org.molgenis documentation.

Last known status of this task. See compute history for details. NB 'ready' means ready for running (cf. 'done').
enum_options: 'generated', 'ready', 'running', 'failed', 'done', 'jobsubmitted', 'cancelled'

submittedID: string (optional)

ID received from the scheduler after submission; used only in clusters

Unique name

id: int (required)

automatically generated internal id, only for internal use.

Associations:

computeRun: ComputeRun (1..1)

The run this task is part of

prevSteps: ComputeTask (0..n)

To keep track of calculation dependencies

Constraints:

unique(id):

Field id is unique within an ComputeTask.

unique(name, computeRun):

The combination of fields name, computeRun is unique within an ComputeTask.

ComputeTaskHistory

implements Autoid

Keep track of the compute history of a task, including resubmissions.

Inherited attributes:

id,

Attributes:

statusTime: datetime (required)

time of state change

runLog: text (optional)

field to show the content of the error file (only applicable on fail/done of a task)

statusCode: enum (optional)

current status of this task.
enum_options: 'generated', 'ready', 'running', 'failed', 'done', 'cancelled'

newStatusCode: enum (required)

current status of this task.
enum_options: 'generated', 'ready', 'running', 'failed', 'done', 'submitted', 'cancelled'

id: int (required)

automatically generated internal id, only for internal use.

Associations:

computeTask: ComputeTask (1..1)

the task for which the history was collected

Constraints:

unique(id):

Field id is unique within an ComputeTaskHistory.

ComputeVM

implements Autoid

Inherited attributes:

id,

Attributes:

serverID: text (optional)

hostName: text (optional)

host of VMs name

floatingIpExtern: text (optional)

IP open to internet

floatingIpTarget: text (optional)

IP open to target environment

startTime: datetime (optional)

time, when VM is started

endTime: datetime (optional)

time, when VM is down

isInUse: bool (optional)

indicate if compute tasks are currently executed on VM

id: int (required)

automatically generated internal id, only for internal use.

Associations:

finishedComputeTask: ComputeTask (0..n)

tasks, which are completed on this VM

failedComputeTask: ComputeTask (0..n)

tasks, which are failed on this VM

computeRun: ComputeRun (1..1)

This VM is used for this run

Constraints:

unique(id):

Field id is unique within an ComputeVM.

ComputeParameterValue

implements Nameable

Related to ComputeTask values

Inherited attributes:

id, name,

Attributes:

value: text (required)

the value of the parameter

Unique name

id: int (required)

automatically generated internal id, only for internal use.

Associations:

computeTask: ComputeTask (1..1)

ComputeTask, to which the value belongs

Constraints:

unique(id):

Field id is unique within an ComputeParameterValue.

ComputeRun

implements Nameable

A set of computetasks to run

Inherited attributes:

id, name,

Attributes:

creationTime: datetime (required)

time of creation

showInDashboard: bool (required)

Show this run in the dashboard

userEnvironment: text (optional)

Environment vars provided by the user

submitScript: text (optional)

The generated submit.sh to use only in the cluster scheduler environment

pollDelay: long (optional)

Delay between two database ComputeTask polls

isActive: bool (required)

isSubmittingPilots: bool (required)

isDone: bool (required)

isCancelled: bool (required)

interpreter: enum (optional)

the interpreter used to run this command. For example 'shellTemplate'
enum_options: 'bash', 'R'

hasFailedJobs: bool (required)

pilotsSubmitted: int (required)

pilotsStarted: int (required)

Unique name

id: int (required)

automatically generated internal id, only for internal use.

Associations:

computeBackend: ComputeBackend (1..1)

Backend where run will be executed

owner: MolgenisUser (1..1)

Constraints:

unique(id):

Field id is unique within an ComputeRun.

unique(name):

Field name is unique within an ComputeRun.

Pilot

implements Autoid

Inherited attributes:

id,

Attributes:

value: text (required)

creationTime: datetime (required)

time when pilot was submitted

lifeTerm: int (required)

term after which pilot id expires in minutes

status: enum (required)

enum_options: 'submitted', 'used', 'expired', 'failed', 'done'

id: int (required)

automatically generated internal id, only for internal use.

Associations:

owner: MolgenisUser (1..1)

backend: ComputeBackend (1..1)

computeRun: ComputeRun (1..1)

computeTask: ComputeTask (0..1)

Constraints:

unique(id):

Field id is unique within an Pilot.

ComputeBackend

implements Nameable

Inherited attributes:

id, name,

Attributes:

backendUrl: string (required)

Backend host

hostType: enum (required)

type of the host
enum_options: 'CLUSTER', 'GRID', 'LOCALHOST', 'CLOUD'

command: string (optional)

Command to be executed

scheduler: string (optional)

scheduler, that is used in backend

rootDir: string (optional)

root directory for all analyses

Unique name

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an ComputeBackend.

unique(name):

Field name is unique within an ComputeBackend.

org.molgenis.omx.core package

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Autoid (interface).

This interface assigns an automatic 'id'.

Constraints:

unique(id):

Field id is unique within an Autoid.

Identifiable (interface).

implements Autoid

This interface assigns an automatic 'id', globally unique identifier 'identifier' field, and possibly not unique 'name' to all entities that implement it.

Inherited attributes:

id,

Attributes:

Identifier: string (required)

user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234

Name: string (required)

human readible name, not necessary unique.

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an Identifiable.

unique(Identifier):

Field Identifier is unique within an Identifiable.

MolgenisEntity

implements Autoid

Referenceable catalog of entity names, menus, forms and plugins.

Inherited attributes:

id,

Attributes:

Name of the entity

type_: string (required)

Type of the entity

className: string (required)

Full name of the entity

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an MolgenisEntity.

unique(className):

Field className is unique within an MolgenisEntity.

unique(name, type_):

The combination of fields name, type_ is unique within an MolgenisEntity.

