TDM Gene Management System 6.0

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MANAGEMENT OF GENETIC DATA

Acknowledgment

Several sections of this page simply cross reference their counterparts on the ICIS 5.4 GEMS narratives. The ICIS 6.0 GEMS schema, however, is modified and follows more closely the nomenclature and architecture of the Generation Challenge Programme Demeter domain model for genotyping data.

Introduction

See ICIS 5.4 GEMS Narrative Introduction.

Molecular Data

See ICIS 5.4 GEMS Narrative Molecular Data.

Molecular Variants

See ICIS 5.4 GEMS Narrative Molecular Variants.

Derived Data

See ICIS 5.4 GEMS Narrative Derived Data.

The Gene Management System Table Structure

Generation Challenge Programme Domain Models

The ICIS 6.0 schema is largely inspired by the structure and class nomenclature of the Generation Challenge Programme Genotype and Genomic Mapping domain models. These models (as Unified Modeling Language diagrams, July 2007 Release 1.8) are replicated here below.

Figure 1. GCP Genotype Model

Figure 2. GCP Genomic Mapping Model

GEMS uses the following table structure to store details on genotype domain model objects (table names and attributes follow the Generation Challenge Programme convention).

Figure 3. ICIS GEMS 6.0 Schema

Notation used:

Table Relationships

The central table of GEMS 6.0 schema is the Entity table (gems_entity) which is the superclass which records all generic information about any data object in the GEMS. The subclass field of this table is an enumeration of each major class of actual GEMS entity: LinkageMap, GenomicFeature, etc.

Table Definitions

GEMS_ENTITY

The GEMS_ENTITY table contains one entry for every major entity object managed by GEMS and keeps track of all generic information about that Entity. In this way the GEMS_ENTITY table is a direct implementation of the GCP Entity class. The subclass field of the table partitions contents of the table (via enum values) into the various non-overlapping classes of GEMS objects, largely described within the GCP Domain Model for Genotyping, including the following:

GenomicFeature: a specific segment (subsequence) of DNA in the genome (specified Germplasm) or generally within a class of organism(i.e. species, e.g. Oryza sativa) of interest. A GenomicFeature may (or may not) have a known location ("locus") on specified maps, a known content ("genotype") in specified Germplasm and/or a specified biological/technical biological (e.g. "gene") or technical (e.g. "SSR marker") function of interest.
LinkageMap: a genetic or physical map of genomic loci
Locus: experimentally observed assignment ("MapFeature") of a specified GenomicFeature to a specific LinkageMap
GenomicFeatureDetector: a specific biological reagent and/or information (e.g. PCR primers) that detect a specific subset of possible GenomicFeatures in a genome.
GenomicFeatureDetectionProtocol: non-biologically specific protocol for using a GenomicFeatureDetector in an experimental assay.
GenomicFeatureAssay: the potentially many-to-many join of GenomicFeatureDetector with available GenomicFeatureDetectionProtocols
DetectedVariant: one specified instance of GenomicFeature content ("allele") detected by a GenomicFeatureDetector. If the variant can be analytically interpreted to belong to a specified GenomicFeature, then it is considered in GCP domain model terms to be a GenomicFeatureVariant

The important rule to note is that although the GEMS_ENTITY table autoincrements its primary keys, any and all subclassed objects (and corresponding table entries) share the identical primary key to the GEMS_ENTITY to which they correspond (e.g. a given entry in the GEMS_LINKAGE_MAP table will have the same primary key value as its corresponding entry in the GEMS_ENTITY table).

The type field of the GEMS_ENTITY serves to designate more specific subtypes of entity within each subclass, for example, a LinkageMap could be a "GeneticMap" (versus a "PhysicalMap"). This will generally refer to an ontology. the description field can be any text that meaningfully describes the object.

The GEMS_ENTITY table has relations with several other tables that provide for the identification, citations and annotation (see the GCP domain model for Entity) that describe the given GEMS_ENTITY entry.

