last update
2025-November-14
VirJenDB
v1.0
VirJenDB Metadata Categories
The VirJenDB metadata are grouped according to tags: Organizational, Sample, Source, Host, Analysis, Taxonomy, Internal, Workflow. Note that fields can overlap between these categories.
-
Contains everything related to the study or project
-
Contains everything related to the description of the specific entry
-
Contains everything related to the data source
-
Contains everything related to the host
-
Contains information related to information generated from the sequence
-
Contains the ICTV, NCBI and GTDB taxonomy trees
-
Contains fields used within VirJenDB
-
Contains information about VirJenDB pipelines
VirJenDB Metadata Fields
Tab-separated files containing the following field descriptions can be downloaded from GitHub in XLSX, JSON, CSV and TXT formats.
Organizational
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| Accession | GenBank Accession of the virus sequence. It equals NCBI Accession, ENA Accession, and DDBJ Accession, which are part of the INSDC. | BVBRC, NCBI Virus |
| Assembly Accession | NCBI Assembly Accession of the virus sequence. | BVBRC, NCBI Virus |
| BV-BRC Accession | Accession of the sequence in the BV-BRC database. | BVBRC |
| Bioproject Accession | References the BioProject Accession that the virus sequence is a part of (INSDC). | BVBRC, NCBI Virus |
| Biosample Accession | References the BioSample Accession that the virus sequence is a part of (INSDC). | BVBRC, NCBI Virus |
| Release Date | Date when the sequence was made public in a repository (e.g. GenBank, BV-BRC). | NCBI Virus |
| SRA Accession | NCBI Sequence Read Archive (SRA) Accession. | BVBRC, NCBI Virus |
| Sequence Source | The name of the source database or tool by which the virus sequence was added in VirJenDB; in the case of PhiSpy-predicted prophages, the value is PhiSpy. | VJDB |
| Sequencing Center | Institution that sequenced the collected sample. | BVBRC |
| Submitter | Name(s) of the submitter(s) of the virus sequence. | NCBI Virus |
| Submitter Organization | Organization the submitter(s) is(are) affiliated with. | NCBI Virus |
| VirJenDB Accession | Unique identifier of the virus sequence, assigned by VirJenDB. | VJDB |
| VirJenDB Metadata Version | Version of the virus sequence record, including metadata, assigned by VirJenDB. | VJDB |
Sample
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| Collection Date | Date when the sample the virus sequence originates from was collected or sampled. | BVBRC, NCBI Virus |
| Collection Geo Location | Country name and additional identifier like a state abbreviation from where the sample the sequence originates from was collected/sampled. | BVBRC, NCBI Virus |
| Collection Source Host Tissue | Tissue, Specimen or Source of the superhost from which the sample the virus sequence originates from was collected or sampled. | NCBI Virus |
| Country | Country or sea area where the sample the virus sequence originates from was collected or sampled. | BVBRC, NCBI Virus |
| Genome Completeness | Wether the sequence is a partial or complete sequence in NCBI GenBank. | NCBI Virus |
| Genotype | The genotype or subtype of a virus sequence, as provided by the sequence submitter. This field comes from the “/serotype” field of the GenBank record and is shown as submitted. Consistency and accuracy may vary. | NCBI Virus |
| Isolate | Name of the virus isolate associated with the sample from which the virus sequence was obtained. | NCBI Virus |
| Molecule Type | Molecule type of the sequence, e.g. ssRNA. Note that there are 15 molecule types corresponding to combinations of the Baltimore Classifications, from NCBI GenBank. | NCBI Virus |
| NCBI Clade | Sub-species designation of the virus sequence, from NCBI GenBank field “clade”. | NCBI Taxonomy |
| NCBI Genotype | Sub-species designation of the virus sequence, from NCBI GenBank field “genotype”. | NCBI Taxonomy |
| NCBI Isolate | Sub-species designation of the virus sequence, from NCBI GenBank field “isolate”. | NCBI Taxonomy |
| NCBI Realm | A ‘Realm’ is the highest taxonomic rank into which virus species can be classified. Defined by the NCBI. | NCBI Taxonomy |
| NCBI Serotype | Sub-species designation of the virus sequence, from NCBI GenBank field “serotype”. | NCBI Taxonomy |
| Organism Name | NCBI GenBank organism name: a taxonomic name at species level or below the species level. | NCBI Virus |
| Segment Name | Name of the virus segment. Can be a number. | NCBI Virus |
| Sequence Length | Length of the virus sequence in basepairs (bp). | BVBRC, NCBI Virus |
| Strain | Name of the virus strain associated with the sample from which the virus sequence was obtained. | BVBRC |
