets linked to this sample.	[optional]
assemblies	List[str]	The genome assemblies to which the referencing files in the file set are utilizing (e.g., GRCh38).	[optional]
transcriptome_annotations	List[str]	The annotation versions of the reference resource.	[optional]
assay_term	str	The assay used to produce data in this measurement set.	[optional]
multiome_size	int	The number of datasets included in the multiome experiment this measurement set is a part of.	[optional]
sequencing_library_types	List[str]	Description of the libraries sequenced in this measurement set.	[optional]
auxiliary_sets	List[str]	The auxiliary sets of files produced alongside raw data from this measurement set.	[optional]
external_image_urls	List[str]	Links to the external site where images produced by this measurement are stored.	[optional]
onlist_method	str	The method by which the onlist files will be combined by the seqspec onlist tool to generate the final barcode inclusion list for the single cell uniform pipeline.	[optional]
onlist_files	List[str]	The barcode region onlist files listed in associated seqspec yaml files.	[optional]
barcode_replacement_file	str	A file containing original barcodes and the new barcodes used to replace the original barcodes. One common application is to use in preprocessing Parse SPLiT-seq data with the single cell uniform pipeline.	[optional]
library_preparation_kit	str	A kit utilized in the library preparation procedure.	[optional]
related_measurement_sets	List[RelatedMeasurementSetGroup]	Measurement sets related to this one, grouped by relationship type.	[optional]
model_name	str	The custom lab name given to this predictive model set.	[optional]
model_version	str	The semantic version number for this predictive model set.	[optional]
prediction_objects	List[str]	The objects this predictive model set is targeting.	[optional]
model_zoo_location	str	The link to the model on the Kipoi repository.	[optional]
assessed_genes	List[str]	A list of gene(s) assessed in this prediction set. This property is used to describe the gene(s) being investigated, especially how the input variables in the prediction set affect some critical functionality of the gene(s). For example, the effect could be predicted from genetic variants on the binding affinity of a transcription factor encoded by a gene (assessed_genes). It differs from small_scale_gene_list and large_scale_gene_list, as these are used when the input variables of the prediction set are genes.	[optional]
external_input_data	str	A tabular file with links to external data utilized for this model.	[optional]
cell_type	str	The ontology term that describes the cell type of the cells in this pseudobulk.	[optional]
cell_qualifier	str	A qualifier that provides additional detail about the cell type annotation or the source biosample.	[optional]
geneid	str	ENSEMBL GeneID of official nomenclature approved gene. The GeneID does not include the current version number suffix.	[optional]
symbol	str	Gene symbol approved by the official nomenclature.	[optional]
study_sets	List[str]	The studies of IGVF that this gene was a part of.	[optional]
locations	List[GeneLocation1]	Gene locations specified using 1-based, closed coordinates for different versions of reference genome assemblies.	[optional]
allele	str	The allele of the gene.	[optional]
version_number	str	Current ENSEMBL GeneID version number of the gene.	[optional]
geneid_with_version	str	The ENSEMBL GeneID concatenated with its version number.	[optional]
geneid_with_allele	str	The ENSEMBL GeneID concatenated with its allele info.	[optional]
caption	str	The caption of the image.	[optional]
download_url	str	Download Url	[optional]
certificate_identifier	str	A unique identifier for the certificate.	[optional]
data_use_limitation	str	Code indicating the limitations on data use for data generated from the applicable samples.	[optional]
data_use_limitation_modifiers	List[str]	Code indicating a modifier on the limitations on data use for data generated from the applicable samples.	[optional]
partner_labs	List[str]	Labs which belong to same institution as the signing PI and can share this institutional certificate.	[optional]
partner_awards	List[str]	Awards granted to at least one lab that belongs to same institution as the signing PI and can share this institutional certificate.	[optional]
data_use_limitation_summary	str	A combination of the data use limitation and its modifiers	[optional]
pi	str	Principle Investigator of the lab.	[optional]
awards	List[str]	Grants associated with the lab.	[optional]
institute_label	str	An abbreviation for the institute the lab is associated with.	[optional]
activated	bool	A boolean indicating whether the modification has been activated by a chemical agent.	[optional]
activating_agent_term_id	str	The CHEBI identifier for the activating agent of the modification.	[optional]
