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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. |
Attributes:
| id: int (required) |
| name: string (required) |
| active: bool (required) |
| Boolean to indicate whether this group is in use. |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisGroup. |
Associations:
|
molgenisUser: MolgenisUser (1..1) |
|
molgenisGroup: MolgenisGroup (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisGroupMember. |
Attributes:
| role: string (required) |
implements Authority
Inherited attributes:
Attributes:
| id: int (required) |
| role: string (required) |
Associations:
|
molgenisUser: MolgenisUser (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an UserAuthority. |
implements Authority
Inherited attributes:
Attributes:
| id: int (required) |
| role: string (required) |
Associations:
|
molgenisGroup: MolgenisGroup (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an GroupAuthority. |
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This interface assigns an automatic 'id'.
Constraints:
| unique(id): |
| Field id is unique within an Autoid. |
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:
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. |
implements Autoid
Referenceable catalog of entity names, menus, forms and plugins.
Inherited attributes:
Attributes:
| name: string (required) |
| 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. |
implements Identifiable
Inherited attributes:
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 . |
implements Autoid
Inherited attributes:
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. |
Observ-OM is a model to uniformly describe any phenotypic, genotypic or molecular observation. The four core concepts are:
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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:
Attributes:
| __Type: enum (required) |
| Subtypes have to be set to allow searching
enum_options: 'Characteristic', 'Patient', 'Individual', 'Panel', 'Variant', 'Chromosome', 'NMRBin', 'Clone', 'DerivedTrait', 'EnvironmentalFactor', 'Gene', 'Transcript', 'Protein', 'Metabolite', 'SNP', 'Marker', 'Polymorphism', 'Spot', 'Probe', 'ProbeSet', 'MassPeak', 'Sample', 'PairedSample', 'ObservationTarget', 'ObservableFeature', 'Category', 'Protocol', 'DataSet', 'Species', 'Accession', 'PersonRole', 'OntologyTerm', 'Institute', 'Person', 'Track' |
| 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. |
extends Characteristic
ObservationTarget defines subjects of observation, such as Individual, Panel, Sample, etc. For instance: 'target 1' IS A 'Individual'.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an ObservationTarget. |
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:
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. |
extends Characteristic
Category is partOf ObservableFeature to define categories for an ObservableFeature, such as the categorical answer codes that are often used in Questionaires. For example the ObservableFeature 'sex' has {code_string = 1, label=male} and {code_string = 2, label=female}. Category can be linked to well-defined ontology terms via the ontologyReference. Category extends ObservationElement such that it can be referenced by ObservedValue.value. The Category class maps to METABASE::Category
Inherited attributes:
Attributes:
| valueCode: string (optional) |
| The value used to store this category in ObservedValue. For example '1', '2'. |
| isMissing: bool (required) |
| whether this value should be treated as missing value. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
observableFeature: ObservableFeature (1..1) |
| The Measurement these permitted values are part of. |
|
definition: OntologyTerm (0..1) |
| The category that is being measured in a specific way. |
Constraints:
| unique(id): |
| Field id is unique within an Category. |
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:
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. |
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:
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. |
implements Autoid
In practice: Observation is one row within a DataSet.
Inherited attributes:
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. |
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:
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. |
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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:
Constraints:
| unique(id): |
| Field id is unique within an Species. |
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:
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. |
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:
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. |
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:
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. |
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:
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. |
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:
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. |
extends OntologyTerm
An external identifier for an annotation. For example: name='R13H8.1', ontology='ensembl' or name='WBgene00000912', ontology='wormbase'.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an Accession. |
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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. |
extends Characteristic
implements ContactInterface
A contact is either a person or an organization. Copied from FuGE::Contact.