RuntimeProperty

implements Identifiable

Inherited attributes:

id, Identifier, Name,

Attributes:

Value: text (required)

Identifier: string (required)

user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234

Name: string (required)

human readible name, not necessary unique.

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an RuntimeProperty.

unique(Identifier):

Field Identifier is unique within an RuntimeProperty.

unique(Name):

Name is unique within its type .

FreemarkerTemplate

implements Autoid

Inherited attributes:

id,

Attributes:

Name: string (required)

Name of the entity

Value: script (required)

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an FreemarkerTemplate.

unique(Name):

Name is unique within its type.

org.molgenis.omx.observ package

Observ-OM is a model to uniformly describe any phenotypic, genotypic or molecular observation. The four core concepts are:

ObservationTarget: the object we are observing.
For example: an Individual, a Panel/Strain, a Sample, a Gene, a Marker.
ObservableFeature: the question asked or characteristic being observed.
For example: 'What is height of [Target]?', 'What is genotype of [Target] at [Marker]?', 'Has [Target] ever used medicine [X]', 'What is QTL p-value association of [Marker] with [Gene Expression]?
Protocol: the procedure of observation
For example: Food Frequency Questionnaire (FFQ), R/QTL mapping method, Genotype array, GWAS protocol.
Observation: the actual act of observation. For example: 'FFQ asked to [Individual:individual1], 'R/QTL applied to [Marker:pvv4]', 'Genotype array applied to [Panel:Mouse RIL BxD 1]. Each observation can have multiple ObservedValue AND be grouped into a DataSet.

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Characteristic

implements Identifiable

Characteristics are yes-no statements about things in the world. These can be used as part of an observation, as parameter of ObservableFeature ('measuredCharacteristic'). For example: 'What is allele of [Marker]', here the [Marker] is a characteristic. Also, Characteristics can be used as target of observation. Typical examples are 'Individual' or 'Panel'. But also 'Marker' can be an Target when asked the question 'QTL p-value for [phenotype]': here both target and feature are characteristic, for example 'leave count' (phenotype characteristic) and 'PVV4' (marker characteristic).

Inherited attributes:

id, Identifier, Name,

Attributes:

__Type: enum (required)

Subtypes have to be set to allow searching
enum_options: 'Characteristic', 'Individual', 'Panel', 'ObservationTarget', 'ObservableFeature', 'Category', 'Protocol', 'DataSet', 'Species', 'Accession', 'PersonRole', 'OntologyTerm', 'Institute', 'Person'

description: text (optional)

(Optional) Rudimentary meta data about the observable feature. Use of ontology terms references to establish unambigious descriptions is recommended

Identifier: string (required)

user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234

Name: string (required)

human readible name, not necessary unique.

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an Characteristic.

unique(Identifier):

Field Identifier is unique within an Characteristic.

ObservationTarget

extends Characteristic

ObservationTarget defines subjects of observation, such as Individual, Panel, Sample, etc. For instance: 'target 1' IS A 'Individual'.

Inherited attributes:

id, Identifier, Name, __Type, description,

Constraints:

unique(id):

Field id is unique within an ObservationTarget.

ObservableFeature

extends Characteristic

ObservableFeature defines anything that can be observed.

In other words, ObservableFeature are the questions asked, e.g. 'What is Height?', 'What is Systolic blood pressure?', or 'Has blue eyes?'.

Some questions may be repeated for multiple characteristics. For example 'What is [MarkerAllele] observed?' can be applied to all elements of a MarkerSet, and 'What is [medicin codes] uses' can be applied to a set of Medicine codes. This can be specified using the measuredCharacteristic field.

The identifier of ObservableFeature is globally unique. It is recommended that each ObservableFeature is named according to a well-defined ontology term or database accession.

Inherited attributes:

id, Identifier, Name, __Type, description,

Attributes:

dataType: enum (required)

(Optional) Reference to the technical data type. E.g. 'int'
enum_options: 'bool', 'categorical', 'date', 'datetime', 'decimal', 'email', 'enum', 'file', 'html', 'hyperlink', 'image', 'int', 'long', 'mref', 'string', 'text', 'xref'

temporal: bool (required)

Whether this feature is time dependent and can have different values when measured on different times (e.g. weight, temporal=true) or generally only measured once (e.g. birth date, temporal=false)

minRange: long (optional)

for numeric values this is used to set the 'min' value of the slider user interface

maxRange: long (optional)

for numeric values this is used to set the 'max' value of the slider user interface

id: int (required)

automatically generated internal id, only for internal use.

Associations:

unit: OntologyTerm (0..1)

(Optional) Reference to the well-defined measurement unit used to observe this feature (if feature is that concrete). E.g. mmHg

definitions: OntologyTerm (0..n)

The concept that is being measured in a specific way.

Constraints:

unique(id):

Field id is unique within an ObservableFeature.

Protocol

extends Characteristic

The Protocol class defines parameterizable descriptions of (analysis)methods. Examples of protocols are: Questionaires, SOPs, Assay platforms, Statistical analyses, etc. Each protocol has a unique identifier. Protocol has an association to OntologyTerm to represent the type of protocol.

Inherited attributes:

id, Identifier, Name, __Type, description,

Attributes:

root: bool (required)

Indicator whether this protocol defines a workflow (e.g is the first protocol of a workflow).

active: bool (required)

whether this protocol is considered active/inactive

id: int (required)

automatically generated internal id, only for internal use.

Associations:

ProtocolType: OntologyTerm (0..1)

classification of protocol

subprotocols: Protocol (0..n)

Subprotocols of this protocol

Features: ObservableFeature (0..n)

parameters (in/out) that are used or produced by this protocol.

RequiredFeatures: ObservableFeature (0..n)

..........

Constraints:

unique(id):

Field id is unique within an Protocol.

DataSet

extends Characteristic

Container for one or more observations that are measured using the same protocol and by the same performer(s). The data set may be a file (having the same identifier) but in most cases it is a data table consisting of rows (Observation). This entity replaces ProtocolApplication.