activating_agent_term_name	str	The CHEBI name for the activating agent of the modification.	[optional]
modality	str	The purpose or intended effect of a modification.	[optional]
tagged_proteins	List[str]	The tagged proteins which are targeted for degradation.	[optional]
cas	str	The name of the CRISPR associated protein used in the modification.	[optional]
fused_domain	str	The name of the molecule fused to a Cas protein.	[optional]
cas_species	str	The originating species of the Cas nuclease.	[optional]
biosamples_modified	List[str]	The biosamples which have been modified with this modification.	[optional]
degron_system	str	The type of degron system implemented.	[optional]
term_id	str	An ontology identifier describing a biological sample	[optional]
term_name	str	Ontology term describing a biological sample, assay, trait, or disease.	[optional]
deprecated_ntr_terms	List[str]	A list of deprecated NTR terms previously associated with this ontology term.	[optional]
is_a	List[str]	A list of ontology terms which are the nearest ancestor to this ontology term.	[optional]
definition	str	Definition for the term that was recorded in an ontology.	[optional]
comments	List[str]	Comment for the term that was recorded in an ontology.	[optional]
ancestors	List[str]	List of term names of ontological terms that precede the given term in the ontological tree. These ancestor terms are typically more general ontological terms under which the term is classified.	[optional]
ontology	str	The ontology in which the term is recorded.	[optional]
assay_slims	List[str]	A broad categorization of the assay term.	[optional]
category_slims	List[str]	The type of feature or interaction measured by the assay.	[optional]
objective_slims	List[str]	The purpose of the assay.	[optional]
company	str	The company that developed and sells the instrument.	[optional]
sequencing_kits	List[str]	The available sequencing kits for this platform.	[optional]
organ_slims	List[str]	Organs associated with the sample term.	[optional]
cell_slims	List[str]	Cells associated with the sample term.	[optional]
developmental_slims	List[str]	Developmental stages associated with the sample term.	[optional]
system_slims	List[str]	Organ systems associated with the sample term.	[optional]
orf_id	str	Open reading frame ID.	[optional]
genes	List[str]	ENSEMBL GeneIDs of official nomenclature approved genes. The GeneIDs do not include the current version number suffix.	[optional]
protein_id	str	ENSEMBL ProteinID of official nomenclature approved protein. The ProteinID does not include the current version number suffix.	[optional]
pct_identical_protein	float	The percentage of identical matches to Ensembl protein.	[optional]
pct_coverage_protein	float	The percentage of ORF covered by Ensembl protein.	[optional]
pct_coverage_orf	float	The percentage of Ensembl protein covered by ORF.	[optional]
parent	str	The parent page associated with this page.	[optional]
layout	PageLayout		[optional]
canonical_uri	str	The path of the page.	[optional]
feature	str	The phenotypic feature observed for the donor.	[optional]
quantity	float	A quantity associated with the phenotypic feature, if applicable.	[optional]
quantity_units	str	The unit of measurement for a quantity associated with the phenotypic feature.	[optional]
quality	str	A quality assessment associated with the phenotypic feature, such as a categorical description.	[optional]
observation_date	str	The date the feature was observed or measured.	[optional]
abstract	str	Abstract of the publication or communication.	[optional]
authors	str	The authors of the publication.	[optional]
date_published	str	The date the publication or communication was published; must be in YYYY-MM-DD format.	[optional]
date_revised	str	The date the publication was revised.	[optional]
issue	str	The issue of the publication.	[optional]
page	str	Pagination of the reference	[optional]
volume	str	The volume of the publication.	[optional]
journal	str	The journal of the publication.	[optional]
publication_identifiers	List[str]	The publication identifiers associated with this publication object.	[optional]
published_by	List[str]	The affiliation of the lab with a larger organization, such as IGVF.	[optional]
website_url	str	A link to an external interactive website hosting data and analytic tools associated with the publication.	[optional]
publication_year	int	The year the publication was published.	[optional]
software	str	Unique name of the software package.	[optional]
quality_metric_of	List[str]	The file(s) to which this quality metric applies.	[optional]
pearson_correlation	float	The correlation of log2 RNA/DNA ratios across tested sequences as a measure of replicable activity signal. Value is the median of replicate comparisons using only oligos with >= 10 barcodes.	[optional]