Inherited attributes:
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. |
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. |
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:
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. |
extends OntologyTerm
Seperate type of ontologyTerm to administrate roles.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an PersonRole. |
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implements Autoid
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an Value. |
extends Value
Inherited attributes:
Attributes:
| Value: bool (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an BoolValue. |
extends Value
Inherited attributes:
Associations:
|
Value: Category (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an CategoricalValue. |
extends Value
Inherited attributes:
Attributes:
| Value: date (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an DateValue. |
extends Value
Inherited attributes:
Attributes:
| Value: datetime (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an DateTimeValue. |
extends Value
Inherited attributes:
Attributes:
| Value: decimal (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an DecimalValue. |
extends Value
Inherited attributes:
Attributes:
| Value: email (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an EmailValue. |
extends Value
Inherited attributes:
Attributes:
| Value: text (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an HtmlValue. |
extends Value
Inherited attributes:
Attributes:
| Value: hyperlink (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an HyperlinkValue. |
extends Value
Inherited attributes:
Attributes:
| Value: int (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an IntValue. |
extends Value
Inherited attributes:
Attributes:
| Value: long (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an LongValue. |
extends Value
Inherited attributes:
Associations:
|
Value: Characteristic (1..n) |
Constraints:
| unique(id): |
| Field id is unique within an MrefValue. |
extends Value
Inherited attributes:
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. |
extends Value
Inherited attributes:
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. |
extends Value
Inherited attributes:
Associations:
|
Value: Characteristic (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an XrefValue. |
Model extension to make it possible to store a DataSetFilter that is linked to a user
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implements Identifiable
Inherited attributes:
Attributes:
| RequestForm: string (required) |
| request form filename |
| RequestDate: datetime (required) |
| request date |
| RequestStatus: enum (required) |
|
enum_options: 'draft', 'submitted', 'approved', 'rejected' |
| 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. |
Associations:
|
Features: ObservableFeature (1..n) |
|
Protocol: Protocol (1..1) |
| protocol used to create request |
|
MolgenisUser: MolgenisUser (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an StudyDataRequest. |
| unique(Identifier): |
| Field Identifier is unique within an StudyDataRequest. |
XGAP, taken from https://raw.github.com/joerivandervelde/molgenis-sdk/omx3/src/main/resources/omx3/xgap.xml at 26 sept 2013. Added: Variant
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extends Characteristic
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an Track. |
extends ObservationTarget
implements Locus
A SNP is a special kind of Marker, but can also be seen as a phenotype to map against in some cases. A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in an individual.
Inherited attributes:
Attributes:
| MutationPosition: int (optional) |
| CdnaPosition: int (optional) |
| AaPosition: int (optional) |
| VariantLength: int (optional) |
| Event: string (optional) |
| NtChange: string (optional) |
| Codonchange: string (optional) |
| CdnaNotation: string (optional) |
| GdnaNotation: string (optional) |
| AaNotation: string (optional) |
| Exon: string (optional) |
| Consequence: string (optional) |
| Inheritance: string (optional) |
| ReportedSNP: bool (optional) |
| EffectOnSplicing: bool (optional) |
| Pathogenicity: string (optional) |
| Gene: string (optional) |
| IdMutation: int (optional) |
| DetailsForMutation: hyperlink (optional) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
Track: Track (1..1) |
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Variant. |
position. Typical examples of such traits are genes, probes and markers. Common structure for entities that have a genomic
Attributes:
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
extends ObservationTarget
Inherited attributes:
Attributes:
| orderNr: int (required) |
| isAutosomal: bool (required) |
| Is 'yes' when number of chromosomes is equal in male and female individuals, i.e., if not a sex chromosome. |
| bpLength: int (optional) |
| Lenght of the chromsome in base pairs. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Species: OntologyTerm (0..1) |
| Reference to the species this chromosome belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Chromosome. |
extends ObservationTarget
Shift of the NMR frequency due to the chemical environment.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an NMRBin. |
extends ObservationTarget
implements Locus
BAC clone fragment.
Inherited attributes:
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Clone. |
extends ObservationTarget
Any meta trait, eg. false discovery rates, P-values, thresholds.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an DerivedTrait. |
extends ObservationTarget
Experimental conditions, such as temperature differences, batch effects etc.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an EnvironmentalFactor. |
extends ObservationTarget
implements Locus
Trait annotations specific for genes.
Inherited attributes:
Attributes:
| Symbol: string (optional) |
| Main symbol this gene is known by (not necessarily unique, in constrast to 'name') |
| Orientation: enum (optional) |
| Orientation of the gene on the genome (F=forward, R=reverse)
enum_options: 'F', 'R' |
| Control: bool (optional) |
| Indicating whether this is a 'housekeeping' gene that can be used as control. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
Associations:
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Gene. |
extends ObservationTarget
Trait annotations specific for transcripts.
