JGI Phytozome Plant Genomics Database

Phytozome plant comparative genomics database. Contains genome annotations, gene models, expression data, and comparative genomics for plant species. DATABASE: plant-db-7 postgresql.public TABLES: 306 KEY FUNCTIONALITY: - Plant genome annotations (Chado-based schema) - Gene models and transcripts - Expression data - Comparative genomics and orthologs - Biomaterial and cell line tracking CHADO SCHEMA: Uses GMOD Chado schema for genomic data with extensions for plant-specific data types.

URI: https://w3id.org/jgi/phytozome

Name: phytozome

Classes

Class	Description
Acquisition	Data acquisition from assay
Analysis	Computational analysis/pipeline
AnalysisFeature	Link between analysis and features it produced
AnalysisGrp	Group of analyses
AnalysisSet	Set of related analyses
ArrayDesign	Microarray or expression platform design
Assay	Expression assay experiment
AssayBiomaterial	Biomaterial used in assay
Biomaterial	Biological material (tissue, cell line, etc
BiomaterialProp	Property of a biomaterial
BiomaterialRelationship	Relationship between biomaterials
BiomaterialTreatment	Treatment applied to biomaterial
CellLine	Cell line information
CellLineFeature	Feature associated with cell line
CellLineProp	Cell line property
Contact	Contact/researcher information
ContactRelationship	Relationship between contacts
CV	Controlled vocabulary (GO, SO, etc
CVTerm	Term from a controlled vocabulary
Feature	Genomic feature (gene, mRNA, exon, CDS, etc
Organism	Plant organism/species

Slots

Slot	Description
abbreviation
acquisition_id
acquisitiondate
algorithm
analysis_id
analysis_set_id
analysisfeature_id
analysisgrp_id
arraydesign_id
assay_biomaterial_id
assay_id
assaydate
biomaterial_id
biomaterial_relationship_id
biomaterial_treatment_id
biomaterialprop_id
biosourceprovider_id
cell_line_feature_id
cell_line_id
cell_lineprop_id
channel_id
comment
common_name
contact_id
contact_relationship_id
cv_id
cvterm_id
dbxref_id
definition
description
feature_id
genus
identity
is_analysis
is_obsolete
manufacturer_id
name	Feature name/symbol
normscore
object_id
organism_id
platformtype_id
program	Analysis program name
programversion
protocol_id
rank
rawscore
residues	Sequence if stored
seqlen
significance
sourcename
sourceuri
sourceversion
species
subject_id
taxon_id
timeaccessioned
timeexecuted
timelastmodified
treatment_id
type_id	SO term for feature type
uniquename	Unique identifier
uri
value
version

Enumerations

Enumeration	Description

Types

Type	Description
Boolean	A binary (true or false) value
Curie	a compact URI
Date	a date (year, month and day) in an idealized calendar
DateOrDatetime	Either a date or a datetime
Datetime	The combination of a date and time
Decimal	A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double	A real number that conforms to the xsd:double specification
Float	A real number that conforms to the xsd:float specification
Integer	An integer
Jsonpath	A string encoding a JSON Path
Jsonpointer	A string encoding a JSON Pointer
Ncname	Prefix part of CURIE
Nodeidentifier	A URI, CURIE or BNODE that represents a node in a model
Objectidentifier	A URI or CURIE that represents an object in the model
Sparqlpath	A string encoding a SPARQL Property Path
String	A character string
Time	A time object represents a (local) time of day, independent of any particular...
Uri	a complete URI
Uriorcurie	a URI or a CURIE

Subsets

Subset	Description