# entry[].resource.title
Values associated with variable, file_manifest.File Format, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, file_manifest.Experimental Strategy, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, file_manifest.Data Type, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, file_manifest.Data Category, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, file_manifest.Data Access, from INCLUDE datasets.

# entry[].resource.concept[].display
Unique INCLUDE global identifier for the participant, assigned by DCC

# entry[].resource.concept[].display
Unique identifier for sample, assigned by data contributor. A sample is a unique biological material; two samples with two different IDs are biologically distinct.

# entry[].resource.concept[].display
INCLUDE global file identifier, assigned by DCC

# entry[].resource.concept[].display
Unique identifier for data file, assigned by data contributor

# entry[].resource.concept[].display
Name of file, assigned by data contributor

# entry[].resource.concept[].display
md5 hash of this file for validation (if known)

# entry[].resource.concept[].display
Type of access control on this file, determined by DCC

# entry[].resource.concept[].display
General category of data in file (e.g. Clinical, Genomics, Proteomics, Metabolomics, Immune profiling, Transcriptomics)

# entry[].resource.concept[].display
Specific type of data contained in file (e.g. Preprocessed metabolite relative abundance, Absolute protein concentration, Aligned reads, Simple nucleotide variations, GVCF, Gene expression quantifications, Gene fusions, Somatic copy number variations, Somatic structural variations)

# entry[].resource.concept[].display
Experimental method used to obtain data in file (e.g. Whole genome sequencing, RNAseq, Multiplex immunoassay, Mass spec metabolomics)

# entry[].resource.concept[].display
Specific platform used to perform experiment (e.g. SOMAscan, MSD, Luminex, Illumina)

# entry[].resource.concept[].display
Format of file (e.g. tsv, cram, gvcf, vcf, maf, txt, pdf, html, png)

# entry[].resource.concept[].display
Size of file, if known (mainly important if large)

# entry[].resource.concept[].display
DOI of publication associated with this file, if published

# entry[].resource.title
Variables associated with table, file_manifest, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, specimen.Volume Unit, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, specimen.Concentration_Unit, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, specimen.Biospecimen Storage, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, specimen.In/Out, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, specimen.Parent Sample Type, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, specimen.Container Availability, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, specimen.Collection Sample Type, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, specimen.Sample Availability, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, specimen.Sample Type, from INCLUDE datasets.

# entry[].resource.concept[].display
Unique INCLUDE global identifier for the participant, assigned by DCC

# entry[].resource.concept[].display
Unique, de-identified identifier for the participant, assigned by data contributor. External IDs must be two steps removed from personal information in the study records.

# entry[].resource.concept[].display
Age in days of participant at time of biospecimen collection

# entry[].resource.concept[].display
INCLUDE global identifier for sample, assigned by DCC

# entry[].resource.concept[].display
Unique identifier for sample, assigned by data contributor. A sample is a unique biological material; two samples with two different IDs are biologically distinct.

# entry[].resource.concept[].display
Type of biological material comprising the Sample (e.g. Plasma, White blood cells, Red blood cells, DNA, RNA, Peripheral blood mononuclear cells, CD4+ Tconv cells, NK cells, Monocytes, CD8+ T cells, B cells, Granulocytes, Treg cells)

# entry[].resource.concept[].display
Whether or not the sample is potentially available for sharing through
      the Virtual Biorepository

# entry[].resource.concept[].display
INCLUDE global identifier for the eldest sample in a lineage, assigned by DCC

# entry[].resource.concept[].display
Identifier for the eldest sample in a lineage of processed, pooled,
      or aliquoted samples - typically the material actually collected from the Participant. This may be the same as Parent Sample ID or Sample ID
      (if no processing was performed). Assigned by data contributor.

# entry[].resource.concept[].display
Type of biological material comprising the Collected Sample (e.g. Whole blood, Not reported, Saliva, Derived cell line)

# entry[].resource.concept[].display
INCLUDE global identifier for specific container/aliquot of sample, assigned by DCC

# entry[].resource.concept[].display
Identifier for specific container/aliquot of sample, assigned by data contributor.
      For example, distinct aliquots of a sample will have the same Sample ID but
      different Container IDs.