| Submitter Country | Country of the submitter’s organization. | NCBI Virus |
| Submitter Region | Region or location of the organization of the submitters. | NCBI Virus |
Source
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| BV-BRC Sequence | Flag indicating if this virus sequence is available in BV-BRC. | VJDB |
| GenBank Sequence | Determines if this virus sequence is available in Genbank. | NCBI Virus |
| ICTV Exemplar | Flag indicating yes if the sequence is an exemplar of the species in the ICTV Taxonomy. | ICTV |
| RefSeq Sequence | Determines if this virus sequence is a reference sequence in the RefSeq database. | BVBRC, NCBI Virus |
Host
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| BV-BRC Host Age | Host Age and Unit from BV-BRC. | BVBRC |
| BV-BRC Host Group | The host’s broader group association in a taxonomic context from BV-BRC. | BVBRC |
| BVBRC Host Sex | Sex of the sampled host from the BV-BRC. | BVBRC |
| Host Accession | Host Accession from NCBI GenBank that refers to the host sequence from which the prophage was predicted. | VJDB |
| Host Age | Host age number only from “BVBRC Host Age”. Caution: not yet standardized by unit! | BVBRC |
| Host Assembly Accession | Host Assembly Accession of the sequence (INSDC). | IMG/VR, PhD, PhiSpy |
| Host Average Sequence Depth | Average sequencing depth across the host sequence. Multiple host associations/predictions separated by semicolons. | IMG/VR, PhD, PhiSpy |
| Host BioProject Accession | References the BioProject Accession associated with the host sequence. | IMG/VR, PhD, PhiSpy |
| Host Biosample Accession | References the BioSample Accession associated with the host sequence. | IMG/VR, PhD, PhiSpy |
| Host Collection Date | Date of collection of the sample from which the host sequence originates. | IMG/VR, PhD, PhiSpy |
| Host Common Name | Common name of the host the virus sequence was collected from, e.g. human. Currently (v1.0) no ontology is applied. | BVBRC, NCBI Virus |
| Host Country | Country or sea area origin of the sample from which the host sequence originates. | IMG/VR, PhD, PhiSpy |
| Host GTDB Species Name | References the Host GTDB Species Name to which the NCBI host taxonomy ID of the virus sequence could be mapped. See the mapping file on the Datasets page. | IMG/VR, PhD, PhiSpy |
| Host IMGM Taxon OID | Associated Host IMGM Taxon OID from which the virus sequence was extracted by IMG/VR. | IMG/VR, PhD, PhiSpy |
| Host NCBI Tax ID | The host sequence NCBI Taxonomy ID. Can be based on the mapping by GTDB of the GTDB Species Name to the NCBI Taxonomy ID. | GTDB |
| Host Species | The scientific species name of the sampled host. | BVBRC |
| ICTV Host Group | The ICTV Host source field content to be combined with other host group data from the other sources. | ICTV |
Analysis
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| Average Depth | Average sequencing depth across the sequence from BVBRC. | BVBRC |
| Cluster Reference | The VirJenDB ID of the representative of its cluster. See documentation for selection details. | VJDB |
| Cluster Representative | Flag indicating yes if the sequence is a representative sequence of a group of sequences, computed by VClust. See documentation for selection details. | VJDB |
| GC Content | Percentage of G and C nucleotides in the sequence from BVBRC. | BVBRC |
| Pangolin Lineage | Lineage determined by Pangolin. | BVBRC, NCBI Virus |
| Platform | Instrument platform used for sequencing the virus; multiple values are seperated by a semicolon (only for assemblies). | BVBRC |
| Predicted Method | The tool used to predict the virus sequence. No value means that it is not a predicted virus sequence. | IMG/VR, PhD, PhiSpy |
| Unique Representative | Flag indicating yes if the sequence is a representative for a group of identical VirJenDB sequences. | VJDB |
Taxonomy
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| ICTV Class | A ‘Class’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Family | A ‘Family’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Genus | A ‘Genus’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Kingdom | A ‘Kingdom’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Lineage Names | Aggregation of the ICTV Taxonomy Names associated with the virus sequence. | VJDB |
| ICTV Order | A ‘Order’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Phylum | A ‘Phylum’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Realm | A ‘Realm’ is the highest taxonomic rank into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Species | 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. Defined by the ICTV. | ICTV |
