EMX format

The default import format for MOLGENIS is 'EMX'. This is a flexible spreadsheet format (Excel, CSV) that allows you to annotate your data with a data model. This works because you can tell MOLGENIS the 'model' of your data via a special sheet named 'attributes'. Optionally, you can also add metadata on entities (i.e., classes, tables), and packages (i.e, models and submodels). It is also possible to provide packages in an emx file via the 'packages' sheet without providing the attributes sheet.

Minimal example

(download)

Note: In order to upload data, at least one group must be created. View the section on groups and roles, for information on creating a group.

For example, if you want to upload an Excel with sheet 'patients':

displayName

firstName

lastName

birthdate

birthplace

john_doe

john

doe

1976-03-13

new york

jane_doe

jane

doe

metropolis

papa_doe

papa

doe

new york

Then you must provide a model of your 'patients' via Excel with sheet named 'attributes':

name

entity

dataType

idAttribute

nillable

description

displayName

patients

TRUE

FALSE

name

firstName

patients

FALSE

first name

lastName

patients

FALSE

family name

birthdate

patients

date

FALSE

day of birth

birthplace

patients

FALSE

place of birth

'entity' should show the name of your data sheet. Each attribute the column headers in your data. Default dataType is 'string' so you only need to provide non-string values (int, date, decimal, etc). And you must always provide one idAttribute that has 'nillable' = 'FALSE'.

You can first upload the 'model' and then the 'data'. Or you can put the both into one file and upload in one go. What you prefer :-) [todo: provide example files for download]

Advanced example

(download)

Lets assume we want to upload multiple data sheets, with relations between them:

Cities:

cityName

lat

lng

new_york

40,712784

-74,005941

metropolis

37,151165

-88,731998

Patients:

displayName

firstName

lastName

birthdate

birthplace

children

disease

john_doe

john

doe

1976-03-13

new_york

none

jane_doe

jane

doe

metropolis

none

papa_doe

papa

doe

new_york

john_doe, jane_doe

cardio

Notes: birthplace refers to elements in the cityName values in the cities table. children contains comma separated values referring to another patient via displayName (trailing spaces will be removed). Warning: when using excel, be sure your decimal separator is a ".", instead of ",", otherwise mrefs might be seen as decimals when their id is a number, this causes molgenis to see a dot between your references and the importer to fail when uploading.

Users:

userName

active

displayName

firstName

lastName

jdoe

TRUE

john_doe

john

doe

jdoe2

jane_doe

jane

doe

pdoe

papa_doe

papa

doe

Note: users looks similar patients, i.e. they are also persons having 'displayName', 'firstName', and 'lastName'. We will use this in the model below.

To model the data advanced data example, again you need to provide the 'attributes' (i.e., columns, properties). Optionally, you can also describe entities (i.e., classes, tables), and packages (i.e, models and submodels) which gives you some advanced options.

Attributes:

name

entity

dataType

nillable

refEntity

idAttribute

description

cityName

cities

FALSE

TRUE

unique city name

lat

cities

decimal

latitude in degrees

lng

cities

decimal

longitude in degrees

displayName

patients

FALSE

TRUE

unique name

firstName

persons

first name

lastName

persons

family name

children

patients

mref

patients

children of a patient

birthdate

patients

date

day of birth

birthplace

patients

xref

cities

place of birth

disease

patients

disease description

userName

users

FALSE

TRUE

unique login name

active

users

bool

whether user is active

The example below defines the model for entities 'city', 'patient' and 'user'. Note that 'users' had some attributes shared with 'patients' so we will use 'object orientation' to say that both 'user' and 'patient' are both a special kind of 'persons'. This will be defined using the 'extends' relation defined in the 'entities' sheet below.

Entities:

name

package

extends

abstract

description

cities

hospital

list of cities

persons

hospital

true

person defines general attributes like firstName, lastName

users

hospital

persons

users extends persons, meaning it 'inherits' attribute definition

patients

hospital

persons

patient extends person, adding patientNumber

In most cases the 'attributes' sheet is all you need. However, in some cases you may want to add more details on the 'entity'. Here we wanted to show use of 'abstract' (i.e., interfaces) to create model class 'persons' and 'extends' (i.e., subclass, inheritance) to define that 'user' and 'patient' have the same attributes as 'persons'. When data model become larger, or when many data sheets are loaded then the 'package' construct enables you to group your (meta)data.

Packages:

name

description

parent

root

my main package

hospital

sub package holding entities to describe all kinds of persons

root

Rules for names

For names in the EMX format, the following rules apply:

  • Name cannot be empty.

  • Only letters (a-z, A-Z), digits (0-9), underscores (_) and dashes (-) are allowed.

  • The keywords: login, logout, csv, base, exist, meta and _idValue are not allowed as

    entity and attribute names.

    attribute names

  • attribute names also allow the hash character (#), e.g. #CHROM is a valid attribute name.

  • In attribute names, the dash (-) is reserved for localization, e.g. description-nl contains the

    Dutch translation of the description attribute.

    labels

    These restrictions only apply to the technical names, labels are not limited by these rules.

