From eafc40d63272f28bfab34899f0e65ca899bfc6de Mon Sep 17 00:00:00 2001
From: spiekos <spiekos@google.com>
Date: Thu, 23 Mar 2023 15:07:59 -0700
Subject: [PATCH] =?UTF-8?q?=E2=80=9CThe=20International=20Committee=20on?=
 =?UTF-8?q?=20Taxonomy=20of=20Viruses=20(ICTV)=20authorizes=20and=20organi?=
 =?UTF-8?q?zes=20the=20taxonomic=20classification=20of=20and=20the=20nomen?=
 =?UTF-8?q?clatures=20for=20viruses.=20The=20ICTV=20has=20developed=20a=20?=
 =?UTF-8?q?universal=20taxonomic=20scheme=20for=20viruses,=20and=20thus=20?=
 =?UTF-8?q?has=20the=20means=20to=20appropriately=20describe,=20name,=20an?=
 =?UTF-8?q?d=20classify=20every=20virus=20that=20affects=20living=20organi?=
 =?UTF-8?q?sms.=20The=20members=20of=20the=20International=20Committee=20o?=
 =?UTF-8?q?n=20Taxonomy=20of=20Viruses=20are=20considered=20expert=20virol?=
 =?UTF-8?q?ogists.=20The=20ICTV=20was=20formed=20from=20and=20is=20governe?=
 =?UTF-8?q?d=20by=20the=20Virology=20Division=20of=20the=20International?=
 =?UTF-8?q?=20Union=20of=20Microbiological=20Societies.=20Detailed=20work,?=
 =?UTF-8?q?=20such=20as=20delimiting=20the=20boundaries=20of=20species=20w?=
 =?UTF-8?q?ithin=20a=20family,=20typically=20is=20performed=20by=20study?=
 =?UTF-8?q?=20groups=20of=20experts=20in=20the=20families.=E2=80=9D=20Desc?=
 =?UTF-8?q?ription=20from=20Wikipedia.?=
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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](https://github.com/datacommonsorg/data/pull/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
---
 biomedical_schema/genome_annotation.mcf   |  10 +-
 biomedical_schema/virus_taxonomy.mcf      | 229 ++++++++++++++++++++++
 biomedical_schema/virus_taxonomy_enum.mcf | 225 +++++++++++++++++++++
 core/dcschema.mcf                         |   7 +
 4 files changed, 466 insertions(+), 5 deletions(-)
 create mode 100644 biomedical_schema/virus_taxonomy.mcf
 create mode 100644 biomedical_schema/virus_taxonomy_enum.mcf

diff --git a/biomedical_schema/genome_annotation.mcf b/biomedical_schema/genome_annotation.mcf
index 809d8ea28..6b15a63c5 100644
--- a/biomedical_schema/genome_annotation.mcf
+++ b/biomedical_schema/genome_annotation.mcf
@@ -51,21 +51,21 @@ name: "Gene"
 typeOf: schema:Class
 subClassOf: dcs:GenomeAnnotation
 description: "Gene symbol of a gene, which is the basic hereditary unit of life."
-sameAs: "https://bioportal.bioontology.org/ontologies/OGG"
+descriptionUrl: "https://bioportal.bioontology.org/ontologies/OGG"
 
 Node: dcid:GeneticVariant
 name: "GeneticVariant"
 typeOf: schema:Class
 subClassOf: dcs:GenomeAnnotation
 description:  "A single-nucleotide polymorphism, which is a substitution of a single nucleotide that occurs at a specific position in the genome, where each variation is present to some appreciable degree within a population. These are defined by dbSNP and includes small indels as well."
-sameAs: "http://rohsdb.usc.edu/GBshape/cgi-bin/hgTables?db=hg19&hgta_group=varRep&hgta_track=snp137&hgta_table=snp137&hgta_doSchema=describe+table+schema"
+descriptionUrl: "http://rohsdb.usc.edu/GBshape/cgi-bin/hgTables?db=hg19&hgta_group=varRep&hgta_track=snp137&hgta_table=snp137&hgta_doSchema=describe+table+schema"
 
 Node: dcid:GeneticVariantGeneAssociation
 name: "GeneticVariantGeneAssociation"
 typeOf: schema:Class
 subClassOf: dcs:GeneticAssociation
 description:  "An association between a genetic variant and a gene in a given tissue. This is determined by performing a regression analysis on paired genome sequencing and RNA-sequencing across a population."
