Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions
Contents:
This page provides a list of the FHIR artifacts defined as part of this implementation guide.
These define the properties by which a RESTful server can be searched. They can also be used for sorting and including related resources.
| GenomicStudyFocusSearchParam |
What the genomic study analysis is about, when it is not about the subject of record |
| GenomicStudyIdentifierSearchParam |
Identifiers for the Study |
| GenomicStudyPatientSearchParam |
Who the study is about |
| GenomicStudyStatusSearchParam |
The status of the study |
| GenomicStudySubjectSearchParam |
Who the study is about |
| MolecularDefinitionIdentifierSearchParam |
The unique identity for a particular sequence |
| MolecularDefinitionMemberSearchParam |
Reference to the state of the molecular member |
| MolecularDefinitionMoleculetypeSearchParam |
Amino Acid Sequence/ DNA Sequence / RNA Sequence |
| MolecularDefinitionTopologySearchParam |
The structural topology of the molecular entity (e.g., linear, circular) |
| MolecularDefinitionTypeSearchParam |
Classification of the molecule into types other than those defined by moleculeType |
'Additional' resources that are not yet published in the FHIR core specification.
| Genomic Study |
A set of analyses performed to analyze and generate genomic data. |
| Molecular Definition |
Definitional content for a molecular entity, such as a nucleotide or protein sequence. |
These define sets of codes used by systems conforming to this implementation guide.
| Amino Acid 1-letter Ambiguous Symbols ValueSet |
Single-letter symbols for amino acids including ambiguous symbols (A, B, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, U, V, W, X, Y, Z). |
| Amino Acid 1-letter Unambiguous Symbols ValueSet |
Single-letter unambiguous symbols for the 20 common amino acids. |
| Amino Acid 3-letter Ambiguous Symbols ValueSet |
Three-letter symbols for amino acids including ambiguous symbols (Ala, Asx, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, Tyr, Sec, Xaa, Glx). |
| Amino Acid 3-letter Unambiguous Symbols ValueSet |
Three-letter unambiguous symbols for the 20 common amino acids. |
| Coordinate System Normalization Method ValueSet |
The normalization method applied when placing a variant within a repetitive sequence region. The binding is extensible to allow new alignment conventions as they emerge. |
| Coordinate System Origin ValueSet |
The reference landmark (origin) from which coordinates are measured in a coordinateInterval. This binding is required because coordinate origin ambiguity directly causes errors in variant interpretation. |
| Genomic Study Change Type VS |
The change type of the GenomicStudy analysis. |
| Genomic Study Data Format VS |
The data formats relevant to Genomic Study analysis. |
| Genomic Study Method Type VS |
The method type of the GenomicStudy analysis. |
| Genomic Study Region Type VS |
The type or status of a set of genomic regions within a GenomicStudy analysis (studied, called, or uncalled). |
| Genomic Study Status VS |
The status of the GenomicStudy. |
| Genomic Study Type VS |
The type of the GenomicStudy. |
| HUGO Gene Nomenclature Committee Gene Names (HGNC) |
This value set includes all HGNC Codes, which includes multiple code systems. The preferred system URL is http://www.genenames.org per the HL7 Terminology (THO) NamingSystem definition (https://terminology.hl7.org/NamingSystem-v3-hgnc.html). Gene IDs are used as CodeableConcepts, which must be sent with the HGNC gene ID including the prefix 'HGNC:' as the code and the HGNC 'gene symbol' as display. CAUTION: HGNC also indexes gene groups by numeric ID (without a prefix), and older systems may send HGNC gene IDs without the prefix, so care must be taken to confirm alignment. The genegroup code system is separately included to draw attention to this ambiguity and potential error. |
| Molecular Definition Literal Encoding VS |
The encoding used in molecular definition literal representations. |
| Molecular Definition Molecule Type |
The broad physical class of molecule represented by a MolecularDefinition resource instance: DNA, RNA, or amino acid (polypeptide). This ValueSet is used for the moleculeType element and is intentionally limited to top-level molecule classes to support consistent searching and profiling across systems. For finer-grained classification, use the type element bound to MolecularDefinitionType. |
| Molecular Definition Organism |
The organism whose genome the genomeAssembly describes. Codes are drawn from the NCBI Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy). The binding is extensible to accommodate any organism with a sequenced genome. Commonly used taxon IDs include 9606 (Homo sapiens) and 10090 (Mus musculus). |
| Molecular Definition Representation Code |
Example codes for representing a molecular entity by accession identifier. Codes are drawn from molecular sequence databases registered in HL7 terminology: NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq) and LRG (http://www.lrg-sequence.org). This binding is example strength — implementations are not constrained to these systems and may use any appropriate molecular sequence identifier system. |
| Molecular Definition Representation Focus VS |
The domain concept that is the focus of the representation in a MolecularDefinition. |
| Molecular Definition Strand |
The strand orientation of a sequenceLocation. 'Forward' corresponds to the plus/sense/Watson strand (5' to 3' in the standard reference orientation); 'reverse' corresponds to the minus/antisense/Crick strand (3' to 5' in the standard reference orientation). |
| Molecular Definition Topology |
The structural topology of a molecular entity as defined by the MolecularDefinition resource. Includes linear, circular, linear-discontiguous (gapped), and branched forms. |