median_barcodes_passing_filtering	float	Median number of barcodes across tested sequences that passed filtering to determine if there was sufficient barcode to oligo coverage. Value is the median of all replicates.	[optional]
median_rna_read_count	float	Median of RNA read count for oligos that passed filtering to determine sufficient coverage in terms of read count. Value is the median of all replicates.	[optional]
fraction_oligos_passing	float	Fraction of tested sequences that passed filtering of the mappable sequences to determine if the designed library was sufficiently recovered. Value is the median of all replicates.	[optional]
median_assigned_barcodes	float	Median number of barcodes assigned to tested sequences in mapping as a quality control measure for the assignment step, whether there is sufficient barcode to oligo coverage.	[optional]
fraction_assigned_oligos	float	Fraction of assigned tested sequences in mapping to determine if the library during the assignment step was sufficiently recovered.	[optional]
total_cells_passing_filters	float	Total Cells Passing Filters	[optional]
pct_cells_assigned_guide	float	Percent Cells Assigned Guide	[optional]
avg_cells_per_target	float	Average Cells Per Target	[optional]
moi	float	The actual multiplicity of infection (MOI) for vectors introduced to this sample. At least one construct library set must be specified in order to specify MOI. This property should capture the actual MOI, and not the targeted MOI.	[optional]
avg_umis_per_cell	float	Average UMIs Per Cell	[optional]
total_guides	float	Total Guides	[optional]
total_targets	float	Total Targets	[optional]
guide_diversity	float	Guide diversity (Gini index)	[optional]
mean_mitochondrial_reads	float	Mean mitochondrial reads.	[optional]
total_reads	float	Total reads (n_processed) reported by Kallisto.	[optional]
paired_reads_mapped	float	Paired reads mapped (n_pseudoaligned) reported by Kallisto.	[optional]
alignment_percentage	float	Alignment percentage (p_pseudoaligned) reported by Kallisto.	[optional]
total_detected_scrna_barcodes	float	Unfiltered total detected scRNA barcodes (numBarcodes) reported by Kallisto.	[optional]
pct_duplicates	float	Percentage of reads that are duplicatively mapped to the same genomic region.	[optional]
n_reads	float	Total number of input reads.	[optional]
n_mapped_reads	float	Reads successfully aligned to the reference genome.	[optional]
n_uniquely_mapped_reads	float	Reads aligned to a single location in the genome.	[optional]
n_reads_with_multi_mappings	float	Reads aligned to multiple locations in the genome.	[optional]
n_candidates	float	Potential mapping locations considered during alignment.	[optional]
n_mappings	float	Total successful alignments, including multiple mappings per read.	[optional]
n_uni_mappings	float	Total alignments where reads map to a single location.	[optional]
n_multi_mappings	float	Total alignments where reads map to multiple locations.	[optional]
n_barcodes_on_onlist	float	Barcodes matching the expected list of valid barcodes.	[optional]
n_corrected_barcodes	float	Barcodes adjusted to match valid entries in the onlist.	[optional]
n_output_mappings	float	Final count of fragments after deduplication and filtering.	[optional]
uni_mappings	float	Number of fragments mapping to single location in the genome.	[optional]
multi_mappings	float	Number of fragments mappig in multiple locations in the genome.	[optional]
total	float	Sum of uni-mappings and multi-mappings.	[optional]
atac_fragments_alignment_stats	ATACFragmentsAlignmentStats		[optional]
atac_bam_summary_stats	ATACBamSummaryStats		[optional]
atac_fragment_summary_stats	ATACFragmentSummaryStats		[optional]
n_records	float	Number of records in BUS file.	[optional]
n_barcodes	float	Total number of valid cell barcodes detected.	[optional]
total_umis	float	Total number of UMIs detected.	[optional]
n_barcode_umis	float	Total number of UMIs associated with cell barcodes.	[optional]
median_reads_per_barcode	float	Median number of reads per cell barcode.	[optional]
mean_reads_per_barcode	float	Mean number of reads per cell barcode.	[optional]
median_umis_per_barcode	float	Median number of UMIs per cell barcode.	[optional]
mean_umis_per_barcode	float	Mean number of UMIs per cell barcode.	[optional]
gt_records	float	Number of BUS records for Good-Toulmin estimation.	[optional]
num_barcodes_on_onlist	float	Number of cell barcodes matching an expected list of barcodes (onlist).	[optional]
percentage_barcodes_on_onlist	float	Percentage of cell barcodes matching an expected list of barcodes (onlist).	[optional]
num_reads_on_onlist	float	Number of reads associated with barcodes on the onlist.	[optional]
percentage_reads_on_onlist	float	Percentage of reads associated with barcodes on the onlist.	[optional]
rnaseq_kb_info	RNASeqKBInfo		[optional]
n_targets	float	Total number of target sequences (e.g., transcripts) in the index.	[optional]