| ICTV Subfamily | A ‘Subfamily’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Subgenus | A ‘Subgenus’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Suborder | A ‘suborder’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Subphylum | A ‘Subphylum’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| NCBI Class | A ‘Class’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | BVBRC |
| NCBI Family | A ‘Family’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | BVBRC, NCBI Virus |
| NCBI Genus | A ‘Genus’ is a rank in the taxonomic hierarchy into which virus a sequence can be classified. Defined by the NCBI. | BVBRC, NCBI Virus |
| NCBI Kingdom | A ‘Kingdom’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | BVBRC |
| NCBI Lineage IDs | NCBI TaxIDs assigned to the virus sequence, from BVBRC. | BVBRC |
| NCBI Lineage Names | Aggregation of the NCBI Taxonomy Names associated with the virus sequence. | BVBRC |
| NCBI Order | A ‘Order’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | BVBRC |
| NCBI Phylum | A ‘Phylum’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | BVBRC |
| NCBI Species | A Species is the lowest taxonomic rank in the hierarchy approved by the NCBI. While subspecies levels of classification may exist for some viruses (e.g. Hepatitis C virus), the NCBI does not classify viruses below the species level. Defined by the NCBI. | BVBRC, NCBI Virus |
| NCBI SpeciesTax ID | The virus species NCBI Taxonomy ID. | BVBRC |
| NCBI Subfamily | A ‘Subfamily’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | NCBI Taxonomy |
| NCBI Subgenus | A ‘Subgenus’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | NCBI |
| NCBI Suborder | A ‘suborder’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | NCBI Taxonomy |
| NCBI Subphylum | A ‘Subphylum’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | NCBI Taxonomy |
Internal
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| Unique Reference | The VirJenDB ID for the unique representative sequence. For the non-phages, the smallest Accession in the group. See documentation for selection details. | VJDB |
Workflows
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| Host Association Method | Method by which the fields “Host Accession ID” from NCBI GenBank or “NCBI Taxonomy Lineage” was associated to the virus sequence. Currently (v1.0) either a host association from the data source or PhiSpy prophage prediction. Multiple host associations/predictions separated by semicolons. | VJDB |
| Host Sequencing Platform | Instrument or sequencing platform used for host sequencing. Multiple host associations/predictions separated by semicolons. | IMG/VR, PhD, PhiSpy |
Metadata Field Mappings
Organizational
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| Accession | GenBank Accession of the virus sequence. It equals NCBI Accession, ENA Accession, and DDBJ Accession, which are part of the INSDC. | BVBRC, NCBI Virus |
| Assembly Accession | NCBI Assembly Accession of the virus sequence. | BVBRC, NCBI Virus |
| BV-BRC Accession | Accession of the sequence in the BV-BRC database. | BVBRC |
| Bioproject Accession | References the BioProject Accession that the virus sequence is a part of (INSDC). | BVBRC, NCBI Virus |
| Biosample Accession | References the BioSample Accession that the virus sequence is a part of (INSDC). | BVBRC, NCBI Virus |
| Release Date | Date when the sequence was made public in a repository (e.g. GenBank, BV-BRC). | NCBI Virus |
| SRA Accession | NCBI Sequence Read Archive (SRA) Accession. | BVBRC, NCBI Virus |
| Sequence Source | The name of the source database or tool by which the virus sequence was added in VirJenDB; in the case of PhiSpy-predicted prophages, the value is PhiSpy. | VJDB |
| Sequencing Center | Institution that sequenced the collected sample. | BVBRC |
| Submitter | Name(s) of the submitter(s) of the virus sequence. | NCBI Virus |
| Submitter Organization | Organization the submitter(s) is(are) affiliated with. | NCBI Virus |
| VirJenDB Accession | Unique identifier of the virus sequence, assigned by VirJenDB. | VJDB |
| VirJenDB Metadata Version | Version of the virus sequence record, including metadata, assigned by VirJenDB. | VJDB |
Sample
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| Collection Date | Date when the sample the virus sequence originates from was collected or sampled. | BVBRC, NCBI Virus |
| Collection Geo Location | Country name and additional identifier like a state abbreviation from where the sample the sequence originates from was collected/sampled. | BVBRC, NCBI Virus |