# entry[].resource.concept[].display
INCLUDE global identifier for the direct parent from which Sample was derived, assigned by DCC

# entry[].resource.concept[].display
Unique identifier for the parent sample, assigned by data contributor

# entry[].resource.concept[].display
Type of biological material comprising the Parent Sample (e.g. Peripheral Whole Blood, Derived Cell Line, Saliva, Whole blood, WBCs)

# entry[].resource.concept[].display
Procedure by which Sample was derived from Parent Sample (e.g. Centrifugation, RBC lysis, Lyse/fix buffer, FACS, PAXgene DNA, PAXgene RNA, Qiagen Allprep, Ficoll)

# entry[].resource.concept[].display
Sample Availability where In indcates available and Out indicates Unavailable

# entry[].resource.concept[].display
Method by which Container is stored (e.g. Minus 80 degrees Celsius, Liquid nitrogen storage)

# entry[].resource.title
Variables associated with table, specimen, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, condition.Condition Data Source, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, condition.Condition Status, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, condition.Condition Interpretation, from INCLUDE datasets.

# entry[].resource.concept[].display
Unique, de-identified identifier for the participant, assigned by data contributor. External IDs must be two steps removed from personal information in the study records.

# entry[].resource.concept[].display
Identifier for event (Visit, Survey completion, Sample collection, etc.) to which the Condition data are linked, if applicable. There may be multiple events linked to a Participant.

# entry[].resource.concept[].display
Type of event for which Event ID is given (Visit, Survey completion, Sample collection, etc.)

# entry[].resource.concept[].display
Co-occurring Condition (phenotype or diagnosis) or Measure (observation with numeric value), as described by data contributor. The Down Syndrome Genetic Diagnosis will be rolled into this field.

# entry[].resource.concept[].display
Age in days at which Condition or Measure was observed, recorded, or diagnosed

# entry[].resource.concept[].display
Whether the Condition is ongoing, has been resolved, or this is a general history of the condition without known dates

# entry[].resource.concept[].display
Whether Condition information was obtained by the investigator or reported by participant/family member

# entry[].resource.concept[].display
Label for Condition in the Human Phenotype Ontology (HPO)

# entry[].resource.concept[].display
Code for Condition in the Human Phenotype Ontology (HPO)

# entry[].resource.concept[].display
Label for Condition in the Mondo Disease Ontology (MONDO)

# entry[].resource.concept[].display
Code for Condition in the Mondo Disease Ontology (Mondo)

# entry[].resource.concept[].display
Label for Condition in the Medical Action Ontology (MAXO)

# entry[].resource.concept[].display
Code for condition in the Medical Action Ontology (MAXO)

# entry[].resource.concept[].display
Label for Condition in another ontology (if no match in HPO, MONDO, or MAXO)

# entry[].resource.concept[].display
Code for Condition in another ontology (if no match in HPO, MONDO, or MAXO)

# entry[].resource.concept[].display
Unit that is associated with Measure Value (e.g. kg, cm, %, x10^9/L, etc.)

# entry[].resource.title
Variables associated with table, condition, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, participant.Outcomes Vital Status, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, participant.Down Syndrome Status, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, participant.Ethnicity, from INCLUDE datasets.

# entry[].resource.concept[].code
Native Hawaiian or Other Pacific Islander

# entry[].resource.concept[].display
Native Hawaiian or Other Pacific Islander

# entry[].resource.title
Values associated with variable, participant.Race, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, participant.Sex, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, participant.Family Relationship, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, participant.Family Type, from INCLUDE datasets.

# entry[].resource.concept[].display
Unique identifer for the study, assigned by DCC

# entry[].resource.concept[].display
Unique INCLUDE global identifier for the participant, assigned by DCC

# entry[].resource.concept[].display
Unique, de-identified identifier for the participant, assigned by data contributor. External IDs must be two steps removed from personal information in the study records.

# entry[].resource.concept[].display
Unique identifer for family to which Participant belongs, assigned by data contributor

# entry[].resource.concept[].display
Structure of family members participating in the study

# entry[].resource.concept[].display
Participant External ID for Participant's father (NA if Participant is not the proband)

# entry[].resource.concept[].display
Participant External ID for Participant's mother (NA if Participant is not the proband)

# entry[].resource.concept[].display
Participant External ID for Participant's sibling(s) (NA if Participant is not the proband)

# entry[].resource.concept[].display
Participant External ID for Participant's other family members (NA if Participant is not the proband)

# entry[].resource.concept[].display
Age in days of Participant at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.). Age at enrollment is preferred, if available.

