Extension to Observ-OM to support Next Gen Sequencing (NGS) projects using the Illumina platform. Each project consists of NGS experiments having one NGS sample. One or more samples are placed on a FlowcellLane, optionally with a barcode. An experiment can be performed one time or may on the same sample. Additionally an experiment can contain a merged collection of experiments done on the same sample.
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implements Autoid
A Project bundles information about one project.
Inherited attributes:
Attributes:
| ProjectName: string (required) |
| The name of a project |
| ProjectComment: string (optional) |
| The comment of a project. |
| ProjectPlannedFinishDate: datetime (optional) |
| The date a project is expected to be finished |
| LaneAmount: int (optional) |
| Number of lanes planned in this project |
| SampleAmount: int (optional) |
| Number of samples planned in this project |
| SampleType: enum (required) |
| Type of sample
enum_options: 'DNA', 'RNA' |
| SeqType: enum (optional) |
| The type of sequencing.
enum_options: 'SR', 'PE', 'MP', 'Unknown' |
| DeclarationNr: string (optional) |
| The Declaration Nr of a project. |
| GccAnalysis: bool (optional) |
| Indication if variant calling has to be performed on the experiment. |
| GccInstructions: string (optional) |
| Specific instructions for GCC members for the analysis. |
| ResultFilesDir: string (optional) |
| File location of the resulting files after analysis occurred (for file download purpose) |
| ResultShippedDate: date (optional) |
| The date the result of the experiment is shipped to the custumor. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
ProjectCustomer: NgsUser (0..1) |
| The user who ordered the project. |
|
ProjectAnalist: NgsUser (0..n) |
| The user which will be responsible for performing the wet-lab activities. |
|
PrepKit: PrepKit (0..1) |
| Preparation kit used on the sample for this experiment |
|
ResultShippedUser: NgsUser (0..1) |
| The user who shipped the date. |
|
ResultShippedTo: NgsUser (0..1) |
| Name of the person to which the data has been shipped. |
Constraints:
| unique(id): |
| Field id is unique within an Project. |
| unique(ProjectName): |
| Field ProjectName is unique within an Project. |
implements Autoid
An NgsUser bundles information about a user.
Inherited attributes:
Attributes:
| UserName: string (required) |
| The name of a user |
| UserEmail: string (optional) |
| The email of a user. |
| UserRole: enum (required) |
| The role the user has.
enum_options: 'Customer', 'Analist', 'Bioinformatician' |
| UserGroup: enum (optional) |
| The group a user belongs to.
enum_options: 'GAF', 'GCC', 'None' |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an NgsUser. |
| unique(UserName): |
| Field UserName is unique within an NgsUser. |
implements Autoid
A Sample bundles information about a sample. Sample can be pooled. A pooled sample is just another sample, but with a additional mref (many to many) linking to the samples inside the pool.
Inherited attributes:
Attributes:
| InternalId: string (required) |
| The number of a sample as used in-house |
| ExternalId: string (optional) |
| The name of a sample as known by the customer |
| SampleComment: text (optional) |
| Comments about the sample |
| ArrayFile: string (optional) |
| Location of arrayfile for the sample in this lane-barcode |
| ArrayId: string (optional) |
| ID of the sample on the arrayFile |
| LabStatus: enum (required) |
| Lab status phase of this sample
enum_options: 'Not Started', 'Sample Prep _ Started', 'Sample Prep _ Failed', 'Ready for Clustering', 'Clustering and Sequencing _ Started', 'Clustering and Sequencing _ Failed', 'Data Post Processing', 'Finished Successfully', 'Other' |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
ProjectId: Project (1..1) |
| the sample that this sample is part of |
|
CapturingKit: CapturingKit (0..1) |
| Capturing kit used. |
|
SampleBarcode: SampleBarcode (0..1) |
| Multiple samples can be on one flowcell using barcodes. |
|
SampleInPool: Sample (0..n) |
| List of samples inside the pool |
Constraints:
| unique(id): |
| Field id is unique within an Sample. |
| unique(InternalId): |
| Field InternalId is unique within an Sample. |
implements Autoid
A FlowcellLaneSampleBarcode bundles information about a sample which is added to a lane on a flowcell.
