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<h1>CIDC Documentation</h1>
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Documentation for CIDC concepts, assays, and manifests.
</div>
<div class="container">
<div class="accordion" id="index_accordion">
<div class="card">
<div class="card-header" id="concepts">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#concepts_card" aria-expanded="false" aria-controls="concepts_card">
Concepts
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<div class="card-body">
<table class="table table-striped">
<tr>
<td width=25%>
<a href='shipping_core.html'>
Core Shipping Details
</a>
</td>
<td>
Core shipping details for a manifest.
</td>
</tr>
<tr>
<td width=25%>
<a href='sample.html'>
Sample
</a>
</td>
<td>
Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products.
</td>
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<td width=25%>
<a href='participant.html'>
Participant
</a>
</td>
<td>
The collection of all data related to a specific participant in the context of a specific clinical trial.
</td>
</tr>
<tr>
<td width=25%>
<a href='clinical_trial.html'>
Clinical Trial
</a>
</td>
<td>
Encapsulates information regarding a clinical trial.
</td>
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<td width=25%>
<a href='available_assays.html'>
Assays available in the network
</a>
</td>
<td>
Reference for every available assay in network.
</td>
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<td width=25%>
<a href='available_analyses.html'>
Analysis outputs for this trial.
</a>
</td>
<td>
Reference for every available assay in network.
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="assays">
<h2 class="mb-0">
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Assays
</button>
</h2>
</div>
<div id="assays_card" class="collapse show" aria-labelledby="assays" data-parent="#index_accordion">
<div class="card-body">
<table class="table table-striped">
<tr>
<td width=25%>
<a href='assays.atacseq.html'>
ATACseq Assay
</a>
</td>
<td>
Assay for Transposase-Accessible Chromatin by Sequencing
</td>
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<td width=25%>
<a href='assays.clinical_data.html'>
Clinical data Assay
</a>
</td>
<td>
Clinical data recorded for a clinical trial
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.ctdna.html'>
Circulating Tumor DNA Assay
</a>
</td>
<td>
Circulating Tumor DNA Assay.
</td>
</tr>
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<td width=25%>
<a href='assays.cytof.html'>
CYTOF Assay
</a>
</td>
<td>
Information about the acquisition and analysis CyTOF data.
</td>
</tr>
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<td width=25%>
<a href='assays.elisa.html'>
ELISA Assay
</a>
</td>
<td>
Enzyme-linked immunosorbent assay (ELISA).
</td>
</tr>
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<td width=25%>
<a href='assays.hande.html'>
H&E Assay
</a>
</td>
<td>
H & E assay
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.ihc.html'>
IHC Assay
</a>
</td>
<td>
Immunohistochemical analysis.
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.mibi.html'>
MIBI Assay
</a>
</td>
<td>
Multiplexed Ion Beam Imaging (MIBI) assay
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.microbiome.html'>
Microbiome Assay
</a>
</td>
<td>
Microbiome Assay.
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.mif.html'>
mIF Assay
</a>
</td>
<td>
Multiplex immunofluorescence.
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.misc_data.html'>
Miscellaneous data
</a>
</td>
<td>
Miscellaneous data not supported directly by any other assay.
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.nanostring.html'>
Nanostring Assay
</a>
</td>
<td>
A microarray assay for expression levels, suitable for smaller samples than RNA-seq
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.olink.html'>
Olink Assay
</a>
</td>
<td>
High-throughput multiplexed assays for protein biomarker discovery.
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.rna.html'>
RNAseq Gene Expression Assay
</a>
</td>
<td>
An RNA assay for expression analysis.
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.tcr.html'>
TCRseq Assay
</a>
</td>
<td>
Additional properties to describe a TCR assay for expression analysis.
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.wes.html'>
WES Assay
</a>
</td>
<td>
Information about the acquisition and analysis of Whole Exome Sequencing data.
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.wes_analysis.html'>
WES analysis combined files
</a>
</td>
<td>
Combined analysis files for the whole WES assay.
</td>
</tr>
<tr>
<td width=25%>
<a href='assays.wes_tumor_only_analysis.html'>
WES tumor-only analysis
</a>
</td>
<td>
Combined analysis files for the whole WES assay.
</td>
</tr>
<tr>
</tr>
<tr>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="manifests">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#manifests_card" aria-expanded="false" aria-controls="manifests_card">
Manifests
</button>
</h2>
</div>
<div id="manifests_card" class="collapse " aria-labelledby="manifests" data-parent="#index_accordion">
<div class="card-body">
<table class="table table-striped">
<tr>
<td width=25%>
<a href='manifests.tumor_tissue_dna_template.html'>
Biospecimen manifest for tumor tissue DNA
</a>
</td>
<td>
Biospecimen manifest for transferring tissue DNA extracted from tumor tissue samples.
</td>
</tr>
<tr>
<td width=25%>
<a href='manifests.pbmc_template.html'>
Biospecimen manifest for PBMC samples
</a>
</td>
<td>
Biospecimen manifest for transferring Peripheral Blood Mononuclear Cell (PBMC) samples.
</td>
</tr>
<tr>
<td width=25%>
<a href='manifests.h_and_e_template.html'>
Biospecimen manifest for H&E
</a>
</td>
<td>
Biospecimen manifest for transferring Hematoxylin and Eosin stained slides.
</td>
</tr>
<tr>
<td width=25%>
<a href='manifests.tumor_tissue_rna_template.html'>
Biospecimen manifest for tumor tissue RNA
</a>
</td>
<td>
Biospecimen manifest for transferring tissue RNA extracted from tumor tissue samples.