Inherited attributes:
Associations:
|
Gene: Gene (0..1) |
| The gene that produces this protein |
Constraints:
| unique(id): |
| Field id is unique within an Transcript. |
extends ObservationTarget
Trait annotations specific for proteins.
Inherited attributes:
Attributes:
| AminoSequence: text (optional) |
| The aminoacid sequence. |
| Mass: decimal (optional) |
| The mass of this metabolite |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Gene: Gene (0..1) |
| The gene that produces this protein |
|
Transcript: Transcript (0..1) |
| The transcript variant that produces this protein |
Constraints:
| unique(id): |
| Field id is unique within an Protein. |
extends ObservationTarget
Trait annotations specific for metabolites.
Inherited attributes:
Attributes:
| Formula: string (optional) |
| The chemical formula of a metabolite. |
| Mass: decimal (optional) |
| The mass of this metabolite |
| Structure: text (optional) |
| The chemical structure of a metabolite (in SMILES representation). |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an Metabolite. |
extends ObservationTarget
implements Locus
Trait annotations specific for markers.
Inherited attributes:
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
ReportsFor: Marker (0..n) |
| The marker (or a subclass like 'SNP') this marker (or a subclass like 'SNP') reports for. |
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Marker. |
extends Marker
A SNP is a special kind of Marker, but can also be seen as a phenotype to map against in some cases. A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in an individual.
Inherited attributes:
Attributes:
| Status: string (optional) |
| The status of this SNP, eg 'confirmed'. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Polymorphism: Polymorphism (0..n) |
| The polymorphism that belongs to this SNP. |
Constraints:
| unique(id): |
| Field id is unique within an SNP. |
extends ObservationTarget
The difference of a single base discovered between two sequenced individuals.
Inherited attributes:
Attributes:
| Base: enum (required) |
| The affected DNA base. Note that you can select the reference base here.
enum_options: 'Reference', 'A', 'T', 'C', 'G' |
| Value: string (optional) |
| The strain/genotype for which this polymorphism was discovered. E.g. 'N2' or 'CB4856'. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an Polymorphism. |
extends ObservationTarget
implements Locus
A piece of sequence that reports for the expression of a gene, typically spotted onto a microarray.
Inherited attributes:
Attributes:
| Mismatch: bool (required) |
| Indicating whether the probe is a match |
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
ProbeSet: ProbeSet (0..1) |
| Optional: probeset this probe belongs to (e.g., in Affymetrix assays). |
|
ReportsFor: Gene (0..1) |
| The gene this probe reports for. |
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Probe. |
extends Probe
This is the spot on a microarray.
Note: We don't distinquish between probes (the sequence) and spots
(the sequence as spotted on the array).
Inherited attributes:
Attributes:
| x: int (required) |
| Row |
| y: int (required) |
| Column |
| GridX: int (optional) |
| Meta Row |
| GridY: int (optional) |
| Meta Column |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an Spot. |
| unique(x, y, GridX, GridY): |
| The combination of fields x, y, GridX, GridY is unique within an Spot. |
extends ObservationTarget
implements Locus
A set of Probes. E.g. an Affymetrix probeset has multiple probes. It implements locus because sometimes you want to give the complete set of probes a range, for example: indicating that this set of probes spans basepair 0 through 10.000.000 on chromosome 3. The same information could arguably also be queried from the probes themselves, but if you have 40k probes, retrieving the same information from only ProbeSet (if annotated so) would be much faster.
Inherited attributes:
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an ProbeSet. |
extends ObservationTarget
A peak that has been selected within a mass spectrometry experiment.
Inherited attributes:
Attributes:
| MZ: decimal (optional) |
| Mass over charge ratio of this peak. |
| RetentionTime: decimal (optional) |
| The retention-time of this peak in minutes. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an MassPeak. |
extends ObservationTarget
Inherited attributes:
Associations:
|
Individual: Individual (0..1) |
| The individual from which this sample was taken. |
|
Tissue: OntologyTerm (0..1) |
| The tissue from which this sample was taken. |
Constraints:
| unique(id): |
| Field id is unique within an Sample. |
extends ObservationTarget
A pair of samples labeled for a two-color microarray experiment.