Table 1. GEMS_ENTITY table

Fieldname	Description	Type
gentity_id	long, primary key, autoincrement	Unique ID for the Entity
subclass	enum (subclasses of entity as noted above)	Major subclass of GEMS Entity (e.g. LinkageMap, GenomicFeature, etc.)
type	cvterm_id foreign key to Chado cv module cvterm table	Minor subclass of object (e.g. DArt marker type)
description	varchar(255)	Description of the specific GEMS Entity

GEMS_NAMES

GEMS_NAMES table serves as a catalogue of marker detector names and molecular variant names. GOBJTYPE contains the table name where all other information regarding the name specified in the GNVAL field can be found. GNID is the unique identifier of a specific name. GOBJID contains the ID of the name in the table name specified in the GOBJTYPE.

Ex.

GNNAMES_ID = 2715
GENTITY_ID = 1200
GNVAL = RM105_143
...
this entry indicates that "RM105_143" is a name with identified by 
unique id = 2715 in the GEMS_NAMES table, that is a name of the entity identified 
by the foreign key unique id = 1200 pointing to the GEMS_Entity table.

Table 2. GEMS_NAMES table

Fieldname	Description	Type
gnames_id	Long	Unique ID of the Name
gentity_id	Long	Unique ID of GEMS_ENTITY to which the name belongs
gntype	Long	Type of Name
gnstat	Long	Status of Name (0- default value 1 - synonyms)
gnval	Varchar(255)	Name Value
gnlocn	Long	Location where Name was assigned
gevidence_id	Long	Unique ID of GEMS_EVIDENCE documenting the support of this name assignment

GEMS_PUB

The GEMS_PUB table is the join table between GEMS_ENTITY and the ICIS BIBLIOREFS table.

Table 3. GEMS_PUB table

Fieldname	Description	Type
gentity_id	Long foreign key to the GEMS_ENTITY table	Unique ID for the GEMS_ENTITY described within the given publication
pub_id	Long foreign key to the ICIS BIBLIOREFS table	Unique ID of the publication

GEMS_ANNOTATION

The GEMS_ANNOTATION table contains the values of GEMS_ENTITY feature annotation (i.e. GCP Feature data attached to the Entity).

Table 4. GEMS_ANNOTATION table

Fieldname	Description	Type
gannot_id	Long, primary key	Unique ID for the annotation
gentity_id	Long foreign key to the GEMS_ENTITY primary key	Unique ID for the annotated GEMS_ENTITY
gfmetadata	Long foreign key to the GEMS_FEATURE_METADATA primary key	Unique Property ID of the annotation type
data_type	Long (foreign key to the Chado cvterm table, or just a constant(??))	Is a controlled vocabulary designating the data type of the feature value
value	Varchar(255)	Value, encoded as a string
value_id	Long foreign key to a pertinent value table	May points to a pertinent entry in another pertinent table, based on the value data_type, if the value cannot be adequately represented in a simple string.
rank	Long	Sequence number for a Feature value series (where the given annotation Feature value is a "vector" of values; rank 0 applies for a single valued feature)

GEMS_FEATURE_METADATA

GEMS_FEATURE_METADATA table defines the Feature type (a.k.a. ICIS "property"), unit (a.k.a. ICIS scale) and supportingEvidence (a.k.a. ICIS method) associated with a given type of GEMS_ENTITY annotation (i.e. GEMS_ANNOTATION entry gmetadata_id foreign key).

Table 5. GEMS_FEATURE_METADATA table

Fieldname	Description	Type
gmetadata_id	Long primary key	Unique ID for the combination of annotation Feature type, unit and supportingEvidence
type_id	Long foreign key into Chado cvterm table	Unique ID for the "type" of annotated Feature
unit_id	Long foreign key into Chado cvterm table	Unique ID for the "unit" of the value of the annotated Feature
supporting_evidence_id	Long foreign key into GEMS_EVIDENCE table	Unique ID for the GEMS_EVIDENCE associated with the Feature

GEMS_EVIDENCE

The GEMS_EVIDENCE table documents the Evidence supporting a given GEMS_ANNOTATION assertion, including the source of the evidence (e.g. publication, study, analysis program, etc.), observation_date, score and the identity of the curator who recorded the evidence.