-sameAs: "https://storage.googleapis.com/gtex_analysis_v6p/single_tissue_eqtl_data/README_eQTL_v6p.txt"
+descriptionUrl: "https://storage.googleapis.com/gtex_analysis_v6p/single_tissue_eqtl_data/README_eQTL_v6p.txt"
 
 Node: Position
 typeOf: dcs:UnitOfMeasure
@@ -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
diff --git a/biomedical_schema/virus_taxonomy.mcf b/biomedical_schema/virus_taxonomy.mcf
new file mode 100644
index 000000000..90d438a7c
--- /dev/null
+++ b/biomedical_schema/virus_taxonomy.mcf
@@ -0,0 +1,229 @@
+# 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"
+descriptionUrl: "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."
+descriptionUrl: "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: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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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
+descriptionUrl: "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."
diff --git a/biomedical_schema/virus_taxonomy_enum.mcf b/biomedical_schema/virus_taxonomy_enum.mcf
new file mode 100644
index 000000000..bba87d486
--- /dev/null
+++ b/biomedical_schema/virus_taxonomy_enum.mcf
@@ -0,0 +1,225 @@
+# GenomeCoverageEnum
+Node: dcid:GenomeCoverageEnum
+name: "GenomeCoverageEnum"
+typeOf: schema:Class
+subClassOf: schema:Enumeration
+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:GenomeCoverageCompleteCodingGenome
+name: "Complete Coding Genome"
+typeOf: dcs:GenomeCoverageEnum
+description: "All of the coding regions (parts of the genome that code for proteins) are covered by sequencing."
+
+Node: dcid:GenomeCoverageCompleteGenome
+name:  "Complete Genome"
+typeOf: dcs:GenomeCoverageEnum
+description: "The entirety of the genome is covered by sequencing."
+
+Node: dcid:GenomeCoverageNoEntryInGenBank
+name: "No Entry In GenBank"
+typeOf: dcs:GenomeCoverageEnum
+description: "The coverage level of a given genome has not been recorded in GenBank."
+
+Node: dcid:GenomeCoveragePartialGenome
+name: "GenomeCoveragePartialGenome"
+typeOf: dcs:GenomeCoverageEnum
+description: "A genome that has been partially sequenced."
+
+
+# VirusGenomeCompositionEnum
+Node: dcid:VirusGenomeCompositionEnum
+name: "VirusGenomeCompositionEnum"
+typeOf: schema:Class
+subClassOf: schema:Enumeration
+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:VirusGenomeCompositionDoubleStrandedDNA
+name: "Double-Stranded DNA"
+typeOf: dcs:VirusGenomeCompositionEnum
+description: "A virus whose genome is composed of double stranded DNA (dsDNA). Belongs to Baltimore classification Group I: double-stranded DNA viruses. All dsDNA viruses have their mRNA synthesized in a three-step process. First, a transcription preinitiation complex binds to the DNA upstream of the site where transcription begins, allowing for the recruitment of a host RNA polymerase. Second, once the RNA polymerase is recruited, it uses the negative strand as a template for synthesizing mRNA strands. Third, the RNA polymerase terminates transcription upon reaching a specific signal, such as a polyadenylation site."
+descriptionUrl: "https://en.wikipedia.org/wiki/Baltimore_classification"
+
+Node: dcid:VirusGenomeCompositionSingleStrandedDNA
+name: "Single-Stranded DNA"
+typeOf: dcs:VirusGenomeCompositionEnum
+description: "A virus whose genome is composed of single stranded DNA (ssDNA), which can be positive or negative. Belongs to Baltimore Classification Group II: single-stranded DNA viruses. ssDNA viruses have the same manner of transcription as dsDNA viruses. However, because the genome is single-stranded, it is first made into a double-stranded form by a DNA polymerase upon entering a host cell. mRNA is then synthesized from the double-stranded form. The double-stranded form of ssDNA viruses may be produced either directly after entry into a cell or as a consequence of replication of the viral genome."