Inherited attributes:

id, Identifier, Name, __Type, description,

Attributes:

startTime: datetime (required)

time when the protocol started.

endTime: datetime (optional)

(Optional) time when the protocol ended.

id: int (required)

automatically generated internal id, only for internal use.

Associations:

ProtocolUsed: Protocol (1..1)

Reference to the protocol that is being used (if available)

Constraints:

unique(id):

Field id is unique within an DataSet.

ObservationSet

implements Autoid

In practice: Observation is one row within a DataSet.

Inherited attributes:

id,

Attributes:

Identifier: string (required)

user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234

Time: datetime (optional)

Time of this observationSet

id: int (required)

automatically generated internal id, only for internal use.

Associations:

partOfDataSet: DataSet (1..1)

DataSet this ValueSet is part of.

Constraints:

unique(id):

Field id is unique within an ObservationSet.

unique(Identifier):

Field Identifier is unique within an ObservationSet.

unique(partOfDataSet, Time):

No single secondary key.

ObservedValue

implements Autoid

Generic storage of values as part of one observation event. Values are atomatic observations, e.g., length (feature) of individual 1 (valueset.target) = 179cm (value). Values can also be qualified by some characteristic, e.g., QTL p-value (feature) between phenotype 'leaf count' (characteristic) and marker 'PVV4' (valueset.target) = 0.1^10+3 (value).

Inherited attributes:

id,

Associations:

ObservationSet: ObservationSet (1..1)

Reference to the observation. For example a particular patient visit or the application of a microarray or the calculation of a QTL model

Feature: ObservableFeature (1..1)

References the ObservableFeature that this observation was made on. For example 'probe123'.

Value: Value (0..1)

The value observed

Constraints:

unique(id):

Field id is unique within an ObservedValue.

org.molgenis.omx.observ.target package

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Species

extends OntologyTerm

Ontology terms for species. E.g. Arabidopsis thaliana. DISCUSSION: should we avoid subclasses of OntologyTerm and instead make a 'tag' filter on terms so we can make pulldowns context dependent (e.g. to only show particular subqueries of ontologies).

Inherited attributes:

id, Identifier, Name, __Type, description, ontology, termAccession, definition,

Constraints:

unique(id):

Field id is unique within an Species.

Individual

extends ObservationTarget

The Individuals class defines the subjects that are used as observation target. The Individual class maps to XGAP:Individual and PaGE:Individual. Groups of individuals can be defined via Panel.

Inherited attributes:

id, Identifier, Name, __Type, description,

Associations:

Mother: Individual (0..1)

Refers to the mother of the individual.

Father: Individual (0..1)

Refers to the father of the individual.

Constraints:

unique(id):

Field id is unique within an Individual.

Panel

extends ObservationTarget

The Panel class defines groups of individuals based on cohort design, case/controls, families, etc. For instance: 'LifeLines cohort', 'middle aged man', 'recombinant mouse inbred Line dba x b6' or 'Smith family'. A Panel can act as a single ObservationTarget. For example: average height (Measurement) in the LifeLines cohort (Panel) is 174cm (ObservedValue). The Panel class maps to XGAP:Strain and PaGE:Panel classes. In METABASE this is assumed there is one panel per study.

Inherited attributes:

id, Identifier, Name, __Type, description,

Attributes:

NumberOfIndividuals: int (required)

id: int (required)

automatically generated internal id, only for internal use.

Associations:

PanelType: OntologyTerm (0..1)

Indicate the type of Panel (example: Sample panel, AssayedPanel, Natural=wild type, Parental=parents of a cross, F1=First generation of cross, RCC=Recombinant congenic, CSS=chromosome substitution)

Species: Species (0..1)

The species this panel is an instance of/part of/extracted from.

Individuals: Individual (0..n)

The list of individuals in this panel

Constraints:

unique(id):

Field id is unique within an Panel.

PanelSource

implements Autoid

PanelSources is partOf Panel to define how panels are related panels, founder panels, such as overlap, selection criteria, getting assayed panel from a sample panel, etc.

Inherited attributes:

id,

Attributes:

NumberOfIndividuals: int (optional)

Number of individuals lifted over from this source

SelectionCriteria: text (required)

Inclusion/exclusion criteria used to select these individuals from source into current panel

id: int (required)

automatically generated internal id, only for internal use.

Associations:

CurrentPanel: Panel (1..1)

Panel for which these sources are defined.

SourcePanel: Panel (1..1)

Source that contributed individuals to current panel

Constraints:

unique(id):

Field id is unique within an PanelSource.

Ontology

implements Identifiable

Ontology defines a reference to an ontology or controlled vocabulary from which well-defined and stable (ontology) terms can be obtained. Each Ontology should have a unique identifer, for instance: Gene Ontology, Mammalian Phenotype, Human Phenotype Ontology, Unified Medical Language System, Medical Subject Headings, etc. Also a abbreviation is required, for instance: GO, MP, HPO, UMLS, MeSH, etc. Use of existing ontologies/vocabularies is recommended to harmonize phenotypic feature and value descriptions. But one can also create a 'local' Ontology. The Ontology class maps to FuGE::Ontology, MAGE-TAB::TermSourceREF.

Inherited attributes:

id, Identifier, Name,

Attributes:

ontologyAccession: string (optional)

A accession that uniquely identifies the ontology (typically an acronym). E.g. GO, MeSH, HPO.

ontologyURI: hyperlink (optional)

(Optional) A URI that references the location of the ontology.

Identifier: string (required)

user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234

Name: string (required)

human readible name, not necessary unique.

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an Ontology.

unique(Identifier):

Field Identifier is unique within an Ontology.