| Molecular Definition Type |
Domain-semantic subtype classifications for a MolecularDefinition resource instance, providing greater specificity than the moleculeType element. For example, an instance with moleculeType 'rna' may have a type of 'mrna' or 'mirna'. This ValueSet is an enumerated, curated set of locally-defined codes covering clinically relevant DNA and RNA subtypes. The binding is extensible: implementers may use codes from other systems when no suitable code exists in this set. |
| Nucleotide DNA 1-letter Ambiguous Symbols ValueSet |
Single-letter ambiguous symbols for DNA residues including all IUPAC codes (G, A, T, C, R, Y, M, K, S, W, H, B, V, D, N). |
| Nucleotide DNA 1-letter Unambiguous Symbols Including N ValueSet |
Single-letter unambiguous symbols for DNA residues, including N for any nucleotide (G, A, T, C, N). |
| Nucleotide DNA 1-letter Unambiguous Symbols ValueSet |
Single-letter unambiguous symbols for DNA residues (G, A, T, C). |
| Nucleotide RNA 1-letter Unambiguous Symbols ValueSet |
Single-letter unambiguous symbols for RNA residues (G, A, U, C). |
These define new code systems used by systems conforming to this implementation guide.
| Amino Acid Symbols |
Single-letter and three-letter symbols for amino acids based on IUPAC nomenclature, including unambiguous and ambiguous symbols. |
| Coordinate System Normalization Method CodeSystem |
The normalization method applied when a variant can be placed at multiple equivalent positions within a repetitive sequence region. Different community standards (VCF, HGVS, VOCA/GA4GH) apply different alignment conventions, and recording which was used is necessary for lossless round-tripping of variant representations across systems. No external vocabulary covers this domain-specific concept, so it is defined here by the CG Working Group. |
| Coordinate System Origin CodeSystem |
The reference landmark (origin) from which coordinates are measured in a coordinateInterval. This identifies the conceptual anchor point on the molecule where numbering begins, independent of whether numbering is 0-based or 1-based (which is captured in coordinateSystem.system). No external vocabulary covers this domain-specific concept, so it is defined here by the CG Working Group. |
| Genomic Study Change Type |
The change type relevant to GenomicStudy analysis. |
| Genomic Study Data Format |
The data format relevant to genomics. These formats and relevant codes were pulled from Integrative Genomics Viewer Documentation by Broad Institute. |
| Genomic Study Method Type |
The method type of the GenomicStudy analysis. These method types and relevant codes were pulled from National Library of Medicine-Genetic Testing Registry (NCBI-GTR) values of describing different testing methods on various levels: major method category, method category, and primary methodology |
| Genomic Study Region Type |
The type or status of a set of genomic regions within a GenomicStudy analysis, indicating the relationship of those regions to the analysis outcome. |
| Genomic Study Status |
The status of the GenomicStudy. |
| Genomic Study Type |
The type relevant to GenomicStudy. |
| Molecular Definition Literal Encoding |
Codes for the encoding used in molecular definition literal representations, based on IUPAC standards for nucleotide and amino acid sequences. |
| Molecular Definition Molecule Type CodeSystem |
The broad physical class of molecule represented by a MolecularDefinition resource instance: DNA, RNA, or amino acid (polypeptide). Codes are intentionally limited to top-level molecule classes to support consistent searching and profiling across systems. For finer-grained classification, use the type element bound to MolecularDefinitionType. |
| Molecular Definition Representation Focus |
The domain concept that is the focus of the representation in a MolecularDefinition. This element is used to disambiguate the representations of different alleles or states at a given location. |
| Molecular Definition Strand CodeSystem |
The strand orientation of a sequenceLocation. Orientation of molecular sequences, indicating directionality for nucleotides (5' to 3' or 3' to 5') or amino acids (N to C terminus). |
| Molecular Definition Topology CodeSystem |
The structural topology of a molecular entity as defined by the MolecularDefinition resource. Includes linear, circular, linear-discontiguous (gapped), and branched forms. |
| Molecular Definition Type CodeSystem |
Domain-semantic subtype classifications for a MolecularDefinition resource instance, providing greater specificity than the moleculeType element. For example, an instance with moleculeType 'rna' may have a type of 'mrna' or 'mirna'. This CodeSystem is an enumerated, curated set covering clinically relevant DNA and RNA subtypes. The binding on this CodeSystem is extensible: implementers may use codes from other systems when no suitable code exists here. |
| NCBI Taxonomy (fragment) |
A fragment of the NCBI Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy) containing taxon IDs referenced by examples and profiles in this IG. Numeric taxon IDs are used as codes; scientific names are used as display text. This fragment covers commonly used research organisms and representative clinical viral pathogens. Add entries here as new examples reference additional taxon IDs. |
| Nucleotide DNA Symbols |
Single-letter symbols for DNA residues based on IUPAC nomenclature, including unambiguous, ambiguous, and N symbols. |
| Nucleotide RNA Symbols |
Single-letter unambiguous symbols for RNA residues based on IUPAC nomenclature. |
These are example instances that show what data produced and consumed by systems conforming with this implementation guide might look like.