Inherited attributes:
Attributes:
| Lane: enum (optional) |
| The lane number that is unique within a flow cell with a range of 1-8.
enum_options: '1', '2', '3', '4', '5', '6', '7', '8' |
| FlowcellLaneComment: text (optional) |
| Comment about the experiment. |
| QcWetMet: enum (required) |
| Quality criteria of the wet lab met
enum_options: 'Not determined', 'Passed', 'Failed' |
| QcWetDate: datetime (optional) |
| The date the QcWetUser selected the QcWetMet value. |
| QcDryMet: enum (required) |
| Variant calling quality criteria
enum_options: 'Not determined', 'Passed', 'Failed' |
| QcDryDate: datetime (optional) |
| The date the QcWetUser selected the QcWetMet value |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Flowcell: Flowcell (0..1) |
| The flowcell to which this lane belongs |
|
Sample: Sample (1..1) |
|
QcWetUser: NgsUser (0..1) |
| The user who checked if the quality score on the wet-lab was met |
|
QcDryUser: NgsUser (0..1) |
| The user who checked if the quality score of the analysis was met |
Constraints:
| unique(id): |
| Field id is unique within an FlowcellLane. |
| unique(Flowcell, Lane, Sample): |
| The combination Flowcell, Lane and Sample is unique.. |
implements Autoid
Inherited attributes:
Attributes:
| FlowcellDirection: enum (optional) |
| The direction used to read sequences
enum_options: 'A', 'B' |
| FlowcellName: string (required) |
| The unique name of a flowcell |
| Run: string (optional) |
| The run number always use 4 digits (with leading 0's) |
| RunDate: datetime (optional) |
| The date the flowcell was run on the machine. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Machine: Machine (0..1) |
| The machine used for sequencing |
Constraints:
| unique(id): |
| Field id is unique within an Flowcell. |
| unique(FlowcellName): |
| Field FlowcellName is unique within an Flowcell. |
implements Autoid
Inherited attributes:
Attributes:
| SampleBarcodeNr: string (optional) |
| The identifier of a barcode given by the supplier |
| SampleBarcodeSequence: string (required) |
| The nucleotide sequence which forms the barcode |
| SampleBarcodeName: string (optional) |
| A concatenated value of Type, Nr and Sequence |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
SampleBarcodeType: SampleBarcodeType (0..1) |
| Type |
Constraints:
| unique(id): |
| Field id is unique within an SampleBarcode. |
| unique(SampleBarcodeName): |
| Field SampleBarcodeName is unique within an SampleBarcode. |
| unique(SampleBarcodeType, SampleBarcodeNr, SampleBarcodeSequence): |
| The combination BarcodeType and SampleBarcodeName is unique.. |
implements Autoid
Inherited attributes:
Attributes:
| SampleBarcodeTypeName: string (required) |
| The name of a barcode type |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an SampleBarcodeType. |
| unique(SampleBarcodeTypeName): |
| Field SampleBarcodeTypeName is unique within an SampleBarcodeType. |
implements Autoid
Inherited attributes:
Attributes:
| CapturingKitName: string (required) |
| The name of a capturing kit |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an CapturingKit. |
| unique(CapturingKitName): |
| Field CapturingKitName is unique within an CapturingKit. |
implements Autoid
Inherited attributes:
Attributes:
| PrepKitName: string (required) |
| The name of a prep kit |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an PrepKit. |
| unique(PrepKitName): |
| Field PrepKitName is unique within an PrepKit. |
implements Autoid
Inherited attributes:
Attributes:
| MachineName: string (required) |
| The name of a sequence machine |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an Machine. |
| unique(MachineName): |
| Field MachineName is unique within an Machine. |
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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
Helper entity to deal with files. Has a decorator to regulate storage and coupling to an Entity. Do not make abstract because of subtyping. This means the names of the subclasses will be used to distinguish MolgenisFiles and place them in the correct folders.