OntologyTerm

extends Characteristic

OntologyTerm defines a single entry (term) from an ontology or a controlled vocabulary (defined by Ontology). The identifier is the ontology term is unique. E.g. 'NCI:Antigen Gene'. Other data entities can reference to this OntologyTerm to harmonize naming of concepts. If no suitable ontology term exists then one can define new terms locally (in which case there is no formal accession for the term limiting its use for cross-Investigation queries).

Inherited attributes:

id, Identifier, Name, __Type, description,

Attributes:

termAccession: string (optional)

(Optional) The accession number assigned to the ontology term in its source ontology. If empty it is assumed to be a locally defined term.

definition: string (optional)

(Optional) The definition of the term.

id: int (required)

automatically generated internal id, only for internal use.

Associations:

ontology: Ontology (0..1)

(Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from.

Constraints:

unique(id):

Field id is unique within an OntologyTerm.

unique(ontology, termAccession):

The term accession is unique within an Ontology.

Accession

extends OntologyTerm

An external identifier for an annotation. For example: name='R13H8.1', ontology='ensembl' or name='WBgene00000912', ontology='wormbase'.

Inherited attributes:

id, Identifier, Name, __Type, description, ontology, termAccession, definition,

Constraints:

unique(id):

Field id is unique within an Accession.

org.molgenis.omx.auth package

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ContactInterface (interface).

A contact is either a person or an organization. Copied from FuGE::Contact.

Attributes:

Address: text (optional)

The address of the Contact.

Phone: string (optional)

The telephone number of the Contact including the suitable area codes.

Email: string (optional)

The email address of the Contact.

Fax: string (optional)

The fax number of the Contact.

tollFreePhone: string (optional)

A toll free phone number for the Contact, including suitable area codes.

City: string (optional)

Added from the old definition of MolgenisUser. City of this contact.

Country: string (optional)

Added from the old definition of MolgenisUser. Country of this contact.

Institute

extends Characteristic
implements ContactInterface

A contact is either a person or an organization. Copied from FuGE::Contact.

Inherited attributes:

Address, Phone, Email, Fax, tollFreePhone, City, Country, id, Identifier, Name, __Type, description,

Attributes:

Name: string (required)

id: int (required)

automatically generated internal id, only for internal use.

Address: text (optional)

The address of the Contact.

Phone: string (optional)

The telephone number of the Contact including the suitable area codes.

Email: string (optional)

The email address of the Contact.

Fax: string (optional)

The fax number of the Contact.

tollFreePhone: string (optional)

A toll free phone number for the Contact, including suitable area codes.

City: string (optional)

Added from the old definition of MolgenisUser. City of this contact.

Country: string (optional)

Added from the old definition of MolgenisUser. Country of this contact.

Constraints:

unique(id):

Field id is unique within an Institute.

unique(Name):

Field Name is unique within an Institute.

PersonInterface (interface).

A contact is either a person or an organization. Copied from FuGE::Contact.

Attributes:

Address: text (optional)

The address of the Contact.

Phone: string (optional)

The telephone number of the Contact including the suitable area codes.

Email: string (optional)

The email address of the Contact.

Fax: string (optional)

The fax number of the Contact.

tollFreePhone: string (optional)

A toll free phone number for the Contact, including suitable area codes.

City: string (optional)

Added from the old definition of MolgenisUser. City of this contact.

Country: string (optional)

Added from the old definition of MolgenisUser. Country of this contact.

FirstName: string (optional)

MidInitials: string (optional)

LastName: string (optional)

Title: string (optional)

An academic title, e.g. Prof.dr, PhD

Department: string (optional)

Added from the old definition of MolgenisUser. Department of this contact.

Associations:

Affiliation: Institute (0..1)

Roles: PersonRole (0..1)

Indicate role of the contact, e.g. lab worker or PI. Changed from mref to xref in oct 2011.

Person

extends Characteristic
implements PersonInterface

Person represents one or more people involved with an Investigation. This may include authors on a paper, lab personnel or PIs. Person has last name, firstname, mid initial, address, contact and email. A Person role is included to represent how a Person is involved with an investigation. For submission to repository purposes an allowed value is 'submitter' and the term is present in the MGED Ontology, an alternative use could represent job title. An Example from ArrayExpress is E-MTAB-506 ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/TABM/E-TABM-506/E-TABM-506.idf.txt. .
The FUGE equivalent to Person is FuGE::Person.

Inherited attributes:

Address, Phone, Email, Fax, tollFreePhone, City, Country, FirstName, MidInitials, LastName, Title, Affiliation, Department, Roles, id, Identifier, Name, __Type, description,

Attributes:

id: int (required)

automatically generated internal id, only for internal use.

Address: text (optional)

The address of the Contact.

Phone: string (optional)

The telephone number of the Contact including the suitable area codes.

Email: string (optional)

The email address of the Contact.

Fax: string (optional)

The fax number of the Contact.

tollFreePhone: string (optional)

A toll free phone number for the Contact, including suitable area codes.

City: string (optional)

Added from the old definition of MolgenisUser. City of this contact.

Country: string (optional)

Added from the old definition of MolgenisUser. Country of this contact.

FirstName: string (optional)

MidInitials: string (optional)

LastName: string (optional)

Title: string (optional)

An academic title, e.g. Prof.dr, PhD

Department: string (optional)

Added from the old definition of MolgenisUser. Department of this contact.

Associations:

Affiliation: Institute (0..1)

Roles: PersonRole (0..1)

Indicate role of the contact, e.g. lab worker or PI. Changed from mref to xref in oct 2011.

Constraints:

unique(id):

Field id is unique within an Person.

unique(Email):

Field Email is unique within an Person.

PersonRole

extends OntologyTerm

Seperate type of ontologyTerm to administrate roles.

Inherited attributes:

id, Identifier, Name, __Type, description, ontology, termAccession, definition,

Constraints:

unique(id):

Field id is unique within an PersonRole.

org.molgenis.omx.observ.value package

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Value

implements Autoid

Inherited attributes:

id,

Constraints:

unique(id):

Field id is unique within an Value.