| Genomic Study Example |
Genomic Study Example |
| Genomic Study Lung Mass Example |
Genomic Study Lung Mass Example |
| Genomic Study PGx Example |
Genomic Study PGx Example |
| Genomic Study Somatic Study Example |
Genomic Study Somatic Study Example |
| Genomic Study Trio Example |
Genomic Study Trio Example |
| Molecular Definition Allele 1 |
Molecular Definition Allele 1 |
| Molecular Definition Allele 2 |
Molecular Definition Allele 2 |
| Molecular Definition Allele 3 |
Molecular Definition Allele 3 |
| Molecular Definition Allele 4 |
Molecular Definition Allele 4 |
| Molecular Definition Allele 5 |
Molecular Definition Allele 5 |
| Molecular Definition Allele 6 |
Molecular Definition Allele 6 |
| Molecular Definition Allele 7 |
Molecular Definition Allele 7 |
| Molecular Definition Allele Sliced 1 |
Molecular Definition Allele Sliced 1 |
| Molecular Definition Allele Sliced CYP2C19 1016 |
Molecular Definition Allele Sliced CYP2C19 1016 |
| Molecular Definition Allele Sliced CYP2C19 661 |
Molecular Definition Allele Sliced CYP2C19 661 |
| Molecular Definition Allele Sliced CYP2C19 Literal Only |
Molecular Definition Allele Sliced CYP2C19 Literal Only |
| Molecular Definition Allele Sliced HLA00381 |
Molecular Definition Allele Sliced HLA00381 |
| Molecular Definition Allele Sliced PGx Variant 1011 |
Molecular Definition Allele Sliced PGx Variant 1011 |
| Molecular Definition Example |
Molecular Definition Example |
| Molecular Definition Genomic CYP2C19 Accession |
Molecular Definition Genomic CYP2C19 Accession |
| Molecular Definition Genotype 1 |
Molecular Definition Genotype 1 |
| Molecular Definition Haplotype 1 |
Molecular Definition Haplotype 1 |
| Molecular Definition Haplotype 2 |
Molecular Definition Haplotype 2 |
| Molecular Definition Replaced Sequence |
Molecular Definition Replaced Sequence |
| Molecular Definition Replacement Sequence |
Molecular Definition Replacement Sequence |
| Molecular Definition Sequence 0 2B Concatenated |
Molecular Definition Sequence 0 2B Concatenated |
| Molecular Definition Sequence 1 |
Molecular Definition Sequence 1 |
| Molecular Definition Sequence 1 2B Concatenated |
Molecular Definition Sequence 1 2B Concatenated |
| Molecular Definition Sequence 2 2B Concatenated |
Molecular Definition Sequence 2 2B Concatenated |
| Molecular Definition Sequence A |
Molecular Definition Sequence A |
| Molecular Definition Sequence A AA IUPAC |
Molecular Definition Sequence A AA IUPAC |
| Molecular Definition Sequence A DNA IUPAC |
Molecular Definition Sequence A DNA IUPAC |
| Molecular Definition Sequence AF1961831 URL |
Molecular Definition Sequence AF1961831 URL |
| Molecular Definition Sequence C |
Molecular Definition Sequence C |
| Molecular Definition Sequence CGG |
Molecular Definition Sequence CGG |
| Molecular Definition Sequence CYP2C19 Accession |
Molecular Definition Sequence CYP2C19 Accession |
| Molecular Definition Sequence CYP2C19 Attached |
Molecular Definition Sequence CYP2C19 Attached |
| Molecular Definition Sequence CYP2C19 Concatenated Regions |
Molecular Definition Sequence CYP2C19 Concatenated Regions |
| Molecular Definition Sequence CYP2C19 Downstream Region |
Molecular Definition Sequence CYP2C19 Downstream Region |
| Molecular Definition Sequence CYP2C19 Gene Region |