+descriptionUrl: "https://en.wikipedia.org/wiki/Baltimore_classification"
+
+Node: dcid:VirusGenomeCompositionSingleStrandedDNAPositive
+name: "Single-Stranded DNA-Positive"
+typeOf: dcs:VirusGenomeCompositionEnum
+description: "A virus whose genome is composed of the positive strand of single stranded DNA (ssDNA). Belongs to Baltimore Classification Group II: single-stranded DNA viruses. ssDNA viruses have the same manner of transcription as dsDNA viruses. However, because the genome is single-stranded, it is first made into a double-stranded form by a DNA polymerase upon entering a host cell. mRNA is then synthesized from the double-stranded form. The double-stranded form of ssDNA viruses may be produced either directly after entry into a cell or as a consequence of replication of the viral genome."
+descriptionUrl: "https://en.wikipedia.org/wiki/Baltimore_classification"
+
+Node: dcid:VirusGenomeCompositionSingleStrandedDNANegative
+name: "Single-Stranded DNA-Negative"
+typeOf: dcs:VirusGenomeCompositionEnum
+description: "A virus whose genome is composed of the negative strand of single stranded DNA (ssDNA). Belongs to Baltimore Classification Group II: single-stranded DNA viruses. ssDNA viruses have the same manner of transcription as dsDNA viruses. However, because the genome is single-stranded, it is first made into a double-stranded form by a DNA polymerase upon entering a host cell. mRNA is then synthesized from the double-stranded form. The double-stranded form of ssDNA viruses may be produced either directly after entry into a cell or as a consequence of replication of the viral genome."
+descriptionUrl: "https://en.wikipedia.org/wiki/Baltimore_classification"
+
+Node: dcid:VirusGenomeCompositionDoubleStrandedDNAReverseTranscription
+name: "Double=Stranded DNA-Reverse Transcription"
+typeOf: dcs:VirusGenomeCompositionEnum
+description: "A virus whose genome is double-stranded DNA that has an RNA intermediate (dsDNA-RT) in its replication cycle. Belongs to Baltimore Classification Group VII: double-stranded DNA viruses with an RNA intermediate. dsDNA-RT viruses have a gap in one strand, which is repaired to create a complete dsDNA genome prior to transcription. dsDNA-RT viruses are transcribed in the same manner as dsDNA viruses, but make use of reverse transcription to replicate their circular genome while it is still in the capsid. The host cell's RNA polymerase II transcribes RNA strands from the genome in the cytoplasm, and the genome is replicated from these RNA strands. The dsDNA genome is produced from pregenomic RNA strands via the same general mechanism as ssRNA-RT viruses, but with replication occurring in a loop around the circular genome. After replication, the dsDNA genome may be packed or sent to the nucleus for further rounds of transcription."
+descriptionUrl: "https://en.wikipedia.org/wiki/Baltimore_classification"
+
+Node: dcid:VirusGenomeCompositionDoubleStrandedRNA
+name: "Double-Stranded RNA"
+typeOf: dcs:VirusGenomeCompositionEnum
+description: "A virus whose genome is composed of double stranded RNA (dsRNA). Belongs to Baltimore Classification Group III: double-stranded RNA viruses. After entering a host cell, the dsRNA genome is transcribed to mRNA from the negative strand by the viral RNA-dependent RNA polymerase (RdRp). The mRNA may be used for translation or replication. Single-stranded mRNA is replicated to form the dsRNA genome. The 5′-end of the genome may be naked, capped, or covalently bound to a viral protein."
+descriptionUrl: "https://en.wikipedia.org/wiki/Baltimore_classification"
+
+Node: dcid:VirusGenomeCompositionSingleStrandedRNA
+name: "Single-Stranded RNA-Positive"
+typeOf: dcs:VirusGenomeCompositionEnum
+description: "A virus whose genome is composed of single stranded RNA (ssRNA). These can be either a positive sense single stranded RNA (+ssRNA) genome belonging to Blatimore Classification Group IV or a negative sense single stranded (-ssRNA) genome belonging to Baltimore Classification Group V."
+
+Node: dcid:VirusGenomeCompositionSingleStrandedRNAPositive
+name: "Single-Stranded RNA-Positive"
+typeOf: dcs:VirusGenomeCompositionEnum
+description: "A virus whose genome is composed of positive sense single stranded RNA (+ssRNA). Belongs to Baltimore Classification Group IV: positive sense single-stranded RNA viruses. For +ssRNA viruses, the genome functions as mRNA, so no transcription is required for translation. +ssRNA viruses will also, however, produce positive sense copies of the genome from negative sense strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. The 5′-end may be naked, capped, or covalently bound to a viral protein, and the 3′-end may be naked or polyadenylated."