| Collection Source Host Tissue | Tissue, Specimen or Source of the superhost from which the sample the virus sequence originates from was collected or sampled. | NCBI Virus |
| Country | Country or sea area where the sample the virus sequence originates from was collected or sampled. | BVBRC, NCBI Virus |
| Genome Completeness | Wether the sequence is a partial or complete sequence in NCBI GenBank. | NCBI Virus |
| Genotype | The genotype or subtype of a virus sequence, as provided by the sequence submitter. This field comes from the “/serotype” field of the GenBank record and is shown as submitted. Consistency and accuracy may vary. | NCBI Virus |
| Isolate | Name of the virus isolate associated with the sample from which the virus sequence was obtained. | NCBI Virus |
| Molecule Type | Molecule type of the sequence, e.g. ssRNA. Note that there are 15 molecule types corresponding to combinations of the Baltimore Classifications, from NCBI GenBank. | NCBI Virus |
| NCBI Clade | Sub-species designation of the virus sequence, from NCBI GenBank field “clade”. | NCBI Taxonomy |
| NCBI Genotype | Sub-species designation of the virus sequence, from NCBI GenBank field “genotype”. | NCBI Taxonomy |
| NCBI Isolate | Sub-species designation of the virus sequence, from NCBI GenBank field “isolate”. | NCBI Taxonomy |
| NCBI Realm | A ‘Realm’ is the highest taxonomic rank into which virus species can be classified. Defined by the NCBI. | NCBI Taxonomy |
| NCBI Serotype | Sub-species designation of the virus sequence, from NCBI GenBank field “serotype”. | NCBI Taxonomy |
| Organism Name | NCBI GenBank organism name: a taxonomic name at species level or below the species level. | NCBI Virus |
| Segment Name | Name of the virus segment. Can be a number. | NCBI Virus |
| Sequence Length | Length of the virus sequence in basepairs (bp). | BVBRC, NCBI Virus |
| Strain | Name of the virus strain associated with the sample from which the virus sequence was obtained. | BVBRC |
| Submitter Country | Country of the submitter’s organization. | NCBI Virus |
| Submitter Region | Region or location of the organization of the submitters. | NCBI Virus |
Source
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| BV-BRC Sequence | Flag indicating if this virus sequence is available in BV-BRC. | VJDB |
| GenBank Sequence | Determines if this virus sequence is available in Genbank. | NCBI Virus |
| ICTV Exemplar | Flag indicating yes if the sequence is an exemplar of the species in the ICTV Taxonomy. | ICTV |
| RefSeq Sequence | Determines if this virus sequence is a reference sequence in the RefSeq database. | BVBRC, NCBI Virus |
Host
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| BV-BRC Host Age | Host Age and Unit from BV-BRC. | BVBRC |
| BV-BRC Host Group | The host’s broader group association in a taxonomic context from BV-BRC. | BVBRC |
| BVBRC Host Sex | Sex of the sampled host from the BV-BRC. | BVBRC |
| Host Accession | Host Accession from NCBI GenBank that refers to the host sequence from which the prophage was predicted. | VJDB |
| Host Age | Host age number only from “BVBRC Host Age”. Caution: not yet standardized by unit! | BVBRC |
| Host Assembly Accession | Host Assembly Accession of the sequence (INSDC). | IMG/VR, PhD, PhiSpy |
| Host Average Sequence Depth | Average sequencing depth across the host sequence. Multiple host associations/predictions separated by semicolons. | IMG/VR, PhD, PhiSpy |
| Host BioProject Accession | References the BioProject Accession associated with the host sequence. | IMG/VR, PhD, PhiSpy |
| Host Biosample Accession | References the BioSample Accession associated with the host sequence. | IMG/VR, PhD, PhiSpy |
| Host Collection Date | Date of collection of the sample from which the host sequence originates. | IMG/VR, PhD, PhiSpy |
| Host Common Name | Common name of the host the virus sequence was collected from, e.g. human. Currently (v1.0) no ontology is applied. | BVBRC, NCBI Virus |
| Host Country | Country or sea area origin of the sample from which the host sequence originates. | IMG/VR, PhD, PhiSpy |
| Host GTDB Species Name | References the Host GTDB Species Name to which the NCBI host taxonomy ID of the virus sequence could be mapped. See the mapping file on the Datasets page. | IMG/VR, PhD, PhiSpy |
| Host IMGM Taxon OID | Associated Host IMGM Taxon OID from which the virus sequence was extracted by IMG/VR. | IMG/VR, PhD, PhiSpy |
| Host NCBI Tax ID | The host sequence NCBI Taxonomy ID. Can be based on the mapping by GTDB of the GTDB Species Name to the NCBI Taxonomy ID. | GTDB |
| Host Species | The scientific species name of the sampled host. | BVBRC |
| ICTV Host Group | The ICTV Host source field content to be combined with other host group data from the other sources. | ICTV |