Molecular Definition Sequence CYP2C19 Gene Region |
| Molecular Definition Sequence CYP2C19 URL |
Molecular Definition Sequence CYP2C19 URL |
| Molecular Definition Sequence CYP2C19 Upstream Region |
Molecular Definition Sequence CYP2C19 Upstream Region |
| Molecular Definition Sequence FMR1 |
Molecular Definition Sequence FMR1 |
| Molecular Definition Sequence FMR1 CGG 20x Edited Referenced |
Molecular Definition Sequence FMR1 CGG 20x Edited Referenced |
| Molecular Definition Sequence FMR1 CGG 20x Repeat |
Molecular Definition Sequence FMR1 CGG 20x Repeat |
| Molecular Definition Sequence G |
Molecular Definition Sequence G |
| Molecular Definition Sequence GGC |
Molecular Definition Sequence GGC |
| Molecular Definition Sequence HLA000011 |
Molecular Definition Sequence HLA000011 |
| Molecular Definition Sequence LRG584 |
Molecular Definition Sequence LRG584 |
| Molecular Definition Sequence MSH2 |
Molecular Definition Sequence MSH2 |
| Molecular Definition Sequence NC00001010 URL |
Molecular Definition Sequence NC00001010 URL |
| Molecular Definition Sequence NM0007694 URL |
Molecular Definition Sequence NM0007694 URL |
| Molecular Definition Sequence Repeat |
Molecular Definition Sequence Repeat |
| Molecular Definition Sequence T |
Molecular Definition Sequence T |
| Molecular Definition Starting Sequence 2B Extracted |
Molecular Definition Starting Sequence 2B Extracted |
| Molecular Definition Starting Sequence 2B Relative |
Molecular Definition Starting Sequence 2B Relative |
| Molecular Definition Variation 1 |
Molecular Definition Variation 1 |
| Molecular Definition Variation CYP2C19 1015 SPDI |
Molecular Definition Variation CYP2C19 1015 SPDI |
| Molecular Definition Variation CYP2C19 1015 VRS |
Molecular Definition Variation CYP2C19 1015 VRS |
| Molecular Definition Variation CYP2C19 1016 VCF |
Molecular Definition Variation CYP2C19 1016 VCF |
| Molecular Definition Variation CYP2C19 661 |
Molecular Definition Variation CYP2C19 661 |
| Molecular Definition Variation CYP2C19 991 HGVS |
Molecular Definition Variation CYP2C19 991 HGVS |
| Molecular Definition Variation PGx Variant 1011 |
Molecular Definition Variation PGx Variant 1011 |
| Molecular Definition Variation PGx Variant 1012 |
Molecular Definition Variation PGx Variant 1012 |
| Molecular Definition Variation PGx Variant 1013 |
Molecular Definition Variation PGx Variant 1013 |
| Molecular Definition Variation PGx Variant 1014 |
Molecular Definition Variation PGx Variant 1014 |
| Molecular Definition Variation PGx Variant 1015 |
Molecular Definition Variation PGx Variant 1015 |
| Molecular Definition Variation PGx Variant 1016 |
Molecular Definition Variation PGx Variant 1016 |
| Molecular Definition Variation PGx Variant 1017 |
Molecular Definition Variation PGx Variant 1017 |
| Molecular Definition Variation PGx Variant 1018 |
Molecular Definition Variation PGx Variant 1018 |
| Molecular Definition Variation PGx Variant 1019 |
Molecular Definition Variation PGx Variant 1019 |
| Molecular Definition Variation PGx Variant 1020 |
Molecular Definition Variation PGx Variant 1020 |
| Molecular Definition Variation PGx Variant 1021 |
Molecular Definition Variation PGx Variant 1021 |
These are resources that are used within this implementation guide that do not fit into one of the other categories.
