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“The International Committee on Taxonomy of Viruses (ICTV) authorizes…
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… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
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spiekos authored and copybara-github committed Mar 27, 2023
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4 changes: 2 additions & 2 deletions biomedical_schema/genome_annotation.mcf
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Expand Up @@ -123,14 +123,14 @@ Node: dcid:genBankAccession
name: "genBankAssemblyAccession"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly,dcs:GenomeAssemblyUnit,dcs:Chromosome
domainIncludes: dcs:BiologicalElement
description: "The accession version of the GenBank assembly or sequence element."

Node: dcid:refSeqAccession
name: "refSeqAssemblyAccession"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly,dcs:GenomeAssemblyUnit,dcs:Chromosome
domainIncludes: dcs:BiologicalElement
description: "The accession version of the RefSeq assembly or sequence element."

Node: dcid:ncbiBioProject
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236 changes: 236 additions & 0 deletions biomedical_schema/virus_taxonomy.mcf
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# Virus Taxonomy
Node: dcid:Virus
name: "Virus"
typeOf: schema:Class
subClassOf: dcs:BiologicalSpecimen
description: "A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. The classification of viruses is developed by the International Committee on the Taxonomy of Viruses (ICTV)."
descriptionUrl: "https://en.wikipedia.org/wiki/Virus"
sameAs: "https://talk.ictvonline.org/taxonomy/w/ictv-taxonomy"

Node: dcid:VirusIsolate
name: "VirusIsolate"
typeOf: schema:Class
subClassOf: dcs:Virus
description: "A virus that has been isolated from an infected host and can be propogated in culture."
sameAs: "https://talk.ictvonline.org/taxonomy/w/ictv-taxonomy"

Node: dcid:VirusGenomeSegment
name: "VirusGenomeSegment"
typeOf: schema:Class
subClassOf: dcs:VirusIsolate
description: "A segment of a virus whose genome is fragmented into two or more nucleic acid molecules."

Node: dcid:abbreviation
name: "abbreviation"
typeOf: schema:Property
domainIncludes: schema:Thing
rangeIncludes: schema:Text
abbreviation: "A shortened form of a word, phrase, or name."

Node: dcid:genomeCoverage
name: "genomeCoverage"
typeOf: schema:Property
domainIncludes: dcs:VirusIsolate
rangeIncludes: dcs:GenomeCoverageEnum
description: "Genome coverage refers to the number of unique reads aligned to a specific locus in a reference genome. Genome coverage can also be used to denote the breadth of coverage of a target genome, which is defined as the percentage of target bases that are sequenced a given number of times."
descriptionUrl: "https://www.nature.com/articles/nrg3642"

Node: dcid:genomeSegmentOf
name: "genomeSegmentOf"
typeOf: schema:Property
domainIncludes: dcs:VirusGenomeSegment
rangeIncludes: dcs:VirusIsolate
description: "The virus isolate from which this genome segment was sequenced."

Node: dcid:isExemplarVirusIsolate
name: "isExemplarVirusIsolate"
typeOf: schema:Property
domainIncludes: dcs:VirusIsolate
rangeIncludes: schema:Boolean
description: "A virus isolate is a virus that has been isolated from an infected host and can be propogated in culture. ICTV chooses examplar isolates to represent a virus species. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source."
descriptionUrl: "https://ictv.global/vmr"

Node: dcid:ofVirusSpecies
name: "ofVirusSpecies"
typeOf: schema:Property
domainIncludes: dcs:VirusIsolate
rangeIncludes: dcs:Virus
description: "The species of a virus isolate."

Node: dcid:proposalForLastChange
name: "proposalForLastChange"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
description: "The file name of the taxonomic proposal that details the justification for the last change. Proposals can be retrieved by appending the file nameand '.pdf' to the end of the following url: 'https://talk.ictvonline.org/ictv/proposals/<replace with file name.pdf'."

Node: dcid:taxonHistoryURL
name: "taxonHistoryURL"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Number
description: "The web url link that provides the complete taxonomic history of the species can be found by appending the number value reported here to the following url 'https://ictv.global/taxonomy/taxondetails?taxnode_id='. The proposal indicated above can be downloaded from the link provided by the last changed entry in the history."

Node: dcid:versionOfLastChange
name: "versionOfLastChange"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Number
description: "The release number of the Master Species List (MSL) where the Last Change occurred. See https://talk.ictvonline.org/taxonomy/p/taxonomy_releases for a list of MSLs and their year of release."