Inherited attributes:
Associations:
|
Subject1: Individual (1..1) |
| The first subject |
|
Label1: OntologyTerm (0..1) |
| Which channel or Fluorescent labeling is associated with the first subject |
|
Subject2: Individual (1..1) |
| The second sample |
|
Label2: OntologyTerm (0..1) |
| Which channel or Fluorescent labeling is associated with the second subject |
Constraints:
| unique(id): |
| Field id is unique within an PairedSample. |
Temporary solution to link mutations to patients for the genome browser.
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extends Individual
Inherited attributes:
Attributes:
| Pheno: string (optional) |
| PubMedID: string (optional) |
| Reference: string (optional) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Allele1: Variant (0..1) |
|
Allele2: Variant (0..1) |
Constraints:
| unique(id): |
| Field id is unique within an Patient. |
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Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| entityClassIdentifier: string (required) |
| Unique identifier for an entityclass |
| fullName: string (required) |
| type: enum (required) |
|
enum_options: 'dataset', 'model', 'format', 'guideline', 'undefined' |
| description: text (optional) |
| homepage: hyperlink (optional) |
Associations:
|
tags: OntologyTerm (0..n) |
|
subEntityClasses: EntityClass (0..n) |
Constraints:
| unique(id): |
| Field id is unique within an EntityClass. |
| unique(entityClassIdentifier): |
| Field entityClassIdentifier is unique within an EntityClass. |
| unique(fullName): |
| Field fullName is unique within an EntityClass. |
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| attributeClassIdentifier: string (required) |
| Unique identifier for an attributeclass |
| fullName: string (required) |
| description: text (optional) |
| nillable: bool (required) |
| dataType: enum (required) |
|
enum_options: 'bool', 'categorical', 'compound', 'date', 'datetime', 'decimal', 'email', 'enum', 'file', 'html', 'hyperlink', 'image', 'int', 'long', 'mref', 'string', 'text', 'xref' |
Associations:
|
entityClass: EntityClass (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an AttributeClass. |
| unique(attributeClassIdentifier): |
| Field attributeClassIdentifier is unique within an AttributeClass. |
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Attributes:
| id: int (required) |
| token: string (required) |
| expirationDate: datetime (optional) |
| When expiration date is null it will never expire |
| creationDate: datetime (required) |
| description: text (optional) |
Associations:
|
molgenisUser: MolgenisUser (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisToken. |
| unique(token): |
| Field token is unique within an MolgenisToken. |
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Mapping of OMIM/ORPHANET diseases to HGNC genes to HPO terms.
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use |
| identifier: string (required) |
| Combination of diseaseId, geneSymbol and HPOId to get unique identifer |
| diseaseId: string (required) |
| OMIM or ORPHANET identifier |
| geneSymbol: string (required) |
| Gene symbol |
| geneId: string (required) |
| Entrez gene identifier |
| HPOId: string (required) |
| HPO term identifier |
| HPODescription: string (required) |
| Description of the HPO term |
| isTypical: bool (required) |
| Boolean to indicate if this term is only found in the TYPICAL disease-gene-phenotype set |
Constraints:
| unique(id): |
| Field id is unique within an DiseaseMapping. |
| unique(identifier): |
| Field identifier is unique within an DiseaseMapping. |
Mapping of OMIM/ORPHANET disease id's to disease names.
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use |
| identifier: string (required) |
| Combination of diseaseName, diseaseId and mappingMethod |
| diseaseId: string (required) |
| OMIM or ORPHANET identifier |
| diseaseName: string (required) |
| OMIM or ORPHANET disease name |
| mappingMethod: string (required) |
| The phenotype mapping method |
Constraints:
| unique(id): |
| Field id is unique within an Disease. |
| unique(identifier): |
| Field identifier is unique within an Disease. |
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All running and finished imports
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| startDate: datetime (required) |
| endDate: datetime (optional) |
| userName: string (required) |
| status: enum (required) |
|
enum_options: 'RUNNING', 'FINISHED', 'FAILED' |
| message: text (optional) |
| progress: int (required) |
Constraints:
| unique(id): |
| Field id is unique within an ImportRun. |
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. |
Attributes:
| id: int (required) |
| name: string (required) |
| active: bool (required) |
| Boolean to indicate whether this group is in use. |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisGroup. |
Associations:
|
molgenisUser: MolgenisUser (1..1) |
|
molgenisGroup: MolgenisGroup (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisGroupMember. |
Attributes:
| role: string (required) |
implements Authority
Inherited attributes:
Attributes:
| id: int (required) |
| role: string (required) |
Associations:
|
molgenisUser: MolgenisUser (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an UserAuthority. |
implements Authority
Inherited attributes:
Attributes:
| id: int (required) |
| role: string (required) |
Associations:
|
molgenisGroup: MolgenisGroup (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an GroupAuthority. |
This interface assigns an automatic 'id'.
