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variants_emx.yaml
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variants_emx.yaml
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name: variants
version: v2.0.0
date: 2022-03-21
defaults:
aggregateable: false
dataType: string
idAttribute: false
labelAttribute: false
lookupAttribute: false
nillable: true
readOnly: false
unique: false
visible: true
entities:
- name: variants
tags: http://purl.obolibrary.org/obo/GENO_0000476
attributes:
- name: Variant identifier
dataType: string
idAttribute: true
nillable: false
tags: http://purl.obolibrary.org/obo/NCIT_C164813
# Should this be a reference to the material, the subject, or sequencing?
- name: Belongs to subject
description: An individual who is the subject of personal data, persons to whom data refers, and from whom data are collected, processed, and stored.
tags: NCIT:C142495 [http://purl.obolibrary.org/obo/NCIT_C142495], IAO:0000136 [http://purl.obolibrary.org/obo/IAO_0000136]
- name: Belongs to materials
dataType: xref
reference: Materials
#description: Name or other identifier of an entry from a biosample database.
description: Reference to the source material from which this sample was prepared.
tags: NCIT:C93400 [http://purl.obolibrary.org/obo/NCIT_C93400], NCIT:C25683 [http://purl.obolibrary.org/obo/NCIT_C25683]
- name: Produced by sequencing
dataType: mref
reference: Sequencing run
description: A unique proper name or character sequence that identifies this particular nucleic acid sequencing assay.
tags: NCIT:C171337 [http://purl.obolibrary.org/obo/NCIT_C171337]
# TODO: get clarification of this attribute
- name: Transcript
description: The initial RNA molecule produced by transcription.
tags: http://purl.obolibrary.org/obo/NCIT_C1936
# TODO: get clarification of this attribute
- name: Cdna
description: Single-stranded DNA that is complementary to messenger RNA or DNA that has been synthesized from messenger RNA by reverse transcriptase.
tags: http://purl.obolibrary.org/obo/NCIT_C324
- name: Protein
description: A group of complex organic macromolecules composed of one or more chains (linear polymers) of alpha-L-amino acids linked by peptide bonds and ranging in size from a few thousand to over 1 million Daltons. Proteins are fundamental genetically encoded components of living cells with specific structures and functions dictated by amino acid sequence.
tags: http://purl.obolibrary.org/obo/NCIT_C17021
# TODO: is this needed here if it's in clinical?
# Perhaps it should be a link to the clinical table?
- name: Molecular diagnosis gene
dataType: mref
refEntity: lookups/Gene.txt
tags: http://purl.obolibrary.org/obo/NCIT_C20826
# TODO: need clarification
- name: Gene specific list
- name: zygosity
description: The genetic condition of a zygote, especially with respect to its being a homozygote or a heterozygote.
dataType: xref
refEntity: lookups/Zygosity.txt
tags: http://purl.obolibrary.org/obo/NCIT_C45824
- name: Human chromosome
description: A structure found in the nucleus of human cells that is comprised of a strand of linearized double-stranded DNA plus proteins that package the DNA in a condensed coil form and regulate chromosomal function.
dataType: xref
refEntity: lookups/Humanchromosome.txt
tags: http://purl.obolibrary.org/obo/NCIT_C13203
- name: Start chromosome band
description: The cytoband that contains the beginning of the range, expressed without the chromosome or arm designation.
dataType: int
tags: http://purl.obolibrary.org/obo/NCIT_C164626
- name: End chromosome band
description: The cytoband that contains the terminus of the range, expressed without the chromosome or arm designation.
dataType: int
tags: http://purl.obolibrary.org/obo/NCIT_C164508
- name: Reference allele
description: An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome.
dataType: xref
refEntity: lookups/
tags: http://purl.obolibrary.org/obo/GENO_0000036
- name: Alternative allele
description:
dataType: xref
refEntity: lookups/
tags: http://ensembl.org/glossary/ENSGLOSSARY_0000109
- name: Allele 1
description: One of a set of sequence features known to exist at a particular genomic location.
dataType: xref
refEntity: lookups/Nucleobase.txt
tags: http://purl.obolibrary.org/obo/GENO_0000512
- name: Allele 2
description: One of a set of sequence features known to exist at a particular genomic location.
dataType: xref
refEntity: lookups/Nucleobase.txt
tags: http://purl.obolibrary.org/obo/GENO_0000512
- name: Maternal allele 1
description: One of a set of sequence features known to exist at a particular genomic location.
dataType: xref
refEntity: lookups/Nucleobase.txt
tags: http://purl.obolibrary.org/obo/GENO_0000512
- name: Maternal allele 2
description: One of a set of sequence features known to exist at a particular genomic location.