# entry[].resource.concept[].display
Event for which Age at First Patient Engagement is given (e.g. enrollment, visit, observation, sample collection, survey completion, etc.). Age at enrollment is preferred, if available.

# entry[].resource.concept[].display
Age in days when participant's vital status was last recorded

# entry[].resource.title
Variables associated with table, participant, from INCLUDE datasets.

# entry[].resource.title
Variables associated with table, DataSet, from INCLUDE datasets.

# entry[].resource.title
Values associated with variable, phenotype.onset_age_range, from study, GREGoR_DD.

# entry[].resource.title
Values associated with variable, phenotype.ontology, from study, GREGoR_DD.

# entry[].resource.title
Values associated with variable, phenotype.presence, from study, GREGoR_DD.

# entry[].resource.concept[].display
modifier of a term where the additional details are not supported/available as a term in HPO

# entry[].resource.title
Variables associated with table, phenotype, from study, GREGoR_DD.

# entry[].resource.title
Values associated with variable, family.consanguinity, from study, GREGoR_DD.

# entry[].resource.concept[].display
Indicate if consanguinity is present or suspected within a family

# entry[].resource.concept[].display
Free text description of any additional consanguinity details

# entry[].resource.concept[].display
name of file (renamed from pedigree_image because it can contain a PED file or image)

# entry[].resource.concept[].display
Free text description of other family structure/pedigree file caption or legend.

# entry[].resource.concept[].display
Details about family history that do not fit into structured fields. Family relationship terms should be relative to the proband.

# entry[].resource.title
Variables associated with table, family, from study, GREGoR_DD.

# entry[].resource.concept[].display
identifier used in the data file (e.g. VCF header / LIMS ID)

# entry[].resource.concept[].display
sequenced read length (bp); GREGoR RCs do paired end sequencing, so is the example of 100bp indicates 2x100bp.

# entry[].resource.concept[].display
Which capture kit is used. Can be missing if RC receives external data

# entry[].resource.concept[].display
name and path of bed file uploaded to workspace

# entry[].resource.concept[].display
Date of data generation (First sequencing date)

# entry[].resource.concept[].display
insert size the protocol targets for DNA fragments

# entry[].resource.concept[].display
sequencing platform used for the experiment

# entry[].resource.title
Variables associated with table, experiment_dna_short_read, from study, GREGoR_DD.

# entry[].resource.concept[].display
unique key for table (anvil requirement)

# entry[].resource.concept[].display
name and path of the file with variant calls

# entry[].resource.concept[].display
variant calling software used including version number

# entry[].resource.concept[].display
brief description of the analysis pipeline used for producing the file; perhaps a link to something like a WDL file or github repository

# entry[].resource.concept[].display
identifier for a set of experiments (primary key)

# entry[].resource.title
Variables associated with table, aligned_dna_short_read_set, from study, GREGoR_DD.

# entry[].resource.title
Values associated with variable, analyte.primary_biosample, from study, GREGoR_DD.

# entry[].resource.title
Values associated with variable, analyte.analyte_type, from study, GREGoR_DD.

# entry[].resource.concept[].display
identifier for an analyte from a primary biosample source (primary key)

# entry[].resource.concept[].display
analyte derived from the primary_biosample. The actual thing you're sticking into a machine to analyze/sequence

# entry[].resource.concept[].display
details about how the analyte or original biosample was extracted or processed

# entry[].resource.concept[].display
Tissue type of biosample taken from the participant that the analyte was extracted or processed from (for unknown can use tissue - UBERON:0000479), e.g. skin, liver, brain

# entry[].resource.concept[].display
Optional ID for the biosample; allows for linking of multiple analytes extracted or processed from the same biosample

# entry[].resource.concept[].display
Free text to capture information not in structured fields

# entry[].resource.concept[].display
If applicable to disease (suspected mosaic), is the tissue from an affected source or an unaffected source?

# entry[].resource.concept[].display
age or participant in years at biosample collection

# entry[].resource.concept[].display
The list of drugs patient is on, at the time of sample collection. This information is helpful during analysis of metabolomics and immune asssays. Free Text

# entry[].resource.concept[].display
If the patient was fasting, when the sample was collected. this is relevant when analyzing metabolomics data. Free Text

# entry[].resource.concept[].display
his is relevant when analyzing metabolomics data

# entry[].resource.concept[].display
passage_number is relevant for fibroblast cultures and possibly iPSC.

# entry[].resource.concept[].display
time (in hours) from collection to freezing the sample. delayed freeze turns out to be useful / important info for PaxGene blood (for RNA isolation).