</td>
</tr>
<tr>
<td width=25%>
<a href='manifests.tissue_slide_template.html'>
Biospecimen manifest for tissue slides
</a>
</td>
<td>
Biospecimen manifest for transferring tissue slides.
</td>
</tr>
<tr>
<td width=25%>
<a href='manifests.normal_blood_dna_template.html'>
Biospecimen manifest for normal blood DNA
</a>
</td>
<td>
Biospecimen manifest for transferring DNA extracted from normal blood samples.
</td>
</tr>
<tr>
<td width=25%>
<a href='manifests.microbiome_dna_template.html'>
Shipping manifest for microbiome DNA extracted from stool samples
</a>
</td>
<td>
Shipping / receiving manifest for transferring microbiome DNA extracted from stool samples.
</td>
</tr>
<tr>
<td width=25%>
<a href='manifests.plasma_template.html'>
Biospecimen manifest for plasma samples
</a>
</td>
<td>
Biospecimen manifest for transferring blood plasma samples.
</td>
</tr>
<tr>
<td width=25%>
<a href='manifests.tumor_normal_pairing_template.html'>
Metadata manifest for WES analysis pairing
</a>
</td>
<td>
Metadata manifest for tumor / normal pairing for WES assay analysis.
</td>
</tr>
<tr>
<td width=25%>
<a href='manifests.normal_tissue_dna_template.html'>
Biospecimen manifest for normal tissue DNA
</a>
</td>
<td>
Biospecimen manifest for transferring DNA extracted from normal tissue samples.
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="files">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#files_card" aria-expanded="false" aria-controls="files_card">
Files
</button>
</h2>
</div>
<div id="files_card" class="collapse " aria-labelledby="files" data-parent="#index_accordion">
<div class="card-body">
<table class="table table-striped">
<tr>
<td width=25%>
<a href='files.clinical_csv.html'>
Generic clinical data CSV artifact
</a>
</td>
<td>
An comma-separated file containing clinical information.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.bed.html'>
BED Artifact
</a>
</td>
<td>
Information about a BED file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.junction.html'>
JUNCTION Artifact
</a>
</td>
<td>
Information about a JUNCTION file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.fastq_gz.html'>
Gzipped FastQ Artifact
</a>
</td>
<td>
Information about a Gzipped FASTQ file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.pdf.html'>
PDF Artifact
</a>
</td>
<td>
Information about a Portable Document Format file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.elisa_xlsx.html'>
ELISA results artifact
</a>
</td>
<td>
Information about an ELISA file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.bigwig.html'>
BIGWIG Artifact
</a>
</td>
<td>
Information about a BIGWIG file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.image.html'>
Image Artifact
</a>
</td>
<td>
Information about an image file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.bam.html'>
BAM Artifact
</a>
</td>
<td>
Information about a BAM file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.rcc.html'>
RCC Artifact
</a>
</td>
<td>
Information about a Nanostring output file. XML-formatted comma-separated tables
</td>
</tr>
<tr>
<td width=25%>
<a href='files.jpg.html'>
JPG Artifact
</a>
</td>
<td>
Information about a JPG file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.log.html'>
LOG Artifact
</a>
</td>
<td>
Information about a log file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.gz.html'>
GZ Artifact
</a>
</td>
<td>
Information about a GZ file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.text.html'>
Text Artifact
</a>
</td>
<td>
Information about a text file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.npx.html'>
NPX Artifact
</a>
</td>
<td>
Information about an NPX file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.cncf.html'>
CNCF Artifact
</a>
</td>
<td>
Information about a CNCF file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.tsv.html'>
TSV Artifact
</a>
</td>
<td>
Information about a tab Separated file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.bam_bai.html'>
BAM.BAI Artifact
</a>
</td>
<td>
Information about a Bam index file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.xlsx.html'>
Excel Artifact
</a>
</td>
<td>
Information about an XLSX file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.binary.html'>
Binary Artifact
</a>
</td>
<td>
Information about a binary file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.core.html'>
Artifact Core
</a>
</td>
<td>
Any file artifact associated with a clinical trial.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.narrowPeak.html'>
narrowPeak Artifact
</a>
</td>
<td>
Information about a narrowPeak file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.clinical_docx.html'>
Generic clinical data DOCX artifact
</a>
</td>
<td>
An Excel file containing clinical information.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.file.html'>
Generic Artifact
</a>
</td>
<td>
Information about a generic file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.csv.html'>
CSV Artifact
</a>
</td>
<td>
Information about a comma separated file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.vcf_gz.html'>
Gzipped VCF Artifact
</a>
</td>
<td>
Information about a Gzipped VCF file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.cns.html'>
CNS Artifact
</a>
</td>
<td>
Information about a CNS file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.png.html'>
PNG Artifact
</a>
</td>
<td>
Information about a PNG file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.zip.html'>
ZIP Artifact
</a>
</td>
<td>
Information about a ZIP file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.json.html'>
JSON Artifact
</a>
</td>
<td>
Information about a JSON file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.fcs.html'>
FCS Artifact
</a>
</td>
<td>
Information about a FCS file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.clinical_xlsx.html'>
Generic clinical data XLSX artifact
</a>
</td>
<td>
An Excel file containing clinical information.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.yaml.html'>
YAML Artifact
</a>
</td>
<td>
Information about a YAML file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.maf.html'>
MAF Artifact
</a>
</td>
<td>
Information about a MAF file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.tbi.html'>
TBI Artifact
</a>
</td>
<td>
Information about a Tabix index file.
</td>
</tr>
<tr>
<td width=25%>
<a href='files.vcf.html'>
VCF Artifact
</a>
</td>
<td>
Information about a VCF file.
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
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