Constraints:
| unique(id): |
| Field id is unique within an Autoid. |
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:
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. |
implements Autoid
Referenceable catalog of entity names, menus, forms and plugins.
Inherited attributes:
Attributes:
| name: string (required) |
| 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. |
implements Identifiable
Inherited attributes:
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 . |
implements Autoid
Inherited attributes:
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. |
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:
Attributes:
| __Type: enum (required) |
| Subtypes have to be set to allow searching
enum_options: 'Characteristic', 'Patient', 'Individual', 'Panel', 'Variant', 'Chromosome', 'NMRBin', 'Clone', 'DerivedTrait', 'EnvironmentalFactor', 'Gene', 'Transcript', 'Protein', 'Metabolite', 'SNP', 'Marker', 'Polymorphism', 'Spot', 'Probe', 'ProbeSet', 'MassPeak', 'Sample', 'PairedSample', 'ObservationTarget', 'ObservableFeature', 'Category', 'Protocol', 'DataSet', 'Species', 'Accession', 'PersonRole', 'OntologyTerm', 'Institute', 'Person', 'Track' |
| 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. |
extends Characteristic
ObservationTarget defines subjects of observation, such as Individual, Panel, Sample, etc. For instance: 'target 1' IS A 'Individual'.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an ObservationTarget. |
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:
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. |
extends Characteristic
Category is partOf ObservableFeature to define categories for an ObservableFeature, such as the categorical answer codes that are often used in Questionaires. For example the ObservableFeature 'sex' has {code_string = 1, label=male} and {code_string = 2, label=female}. Category can be linked to well-defined ontology terms via the ontologyReference. Category extends ObservationElement such that it can be referenced by ObservedValue.value. The Category class maps to METABASE::Category
Inherited attributes:
Attributes:
| valueCode: string (optional) |
| The value used to store this category in ObservedValue. For example '1', '2'. |
| isMissing: bool (required) |
| whether this value should be treated as missing value. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
observableFeature: ObservableFeature (1..1) |
| The Measurement these permitted values are part of. |
|
definition: OntologyTerm (0..1) |
| The category that is being measured in a specific way. |
Constraints:
| unique(id): |
| Field id is unique within an Category. |
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:
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. |
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:
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. |
implements Autoid
In practice: Observation is one row within a DataSet.
Inherited attributes:
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. |
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:
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. |
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:
Constraints:
| unique(id): |
| Field id is unique within an Species. |
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:
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. |
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:
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. |
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:
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. |
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:
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. |
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:
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. |
extends OntologyTerm
An external identifier for an annotation. For example: name='R13H8.1', ontology='ensembl' or name='WBgene00000912', ontology='wormbase'.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an Accession. |
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. |
extends Characteristic
implements ContactInterface
A contact is either a person or an organization. Copied from FuGE::Contact.