# entry[].resource.title
Variables associated with table, analyte, from study, GREGoR_DD.

# entry[].resource.title
Values associated with variable, participant.affected_status, from study, GREGoR_DD.

# entry[].resource.concept[].code
Native Hawaiian or Other Pacific Islander

# entry[].resource.concept[].display
Native Hawaiian or Other Pacific Islander

# entry[].resource.title
Values associated with variable, participant.reported_race, from study, GREGoR_DD.

# entry[].resource.title
Values associated with variable, participant.sex, from study, GREGoR_DD.

# entry[].resource.title
Values associated with variable, participant.recontactable, from study, GREGoR_DD.

# entry[].resource.title
Values associated with variable, participant.consent_code, from study, GREGoR_DD.

# entry[].resource.title
Values associated with variable, participant.gregor_center, from study, GREGoR_DD.

# entry[].resource.concept[].display
An identifier used by GREGoR research centers to identify a set of participants for their internal tracking

# entry[].resource.concept[].display
GREGoR Center to which the participant is originally associated

# entry[].resource.concept[].display
Consent group pertaining to this participant's data

# entry[].resource.concept[].display
Is the originating GREGoR Center likely able to recontact this participant

# entry[].resource.concept[].display
Text description of any genetic testing for individual conducted prior to enrollment

# entry[].resource.concept[].display
participant_id for father; 0 if not available

# entry[].resource.concept[].display
participant_id for mother; 0 if not available

# entry[].resource.concept[].display
participant_id for twins, triplets, etc; 0 if not available

# entry[].resource.concept[].display
Text description of individual relationship to proband in family, especially useful to capture relationships when connecting distant relatives and connecting relatives not studied

# entry[].resource.concept[].display
Other proband relationship not captured in enumeration above

# entry[].resource.concept[].display
Biological sex assigned at birth (aligned with All of Us). If individual has a known DSD / not expected sex chromosome karyotype, this can be noted in the phenotype information section.

# entry[].resource.concept[].display
Optional free-text field to describe known discrepancies between 'sex' value (female=>XX, male=>XY) and actual sex chromosome karyotype

# entry[].resource.concept[].display
Additional specific ancestry description free text beyond what is captured by OMB race/ethnicity categories

# entry[].resource.concept[].display
Age at last observation, aka age in years at the last time the center can vouch for the accuracy phenotype data. For conditions with later age of onset, this field lets users know if individuals marked as unaffected were younger or older than the age when the phenotype is expected to appear.

# entry[].resource.concept[].display
Indicate affected status of individual (overall with respect to primary phenotype in the family). Note: Affected participants must have entry in phenotype table.

# entry[].resource.concept[].display
human-readable 'Phenotypic one-line summary' for why this individual is of interest. Could be the same as the term_details value in the Phenotype table. Strongly encourage/required for proband.

# entry[].resource.concept[].display
age in years at which consent was originally obtained

# entry[].resource.title
Variables associated with table, participant, from study, GREGoR_DD.

# entry[].resource.title
Variables associated with table, DataSet, from study, GREGoR_DD.

# entry[].resource.title
Values associated with variable, sequencing.sex, from study, CCDG_DD.

# entry[].resource.title
Values associated with variable, sequencing.sequencing_assay, from study, CCDG_DD.

# entry[].resource.title
Values associated with variable, sequencing.analyte_type, from study, CCDG_DD.

# entry[].resource.concept[].display
Identifier for sample (this should be the same sample_id used to link the sample information to the subject information in the provided phenotype data)

# entry[].resource.concept[].display
filename containing the sequence information

# entry[].resource.concept[].display
Does this meet the functional equivalence standard?

# entry[].resource.concept[].display
Date of data generation (First sequencing date)

# entry[].resource.concept[].display
tissue from which DNA (or RNA) extracted

# entry[].resource.concept[].display
number of independent libraries sequenced

# entry[].resource.concept[].display
Sex of sample subject (Note: this field is also required for the phenotype information, but is requested in sequence metadata for QC purposes)