dataType: xref
refEntity: lookups/Nucleobase.txt
tags: http://purl.obolibrary.org/obo/GENO_0000512
- name: Paternal allele 1
description: One of a set of sequence features known to exist at a particular genomic location.
dataType: xref
refEntity: lookups/Nucleobase.txt
tags: http://purl.obolibrary.org/obo/GENO_0000512
- name: Paternal allele 2
description: One of a set of sequence features known to exist at a particular genomic location.
dataType: xref
refEntity: lookups/Nucleobase.txt
tags: http://purl.obolibrary.org/obo/GENO_0000512
# we mainly need Father, Mother, DeNovo, but it would be better to create the full reference list
- name: Allele origin
description: A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent.
dataType: xref
refEntity: lookups/AlleleOrigin.txt
tags: http://purl.obolibrary.org/obo/GENO_0000877
- name: Exon
description: The sequences of a gene that are present in the final, mature, spliced messenger RNA molecule from that gene.
dataType: int
tags: http://purl.obolibrary.org/obo/NCIT_C13231
- name: Genetic reference sequence
description: A published genetic sequence that is used as a reference sequence against which other sequences are compared.
tags: http://purl.obolibrary.org/obo/NCIT_C164388
# "genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information"
# probably, this better fits in Clinical or Subject
- name: Allele information
description: a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
dataType: xref
refEntity: alleleinformation
tags: http://purl.obolibrary.org/obo/OBI_0001352
# in variantDB code is: Effect
# lookup contains two items: synonymous and non-synonymous
- name: Coding variant quality
description: An attribute of a coding genomic variant.
dataType: xref
refEntity: lookupgs/CodingVariantQuality.txt
tags: http://purl.obolibrary.org/obo/SO_0001814
# need clarification
- name: panel
- name: Pipeline version
tags: http://purl.obolibrary.org/obo/GENEPIO_0000152
# is this an appropriate term? Original "classification (by algorithm)"
- name: Variant classification
description:
tags: http://edamontology.org/operation_3225
- name: Date of analysis
description: The particular day, month and year an event has happened or will happen.
dataType: date
tags: http://purl.obolibrary.org/obo/NCIT_C25164
# this is an enum in EMX1
- name: Pipeline name
tags: http://purl.obolibrary.org/obo/GENEPIO_0000151
- name: Assessment
description: The final result of a determination of the value, significance, or extent of.
tags: http://purl.obolibrary.org/obo/NCIT_C25217
- name: Date of Assessment
description: The date (and time) on which an assessment is completed.
dataType: date
tags: http://purl.obolibrary.org/obo/NCIT_C93511
- name: Reviewed by
description: Indicates the person or authoritative body who appraised, evaluated, or analyzed the item.
tags: http://purl.obolibrary.org/obo/NCIT_C42728
# need clarification
- name: assesmentLab
- name: curatedText
# Or maybe the NCIT Date term?
- name: Date of curation
description: A classification datum is a facet that classifies some entity.
dataType: date
tags: http://purl.allotrope.org/ontologies/result#AFR_0001277
- name: Curator
description: The person in charge of the care and superintendence of something, especially a collection.
dataType: xref
refEntity: Person
tags: http://purl.obolibrary.org/obo/NCIT_C69141
- name: Classification
description: A method of generalization, the systematic arrangement of entities into classes or groups based on mutual similarity and certain differing characteristics.
dataType: xref
refEntity: Classification
tags: http://purl.obolibrary.org/obo/NCIT_C25161
- name: Vus plus
dataType: bool
- name: Classification changed
datatype: bool
- name: Variant comment
description: A written explanation, observation or criticism added to textual material.
tags: http://purl.obolibrary.org/obo/NCIT_C25393
- name: Cadd score
dataType: decimal
- name: Gnomad
description: An aggregation of publicly available whole genome and whole exome variant calling experiments in human. GnomAD was previously known as ExAC, when it contained only exome data. Ensembl display population frequencies from gnomAD.
tags: http://ensembl.org/glossary/ENSGLOSSARY_0000238
- name: Gnomad link
dataType: xref
refEntity: Link
- name: HGMD
dataType: enum
enumOptions: Yes,No,Non-contributory
- name: HGMD link
- name: Phylop score
datatype: decimal
- name: Omim Inheritance
dataType: xref
refEntity: omiminheritance
- name: Omim morbid
dataType: xref
refEntity: link
- name: Clinvar
description: NCBI resource that aggregates information about genomic variation and its relationship to human health. Ensembl display clinical significance and phenotypes from ClinVar. https://www.ncbi.nlm.nih.gov/clinvar/
dataType: xref
refEntity: link
tags: http://ensembl.org/glossary/ENSGLOSSARY_0000242
- name: Pubmed
description: A web application from the National Library of Medicine (NLM). It provides a single query interface to over 15 million citations for biomedical articles back to the 1950's. These citations are from MEDLINE and additional life science journals. PubMed includes links to many sites providing full text articles and other related resources.