Table 6. GEMS_EVIDENCE table

Fieldname	Description	Type
gevidence_id	Long, primary key	Unique ID for the Evidence entry
curator	Long foreign key into the ICIS user table	Curator of the specific evidence
source_type	Long	Specifies the data type of the source_id (i.e. table identification for the source_id foreign key, e.g. BIBLIOREFS, STUDY, etc)
source_id	Unique Property ID of the pertinent entry in the Evidence source table
observation_date	date	Date when the Feature Evidence was asserted
score	varchar(64)	Some source specific measurement of statistical confidence of the source assertion of the annotation Feature value

GEMS_GENOMIC_FEATURE

GEMS_GENOMIC_FEATURE table documents the LinkageMap location, content and function of a specified DNA segment in a genome. Given that all of the documentation of this object may be represented in the GEMS_ENTITY table and its table relationships, the GEMS_GENOMIC_FEATURE may be represented solely as a subclass indexed set of entries in the GEMS_ENTITY table, hence this table is redundant (i.e. doesn't need to be implemented directly).

Table 7. GEMS_GENOMIC_FEATURE table

Fieldname	Description	Type
gfeature_id	Long	Unique ID for the GenomicFeature

GEMS_LINKAGE_MAP

GEMS_LINKAGE_MAP table contains information on genetic, physical, or other kinds of LinkageMap objects (see GCP genomic map domain model description).

Table 8. GEMS_LINKAGE_MAP table

Fieldname	Description	Type
gmap_id	Long	Unique ID for the LinkageMap
parent_map_id	Long foreign key pointing reflexively into the GEMS_LINKAGE_MAP	Unique ID for the LinkageMap within which the given LinkageMap entry resides. For most linkage groups, this is the parent chromosome map. For chromosome maps, the given genome map (set).

GEMS_LOCUS

GEMS_LOCUS table contains information on genetic, physical, or other kinds of Locus objects (GCP MapFeature) (see GCP genomic map domain model description).

Table 9. GEMS_LINKAGE_MAP table

Fieldname	Description	Type
glocus_id	Long, primary key	Unique ID for the a Locus
glmap_id	Long foreign key to the LinkageMap	Unique ID for the a LinkageMap
gfeature_id	Long foreign key to the GenomicFeature	Unique ID for the a GenomicFeature

GEMS_GENOMIC_FEATURE_DETECTOR

GEMS_GENOMIC_FEATURE_DETECTOR table documents the biologically specific reagents/information required to detect a specified subset of GenomicFeature entities in a genome. Given that all of the documentation of this object may be represented in the GEMS_ENTITY table and its table relationships, the GEMS_GENOMIC_FEATURE_DETECTOR may be represented solely as a subclass indexed set of entries in the GEMS_ENTITY table, hence this table is redundant (i.e. doesn't need to be implemented directly)

Table 10. GEMS_GENOMIC_FEATURE_DETECTOR table

Fieldname	Description	Type
gfdetector_id	Long, primary key	Unique ID of the Genomic Feature Detector

GEMS_GENOMIC_FEATURE_DETECTION_PROTOCOL

GEMS_GENOMIC_FEATURE_DETECTION_PROTOCOL documents all the generic (non-biological) reagents and methodology for using instances of GenomicFeatureDetector to identify instances of GenomicFeature experimentally. Such reagents and protocols can typically be reused with many distinct GenomicFeatureDetector instances, hence, are reusable across several GenomicFeatureAssays. Given that all of the documentation of this object may be represented in the GEMS_ENTITY table and its table relationships, the GEMS_GENOMIC_FEATURE_DETECTION_PROTOCOL may be represented solely as a subclass indexed set of entries in the GEMS_ENTITY table, hence this table is redundant (i.e. doesn't need to be implemented directly).

Table 11. GEMS_GENOMIC_FEATURE_DETECTION_PROTOCOL table

Fieldname	Description	Type
gfdprotocol_id	Long, primary key	Unique identifier of the given protocol

GEMS_GENOMIC_FEATURE_ASSAY

GEMS_GENOMIC_FEATURE_ASSAY (Polymorphic Detector) contains the different combination of GenomicFeatureDetector with GenomicFeatureDetectionProtocol. That is, a GenomicFeatureDetector can have one or more applied conditions (or protocols) for experimental assay. A protocol/condition can also be used for different GenomicFeatureDetector instances. This creates a many-to-many relationship between the markers and protocols, modeled by this join table.