# entry[].resource.title
Variables associated with table, sequencing, from study, CCDG_DD.

# entry[].resource.title
Values associated with variable, sample.sample_source, from study, CCDG_DD.

# entry[].resource.concept[].display
Sample identifier used in dbGaP (if previously submitted)

# entry[].resource.title
Variables associated with table, sample, from study, CCDG_DD.

# entry[].resource.title
Values associated with variable, subject.affected_status, from study, CCDG_DD.

# entry[].resource.concept[].code
Native Hawaiian or Other Pacific Islander

# entry[].resource.concept[].display
Native Hawaiian or Other Pacific Islander

# entry[].resource.title
Values associated with variable, subject.race_ethnicity, from study, CCDG_DD.

# entry[].resource.title
Values associated with variable, subject.sex, from study, CCDG_DD.

# entry[].resource.title
Values associated with variable, subject.dbgap_consent_id, from study, CCDG_DD.

# entry[].resource.concept[].display
Reported race/ethnicity defined by NIH Racial and Ethnic Categories and Definitions (NOT-OD-15-089)

# entry[].resource.concept[].display
Additional specific race/ethnicity description free text

# entry[].resource.concept[].display
Disease name or free text description of disease

# entry[].resource.concept[].display
Detail, such as subtype, regarding affected status

# entry[].resource.concept[].display
Age as given by study, but unspecified as to when. Most likely corresponds to age at the only visit

# entry[].resource.title
Variables associated with table, subject, from study, CCDG_DD.

# entry[].resource.title
Variables associated with table, DataSet, from study, CCDG_DD.

# entry[].resource.title
Values associated with variable, discovery.significance, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, discovery.sv_type, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, discovery.zygosity, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, discovery.gene_class, from study, CMG_DD.

# entry[].resource.concept[].display
Indicate of the gene listed is a candidate or known

# entry[].resource.concept[].display
The genome build for identifying the variant position

# entry[].resource.concept[].display
Clinical significance of variant described

# entry[].resource.title
Variables associated with table, discovery, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, family.family_history, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, family.consanguinity, from study, CMG_DD.

# entry[].resource.concept[].display
Indicate if consanguinity is present or suspected within a family

# entry[].resource.concept[].display
Free text description of any additional consanguinity details

# entry[].resource.concept[].display
Free text description of other family structure/pedigree image caption

# entry[].resource.concept[].display
Flag if there is a known family history for the phenotype (useful if only proband sequenced but extended family history suggestion mode of inheritance was reported)

# entry[].resource.concept[].display
Information regarding age of onset for affected individuals in family if relevant for phenotype

# entry[].resource.title
Variables associated with table, family, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, sequencing.sequencing_assay, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, sequencing.analyte_type, from study, CMG_DD.

# entry[].resource.concept[].display
Is this a functional equivalence standard?

# entry[].resource.title
Variables associated with table, sequencing, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, sample.tissue_affected_status, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, sample.sample_source, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, sample.sequencing_center (formerly sample_provider), from study, CMG_DD.

# entry[].resource.concept[].display
Sample identifier used in dbGaP (if previously submitted)

# entry[].resource.concept[].display
If applicable to disease, is the tissue from an affected source or an unaffected source?

# entry[].resource.title
Variables associated with table, sample, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, subject.solve_state, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, subject.congenital_status, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, subject.affected_status, from study, CMG_DD.

# entry[].resource.concept[].code
Native Hawaiian or Other Pacific Islander

# entry[].resource.concept[].display
Native Hawaiian or Other Pacific Islander

# entry[].resource.title
Values associated with variable, subject.ancestry, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, subject.sex, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, subject.proband_relationship, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, subject.multiple_datasets, from study, CMG_DD.

# entry[].resource.title
Values associated with variable, subject.dbgap_submission, from study, CMG_DD.

# entry[].resource.concept[].display
Text description of any genetic testing for individual conducted prior to enrollment

# entry[].resource.concept[].display
Information field about cohort. Suggested use case is for the identification of a set of subjects from a specific data provider in order to identify this subset within searches (and for manuscript referencing)

# entry[].resource.concept[].display
Flag if sample has been submitted to dbGaP

# entry[].resource.concept[].display
Subject identifier used in dbGaP (if previously submitted)

# entry[].resource.concept[].display
Flag if an individual has data represented in multiple data types (Ex: Yes if both exome and genome data is available for an individual)

# entry[].resource.concept[].display
Text description of individual relationship to proband in family, especially useful to capture relationships when connecting distant relatives and connecting relatives not studied

# entry[].resource.concept[].display
Reported ancestry defined by NIH Racial and Ethnic Categories and Definitions (NOT-OD-15-089)

# entry[].resource.concept[].display
Additional specific ancestry description free text

# entry[].resource.concept[].display
Age at last observation. For conditions with later age of onset, this field lets users know if individuals marked as unaffected were younger or older than the age when the phenotype is expected to appear.