Inherited attributes:
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. |
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. |
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:
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. |
extends OntologyTerm
Seperate type of ontologyTerm to administrate roles.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an PersonRole. |
implements Autoid
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an Value. |
extends Value
Inherited attributes:
Attributes:
| Value: bool (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an BoolValue. |
extends Value
Inherited attributes:
Associations:
|
Value: Category (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an CategoricalValue. |
extends Value
Inherited attributes:
Attributes:
| Value: date (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an DateValue. |
extends Value
Inherited attributes:
Attributes:
| Value: datetime (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an DateTimeValue. |
extends Value
Inherited attributes:
Attributes:
| Value: decimal (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an DecimalValue. |
extends Value
Inherited attributes:
Attributes:
| Value: email (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an EmailValue. |
extends Value
Inherited attributes:
Attributes:
| Value: text (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an HtmlValue. |
extends Value
Inherited attributes:
Attributes:
| Value: hyperlink (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an HyperlinkValue. |
extends Value
Inherited attributes:
Attributes:
| Value: int (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an IntValue. |
extends Value
Inherited attributes:
Attributes:
| Value: long (required) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an LongValue. |
extends Value
Inherited attributes:
Associations:
|
Value: Characteristic (1..n) |
Constraints:
| unique(id): |
| Field id is unique within an MrefValue. |
extends Value
Inherited attributes:
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. |
extends Value
Inherited attributes:
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. |
extends Value
Inherited attributes:
Associations:
|
Value: Characteristic (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an XrefValue. |
implements Identifiable
Inherited attributes:
Attributes:
| RequestForm: string (required) |
| request form filename |
| RequestDate: datetime (required) |
| request date |
| RequestStatus: enum (required) |
|
enum_options: 'draft', 'submitted', 'approved', 'rejected' |
| 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. |
Associations:
|
Features: ObservableFeature (1..n) |
|
Protocol: Protocol (1..1) |
| protocol used to create request |
|
MolgenisUser: MolgenisUser (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an StudyDataRequest. |
| unique(Identifier): |
| Field Identifier is unique within an StudyDataRequest. |
extends Characteristic
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an Track. |
extends ObservationTarget
implements Locus
A SNP is a special kind of Marker, but can also be seen as a phenotype to map against in some cases. A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in an individual.
Inherited attributes:
Attributes:
| MutationPosition: int (optional) |
| CdnaPosition: int (optional) |
| AaPosition: int (optional) |
| VariantLength: int (optional) |
| Event: string (optional) |
| NtChange: string (optional) |
| Codonchange: string (optional) |
| CdnaNotation: string (optional) |
| GdnaNotation: string (optional) |
| AaNotation: string (optional) |
| Exon: string (optional) |
| Consequence: string (optional) |
| Inheritance: string (optional) |
| ReportedSNP: bool (optional) |
| EffectOnSplicing: bool (optional) |
| Pathogenicity: string (optional) |
| Gene: string (optional) |
| IdMutation: int (optional) |
| DetailsForMutation: hyperlink (optional) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
Track: Track (1..1) |
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Variant. |
position. Typical examples of such traits are genes, probes and markers. Common structure for entities that have a genomic
Attributes:
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
extends ObservationTarget
Inherited attributes:
Attributes:
| orderNr: int (required) |
| isAutosomal: bool (required) |
| Is 'yes' when number of chromosomes is equal in male and female individuals, i.e., if not a sex chromosome. |
| bpLength: int (optional) |
| Lenght of the chromsome in base pairs. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Species: OntologyTerm (0..1) |
| Reference to the species this chromosome belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Chromosome. |
extends ObservationTarget
Shift of the NMR frequency due to the chemical environment.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an NMRBin. |
extends ObservationTarget
implements Locus
BAC clone fragment.
Inherited attributes:
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Clone. |
extends ObservationTarget
Any meta trait, eg. false discovery rates, P-values, thresholds.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an DerivedTrait. |
extends ObservationTarget
Experimental conditions, such as temperature differences, batch effects etc.
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an EnvironmentalFactor. |
extends ObservationTarget
implements Locus
Trait annotations specific for genes.
Inherited attributes:
Attributes:
| Symbol: string (optional) |
| Main symbol this gene is known by (not necessarily unique, in constrast to 'name') |
| Orientation: enum (optional) |
| Orientation of the gene on the genome (F=forward, R=reverse)
enum_options: 'F', 'R' |
| Control: bool (optional) |
| Indicating whether this is a 'housekeeping' gene that can be used as control. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
Associations:
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Gene. |
extends ObservationTarget
Trait annotations specific for transcripts.
Inherited attributes:
Associations:
|
Gene: Gene (0..1) |
| The gene that produces this protein |
Constraints:
| unique(id): |
| Field id is unique within an Transcript. |
extends ObservationTarget
Trait annotations specific for proteins.