+descriptionUrl: "https://en.wikipedia.org/wiki/Baltimore_classification"
+
+Node: dcid:VirusGenomeCompositionSingleStrandedRNANegative
+name: "Single-Stranded RNA-Negative"
+typeOf: dcs:VirusGenomeCompositionEnum
+description: "A virus whose genome is composed of negative sense single stranded RNA (-ssRNA). Belongs to Baltimore Classification Group V: negative sense single-stranded RNA viruses. mRNA, which is positive sense, is transcribed directly from the negative sense genome. The first process for -ssRNA transcription involves RdRp binding to a leader sequence on the 3′ end of the genome, transcribing a 5′ triphosphate-leader RNA that is capped, then stopping and restarting on a transcription signal which is capped, continuing until a stop signal is reached.[31] The second manner is similar but instead of synthesizing a cap, RdRp may make use of cap snatching, whereby a short sequence of host cell mRNA is taken and used as the 5′ cap of the viral mRNA.[32] Genomic -ssRNA is replicated from the positive sense antigenome in a similar manner as transcription, except in reverse using the antigenome as a template for the genome. RdRp moves from the 3′-end to the 5′-end of the antigenome and ignores all transcription signals when synthesizing genomic -ssRNA."
+descriptionUrl: "https://en.wikipedia.org/wiki/Baltimore_classification"
+
+Node: dcid:VirusGenomeCompositionSingleStrandedRNAReverseTranscription
+name: "Single-Stranded RNA-Reverse Transcription"
+typeOf: dcs:VirusGenomeCompositionEnum
+description: "A virus whose genome is positive-sense single-stranded RNA that has a DNA intermediate ((+)ssRNA-RT) in its replication cycle. Belongs to Baltimore Classification Group VI: single-stranded RNA viruses with a DNA intermediate. ssRNA-RT viruses are transcribed in the same manner as DNA viruses, but their linear genomes are first converted to a dsDNA form through a process called reverse transcription. The viral reverse transcriptase enzyme synthesizes a DNA strand from the ssRNA strand, and the RNA strand is degraded and replaced with a DNA strand to create a dsDNA genome. The genome is then integrated into the DNA of the host cell, where it is now called a provirus. The host cell's RNA polymerase II then transcribes RNA in the nucleus from the proviral DNA. Some of this RNA may become mRNA whereas other strands will become copies of the viral genome for replication."
+descriptionUrl: "https://en.wikipedia.org/wiki/Baltimore_classification"
+
+
+# VirusHostEnum
+Node: dcid:VirusHostEnum
+name: "VirusHostEnum"
+typeOf: schema:Class
+subClassOf: schema:Enumeration
+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:VirusHostAlgae
+name: "Algae"
+typeOf: dcs:VirusHostEnum
+
+Node: dcid:VirusHostArchea
+name: "Archea"
+typeOf: dcs:VirusHostEnum
+
+Node: dcid:VirusHostBacteria
+name: "Bacteria"
+typeOf: dcs:VirusHostEnum
+
+Node: dcid:VirusHostFungi
+name: "Fungi"
+typeOf: dcs:VirusHostEnum
+
+Node: dcid:VirusHostInvertebrates
+name: "Invertebrates"
+typeOf: dcs:VirusHostEnum
+
+Node: dcid:VirusHostPlants
+name: "Plants"
+typeOf: dcs:VirusHostEnum
+
+Node: dcid:VirusHostProtists
+name: "Protists"
+typeOf: dcs:VirusHostEnum
+
+Node: dcid:VirusHostVertebrates
+name: "Vertebrates"
+typeOf: dcs:VirusHostEnum
+
+
+# VirusSourceEnum
+Node: dcid:VirusSourceEnum
+name: "VirusSourceEnum"
+typeOf: schema:Class
+subClassOf: schema:Enumeration
+description: "The source envrionment from which the virus was isolated."