Inherited attributes:
Attributes:
| Extension: string (required) |
| The file extension. This will be mapped to MIME type at runtime. For example, a type 'png' will be served out as 'image/png'. |
| 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 MolgenisFile. |
| unique(Identifier): |
| Field Identifier is unique within an MolgenisFile. |
| unique(Name): |
| Field Name is unique within an MolgenisFile. |
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 . |
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', 'Individual', 'Panel', 'ObservationTarget', 'ObservableFeature', 'Category', 'Protocol', 'DataSet', 'Species', 'Accession', 'PersonRole', 'OntologyTerm', 'Person', 'Institute' |
| 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) |
| 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 |
|
definition: OntologyTerm (0..1) |
| 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:
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. |
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 dataset 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:
| 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(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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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. |
show fullscreen
implements Identifiable
Inherited attributes:
Attributes:
| __Type: enum (required) |
| Subtypes have to be set to allow searching
enum_options: 'MolgenisRole', 'MolgenisGroup', 'MolgenisUser' |
| Name: string (required) |
| Identifier: string (required) |
| user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234 |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisRole. |
| unique(Identifier): |
| Field Identifier is unique within an MolgenisRole. |
| unique(Name): |
| Field Name is unique within an MolgenisRole. |
extends MolgenisRole
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an MolgenisGroup. |
implements Identifiable
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. |
Associations:
|
group_: MolgenisGroup (1..1) |
|
role_: MolgenisRole (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisRoleGroupLink. |
| unique(Identifier): |
| Field Identifier is unique within an MolgenisRoleGroupLink. |
| unique(group_, role_): |
| The combination of fields group_, role_ is unique within an MolgenisRoleGroupLink. |
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. |
Attributes:
| FirstName: string (optional) |
| First Name |
| MidInitials: string (optional) |
| Mid Initials |
| LastName: string (optional) |
| Last Name |
| 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 Contact, PersonContact
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) |
| First Name |
| MidInitials: string (optional) |
| Mid Initials |
| LastName: string (optional) |
| Last Name |
| 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. |
extends Characteristic
implements Contact
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. |
extends MolgenisRole
implements Contact, PersonContact
Anyone who can login
Inherited attributes:
Attributes:
| 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) |
| 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) |
| First Name |
| MidInitials: string (optional) |
| Mid Initials |
| LastName: string (optional) |
| Last Name |
| 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 MolgenisUser. |
| unique(Email): |
| Field Email is unique within an MolgenisUser. |
implements Identifiable
Inherited attributes:
Attributes:
| permission: enum (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. |
Associations:
|
role_: MolgenisRole (1..1) |
|
entity: MolgenisEntity (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisPermission. |
| unique(Identifier): |
| Field Identifier is unique within an MolgenisPermission. |
| unique(role_, entity, permission): |
| The combination of fields role_, entity, permission is unique within an MolgenisPermission. |
Interface for row level security
Associations:
|
canRead: MolgenisRole (0..1) |
|
canWrite: MolgenisRole (0..1) |
|
owns: MolgenisRole (1..1) |
implements Autoid
A Project bundles information about one project.
Inherited attributes:
Attributes:
| ProjectName: string (required) |
| The name of a project |
| ProjectComment: string (optional) |
| The comment of a project. |
| ProjectPlannedFinishDate: datetime (optional) |
| The date a project is expected to be finished |
| LaneAmount: int (optional) |
| Number of lanes planned in this project |
| SampleAmount: int (optional) |
| Number of samples planned in this project |
| SampleType: enum (required) |
| Type of sample
enum_options: 'DNA', 'RNA' |
| SeqType: enum (optional) |
| The type of sequencing.
enum_options: 'SR', 'PE', 'MP', 'Unknown' |
| DeclarationNr: string (optional) |
| The Declaration Nr of a project. |
| GccAnalysis: bool (optional) |
| Indication if variant calling has to be performed on the experiment. |
| GccInstructions: string (optional) |
| Specific instructions for GCC members for the analysis. |
| ResultFilesDir: string (optional) |
| File location of the resulting files after analysis occurred (for file download purpose) |
| ResultShippedDate: date (optional) |
| The date the result of the experiment is shipped to the custumor. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
ProjectCustomer: NgsUser (0..1) |
| The user who ordered the project. |
|
ProjectAnalist: NgsUser (0..n) |
| The user which will be responsible for performing the wet-lab activities. |
|
PrepKit: PrepKit (0..1) |
| Preparation kit used on the sample for this experiment |
|
ResultShippedUser: NgsUser (0..1) |
| The user who shipped the date. |
|
ResultShippedTo: NgsUser (0..1) |
| Name of the person to which the data has been shipped. |
Constraints:
| unique(id): |
| Field id is unique within an Project. |
| unique(ProjectName): |
| Field ProjectName is unique within an Project. |
implements Autoid
An NgsUser bundles information about a user.