Analysis
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| Average Depth | Average sequencing depth across the sequence from BVBRC. | BVBRC |
| Cluster Reference | The VirJenDB ID of the representative of its cluster. See documentation for selection details. | VJDB |
| Cluster Representative | Flag indicating yes if the sequence is a representative sequence of a group of sequences, computed by VClust. See documentation for selection details. | VJDB |
| GC Content | Percentage of G and C nucleotides in the sequence from BVBRC. | BVBRC |
| Pangolin Lineage | Lineage determined by Pangolin. | BVBRC, NCBI Virus |
| Platform | Instrument platform used for sequencing the virus; multiple values are seperated by a semicolon (only for assemblies). | BVBRC |
| Predicted Method | The tool used to predict the virus sequence. No value means that it is not a predicted virus sequence. | IMG/VR, PhD, PhiSpy |
| Unique Representative | Flag indicating yes if the sequence is a representative for a group of identical VirJenDB sequences. | VJDB |
Taxonomy
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| ICTV Class | A ‘Class’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Family | A ‘Family’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Genus | A ‘Genus’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Kingdom | A ‘Kingdom’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Lineage Names | Aggregation of the ICTV Taxonomy Names associated with the virus sequence. | VJDB |
| ICTV Order | A ‘Order’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Phylum | A ‘Phylum’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Realm | A ‘Realm’ is the highest taxonomic rank into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Species | 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. Defined by the ICTV. | ICTV |
| ICTV Subfamily | A ‘Subfamily’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Subgenus | A ‘Subgenus’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Suborder | A ‘suborder’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| ICTV Subphylum | A ‘Subphylum’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the ICTV. | ICTV |
| NCBI Class | A ‘Class’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | BVBRC |
| NCBI Family | A ‘Family’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | BVBRC, NCBI Virus |
| NCBI Genus | A ‘Genus’ is a rank in the taxonomic hierarchy into which virus a sequence can be classified. Defined by the NCBI. | BVBRC, NCBI Virus |
| NCBI Kingdom | A ‘Kingdom’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | BVBRC |
| NCBI Lineage IDs | NCBI TaxIDs assigned to the virus sequence, from BVBRC. | BVBRC |
| NCBI Lineage Names | Aggregation of the NCBI Taxonomy Names associated with the virus sequence. | BVBRC |
| NCBI Order | A ‘Order’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | BVBRC |
| NCBI Phylum | A ‘Phylum’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | BVBRC |
| NCBI Species | A Species is the lowest taxonomic rank in the hierarchy approved by the NCBI. While subspecies levels of classification may exist for some viruses (e.g. Hepatitis C virus), the NCBI does not classify viruses below the species level. Defined by the NCBI. | BVBRC, NCBI Virus |
| NCBI SpeciesTax ID | The virus species NCBI Taxonomy ID. | BVBRC |
| NCBI Subfamily | A ‘Subfamily’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | NCBI Taxonomy |
| NCBI Subgenus | A ‘Subgenus’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | NCBI |
| NCBI Suborder | A ‘suborder’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | NCBI Taxonomy |
| NCBI Subphylum | A ‘Subphylum’ is a rank in the taxonomic hierarchy into which a virus sequence can be classified. Defined by the NCBI. | NCBI Taxonomy |
Internal
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| Unique Reference | The VirJenDB ID for the unique representative sequence. For the non-phages, the smallest Accession in the group. See documentation for selection details. | VJDB |
Workflows
| VirJenDB Field Name | Description | Sources |
|---|---|---|
| Host Association Method | Method by which the fields “Host Accession ID” from NCBI GenBank or “NCBI Taxonomy Lineage” was associated to the virus sequence. Currently (v1.0) either a host association from the data source or PhiSpy prophage prediction. Multiple host associations/predictions separated by semicolons. | VJDB |
| Host Sequencing Platform | Instrument or sequencing platform used for host sequencing. Multiple host associations/predictions separated by semicolons. | IMG/VR, PhD, PhiSpy |