tags: http://purl.obolibrary.org/obo/NCIT_C42881
- name: Vkgl
dataType: xref
refEntity: link
- name: dbSNP
dataType: xref
refEntity: link
- name: Polyphen 2 prediction
dataType: enum
enumOptions: benign,possibly_damaging,probably_damaging
# ???
- name: Mutation taster
- name: Modulaire pipeline
dataType: compound
- name: Url to report
description: A Uniform Resource Locator (URL)
dataType: hyperlink
tags: http://edamontology.org/data_1052
- name: referenceGenomeUsed
dataType: xref
refEntity: Lookups/GenomeAccessions.txt
description: The specific build of the human genome used as reference for sequence alignment and variant calling.
tags: http://edamontology.org/data_2340
# removed grBuild_release attribute as it's linked via `referenceGenomeUsed`
- name: HGVS genomic nomenclature
description: A set of recomendations for variant naming. The nomenclature describes the change a variant allele has on a named (genomic, transcript or protein) sequence. Can be used as an input for the VEP and displayed for known variants. http://varnomen.hgvs.org/
tags: http://ensembl.org/glossary/ENSGLOSSARY_0000274
- name: HGVS protein nomenclature
description: A set of recomendations for variant naming. The nomenclature describes the change a variant allele has on a named (genomic, transcript or protein) sequence. Can be used as an input for the VEP and displayed for known variants. http://varnomen.hgvs.org/
tags: http://ensembl.org/glossary/ENSGLOSSARY_0000274
# ??? example: Hnf1a+/- --> wont include, should make additional Annotation records
- name: Other transcriptions
- name: Gene identifier
description: A unique gene name within a specific repository, database, or collection.
tags: http://purl.obolibrary.org/obo/NCIT_C48664
- name: allelinfo
label: Extra Allel Info
description: Depth and frequency
tags: http://purl.obolibrary.org/obo/OBI_0001352
attributes:
- name: id
label: allel identifier
description: UMCGnr_#CHROM-start-REF-ALT
dataType: string
aggregateable: true
labelAttribute: true
lookupAttribute: true
nillable: false
readOnly: true
unique: true
tags: http://purl.obolibrary.org/obo/NCIT_C25364
# - name: freqAllel1
# label: Allele Frequency Allele 1
- name: variantFrequencyAllele1 # is 1 needed?
dataType: decimal
tags: http://purl.obolibrary.org/obo/NCIT_C154665
# - name: freqAllel2
# label: Allele Frequency Allele 2
- name: variantFrequencyAllele2
dataType: decimal
tags: http://purl.obolibrary.org/obo/NCIT_C154665
# TODO: is this the correct tag?
# - name: depthAllel1
# label: Allelic Depth Allele 1
- name: alternativeSequenceReadDepth1
dataType: int
tags: http://purl.obolibrary.org/obo/NCIT_C164666
# TODO: is this the correct tag?
# - name: depthAllel2
# label: Allelic Depth Allele 2
- name: alternativeSequenceReadDepth2
dataType: int
tags: http://purl.obolibrary.org/obo/NCIT_C164666
# In the variantDB, this is chromosomeType
- name: Inheritance pattern
dataType: xref
refEntity: lookups/InheritancePattern.txt
nillable: false
lookupAttribute: true
# TODO: is this the correct tag?
- name: mother
label: Mother AllelInfo
dataType: compound
tags: http://purl.obolibrary.org/obo/GENO_0000878
- name: MotherDepth
label: Mother Read Depth
dataType: int
partOfAttribute: mother
- name: MotherfreqAllel1
label: Mother Allele Frequency Allele 1
dataType: decimal
partOfAttribute: mother
- name: MotherfreqAllel2
label: Mother Allele Frequency Allele 2
dataType: decimal
partOfAttribute: mother
- name: MotherdepthAllel1
label: Mother Allelic Depth Allele 1
dataType: int
partOfAttribute: mother
- name: MotherdepthAllel2
label: Mother Allelic Depth Allele 2
dataType: int
partOfAttribute: mother
# TODO: is this the correct tag?
- name: father
label: Father AllelInfo
dataType: compound
tags: http://purl.obolibrary.org/obo/GENO_0000879
- name: FatherDepth
label: Father Read Depth
dataType: int
partOfAttribute: father
- name: FatherfreqAllel1
label: Father Allele Frequency Allele 1
dataType: decimal
partOfAttribute: father
- name: FatherfreqAllel2
label: Father Allele Frequency Allele 2
dataType: decimal
partOfAttribute: father
- name: FatherdepthAllel1
label: Father Allelic Depth Allele 1
dataType: int
partOfAttribute: father
- name: FatherdepthAllel2
label: Father Allelic Depth Allele 2
dataType: int
partOfAttribute: father
# need to pull child terms
- name: Allele Origin
description: A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent.