Inherited attributes:
Attributes:
| UserName: string (required) |
| The name of a user |
| UserEmail: string (optional) |
| The email of a user. |
| UserRole: enum (required) |
| The role the user has.
enum_options: 'Customer', 'Analist', 'Bioinformatician' |
| UserGroup: enum (optional) |
| The group a user belongs to.
enum_options: 'GAF', 'GCC', 'None' |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an NgsUser. |
| unique(UserName): |
| Field UserName is unique within an NgsUser. |
implements Autoid
A Sample bundles information about a sample. Sample can be pooled. A pooled sample is just another sample, but with a additional mref (many to many) linking to the samples inside the pool.
Inherited attributes:
Attributes:
| InternalId: string (required) |
| The number of a sample as used in-house |
| ExternalId: string (optional) |
| The name of a sample as known by the customer |
| SampleComment: text (optional) |
| Comments about the sample |
| ArrayFile: string (optional) |
| Location of arrayfile for the sample in this lane-barcode |
| ArrayId: string (optional) |
| ID of the sample on the arrayFile |
| LabStatus: enum (required) |
| Lab status phase of this sample
enum_options: 'Not Started', 'Sample Prep _ Started', 'Sample Prep _ Failed', 'Ready for Clustering', 'Clustering and Sequencing _ Started', 'Clustering and Sequencing _ Failed', 'Data Post Processing', 'Finished Successfully', 'Other' |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
ProjectId: Project (1..1) |
| the sample that this sample is part of |
|
CapturingKit: CapturingKit (0..1) |
| Capturing kit used. |
|
SampleBarcode: SampleBarcode (0..1) |
| Multiple samples can be on one flowcell using barcodes. |
|
SampleInPool: Sample (0..n) |
| List of samples inside the pool |
Constraints:
| unique(id): |
| Field id is unique within an Sample. |
| unique(InternalId): |
| Field InternalId is unique within an Sample. |
implements Autoid
A FlowcellLaneSampleBarcode bundles information about a sample which is added to a lane on a flowcell.
Inherited attributes:
Attributes:
| Lane: enum (optional) |
| The lane number that is unique within a flow cell with a range of 1-8.
enum_options: '1', '2', '3', '4', '5', '6', '7', '8' |
| FlowcellLaneComment: text (optional) |
| Comment about the experiment. |
| QcWetMet: enum (required) |
| Quality criteria of the wet lab met
enum_options: 'Not determined', 'Passed', 'Failed' |
| QcWetDate: datetime (optional) |
| The date the QcWetUser selected the QcWetMet value. |
| QcDryMet: enum (required) |
| Variant calling quality criteria
enum_options: 'Not determined', 'Passed', 'Failed' |
| QcDryDate: datetime (optional) |
| The date the QcWetUser selected the QcWetMet value |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Flowcell: Flowcell (0..1) |
| The flowcell to which this lane belongs |
|
Sample: Sample (1..1) |
|
QcWetUser: NgsUser (0..1) |
| The user who checked if the quality score on the wet-lab was met |
|
QcDryUser: NgsUser (0..1) |
| The user who checked if the quality score of the analysis was met |
Constraints:
| unique(id): |
| Field id is unique within an FlowcellLane. |
| unique(Flowcell, Lane, Sample): |
| The combination Flowcell, Lane and Sample is unique.. |
implements Autoid
Inherited attributes:
Attributes:
| FlowcellDirection: enum (optional) |
| The direction used to read sequences
enum_options: 'A', 'B' |
| FlowcellName: string (required) |
| The unique name of a flowcell |
| Run: string (optional) |
| The run number always use 4 digits (with leading 0's) |
| RunDate: datetime (optional) |
| The date the flowcell was run on the machine. |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
Machine: Machine (0..1) |
| The machine used for sequencing |
Constraints:
| unique(id): |
| Field id is unique within an Flowcell. |
| unique(FlowcellName): |
| Field FlowcellName is unique within an Flowcell. |
implements Autoid
Inherited attributes:
Attributes:
| SampleBarcodeNr: string (optional) |
| The identifier of a barcode given by the supplier |
| SampleBarcodeSequence: string (required) |
| The nucleotide sequence which forms the barcode |
| SampleBarcodeName: string (optional) |
| A concatenated value of Type, Nr and Sequence |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Associations:
|
SampleBarcodeType: SampleBarcodeType (0..1) |
| Type |
Constraints:
| unique(id): |
| Field id is unique within an SampleBarcode. |
| unique(SampleBarcodeName): |
| Field SampleBarcodeName is unique within an SampleBarcode. |
| unique(SampleBarcodeType, SampleBarcodeNr, SampleBarcodeSequence): |
| The combination BarcodeType and SampleBarcodeName is unique.. |
implements Autoid
Inherited attributes:
Attributes:
| SampleBarcodeTypeName: string (required) |
| The name of a barcode type |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an SampleBarcodeType. |
| unique(SampleBarcodeTypeName): |
| Field SampleBarcodeTypeName is unique within an SampleBarcodeType. |
implements Autoid
Inherited attributes:
Attributes:
| CapturingKitName: string (required) |
| The name of a capturing kit |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an CapturingKit. |
| unique(CapturingKitName): |
| Field CapturingKitName is unique within an CapturingKit. |
implements Autoid
Inherited attributes:
Attributes:
| PrepKitName: string (required) |
| The name of a prep kit |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an PrepKit. |
| unique(PrepKitName): |
| Field PrepKitName is unique within an PrepKit. |
implements Autoid
Inherited attributes:
Attributes:
| MachineName: string (required) |
| The name of a sequence machine |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an Machine. |
| unique(MachineName): |
| Field MachineName is unique within an Machine. |
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
Helper entity to deal with files. Has a decorator to regulate storage and coupling to an Entity. Do not make abstract because of subtyping. This means the names of the subclasses will be used to distinguish MolgenisFiles and place them in the correct folders.