Table 12. GEMS_GENOMIC_FEATURE_ASSAY table

Fieldname	Description	Type
gfassay_id	Long, primary key	Unique identifier
gfdetector_id	Long foreign key into the GEMS_GENOMIC_FEATURE_DETECTOR table	Unique detector identifier
gfdprotocol_id	Long foreign key into the GEMS_GENOMIC_FEATURE_DETECTION_PROTOCOL table	Unique detector identifier

GEMS_DETECTED_VARIANT

GEMS_DETECTED_VARIANT stores information on molecular variants associated with GenomicFeature instances that are detected by GenomicFeatureDetector systems. Each molecular variant is uniquely identified by the gvariant_id field. Each gvariant_id is associated with the GenomicFeatureDetector that resolves it, using the gfdetector_id foreign key. If analysis can assign the specific molecular variant to a specified GenomicFeature, then the gfeature_id field that links the variant to an entry in the GEMS_GENOMIC_FEATURE table (this makes the entry a full GCP GenomicFeatureVariant instance).

Table 13. GEMS_DETECTED_VARIANT table

Fieldname	Description	Type
gvariant_id	Long	Unique Molecular Variant ID
gfdetector_id	Long foreign key into the GEMS_GENOME_FEATURE_DETECTOR table	GenomicFeatureDetector that identified the variant
gfeature_id	Long foreign key into the GEMS_GENOME_FEATURE table	GenomicFeature to which the variant is specifically assigned (if any)

Semantic Correspondence between ICIS GEMS 5.4 and ICIS GEMS 6.0

The table below attempts to map the tables and attributes of the ICIS GEMS 5.4 schema onto the above ICIS GEMS 6.0 schema.

Table Mappings

Table 14. Approximate Semantic Mapping of ICIS GEMS 5.4 Tables onto ICIS GEMS 6.0 Tables

ICIS 5.4 Table	ICIS 6.0 Table
no counterpart in 5.4	GEMS_ENTITY
GEMS_NAMES	GEMS_NAMES
no counterpart in 5.4	GEMS_PUB (join table between GEMS_ENTITY and ICIS_BIBREFS)
GEMS_COMP	GEMS_ANNOTATION used at GEMS_ENTITY level
GEMS_PROP	GEMS_FEATURE_METADATA + Controlled vocabulary term foreign key for Property itself (Chado cvterm table)
GEMS_SCALE	Controlled vocabulary term foreign key (Chado cvterm table)
GEMS_METHOD	GEMS_EVIDENCE + Controlled vocabulary term foreign key for Method itself (Chado cvterm table)
GEMS_MARKER_DETECTOR	GEMS_GENOMIC_FEATURE_DETECTOR
GEMS_MV	GEMS_DETECTED_VARIANT
GEMS_PD	GEMS_GENOMIC_FEATURE_ASSAY
GEMS_PD_COMP	GEMS_GENOMIC_FEATURE_DETECTION_PROTOCOL
no counterpart in 5.4	GEMS_LINKAGE_MAP
GEMS_LOCUS	GEMS_GENOMIC_FEATURE for DNA identity with map location information stored in GEMS_LOCUS