tags: http://purl.obolibrary.org/obo/GENO_0000877
attributes:
- name: value
idAttribute: true
nillable: false
lookupAttribute: true
labelAttribute: true
tags: http://purl.obolibrary.org/obo/NCIT_C49100
description: The information contained in a data field. It may represent a numeric quantity, a textual characterization, a date or time measurement, or some other state, depending on the nature of the attribute.
- name: description
dataType: text
tags: http://purl.obolibrary.org/obo/NCIT_C25365
description: A written or verbal account, representation, statement, or explanation of something
- name: codesystem
tags: http://purl.obolibrary.org/obo/NCIT_C70895
description: A systematized collection of concepts that define corresponding codes.
- name: code
tags: http://purl.obolibrary.org/obo/NCIT_C25162
description: A symbol or combination of symbols which is assigned to the members of a collection.
- name: iri
dataType: hyperlink
tags: http://purl.obolibrary.org/obo/NCIT_C165071
description: A unique symbol that establishes identity of the resource.
# not in Fair Genomes. Needs a better lookup table though
- name: Clinical classification
tags: http://purl.obolibrary.org/obo/NCIT_C118969
attributes:
- name: value
idAttribute: true
nillable: false
lookupAttribute: true
labelAttribute: true
tags: http://purl.obolibrary.org/obo/NCIT_C49100
description: The information contained in a data field. It may represent a numeric quantity, a textual characterization, a date or time measurement, or some other state, depending on the nature of the attribute.
- name: description
dataType: text
tags: http://purl.obolibrary.org/obo/NCIT_C25365
description: A written or verbal account, representation, statement, or explanation of something
- name: codesystem
tags: http://purl.obolibrary.org/obo/NCIT_C70895
description: A systematized collection of concepts that define corresponding codes.
- name: code
tags: http://purl.obolibrary.org/obo/NCIT_C25162
description: A symbol or combination of symbols which is assigned to the members of a collection.
- name: iri
dataType: hyperlink
tags: http://purl.obolibrary.org/obo/NCIT_C165071
description: A unique symbol that establishes identity of the resource.
# same as FairGenomes
- name: Gene
tags: http://purl.obolibrary.org/obo/NCIT_C16612
attributes:
- name: value
idAttribute: true
nillable: false
lookupAttribute: true
labelAttribute: true
tags: http://purl.obolibrary.org/obo/NCIT_C49100
description: The information contained in a data field. It may represent a numeric quantity, a textual characterization, a date or time measurement, or some other state, depending on the nature of the attribute.
- name: description
dataType: text
tags: http://purl.obolibrary.org/obo/NCIT_C25365
description: A written or verbal account, representation, statement, or explanation of something
- name: codesystem
tags: http://purl.obolibrary.org/obo/NCIT_C70895
description: A systematized collection of concepts that define corresponding codes.
- name: code
tags: http://purl.obolibrary.org/obo/NCIT_C25162
description: A symbol or combination of symbols which is assigned to the members of a collection.
- name: iri
dataType: hyperlink
tags: http://purl.obolibrary.org/obo/NCIT_C165071
description: A unique symbol that establishes identity of the resource.
# pull list of child terms at link
- name: Human chromosome
description: A structure found in the nucleus of human cells that is comprised of a strand of linearized double-stranded DNA plus proteins that package the DNA in a condensed coil form and regulate chromosomal function.
tags: http://purl.obolibrary.org/obo/NCIT_C13203
attributes:
- name: value
idAttribute: true
nillable: false
lookupAttribute: true
labelAttribute: true
tags: http://purl.obolibrary.org/obo/NCIT_C49100
description: The information contained in a data field. It may represent a numeric quantity, a textual characterization, a date or time measurement, or some other state, depending on the nature of the attribute.
- name: description
dataType: text
tags: http://purl.obolibrary.org/obo/NCIT_C25365
description: A written or verbal account, representation, statement, or explanation of something
- name: codesystem
tags: http://purl.obolibrary.org/obo/NCIT_C70895
description: A systematized collection of concepts that define corresponding codes.