BoolValue

extends Value

Inherited attributes:

id, __Type,

Attributes:

Value: bool (required)

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

extends Value

Inherited attributes:

id, __Type,

Associations:

Value: Characteristic (1..n)

Constraints:

unique(id):

Field id is unique within an MrefValue.

StringValue

extends Value

Inherited attributes:

id, __Type,

Attributes:

Value: string (required)

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an StringValue.

TextValue

extends Value

Inherited attributes:

id, __Type,

Attributes:

Value: text (required)

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an TextValue.

XrefValue

extends Value

Inherited attributes:

id, __Type,

Associations:

Value: Characteristic (1..1)

Constraints:

unique(id):

Field id is unique within an XrefValue.

org.molgenis.omx.auth package

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MolgenisUser

Anyone who can login

Attributes:

id: int (required)

automatically generated internal id, only for internal use.

username: string (required)

password_: string (required)

big fixme: password type

activationCode: string (optional)

Used as alternative authentication mechanism to verify user email and/or if user has lost password.

active: bool (required)

Boolean to indicate if this account can be used to login

superuser: bool (required)

FirstName: string (optional)

MiddleNames: string (optional)

LastName: string (optional)

Title: string (optional)

An academic title, e.g. Prof.dr, PhD

Affiliation: string (optional)

Department: string (optional)

Added from the old definition of MolgenisUser. Department of this contact.

Role: string (optional)

Indicate role of the contact, e.g. lab worker or PI.

Address: text (optional)

The address of the Contact.

Phone: string (optional)

The telephone number of the Contact including the suitable area codes.

Email: email (required)

The email address of the Contact.

Fax: string (optional)

The fax number of the Contact.

tollFreePhone: string (optional)

A toll free phone number for the Contact, including suitable area codes.

City: string (optional)

Added from the old definition of MolgenisUser. City of this contact.

Country: string (optional)

Added from the old definition of MolgenisUser. Country of this contact.

changePassword: bool (required)

If true the user must first change his password before he can proceed

Constraints:

unique(id):

Field id is unique within an MolgenisUser.

unique(username):

Field username is unique within an MolgenisUser.

unique(Email):

Field Email is unique within an MolgenisUser.

MolgenisGroup

Attributes:

id: int (required)

active: bool (required)

Boolean to indicate whether this group is in use.

Constraints:

unique(id):

Field id is unique within an MolgenisGroup.

MolgenisGroupMember

Associations:

molgenisUser: MolgenisUser (1..1)

molgenisGroup: MolgenisGroup (1..1)

Constraints:

unique(id):

Field id is unique within an MolgenisGroupMember.

Authority (interface).

Attributes:

role: string (required)

UserAuthority

implements Authority

Inherited attributes:

role,

Attributes:

id: int (required)

role: string (required)

Associations:

molgenisUser: MolgenisUser (1..1)

Constraints:

unique(id):

Field id is unique within an UserAuthority.

GroupAuthority

implements Authority

Inherited attributes:

role,

Attributes:

id: int (required)

role: string (required)

Associations:

molgenisGroup: MolgenisGroup (1..1)

Constraints:

unique(id):

Field id is unique within an GroupAuthority.

org.molgenis package

Nameable (interface).

implements Autoid

Inherited attributes:

id,

Attributes:

Unique name

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an Nameable.

ComputeTask

implements Nameable

A protocolApplication that reports the application of running a ComputeProtocol.

Inherited attributes:

id, name,

Attributes:

computeScript: text (required)

The actual command to be sent to the cluster, is a filled in version of the one define in the ComputeProtocol

outputEnvironment: text (optional)

Environment vars created by this step

RunInfo: text (optional)

Summary of the task execution

runLog: text (optional)

Log of the task execution

failedLog: text (optional)

Failed log of the task execution

interpreter: enum (required)

the interpreter used to run this command. For example 'shellTemplate'
enum_options: 'bash', 'R'

statusCode: enum (required)

submittedID: string (optional)

ID received from the scheduler after submission; used only in clusters

Unique name

id: int (required)

automatically generated internal id, only for internal use.

Associations:

computeRun: ComputeRun (1..1)

The run this task is part of

prevSteps: ComputeTask (0..n)

To keep track of calculation dependencies

Constraints:

unique(id):

Field id is unique within an ComputeTask.

unique(name, computeRun):

The combination of fields name, computeRun is unique within an ComputeTask.

ComputeTaskHistory

implements Autoid

Keep track of the compute history of a task, including resubmissions.

Inherited attributes:

id,

Attributes:

statusTime: datetime (required)

time of state change

runLog: text (optional)

field to show the content of the error file (only applicable on fail/done of a task)

statusCode: enum (optional)

current status of this task.
enum_options: 'generated', 'ready', 'running', 'failed', 'done', 'cancelled'

newStatusCode: enum (required)

current status of this task.
enum_options: 'generated', 'ready', 'running', 'failed', 'done', 'submitted', 'cancelled'

id: int (required)

automatically generated internal id, only for internal use.

Associations:

computeTask: ComputeTask (1..1)

the task for which the history was collected

Constraints:

unique(id):

Field id is unique within an ComputeTaskHistory.

ComputeVM

implements Autoid

Inherited attributes:

id,

Attributes:

serverID: text (optional)

hostName: text (optional)

host of VMs name

floatingIpExtern: text (optional)

IP open to internet

floatingIpTarget: text (optional)

IP open to target environment

startTime: datetime (optional)

time, when VM is started

endTime: datetime (optional)

time, when VM is down

isInUse: bool (optional)

indicate if compute tasks are currently executed on VM

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an ComputeVM.

ComputeParameterValue

implements Nameable

Related to ComputeTask values

Inherited attributes:

id, name,

Attributes:

value: text (required)

the value of the parameter

Unique name

id: int (required)

automatically generated internal id, only for internal use.