# entry[].resource.concept[].display
Optional submitter-defined field for samples that could be grouped together in a single analysis based on overlap in phenotypic features.

# entry[].resource.concept[].display
Concept code for disease (e.g. OMIM, Orphanet)

# entry[].resource.concept[].display
Disease name or free text description of disease (especially if concept code not available)

# entry[].resource.concept[].display
Age of onset bucket range (if affected with non-congenital disorder)

# entry[].resource.concept[].display
Age of onset (if affected with non-congenital disorder)

# entry[].resource.concept[].display
Phenotype term or free text description for additional phenotype information

# entry[].resource.title
Variables associated with table, subject, from study, CMG_DD.

# entry[].resource.title
Variables associated with table, DataSet, from study, CMG_DD.

# entry[].resource.description
NCI Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities.

# entry[].resource.text.div
This code system http://purl.obolibrary.org/obo/ncit.owl provides a fragment that includes following codes:

Code | Display
C3270 | Neuroblastoma
C5437 | Extracranial Neuroblastoma
C84505 | Tetralogy of Fallot
C142710 | Study Participant

# entry[].resource.text.div
This code system https://nih-ncpi.github.io/ncpi-fhir-ig/CodeSystem/ncpi-data-types defines many codes, of which the following are a subset:

Code | Display
Exome | Exome Sequence Data
WholeGenome | Whole Genome Sequence Data
GWAS | Genome-Wide Association Studies

# entry[].resource.concept[].display
Autosomal dominant inheritance (with paternal imprinting)

# entry[].resource.concept[].display
Autosomal dominant inheritance (with maternal imprinting)

# entry[].resource.concept[].display
Autosomal dominant inheritance (primarily or exclusively de novo)

# entry[].resource.concept[].display
X-linked inheritance (primarily recessive with milder female expression)

# entry[].resource.concept[].display
Autosomal dominant inheritance (with genetic anticipation)

# entry[].resource.concept[].display
Autosomal recessive inheritance (with genetic anticipation)

# entry[].resource.description
A set of terms that describe the transmission pattern of a condition in a pedigree.

# entry[].resource.text.div
This code system https://nih-ncpi.github.io/ncpi-fhir-ig/CodeSystem/ConditionInheritanceMode defines the following codes:

Code | Display
GENO:0000143 | Codominant inheritance
GENO:0000889 | Unknown inheritance
GENO:0000892 | Mitochondrial inheritance (primarily or exclusively heteroplasmic)
GENO:0000893 | Mitochondrial inheritance (primarily or exclusively homoplasmic)
HP:0000006 | Autosomal dominant inheritance
HP:0000007 | Autosomal recessive inheritance
HP:0001417 | X-linked inheritance
HP:0001419 | X-linked inheritance (recessive)
HP:0001423 | X-linked inheritance (dominant)
HP:0001426 | Multifactorial inheritance
HP:0001427 | Mitochondrial inheritance
HP:0001428 | Somatic mutation
HP:0001450 | Y-linked inheritance
HP:0001470 | Autosomal dominant inheritance (sex-limited)
HP:0003743 | Genetic anticipation
HP:0003745 | Sporadic
HP:0010983 | Oligogenic
HP:0012274 | Autosomal dominant inheritance (with paternal imprinting)
HP:0012275 | Autosomal dominant inheritance (with maternal imprinting)
HP:0025352 | Autosomal dominant inheritance (primarily or exclusively de novo)
HP:0031362 | Autosomal recessive inheritance (sex-limited)
SEPIO-CG:97020 | Semidominant inheritance
SEPIO-CG:97021 | X-linked inheritance (primarily recessive with milder female expression)
SEPIO-CG:97022 | Autosomal dominant inheritance (with genetic anticipation)
SEPIO-CG:97023 | Autosomal recessive inheritance (with genetic anticipation)

# entry[].resource.description
The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. The name Mondo comes from the latin word 'mundus' and means 'for the world.'