Inherited attributes:
Attributes:
| Extension: string (required) |
| The file extension. This will be mapped to MIME type at runtime. For example, a type 'png' will be served out as 'image/png'. |
| 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 MolgenisFile. |
| unique(Identifier): |
| Field Identifier is unique within an MolgenisFile. |
| unique(Name): |
| Field Name is unique within an MolgenisFile. |
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 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', 'Individual', 'Panel', 'ObservationTarget', 'ObservableFeature', 'Category', 'Protocol', 'DataSet', 'Species', 'Accession', 'PersonRole', 'OntologyTerm', 'Person', 'Institute' |
| 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) |
| 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 |
|
definition: OntologyTerm (0..1) |
| 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:
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. |
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 dataset 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:
| 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(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. |
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:
| __Type: enum (required) |
| Subtypes have to be set to allow searching
enum_options: 'MolgenisRole', 'MolgenisGroup', 'MolgenisUser' |
| Name: string (required) |
| Identifier: string (required) |
| user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234 |
| id: int (required) |
| automatically generated internal id, only for internal use. |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisRole. |
| unique(Identifier): |
| Field Identifier is unique within an MolgenisRole. |
| unique(Name): |
| Field Name is unique within an MolgenisRole. |
extends MolgenisRole
Inherited attributes:
Constraints:
| unique(id): |
| Field id is unique within an MolgenisGroup. |
implements Identifiable
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. |
Associations:
|
group_: MolgenisGroup (1..1) |
|
role_: MolgenisRole (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisRoleGroupLink. |
| unique(Identifier): |
| Field Identifier is unique within an MolgenisRoleGroupLink. |
| unique(group_, role_): |
| The combination of fields group_, role_ is unique within an MolgenisRoleGroupLink. |
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. |
Attributes:
| FirstName: string (optional) |
| First Name |
| MidInitials: string (optional) |
| Mid Initials |
| LastName: string (optional) |
| Last Name |
| 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 Contact, PersonContact
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) |
| First Name |
| MidInitials: string (optional) |
| Mid Initials |
| LastName: string (optional) |
| Last Name |
| 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. |
extends Characteristic
implements Contact
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. |
extends MolgenisRole
implements Contact, PersonContact
Anyone who can login
Inherited attributes:
Attributes:
| 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) |
| 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) |
| First Name |
| MidInitials: string (optional) |
| Mid Initials |
| LastName: string (optional) |
| Last Name |
| 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 MolgenisUser. |
| unique(Email): |
| Field Email is unique within an MolgenisUser. |
implements Identifiable
Inherited attributes:
Attributes:
| permission: enum (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. |
Associations:
|
role_: MolgenisRole (1..1) |
|
entity: MolgenisEntity (1..1) |
Constraints:
| unique(id): |
| Field id is unique within an MolgenisPermission. |
| unique(Identifier): |
| Field Identifier is unique within an MolgenisPermission. |
| unique(role_, entity, permission): |
| The combination of fields role_, entity, permission is unique within an MolgenisPermission. |
Interface for row level security
Associations:
|
canRead: MolgenisRole (0..1) |
|
canWrite: MolgenisRole (0..1) |
|
owns: MolgenisRole (1..1) |