Field Mappings

Table 6. Semantic Mapping of ICIS GEMS 5.4 onto ICIS GEMS 6.0

ICIS 5.4 Table	ICIS 5.4 Field	ICIS 6.0 Table	ICIS 6.0 Field
GEMS_NAMES	gnid	GEMS_NAMES	gnames_id
GEMS_NAMES	gobjid	GEMS_NAMES	gentity_id
not present	n/a	GEMS_NAMES	source_id (foreign key to GEMS_EVIDENCE table)
GEMS_NAMES	gndate	GEMS_EVIDENCE	observation_date
GEMS_NAMES	gnuid	GEMS_EVIDENCE	curator_id (foreign key to ICIS users table)
not present	n/a	GEMS_EVIDENCE	source_type
GEMS_NAMES	gnref	GEMS_EVIDENCE	source_id (foreign key to pertinent table, as per source_type)
GEMS_COMP	cid	GEMS_ANNOTATION	gannot_id
GEMS_COMP	condid	GEMS_ANNOTATION	type_id (foreign key to cvterm table)
GEMS_COMP	comid	GEMS_ENTITY	type
GEMS_COMP	pid	GEMS_ANNOTATION	gmetadata_id
GEMS_COMP	comval	GEMS_ANNOTATION	value
GEMS_COMP	comuid	GEMS_EVIDENCE	curator_id
GEMS_COMP	comref	GEMS_EVIDENCE	source_id (foreign key to ICIS BIBREFS)
GEMS_PROP	Pid	GEMS_FEATURE_METADATA	gmetadata_id
GEMS_PROP	propid	GEMS_FEATURE_METADATA	type_id (foreign key to cvterm table)
GEMS_PROP	propname	Chado cvterm table	name in cvterm table via type_id
GEMS_PROP	scaleid	GEMS_FEATURE_METADATA	unit_id (foreign key to cvterm table)
GEMS_PROP	methid	GEMS_FEATURE_METADATA	supportingEvidence_id (foreign key to GEMS_EVIDENCE table)
GEMS_METHOD, GEMS_SCALE	all fields	Chado cvterm table	Controlled vocabulary terms with pertinent documentation
GEMS_LOCUS	locusid	GEMS_LOCUS	glocus_id (see also GEMS_GENOMIC_FEATURE below)
GEMS_LOCUS	chromosome	GEMS_LOCUS	glmap_id (foreign key to GEMS_LINKAGE_MAP table - chromosome treated as another map)
GEMS_LOCUS	position	GEMS_ANNOTATION	locus metadata, including position data, is recorded as GEMS_ANNOTATION of the corresponding GEMS_ENTITY (with associated GEMS_FEATURE_METADATA and supporting GEMS_EVIDENCE)
not present	n/a	GEMS_GENOMIC_FEATURE	genomic_locus_id foreign key to GEMS_LOCUS
GEMS_MARKER_DETECTOR	mdid	GEMS_GENOMIC_FEATURE_DETECTOR	gfdetector_id
GEMS_MARKER_DETECTOR	all other fields	GEMS_ANNOTATION	detector metadata recorded as GEMS_ANNOTATION of the corresponding GEMS_ENTITY (with associated GEMS_FEATURE_METADATA and supporting GEMS_EVIDENCE)
GEMS_MV	mvid	GEMS_DETECTED_VARIANT	gvariant_id
GEMS_MV	locusid	GEMS_DETECTED_VARIANT	gfeature_id (foreign key to GEMS_GENOMIC_FEATURE table)
GEMS_MV	mvtype	GEMS_ENTITY	type
GEMS_MV	mdid	GEMS_DETECTED_VARIANT	gfdetector_id (foreign key to GEMS_GENOMIC_FEATURE_DETECTOR table)
GEMS_MV	all other fields	GEMS_ANNOTATION	GEMS_DETECTED_VARIANT metadata recorded as GEMS_ANNOTATION of the corresponding GEMS_ENTITY (with associated GEMS_FEATURE_METADATA and supporting GEMS_EVIDENCE)
GEMS_PD	pdid	GEMS_GENOMIC_FEATURE_ASSAY	gfassay_id
GEMS_PD	condid	GEMS_GENOMIC_FEATURE_ASSAY	gfdprotocol_id (foreign key to GEMS_GENOMIC_FEATURE_DETECTION_PROTOCOL table)
GEMS_PD	mdid	GEMS_GENOMIC_FEATURE_ASSAY	gfdetector_id (foreign key to GEMS_GENOMIC_FEATURE_DETECTOR table)
GEMS_PD	all other fields	GEMS_ANNOTATION	GEMS_GENOMIC_FEATURE_ASSAY metadata recorded as GEMS_ANNOTATION of the corresponding GEMS_ENTITY (with associated GEMS_FEATURE_METADATA and supporting GEMS_EVIDENCE)
GEMS_PD_COMP	pdcomp	GEMS_GENOMIC_FEATURE_DETECTION_PROTOCOL	gfdprotocol_id
GEMS_PD_COMP	pdid	not present	not needed, since GEMS_GENOMIC_FEATURE_ASSAY points to the protocol, not vice-versa
GEMS_PD_COMP	all other fields	GEMS_ANNOTATION	GEMS_GENOMIC_FEATURE_DETECTION_PROTOCOL metadata recorded as GEMS_ANNOTATION of the corresponding GEMS_ENTITY (with associated GEMS_FEATURE_METADATA and supporting GEMS_EVIDENCE)
not present	n/a	GEMS_PUB	gpub_id is a foreign key into the ICIS BIBREFS table
not present	n/a	GEMS_PUB	gentity_id is a foreign key into the GEMS_ENTITY