Inherited attributes:
Attributes:
| AminoSequence: text (optional) |
| The aminoacid sequence. |
| Mass: decimal (optional) |
| The mass of this metabolite |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Gene: Gene (0..1) |
| The gene that produces this protein |
|
Transcript: Transcript (0..1) |
| The transcript variant that produces this protein |
Constraints:
| unique(id): |
| Field id is unique within an Protein. |
extends ObservationTarget
Trait annotations specific for metabolites.
Inherited attributes:
Attributes:
| Formula: string (optional) |
| The chemical formula of a metabolite. |
| Mass: decimal (optional) |
| The mass of this metabolite |
| Structure: text (optional) |
| The chemical structure of a metabolite (in SMILES representation). |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an Metabolite. |
extends ObservationTarget
implements Locus
Trait annotations specific for markers.
Inherited attributes:
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
ReportsFor: Marker (0..n) |
| The marker (or a subclass like 'SNP') this marker (or a subclass like 'SNP') reports for. |
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Marker. |
extends Marker
A SNP is a special kind of Marker, but can also be seen as a phenotype to map against in some cases. A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in an individual.
Inherited attributes:
Attributes:
| Status: string (optional) |
| The status of this SNP, eg 'confirmed'. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Polymorphism: Polymorphism (0..n) |
| The polymorphism that belongs to this SNP. |
Constraints:
| unique(id): |
| Field id is unique within an SNP. |
extends ObservationTarget
The difference of a single base discovered between two sequenced individuals.
Inherited attributes:
Attributes:
| Base: enum (required) |
| The affected DNA base. Note that you can select the reference base here.
enum_options: 'Reference', 'A', 'T', 'C', 'G' |
| Value: string (optional) |
| The strain/genotype for which this polymorphism was discovered. E.g. 'N2' or 'CB4856'. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an Polymorphism. |
extends ObservationTarget
implements Locus
A piece of sequence that reports for the expression of a gene, typically spotted onto a microarray.
Inherited attributes:
Attributes:
| Mismatch: bool (required) |
| Indicating whether the probe is a match |
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
ProbeSet: ProbeSet (0..1) |
| Optional: probeset this probe belongs to (e.g., in Affymetrix assays). |
|
ReportsFor: Gene (0..1) |
| The gene this probe reports for. |
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an Probe. |
extends Probe
This is the spot on a microarray.
Note: We don't distinquish between probes (the sequence) and spots
(the sequence as spotted on the array).
Inherited attributes:
Attributes:
| x: int (required) |
| Row |
| y: int (required) |
| Column |
| GridX: int (optional) |
| Meta Row |
| GridY: int (optional) |
| Meta Column |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an Spot. |
| unique(x, y, GridX, GridY): |
| The combination of fields x, y, GridX, GridY is unique within an Spot. |
extends ObservationTarget
implements Locus
A set of Probes. E.g. an Affymetrix probeset has multiple probes. It implements locus because sometimes you want to give the complete set of probes a range, for example: indicating that this set of probes spans basepair 0 through 10.000.000 on chromosome 3. The same information could arguably also be queried from the probes themselves, but if you have 40k probes, retrieving the same information from only ProbeSet (if annotated so) would be much faster.
Inherited attributes:
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| cM: decimal (optional) |
| genetic map position in centi morgan (cM). |
| bpStart: long (optional) |
| numeric basepair postion (5') on the chromosome |
| bpEnd: long (optional) |
| numeric basepair postion (3') on the chromosome |
| Seq: text (optional) |
| The FASTA text representation of the sequence. |
| Symbol: string (optional) |
| todo |
Associations:
|
Chromosome: Chromosome (0..1) |
| Reference to the chromosome this position belongs to. |
Constraints:
| unique(id): |
| Field id is unique within an ProbeSet. |
extends ObservationTarget
A peak that has been selected within a mass spectrometry experiment.
Inherited attributes:
Attributes:
| MZ: decimal (optional) |
| Mass over charge ratio of this peak. |
| RetentionTime: decimal (optional) |
| The retention-time of this peak in minutes. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an MassPeak. |
extends ObservationTarget
Inherited attributes:
Associations:
|
Individual: Individual (0..1) |
| The individual from which this sample was taken. |
|
Tissue: OntologyTerm (0..1) |
| The tissue from which this sample was taken. |
Constraints:
| unique(id): |
| Field id is unique within an Sample. |
extends ObservationTarget
A pair of samples labeled for a two-color microarray experiment.