| CNVAnalysis-called |
CNVAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline. |
| De Novo Child Patient |
De Novo Child Patient |
| De Novo Encounter |
De Novo Encounter |
| De Novo Father Patient |
De Novo Father Patient |
| De Novo Father Related Person |
De Novo Father Related Person |
| De Novo Mother Patient |
De Novo Mother Patient |
| De Novo Mother Related Person |
De Novo Mother Related Person |
| De Novo Specimen 1 |
De Novo Specimen 1 |
| De Novo Specimen 2 |
De Novo Specimen 2 |
| De Novo Specimen 3 |
De Novo Specimen 3 |
| Denovo Mutation Example Group |
[markdown] |
| Father Patient |
Father Patient |
| Father Specimen |
Father Specimen |
| Genomic Encounter |
Genomic Encounter |
| Genomic Patient |
Genomic Patient |
| Genomic Service Request |
Genomic Service Request |
| Genomic Service Request 2 |
Genomic Service Request 2 |
| Genomic Service Request 3 |
Genomic Service Request 3 |
| Genomic Service Request 4 |
Genomic Service Request 4 |
| Genomic Service Request Father |
Genomic Service Request Father |
| Genomic Service Request Mother |
Genomic Service Request Mother |
| Genomic Service Request Proband |
Genomic Service Request Proband |
| Genomic Specimen |
Genomic Specimen |
| Genomic Study Examples List |
Genomic Study Examples List |
| Genomic Study Operations List |
Genomic Study Operations List |
| Molecular Definition Examples List |
Molecular Definition Examples List |
| Molecular Definition Operations List |
Molecular Definition Operations List |
| Mother Patient |
Mother Patient |
| Mother Specimen |
Mother Specimen |
| NGS Sequencing Device |
NGS Sequencing Device |
| Normal Specimen |
Normal Specimen |
| PGx Patient |
PGx Patient |
| PGx Service Request |
PGx Service Request |
| PGx Specimen |
PGx Specimen |
| Practitioner 01 |
Practitioner 01 |
| Practitioner 02 |
Practitioner 02 |
| Proband Patient |
Proband Patient |
| Proband Specimen |
Proband Specimen |
| SimpleVariantAnalysis-called |
SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline. |
| Somatic Patient |
Somatic Patient |
| Somatic Service Request |
Somatic Service Request |
| Triodenovo Software Device |
Triodenovo Software Device |
| Tumor Specimen |
Tumor Specimen |
| WES-FullSequencedRegion-GRCh38 |
WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline. |
| example-genomicFile-af1961831-url |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. Homo sapiens MHC class I antigen (HLA-B) gene |
| example-genomicFile-cyp2c19-accession |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. CYP2C19 gene sequence |
| example-genomicFile-cyp2c19-attached |
CYP2C19 gene sequence |
| example-genomicFile-cyp2c19-url |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. CYP2C19 gene sequence |
| example-genomicFile-hla00001 |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. |
| example-genomicFile-mw7162561 |
A sample Document Reference instance representing Homo sapiens isolate 7 BRCA1 (BRCA1) gene, exon 10 and partial cds. |
| example-genomicFile-ng0083843 |
A sample Document Reference instance representing Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), RefSeqGene (LRG_584) on chromosome 10. |
| example-genomicFile-nm0002513 |
A sample Document Reference instance representing Homo sapiens mutS homolog 2 (MSH2), transcript variant 1, mRNA. |
| example-genomicFile-nm0007694 |
(CYP2C19), mRNA |
| example-genomicFile-nm0020245 |
A sample Document Reference instance representing Homo sapiens FMRP translational regulator 1 (FMR1), transcript variant ISO1, mRNA. |
| example-genomicfile-nc00001010-url |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. |
| genomicBEDfile |
A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline. |
| genomicFile1 |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. |
| genomicFile2 |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. |
| genomicFile3 |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. |
| genomicFile4 |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. |
| genomicFileFather |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. |
| genomicFileGroupAsSubject |
Combined VCF file of a Proband and Parents that may be used as input or output of a genomic analysis pipeline. |
| genomicFileMother |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. |
| genomicFileProband |
A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. |
| genomicVCFfile |
A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline. |
| genomicVCFfile-cnv |
genomicVCFfile_cnv: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline. |
| genomicVCFfile-simple |
genomicVCFfile_simple: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline. |
| pgxVCFfile |
VCF file containing PGX variant calls for CYP2C19, CYP2C9, and VKORC1 |
| somaticCalledRegions |
BED file describing regions that passed coverage and quality thresholds in the tumor/normal DNA analysis |
| somaticFusionFile |
VCF file containing gene fusions and transcript variants identified from tumor RNA sequencing |
| somaticRNAstudiedRegions |
BED file describing studied regions for RNA sequencing (fusion and transcript variant detection) |
| somaticVCFfile |
VCF file containing somatic variants identified from tumor/normal paired DNA sequencing |