# entry[].resource.text.div
This code system http://purl.obolibrary.org/obo/mondo.owl defines many codes, of which the following are a subset:

Code | Display
MONDO:0005072 | neuroblastoma
MONDO:0002749 | extracranial neuroblastoma
MONDO:0008542 | tetralogy of fallot

# entry[].resource.concept[].definition
A means to bundle several observations such as one would find in a genetics test panel.

# entry[].resource.concept[].definition
This is actually LOINC code 79742-3. And the IG will be updated

# entry[].resource.concept[].definition
Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance.

# entry[].resource.concept[].definition
Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions.

# entry[].resource.concept[].definition
The non-medication therapy (procedure) associated with this implication.

# entry[].resource.concept[].definition
Given as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence.

# entry[].resource.concept[].definition
Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537.

# entry[].resource.concept[].definition
The genomic coordinates of the exact genomic range in which the variant resides.

# entry[].resource.concept[].definition
The genomic coordinates of the inner genomic range in which the variant might reside.

# entry[].resource.concept[].definition
The genomic coordinates of the outer genomic range in which the variant might reside.

# entry[].resource.concept[].definition
A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762.

# entry[].resource.concept[].definition
An observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition.

# entry[].resource.concept[].definition
An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy.

# entry[].resource.description
These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.

# entry[].resource.text.div
This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes defines the following codes:

Code | Display | Definition
grouper | grouper | A means to bundle several observations such as one would find in a genetics test panel.
mode-of-inheritance | mode-of-inheritance | This is actually LOINC code 79742-3. And the IG will be updated
effect-transporter-function | effect-transporter-function | Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance.
effect-medication-efficacy | Medication Efficacy |
effect-medication-metabolism | Medication Metabolism |
effect-medication-transporter | Medication Transporter Function |
effect-high-risk-allele | High Risk Allele |
prognostic-implication | Prognostic Implication component | Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions.
associated-cancer | associated-cancer |
associated-therapy | Genomically linked therapy | The non-medication therapy (procedure) associated with this implication.
region-coverage | region-coverage | Given as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence.
functional-annotation | functional-annotation | Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537.
exact-start-end | Variant exact start and end | The genomic coordinates of the exact genomic range in which the variant resides.
inner-start-end | Variant inner start and end | The genomic coordinates of the inner genomic range in which the variant might reside.
outer-start-end | Variant outer start and end | The genomic coordinates of the outer genomic range in which the variant might reside.
variant-inheritance | Variant inheritance | A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762.
diagnostic-implication | Diagnostic Implication | An observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition.
therapeutic-implication | Therapeutic Implication | An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy.

# entry[].resource.concept[].display
Number of cohorts that are part of this study

# entry[].resource.concept[].display
Number of sub-studies that are part of this study

# entry[].resource.concept[].display
Number of samples that are part of this study

# entry[].resource.concept[].display
Number of participants that are part of this study

# entry[].resource.concept[].display
Number of variables that are part of this study

# entry[].resource.concept[].display
Number of analyses that are part of this study

# entry[].resource.concept[].display
Number of molecular datasets that are part of this study

# entry[].resource.concept[].display
Number of phenotype datasets that are part of this study

# entry[].resource.text.div
This code system https://nih-ncpi.github.io/ncpi-fhir-ig/CodeSystem/ncpi defines many codes, of which the following are a subset:

Code | Display
Consortium | Study Consortium
StudyCohort | Study Cohort
ConsentGroup | Study Consent Group
Summary | Summary Data
CohortCount | Number of cohorts that are part of this study
SubStudyCount | Number of sub-studies that are part of this study
SampleCount | Number of samples that are part of this study
Participant | Number of participants that are part of this study
VariableCount | Number of variables that are part of this study
AnalysesCount | Number of analyses that are part of this study
MolecularDatasetCount | Number of molecular datasets that are part of this study
PhenotypeDatasetCount | Number of phenotype datasets that are part of this study
StorageSize | Size on Disk
ConsentCodes | Consent Codes
TerraWorkspace | Terra Workspace Name
PrimaryDisease | Primary Disease
AccessType | Access Type
StudyDesign | Study Design