Inherited attributes:
Associations:
|
Subject1: Individual (1..1) |
| The first subject |
|
Label1: OntologyTerm (0..1) |
| Which channel or Fluorescent labeling is associated with the first subject |
|
Subject2: Individual (1..1) |
| The second sample |
|
Label2: OntologyTerm (0..1) |
| Which channel or Fluorescent labeling is associated with the second subject |
Constraints:
| unique(id): |
| Field id is unique within an PairedSample. |
extends Individual
Inherited attributes:
Attributes:
| Pheno: string (optional) |
| PubMedID: string (optional) |
| Reference: string (optional) |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Allele1: Variant (0..1) |
|
Allele2: Variant (0..1) |
Constraints:
| unique(id): |
| Field id is unique within an Patient. |
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| entityClassIdentifier: string (required) |
| Unique identifier for an entityclass |
| fullName: string (required) |
| type: enum (required) |
|
enum_options: 'dataset', 'model', 'format', 'guideline', 'undefined' |
| description: text (optional) |
| homepage: hyperlink (optional) |
Associations:
|
tags: OntologyTerm (0..n) |
|
subEntityClasses: EntityClass (0..n) |
Constraints:
| unique(id): |
| Field id is unique within an EntityClass. |
| unique(entityClassIdentifier): |
| Field entityClassIdentifier is unique within an EntityClass. |
| unique(fullName): |
| Field fullName is unique within an EntityClass. |
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| attributeClassIdentifier: string (required) |
| Unique identifier for an attributeclass |
| fullName: string (required) |
| description: text (optional) |
| nillable: bool (required) |
| dataType: enum (required) |
|
enum_options: 'bool', 'categorical', 'compound', 'date', 'datetime', 'decimal', 'email', 'enum', 'file', 'html', 'hyperlink', 'image', 'int', 'long', 'mref', 'string', 'text', 'xref' |
Associations:
|
entityClass: EntityClass (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an AttributeClass. |
| unique(attributeClassIdentifier): |
| Field attributeClassIdentifier is unique within an AttributeClass. |
Attributes:
| id: int (required) |
| token: string (required) |
| expirationDate: datetime (optional) |
| When expiration date is null it will never expire |
| creationDate: datetime (required) |
| description: text (optional) |
Associations:
|
molgenisUser: MolgenisUser (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisToken. |
| unique(token): |
| Field token is unique within an MolgenisToken. |
Mapping of OMIM/ORPHANET diseases to HGNC genes to HPO terms.
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use |
| identifier: string (required) |
| Combination of diseaseId, geneSymbol and HPOId to get unique identifer |
| diseaseId: string (required) |
| OMIM or ORPHANET identifier |
| geneSymbol: string (required) |
| Gene symbol |
| geneId: string (required) |
| Entrez gene identifier |
| HPOId: string (required) |
| HPO term identifier |
| HPODescription: string (required) |
| Description of the HPO term |
| isTypical: bool (required) |
| Boolean to indicate if this term is only found in the TYPICAL disease-gene-phenotype set |
Constraints:
| unique(id): |
| Field id is unique within an DiseaseMapping. |
| unique(identifier): |
| Field identifier is unique within an DiseaseMapping. |
Mapping of OMIM/ORPHANET disease id's to disease names.
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use |
| identifier: string (required) |
| Combination of diseaseName, diseaseId and mappingMethod |
| diseaseId: string (required) |
| OMIM or ORPHANET identifier |
| diseaseName: string (required) |
| OMIM or ORPHANET disease name |
| mappingMethod: string (required) |
| The phenotype mapping method |
Constraints:
| unique(id): |
| Field id is unique within an Disease. |
| unique(identifier): |
| Field identifier is unique within an Disease. |
All running and finished imports
Attributes:
| id: int (required) |
| automatically generated internal id, only for internal use. |
| startDate: datetime (required) |
| endDate: datetime (optional) |
| userName: string (required) |
| status: enum (required) |
|
enum_options: 'RUNNING', 'FINISHED', 'FAILED' |
| message: text (optional) |
| progress: int (required) |
Constraints:
| unique(id): |
| Field id is unique within an ImportRun. |