n_bootstraps	float	Number of bootstrap iterations used to estimate expression uncertainty.	[optional]
n_processed	float	Number of valid reads processed by Kallisto.	[optional]
n_pseudoaligned	float	Number of reads that could be pseudoaligned to the transcriptome index.	[optional]
n_unique	float	Number of reads that could be pseudoaligned to a unique target sequence.	[optional]
p_pseudoaligned	float	Percentage of reads that could be pseudoaligned to the transcriptome index.	[optional]
p_unique	float	Percentage of reads that could be pseudoaligned to a unique target sequence.	[optional]
index_version	float	Version of Kallisto index command used for building the transcriptome index.	[optional]
kmer_length	float	Length of k-mers used for building the transcriptome index.	[optional]
coverage	float	Coverage of the library.	[optional]
coverage_per_basepair	float	Coverage at basepair level.	[optional]
rna_correlation_in_peaks	float	Correlation of RNA only over regions called as peaks in DNA.	[optional]
annotated_from	str	Links to the sample that was used as a reference for annotating this sample.	[optional]
lower_bound_age	float	Lower bound of age of the organism at the time of collection of the sample.	[optional]
upper_bound_age	float	Upper bound of age of the organism at the time of collection of the sample.	[optional]
age_units	str	The units of time associated with age of the biosample.	[optional]
sample_terms	List[str]	Ontology terms identifying a biosample.	[optional]
disease_terms	List[str]	Ontology term of the disease associated with the biosample.	[optional]
pooled_from	List[str]	The biosamples this biosample is pooled from.	[optional]
originated_from	str	Links to a biosample that was originated from due to differentiation, dedifferentiation, reprogramming, or the introduction of a genetic modification.	[optional]
treatments	List[str]	A list of treatments applied to the biosample with the purpose of perturbation.	[optional]
biomarkers	List[str]	Biological markers that are associated with this sample.	[optional]
embryonic	bool	Biosample is embryonic.	[optional]
modifications	List[str]	Links to modifications applied to this biosample.	[optional]
cellular_sub_pool	str	Cellular sub-pool fraction of the sample. Also known as PKR and sub-library.	[optional]
starting_amount	float	The initial quantity of samples obtained.	[optional]
starting_amount_units	str	The units used to quantify the amount of samples obtained.	[optional]
date_obtained	str	The date the sample was harvested, dissected or created, depending on the type of the sample.	[optional]
part_of	str	Links to a sample which represents a larger sample from which this sample was taken regardless of whether it is a tissue taken from an organism or smaller slices of a piece of tissue or aliquots of a cell growth.	[optional]
sorted_from	str	Links to a larger sample from which this sample was obtained through sorting.	[optional]
sorted_from_detail	str	Detail for sample sorted into fractions capturing information about sorting.	[optional]
nucleic_acid_delivery	str	Method of introduction of nucleic acid into the cell.	[optional]
time_post_library_delivery	float	The time that elapsed past the time-point when the construct library sets were introduced.	[optional]
time_post_library_delivery_units	str	The units of time that elapsed past the point when the construct library sets were introduced.	[optional]
selection_conditions	List[str]	The conditions used for selecting the sample.	[optional]
classifications	List[str]	The general category of this type of sample.	[optional]
time_post_change	float	The time that elapsed past the time-point when the cell fate change treatments were introduced.	[optional]
time_post_change_units	str	The units of time that elapsed past the point when the cell fate change treatments were introduced.	[optional]
cell_fate_change_protocol	str	A protocol applied to the biosample with the purpose of differentiation, dedifferentiation, or reprogramming.	[optional]
demultiplexed_from	str	The biosample this in vitro system sample was demultiplexed from using computational methods.	[optional]
passage_number	int	Number of passages including the passages from the source.	[optional]
targeted_sample_term	str	Ontology term identifying the targeted endpoint biosample resulting from differentation or reprogramming.	[optional]
growth_medium	str	A growth medium of the in vitro system.	[optional]
biosample_qualifiers	List[str]	An array of various cell states. This property provides additional information about a cell at a finer-grained level compared to what ontologies currently capture. For example, exhausted T-cells.	[optional]
time_post_culture	float	The time that elapsed since the biosample was placed into culture.	[optional]
time_post_culture_units	str	The units of time that elapsed since the biosample was placed into culture.	[optional]