Associations:

computeTask: ComputeTask (1..1)

ComputeTask, to which the value belongs

Constraints:

unique(id):

Field id is unique within an ComputeParameterValue.

ComputeRun

implements Nameable

A set of computetasks to run

Inherited attributes:

id, name,

Attributes:

creationTime: datetime (required)

time of creation

showInDashboard: bool (required)

Show this run in the dashboard

userEnvironment: text (optional)

Environment vars provided by the user

submitScript: text (optional)

The generated submit.sh to use only in the cluster scheduler environment

pollDelay: long (optional)

Delay between two database ComputeTask polls

isActive: bool (required)

isSubmittingPilots: bool (required)

isDone: bool (required)

isCancelled: bool (required)

interpreter: enum (optional)

the interpreter used to run this command. For example 'shellTemplate'
enum_options: 'bash', 'R'

hasFailedJobs: bool (required)

pilotsSubmitted: int (required)

pilotsStarted: int (required)

Unique name

id: int (required)

automatically generated internal id, only for internal use.

Associations:

computeBackend: ComputeBackend (1..1)

Backend where run will be executed

owner: MolgenisUser (1..1)

Constraints:

unique(id):

Field id is unique within an ComputeRun.

unique(name):

Field name is unique within an ComputeRun.

Pilot

implements Autoid

Inherited attributes:

id,

Attributes:

value: text (required)

creationTime: datetime (required)

time when pilot was submitted

lifeTerm: int (required)

term after which pilot id expires in minutes

status: enum (required)

enum_options: 'submitted', 'used', 'expired', 'failed', 'done'

id: int (required)

automatically generated internal id, only for internal use.

Associations:

owner: MolgenisUser (1..1)

backend: ComputeBackend (1..1)

computeRun: ComputeRun (1..1)

computeTask: ComputeTask (0..1)

Constraints:

unique(id):

Field id is unique within an Pilot.

ComputeBackend

implements Nameable

Inherited attributes:

id, name,

Attributes:

backendUrl: string (required)

Backend host

hostType: enum (required)

type of the host
enum_options: 'CLUSTER', 'GRID', 'LOCALHOST', 'CLOUD'

command: string (optional)

Command to be executed

scheduler: string (optional)

scheduler, that is used in backend

rootDir: string (optional)

root directory for all analyses

Unique name

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an ComputeBackend.

unique(name):

Field name is unique within an ComputeBackend.

Autoid (interface).

This interface assigns an automatic 'id'.

Constraints:

unique(id):

Field id is unique within an Autoid.

Identifiable (interface).

implements Autoid

This interface assigns an automatic 'id', globally unique identifier 'identifier' field, and possibly not unique 'name' to all entities that implement it.

Inherited attributes:

id,

Attributes:

Identifier: string (required)

user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234

Name: string (required)

human readible name, not necessary unique.

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an Identifiable.

unique(Identifier):

Field Identifier is unique within an Identifiable.

MolgenisEntity

implements Autoid

Referenceable catalog of entity names, menus, forms and plugins.

Inherited attributes:

id,

Attributes:

Name of the entity

type_: string (required)

Type of the entity

className: string (required)

Full name of the entity

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an MolgenisEntity.

unique(className):

Field className is unique within an MolgenisEntity.

unique(name, type_):

The combination of fields name, type_ is unique within an MolgenisEntity.

RuntimeProperty

implements Identifiable

Inherited attributes:

id, Identifier, Name,

Attributes:

Value: text (required)

Identifier: string (required)

user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234

Name: string (required)

human readible name, not necessary unique.

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an RuntimeProperty.

unique(Identifier):

Field Identifier is unique within an RuntimeProperty.

unique(Name):

Name is unique within its type .

FreemarkerTemplate

implements Autoid

Inherited attributes:

id,

Attributes:

Name: string (required)

Name of the entity

Value: script (required)

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an FreemarkerTemplate.

unique(Name):

Name is unique within its type.

Characteristic

implements Identifiable

Inherited attributes:

id, Identifier, Name,

Attributes:

__Type: enum (required)

description: text (optional)

(Optional) Rudimentary meta data about the observable feature. Use of ontology terms references to establish unambigious descriptions is recommended

Identifier: string (required)

user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234

Name: string (required)

human readible name, not necessary unique.

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an Characteristic.

unique(Identifier):

Field Identifier is unique within an Characteristic.

ObservationTarget

extends Characteristic

ObservationTarget defines subjects of observation, such as Individual, Panel, Sample, etc. For instance: 'target 1' IS A 'Individual'.

Inherited attributes:

id, Identifier, Name, __Type, description,

Constraints:

unique(id):

Field id is unique within an ObservationTarget.

ObservableFeature

extends Characteristic

ObservableFeature defines anything that can be observed.

In other words, ObservableFeature are the questions asked, e.g. 'What is Height?', 'What is Systolic blood pressure?', or 'Has blue eyes?'.

The identifier of ObservableFeature is globally unique. It is recommended that each ObservableFeature is named according to a well-defined ontology term or database accession.

Inherited attributes:

id, Identifier, Name, __Type, description,

Attributes:

dataType: enum (required)

temporal: bool (required)

Whether this feature is time dependent and can have different values when measured on different times (e.g. weight, temporal=true) or generally only measured once (e.g. birth date, temporal=false)

minRange: long (optional)

for numeric values this is used to set the 'min' value of the slider user interface

maxRange: long (optional)

for numeric values this is used to set the 'max' value of the slider user interface

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an ObservableFeature.

Protocol

extends Characteristic

Inherited attributes:

id, Identifier, Name, __Type, description,

Attributes:

root: bool (required)

Indicator whether this protocol defines a workflow (e.g is the first protocol of a workflow).

active: bool (required)

whether this protocol is considered active/inactive

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an Protocol.

DataSet

extends Characteristic

Inherited attributes:

id, Identifier, Name, __Type, description,

Attributes:

startTime: datetime (required)

time when the protocol started.

endTime: datetime (optional)

(Optional) time when the protocol ended.

id: int (required)

automatically generated internal id, only for internal use.