+
+Node: dcid:VirusSourceInvertebrates
+name: "Invertebrates"
+typeOf: dcs:VirusSourceEnum
+
+Node: dcid:VirusSourceMarine
+name: "Marine"
+typeOf: dcs:VirusSourceEnum
+
+Node: dcid:VirusSourcePhytobiome
+name: "Phytobiome"
+typeOf: dcs:VirusSourceEnum
+
+Node: dcid:VirusSourcePlants
+name: "Plants"
+typeOf: dcs:VirusSourceEnum
+
+Node: dcid:ViruSourceProtists
+name: "Protists"
+typeOf: dcs:VirusSourceEnum
+
+Node: dcid:VirusSourceSewage
+name: "Sewage"
+typeOf: dcs:VirusSourceEnum
+
+Node: dcid:VirusSourceSoil
+name: "Soil"
+typeOf: dcs:VirusSourceEnum
+
+
+# VirusLastTaxonomicChangeEnum
+Node: dcid:VirusLastTaxonomicChangeEnum
+name: "VirusLastTaxonomicChangeEnum"
+typeOf: schema:Class
+subClassOf: schema:Enumeration
+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:VirusLastTaxonomicChangeAbolished
+name: "Abolished"
+typeOf: dcs:VirusLastTaxonomicChangeEnum
+description: "The taxon is abolished (deleted) from the MSL. All constituent taxa need to be moved, otherwise they will also be deleted."
+
+Node: dcid:VirusLastTaxonomicChangeDemoted
+name: "Demoted"
+typeOf: dcs:VirusLastTaxonomicChangeEnum
+description: "A higher rank taxon is moved to a lower rank (potentially requiring a rename). This does NOT necessarily imply that the constituent members of the promoted taxon are subject to any change. This change type was added in 2020."
+
+Node: dcid:VirusLastTaxonomicChangeMerged
+name: "Merged"
+typeOf: dcs:VirusLastTaxonomicChangeEnum
+description: "Two separate taxa will be merged into a single taxon. The single taxon may be one of the initial two, or it could be a newly created taxon. All constituent, lower rank members will be automatically moved into the merged taxon."
+
+Node: dcid:VirusLastTaxonomicChangeMoved
+name: "Moved"
+typeOf: dcs:VirusLastTaxonomicChangeEnum
+description: "A lower rank taxon and its constituent members is moved from one higher rank taxon to another. (The move usually, but not necessarily, is to a taxon (existing or new) at the same rank as the original parent.)"
+
+Node: dcid:VirusLastTaxonomicChangeNew
+name: "New"
+typeOf: dcs:VirusLastTaxonomicChangeEnum
+description: "Creation of a new taxon. New ranks higher than Species must contain new (or moved) lower-rank members."
+
+Node: dcid:VirusLastTaxonomicChangePromoted
+name: "Promoted"
+typeOf: dcs:VirusLastTaxonomicChangeEnum
+description: "A lower rank taxon is moved to a higher rank (usually also requiring a rename). This does NOT necessarily imply that the constituent members of the promoted taxon are subject to any change."
+
+Node: dcid:VirusLastTaxonomicChangeRemoved
+name: "Removed"
+typeOf: dcs:VirusLastTaxonomicChangeEnum
+description: "A taxon is removed as type species."
+
+Node: dcid:VirusLastTaxonomicChangeRenamed
+name: "Renamed"
+typeOf: dcs:VirusLastTaxonomicChangeEnum
+description: "A taxon is renamed. The new name must adhere to the naming rules of the ICTV Code of Virus Classification and Nomenclature."
+
+Node: dcid:VirusLastTaxonomicChangeSplit
+name: "Split"
+typeOf: dcs:VirusLastTaxonomicChangeEnum
+description: "A taxon, along with its constituent members, are split into two or more taxa. The original taxon that was split may, or may not, be retained, and the resulting set of taxa into which the original was split, may consist of existing or new taxa. The change must be accompanied with an indication of where each of the constituent member taxa are to be moved. Theoretically, this action could be accomplished with a combination of changes involving Moved, Abolished, and New, but was created to maintain the history of all changes to the original taxon and its members."
diff --git a/core/dcschema.mcf b/core/dcschema.mcf
index 4515d9148..be219fced 100644
--- a/core/dcschema.mcf
+++ b/core/dcschema.mcf
@@ -2985,3 +2985,10 @@ name: "isFallbackRoot"
 description: "Indicates that a StatVarGroup is to act as the root for all StatisticalVariable nodes that are not explicitly assigned to be a member of a StatVarGroup. This is relevant only in the context of a Custom Data Commons instance."
 domainIncludes: dcs:StatVarGroup
 rangeIncludes: schema:Boolean
+
+Node: dcid:abbreviation
+name: "abbreviation"
+typeOf: schema:Property
+domainIncludes: schema:Thing
+rangeIncludes: schema:Text
+abbreviation: "A shortened form of a word, phrase, or name."