- name: code
tags: http://purl.obolibrary.org/obo/NCIT_C25162
description: A symbol or combination of symbols which is assigned to the members of a collection.
- name: iri
dataType: hyperlink
tags: http://purl.obolibrary.org/obo/NCIT_C165071
description: A unique symbol that establishes identity of the resource.
# not in FairGenomes
# need lookup for: Autosomal,Dominant,X-linked,Y-linked,Codominant,Mitchondrial,Inherited_Unresolved
# pull child terms
- name: Inheritance pattern
description: The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment.
tags: http://purl.obolibrary.org/obo/GENO_0000141
attributes:
- name: value
idAttribute: true
nillable: false
lookupAttribute: true
labelAttribute: true
tags: http://purl.obolibrary.org/obo/NCIT_C49100
description: The information contained in a data field. It may represent a numeric quantity, a textual characterization, a date or time measurement, or some other state, depending on the nature of the attribute.
- name: description
dataType: text
tags: http://purl.obolibrary.org/obo/NCIT_C25365
description: A written or verbal account, representation, statement, or explanation of something
- name: codesystem
tags: http://purl.obolibrary.org/obo/NCIT_C70895
description: A systematized collection of concepts that define corresponding codes.
- name: code
tags: http://purl.obolibrary.org/obo/NCIT_C25162
description: A symbol or combination of symbols which is assigned to the members of a collection.
- name: iri
dataType: hyperlink
tags: http://purl.obolibrary.org/obo/NCIT_C165071
description: A unique symbol that establishes identity of the resource.
# I'm not sure this is the correct name/tag
# --> cant include because of all indel possibilities
- name: Nucleobase
tags: http://purl.obolibrary.org/obo/RNAO_0000017
- name: Omim Inheritance
attributes:
- name: id
idAttribute: true
lookupAttribute: true
nillable: false
readOnly: true
unique: true
tags: http://purl.obolibrary.org/obo/NCIT_C25364
- name: label
lookupAttribute: true
labelAttribute: true
nillable: false
readOnly: true
unique: true
tags: http://purl.obolibrary.org/obo/NCIT_C45561
data:
- id: 1
label: AD
- id: 2
label: AR
- id: 3
label: AD/AR
- id: 4
label: XL
- name: Person
description: researcher or contactperson involved in the study and/or affliated with organisation
tags: http://purl.obolibrary.org/obo/NCIT_C25461, http://purl.obolibrary.org/obo/NCIT_C25936
attributes:
- name: identifier
description: identifier
nillable: false
idAttribute: true
lookupAttribute: true
tags: http://purl.obolibrary.org/obo/NCIT_C25364
- name: fullName
label: Full Name
description: full name. E.g. Morris Swertz
tags: http://purl.obolibrary.org/obo/GSSO_001755
- name: alternativeIdentifier
label: Alternative ID
description: alternative identifier. E.g. ORCID:1234
tags: http://purl.obolibrary.org/obo/NCIT_C90353
- name: firstName
tags: http://purl.obolibrary.org/obo/NCIT_C40974
- name: middleInitials
label: Initials
description: middle initiatials. E.g. A.
tags: http://purl.obolibrary.org/obo/NCIT_C166237
- name: lastName
label: Lastname
description: last name. E.g. Swertz
tags: http://purl.obolibrary.org/obo/NCIT_C40975
- name: email
label: Email
description: email address. E.g. [email protected]
nillable: false
labelAttribute: true
tags: http://purl.obolibrary.org/obo/NCIT_C42775
# pull child terms
- name: Zygosity
description: An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different).
tags: http://purl.obolibrary.org/obo/GENO_0000133
attributes:
- name: value
idAttribute: true
nillable: false
lookupAttribute: true
labelAttribute: true
tags: http://purl.obolibrary.org/obo/NCIT_C49100
description: The information contained in a data field. It may represent a numeric quantity, a textual characterization, a date or time measurement, or some other state, depending on the nature of the attribute.
- name: description
dataType: text
tags: http://purl.obolibrary.org/obo/NCIT_C25365
description: A written or verbal account, representation, statement, or explanation of something
- name: codesystem
tags: http://purl.obolibrary.org/obo/NCIT_C70895
description: A systematized collection of concepts that define corresponding codes.
- name: code
tags: http://purl.obolibrary.org/obo/NCIT_C25162
description: A symbol or combination of symbols which is assigned to the members of a collection.
- name: iri
dataType: hyperlink
tags: http://purl.obolibrary.org/obo/NCIT_C165071
description: A unique symbol that establishes identity of the resource.