Node: dcid:virusGenomeComposition
name: "virusGenomeComposition"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: dcs:VirusGenomeCompositionEnum
description: "Composition of the virus genome and it's replication method. This follows the Baltimore Classification system, which groups viruses together based on their manner of mRNA synthesis. Characteristics directly related to this include whether the genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), the strandedness of the genome, which can be either single- or double-stranded, and the sense of a single-stranded genome, which is either positive or negative."
descriptionUrl: "https://en.wikipedia.org/wiki/Baltimore_classification"

Node: dcid:virusHost
name: "virusHost"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: dcs:VirusHostEnum
description: "A specific organism or taxonomic group of organisms that are susceptible to be infected by a virus. Viruses require infection of living host cells to replicate and survive."
descriptionUrl: "https://www.uniprot.org/help/virus_host"

Node: dcid:virusIsolateDesignation
name: "virusIsolateDesignation"
typeOf: schema:Property
domainIncludes: dcs:VirusIsolate
rangeIncludes: schema:Text
description: "The designation of the virus isolate (often also referred to as variants or strains). May be empty if there is no physical isolate."

Node: dcid:virusLastTaxonomicChange
name: "virusLastTaxonomicChange"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: dcs:VirusLastTaxonomicChangeEnum
description: "The last change made to each virus species across the entire history of the taxon. Possible changes include a combination of the following: abolished, demoted, merged, moved, new, promoted, removed, renamed, or split."

Node: dcid:virusSource
name: "virusSource"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: dcs:VirusSourceEnum
description: "The source envrionment from which the virus was isolated."

Node: dcid:virusRealm
name: "virusRealm"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'realm' is the highest taxonomic rank into which virus species can be classified. Use of the taxonomic rank 'realm' is optional. If left blank, lower taxonomic levels of have not been assigned to a realm. The realm rank suffix is '-viria'."

Node: dcid:virusSubrealm
name: "virusSubrealm"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'subrealm' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'subrealm' is optional. If left blank, lower taxonomic levels of have not been assigned to a subrealm.The subrealm rank suffix is '-vira'."

Node: dcid:virusKingdom
name: "virusKingdom"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'kingdom' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'kingdom' is optional. If left blank, lower taxonomic levels of have not been assigned to a kingdom. The kingdom rank suffix is '-virae'."

Node: dcid:virusSubkingdom
name: "virusSubkingdom"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'subkingdom' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'subkingdom' is optional. If left blank, lower taxonomic levels of have not been assigned to a subkingdom. The subkingdom rank suffix is '-virites'."

Node: dcid:virusPhylum
name: "virusPhylum"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'phylum' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'phylum' is optional. If left blank, lower taxonomic levels of have not been assigned to a phylum.The phylum rank suffix is '-viricota'."

Node: dcid:virusSubphylum
name: "virusSubphylum"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'subphylum' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'subphylum' is optional. If left blank, lower taxonomic levels of have not been assigned to a subphylum.The subphylum rank suffix is '-viricotina'."

Node: dcid:virusClass
name: "virusClass"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'class' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'class' is optional. If left blank, lower taxonomic levels of have not been assigned to a class.The class rank suffix is '-viricetes'."

Node: dcid:virusSubclass
name: "virusSubclass"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'subclass' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'subclass' is optional. If left blank, lower taxonomic levels of have not been assigned to a subclass.The subclass rank suffix is '-viricetidae'."

Node: dcid:virusOrder
name: "virusOrder"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "An 'order' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'order' is optional. If left blank, lower taxonomic levels of have not been assigned to a order. The order rank suffix is '-virales'."

Node: dcid:virusSuborder
name: "virusSuborder"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'suborder' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'suborder' is optional. If left blank, lower taxonomic levels of have not been assigned to a suborder. The suborder rank suffix is '-virineae'."

Node: dcid:virusFamily
name: "virusFamily"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'family' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'family' is optional. If left blank, lower taxonomic levels of have not been assigned to a family.The family rank suffix is '-viridae'."

Node: dcid:virusSubfamily
name: "virusSubfamily"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'subfamily' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'subfamily' is optional. If left blank, lower taxonomic levels of have not been assigned to a subfamily. The subfamily rank suffix is '-virinae'."

Node: dcid:virusGenus
name: "virusGenus"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'genus' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'genus' is mandatory. Every species should be assigned to a genus. The genus rank suffix is '-virus'."

Node: dcid:virusSubgenus
name: "virusSubgenus"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A 'subgenus' is a rank in the taxonomic hierarchy into which virus species can be classified. Use of the taxonomic rank 'subgenus' is optional. If left blank, species have not been assigned to a subgenus. The genus rank suffix is '-virus'."

Node: dcid:virusSpecies
name: "virusSpecies"
typeOf: schema:Property
domainIncludes: dcs:Virus
rangeIncludes: schema:Text
sameAs: "https://ictv.global/taxonomy"
description: "A Species is the lowest taxonomic rank in the hierarchy approved by the ICTV. While subspecies levels of classification may exist for some viruses (e.g. Hepatitis C virus), the ICTV does not classify viruses below the species level."
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