multiplexed_in	List[str]	The multiplexed samples in which this sample is included.	[optional]
parts	List[str]	The parts into which this sample has been divided.	[optional]
sorted_fractions	List[str]	The fractions into which this sample has been sorted.	[optional]
origin_of	List[str]	The samples which originate from this sample, such as through a process of cell fate change or the introduction of a genetic material.	[optional]
institutional_certificates	List[str]	The institutional certificates under which use of this sample is approved.	[optional]
age	str	Age of organism at the time of collection of the sample.	[optional]
upper_bound_age_in_hours	float	Upper bound of age of organism in hours at the time of collection of the sample.	[optional]
lower_bound_age_in_hours	float	Lower bound of age of organism in hours at the time of collection of the sample .	[optional]
pooled_in	List[str]	The pooled samples in which this sample is included.	[optional]
demultiplexed_to	List[str]	The in vitro system samples this multiplexed sample has been demultiplexed into.	[optional]
multiplexed_samples	List[str]	The samples multiplexed together to produce this sample.	[optional]
multiplexing_methods	List[str]	The methods used for multiplexing and demultiplexing.	[optional]
sample_material	str		[optional]
pmi	int	The amount of time elapsed since death.	[optional]
pmi_units	str	The unit in which the PMI time was reported.	[optional]
preservation_method	str	The method by which the tissue/organ was preserved: cryopreservation (slow-freeze) or flash-freezing.	[optional]
used_by	List[str]	The component(s) of the IGVF consortium that utilize this software.	[optional]
categories	List[str]	The general categories of this software.	[optional]
versions	List[str]	A list of versions that have been released for this software.	[optional]
version	str	The version of a particular software.	[optional]
amount	float	Specific quantity of the applied treatment (used in conjunction with amount_units).	[optional]
amount_units	str	A unit for an amount other than those for time or temperature.	[optional]
duration	float	Duration indicates the time elapsed between the start and end of the treatment.	[optional]
duration_units	str	A unit of time.	[optional]
p_h	float	Final pH of the solution containing a chemical compound (if applicable)	[optional]
purpose	str	The intended purpose for treating the samples.	[optional]
post_treatment_time	float	Post treatment time in conjunction with post treatment time units is used to specify the time that has passed between the point when biosamples were removed from the treatment solution before being sampled or treated with the next treatment.	[optional]
post_treatment_time_units	str	A unit of time.	[optional]
temperature	float	The temperature in Celsius to which the sample was exposed	[optional]
temperature_units	str	A unit of temperature.	[optional]
treatment_type	str	The classification of treatment agent that specifies its exact molecular nature.	[optional]
treatment_term_id	str	Ontology identifier describing a component in the treatment.	[optional]
treatment_term_name	str	Ontology term describing a component in the treatment that is the principal component affecting the biosample being treated. Examples: interferon gamma, interleukin-4, Fibroblast growth factor 2, 20-hydroxyecdysone, 5-bromouridine etc.	[optional]
depletion	bool	Treatment is depleted.	[optional]
biosamples_treated	List[str]	The samples which have been treated using this treatment.	[optional]
email	str	The email associated with the user's account.	[optional]
first_name	str	The user's first (given) name.	[optional]
last_name	str	The user's last (family) name.	[optional]
submits_for	List[str]	Labs user is authorized to submit data for.	[optional]
groups	List[str]	Additional access control groups	[optional]
viewing_groups	List[str]	The group that determines which set of data the user has permission to view.	[optional]
job_title	str	The role of the user in their lab or organization.	[optional]
workflow_repositories	List[str]	Resources hosting the workflow.	[optional]
standards_page	str	A link to a page describing the standards for this workflow.	[optional]
workflow_version	str	The version of this workflow.	[optional]
uniform_pipeline	bool	Indicates whether the pipeline is developed by the IGVF consortium.	[optional]

Example

from igvf_client.models.item import Item

# TODO update the JSON string below
json = "{}"
# create an instance of Item from a JSON string
item_instance = Item.from_json(json)
# print the JSON string representation of the object
print(Item.to_json())

# convert the object into a dict
item_dict = item_instance.to_dict()
# create an instance of Item from a dict
item_from_dict = Item.from_dict(item_dict)

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