Associations:

ProtocolUsed: Protocol (1..1)

Reference to the protocol that is being used (if available)

Constraints:

unique(id):

Field id is unique within an DataSet.

ObservationSet

implements Autoid

In practice: Observation is one row within a DataSet.

Inherited attributes:

id,

Attributes:

Identifier: string (required)

user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234

Time: datetime (optional)

Time of this observationSet

id: int (required)

automatically generated internal id, only for internal use.

Associations:

partOfDataSet: DataSet (1..1)

DataSet this ValueSet is part of.

Constraints:

unique(id):

Field id is unique within an ObservationSet.

unique(Identifier):

Field Identifier is unique within an ObservationSet.

unique(partOfDataSet, Time):

No single secondary key.

ObservedValue

implements Autoid

Inherited attributes:

id,

Constraints:

unique(id):

Field id is unique within an ObservedValue.

Species

extends OntologyTerm

Inherited attributes:

id, Identifier, Name, __Type, description, ontology, termAccession, definition,

Constraints:

unique(id):

Field id is unique within an Species.

Individual

extends ObservationTarget

The Individuals class defines the subjects that are used as observation target. The Individual class maps to XGAP:Individual and PaGE:Individual. Groups of individuals can be defined via Panel.

Inherited attributes:

id, Identifier, Name, __Type, description,

Associations:

Mother: Individual (0..1)

Refers to the mother of the individual.

Father: Individual (0..1)

Refers to the father of the individual.

Constraints:

unique(id):

Field id is unique within an Individual.

Panel

extends ObservationTarget

Inherited attributes:

id, Identifier, Name, __Type, description,

Attributes:

NumberOfIndividuals: int (required)

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an Panel.

PanelSource

implements Autoid

PanelSources is partOf Panel to define how panels are related panels, founder panels, such as overlap, selection criteria, getting assayed panel from a sample panel, etc.

Inherited attributes:

id,

Attributes:

NumberOfIndividuals: int (optional)

Number of individuals lifted over from this source

SelectionCriteria: text (required)

Inclusion/exclusion criteria used to select these individuals from source into current panel

id: int (required)

automatically generated internal id, only for internal use.

Associations:

CurrentPanel: Panel (1..1)

Panel for which these sources are defined.

SourcePanel: Panel (1..1)

Source that contributed individuals to current panel

Constraints:

unique(id):

Field id is unique within an PanelSource.

Ontology

implements Identifiable

Inherited attributes:

id, Identifier, Name,

Attributes:

ontologyAccession: string (optional)

A accession that uniquely identifies the ontology (typically an acronym). E.g. GO, MeSH, HPO.

ontologyURI: hyperlink (optional)

(Optional) A URI that references the location of the ontology.

Identifier: string (required)

user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234

Name: string (required)

human readible name, not necessary unique.

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an Ontology.

unique(Identifier):

Field Identifier is unique within an Ontology.

OntologyTerm

extends Characteristic

Inherited attributes:

id, Identifier, Name, __Type, description,

Attributes:

termAccession: string (optional)

(Optional) The accession number assigned to the ontology term in its source ontology. If empty it is assumed to be a locally defined term.

definition: string (optional)

(Optional) The definition of the term.

id: int (required)

automatically generated internal id, only for internal use.

Associations:

ontology: Ontology (0..1)

(Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from.

Constraints:

unique(id):

Field id is unique within an OntologyTerm.

unique(ontology, termAccession):

The term accession is unique within an Ontology.

Accession

extends OntologyTerm

An external identifier for an annotation. For example: name='R13H8.1', ontology='ensembl' or name='WBgene00000912', ontology='wormbase'.

Inherited attributes:

id, Identifier, Name, __Type, description, ontology, termAccession, definition,

Constraints:

unique(id):

Field id is unique within an Accession.

ContactInterface (interface).

A contact is either a person or an organization. Copied from FuGE::Contact.

Attributes:

Address: text (optional)

The address of the Contact.

Phone: string (optional)

The telephone number of the Contact including the suitable area codes.

Email: string (optional)

The email address of the Contact.

Fax: string (optional)

The fax number of the Contact.

tollFreePhone: string (optional)

A toll free phone number for the Contact, including suitable area codes.

City: string (optional)

Added from the old definition of MolgenisUser. City of this contact.

Country: string (optional)

Added from the old definition of MolgenisUser. Country of this contact.

Institute

extends Characteristic
implements ContactInterface

A contact is either a person or an organization. Copied from FuGE::Contact.

Inherited attributes:

Address, Phone, Email, Fax, tollFreePhone, City, Country, id, Identifier, Name, __Type, description,

Attributes:

Name: string (required)

id: int (required)

automatically generated internal id, only for internal use.

Address: text (optional)

The address of the Contact.

Phone: string (optional)

The telephone number of the Contact including the suitable area codes.

Email: string (optional)

The email address of the Contact.

Fax: string (optional)

The fax number of the Contact.

tollFreePhone: string (optional)

A toll free phone number for the Contact, including suitable area codes.

City: string (optional)

Added from the old definition of MolgenisUser. City of this contact.

Country: string (optional)

Added from the old definition of MolgenisUser. Country of this contact.

Constraints:

unique(id):

Field id is unique within an Institute.

unique(Name):

Field Name is unique within an Institute.

PersonInterface (interface).

A contact is either a person or an organization. Copied from FuGE::Contact.

Attributes:

Address: text (optional)

The address of the Contact.

Phone: string (optional)

The telephone number of the Contact including the suitable area codes.

Email: string (optional)

The email address of the Contact.

Fax: string (optional)

The fax number of the Contact.

tollFreePhone: string (optional)

A toll free phone number for the Contact, including suitable area codes.

City: string (optional)

Added from the old definition of MolgenisUser. City of this contact.

Country: string (optional)

Added from the old definition of MolgenisUser. Country of this contact.

FirstName: string (optional)

MidInitials: string (optional)

LastName: string (optional)

Title: string (optional)

An academic title, e.g. Prof.dr, PhD

Department: string (optional)

Added from the old definition of MolgenisUser. Department of this contact.

Associations:

Affiliation: Institute (0..1)

Roles: PersonRole (0..1)

Indicate role of the contact, e.g. lab worker or PI. Changed from mref to xref in oct 2011.

Person

extends Characteristic
implements PersonInterface

Inherited attributes:

Address, Phone, Email, Fax, tollFreePhone, City, Country, FirstName, MidInitials, LastName, Title, Affiliation, Department, Roles, id, Identifier, Name, __Type, description,

Attributes:

id: int (required)

automatically generated internal id, only for internal use.

Address: text (optional)

The address of the Contact.

Phone: string (optional)

The telephone number of the Contact including the suitable area codes.

Email: string (optional)

The email address of the Contact.

Fax: string (optional)

The fax number of the Contact.

tollFreePhone: string (optional)

A toll free phone number for the Contact, including suitable area codes.

City: string (optional)

Added from the old definition of MolgenisUser. City of this contact.

Country: string (optional)

Added from the old definition of MolgenisUser. Country of this contact.

FirstName: string (optional)

MidInitials: string (optional)

LastName: string (optional)

Title: string (optional)

An academic title, e.g. Prof.dr, PhD

Department: string (optional)

Added from the old definition of MolgenisUser. Department of this contact.

Associations:

Affiliation: Institute (0..1)

Roles: PersonRole (0..1)

Indicate role of the contact, e.g. lab worker or PI. Changed from mref to xref in oct 2011.

Constraints:

unique(id):

Field id is unique within an Person.

unique(Email):

Field Email is unique within an Person.

PersonRole

extends OntologyTerm

Seperate type of ontologyTerm to administrate roles.

Inherited attributes:

id, Identifier, Name, __Type, description, ontology, termAccession, definition,

Constraints:

unique(id):

Field id is unique within an PersonRole.

Value

implements Autoid

Inherited attributes:

id,

Constraints:

unique(id):

Field id is unique within an Value.

BoolValue

extends Value

Inherited attributes:

id, __Type,

Attributes:

Value: bool (required)

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

extends Value

Inherited attributes:

id, __Type,

Associations:

Value: Characteristic (1..n)

Constraints:

unique(id):

Field id is unique within an MrefValue.

StringValue

extends Value

Inherited attributes:

id, __Type,

Attributes:

Value: string (required)

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an StringValue.

TextValue

extends Value

Inherited attributes:

id, __Type,

Attributes:

Value: text (required)

id: int (required)

automatically generated internal id, only for internal use.

Constraints:

unique(id):

Field id is unique within an TextValue.

XrefValue

extends Value

Inherited attributes:

id, __Type,

Associations:

Value: Characteristic (1..1)

Constraints:

unique(id):

Field id is unique within an XrefValue.

MolgenisUser

Anyone who can login

Attributes:

id: int (required)

automatically generated internal id, only for internal use.

username: string (required)

password_: string (required)

big fixme: password type

activationCode: string (optional)

Used as alternative authentication mechanism to verify user email and/or if user has lost password.

active: bool (required)

Boolean to indicate if this account can be used to login

superuser: bool (required)

FirstName: string (optional)

MiddleNames: string (optional)

LastName: string (optional)

Title: string (optional)

An academic title, e.g. Prof.dr, PhD

Affiliation: string (optional)

Department: string (optional)

Added from the old definition of MolgenisUser. Department of this contact.

Role: string (optional)

Indicate role of the contact, e.g. lab worker or PI.

Address: text (optional)

The address of the Contact.

Phone: string (optional)

The telephone number of the Contact including the suitable area codes.

Email: email (required)

The email address of the Contact.

Fax: string (optional)

The fax number of the Contact.

tollFreePhone: string (optional)

A toll free phone number for the Contact, including suitable area codes.

City: string (optional)

Added from the old definition of MolgenisUser. City of this contact.

Country: string (optional)

Added from the old definition of MolgenisUser. Country of this contact.

changePassword: bool (required)

If true the user must first change his password before he can proceed

Constraints:

unique(id):

Field id is unique within an MolgenisUser.

unique(username):

Field username is unique within an MolgenisUser.

unique(Email):

Field Email is unique within an MolgenisUser.

MolgenisGroup

Attributes:

id: int (required)

active: bool (required)

Boolean to indicate whether this group is in use.

Constraints:

unique(id):

Field id is unique within an MolgenisGroup.

MolgenisGroupMember

Associations:

molgenisUser: MolgenisUser (1..1)

molgenisGroup: MolgenisGroup (1..1)

Constraints:

unique(id):

Field id is unique within an MolgenisGroupMember.

Authority (interface).

Attributes:

role: string (required)

UserAuthority

implements Authority

Inherited attributes:

role,

Attributes:

id: int (required)

role: string (required)

Associations:

molgenisUser: MolgenisUser (1..1)

Constraints:

unique(id):

Field id is unique within an UserAuthority.

GroupAuthority

implements Authority

Inherited attributes:

role,

Attributes:

id: int (required)

role: string (required)

Associations:

molgenisGroup: MolgenisGroup (1..1)

Constraints:

unique(id):

Field id is unique within an GroupAuthority.

Supplementary figure: complete data model

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Documentation generated on July 13, 2015 by MOLGENIS http://www.molgenis.org

org.molgenis documentation.

Table of contents

Autoid (interface).

Nameable (interface).

Autoid (interface).

Identifiable (interface).

ContactInterface (interface).

PersonInterface (interface).

Authority (interface).

Nameable (interface).

Autoid (interface).

Identifiable (interface).

ContactInterface (interface).

PersonInterface (interface).

Authority (interface).

Supplementary figure: complete data model