Packages without a parent

Creating a package without a parent package (also known as a root package) automatically results in the creation of a group. Initially the group name is set to the package identifier, unless the package identifier is not a valid group name. In this case a unique group name is generated. The initial group label is set to the package label. Otherwise the group creation is the same as when created using the security manager plugin. Both name and label can be modified afterwards.

View the section on groups and roles, for information on creating a group.

Attributes options

Required columns

entity

Name of the entity this attribute is part of

name

Name of attribute, unique per entity.

Optional columns (can be omitted)

DataType

Defines the data type (default: string)

Data type

Description

Expected formatting

string

The default data type in MOLGENIS, describing a character string of <255 characters.

A string of characters with a length of less than 255

text

When having a string with a length of more than 255 characters, this data type is recommended.

A string with characters with a maximum length of 65535

int

Integers. Natural numbers like 1, 2, 3, -1, -2, -3. rangeMin and rangeMax can be defined.

Non decimal numbers in range[-2^31 , 2^31 -1]

long

Non-decimal number of type long

Non decimal numbers in range[-2^63 , 2^63 -1]

decimal

Decimal numbers/floats.

Decimal numbers with double-precision ('NaN' not allowed)

bool

A boolean value: true/false

TRUE/FALSE

date

A date without a time-zone in the ISO-8601 calendar system

yyyy-mm-dd

datetime

An instant in time. Time zone information may be used to specify the instant but is not stored.

yyyy-mm-ddThh:mm:ss+timezone e.g. 1985-08-12T11:12:13+0500

xref

Reference to an attribute of another entity. Using this type requires another entity (refEntity) with information that is linked to the selected entity. Although you should always refer to the id of an attribute defined as xref, in your data explorer the label of the refEntity will be presented instead. When label is not specified, id will be used as label. When searching for a specific xref value in the filter wizard, the value has to be typed partly and then selected out of a list with suggestions.

Id of the attribute you wish to link, this id should always be available in the refEntity.

mref

Reference to several attributes of another entity. Using this type requires another entity (refEntity) with information that is linked to the selected entity. Although you should always refer to the id of an attribute defined as mref, in your visualisation, the defined label for the refEntity will be presented, when label is not given, id will be used as label. When searching for a specific mref value in the filter wizard, the value has to be typed partly and then selected out of a list with suggestions.

A comma separated list of id’s, these id’s should always be available in the refEntity.

categorical

Reference to an attribute of another entity. Using this type requires another entity (refEntity) with information that is linked to the selected entity. Although you should always refer to the id of an attribute defined as categorical, in your visualisation, the defined label for the refEntity will be presented, when label is not given, id will be used as label. This type is typically used when answers are fixed like: “Yes”, “No”, “Unknown”. When searching for a specific categorical value in the filter wizard of molgenis a checkbox can be marked.

Id of the attribute you wish to link, this id should always be available in the refEntity.

categorical_mref

Reference to several attributes of another entity. Using this type requires another entity (refEntity) with information that is linked to the selected entity. Although you should always refer to the id of an attribute defined as categorical_mref, in your visualisation, the defined label for the refEntity will be presented, when label is not given, id will be used as label. When searching for a specific categorical value in the filter wizard of molgenis a checkbox can be marked.

A comma separated list of id’, these id’s should always be available in the refEntity.

compound

This type can be used to group parts of your data together. Your dataset will consist of several compounds all containing certain attributes. Don’t forget to specify the partOfAttribute column for the attributes you wish to put in the compound.

Nothing

file

A file. Create a column of the 'file' data type requires refEntity FileMeta.

Id of the FileMeta entity you wish to link, this id should always be available in FileMeta.

email

An e-mail adress

E-mail adress

enum

An item chosen from a fixed list of options that can be selected for this data type. The options should be given in an extra column called “enumOptions”. These options cannot be updated without changing meta-data (so deleting the data and meta data and a new upload are required in MOLGENIS 1.x).

A value chosen from the enumOptions list specified as a comma separated list of options in the model.

hyperlink

A link to a website

A link to a website

one_to_many

This data type is only supported in MOLGENIS 2.0. A data type that defines the one to many relationship between two columns in two separate tables. Having this data types requires having another table with an xref column which is linked to the one_to_many. The one_to_many requires a refEntity like the other referring data types, but unlike the others, it also requires a “mappedBy” column. In this column the name of the xref in the other column should be specified. For instance, an author can write several books. Books are stored in one table (called “books”) with “author” as xref and as refEntity “authors”. In the authors table authors are stored with books as one_to_many. The books attribute has the refEntity “books” and is mappedBy “author”.

A comma separated list of id’s. Requires having an xref to this attribute in another table. Since one_to_many attributes are mapped by a xref attribute they cannot be specified in data sheets.

refEntity

Used in combination with xref, mref, categorical, categorical_mref or one_to_many. Should refer to an entity.

nillable

Whether the column may be left empty. Default: true

idAttribute

Whether this field is the unique key for the entity. Default: false. Use 'AUTO' for auto generated (string) identifiers.

auto

Whether the value for this field is automatically generated. Default: false. Can be set to true when idAttribute is true or data type is one of [string, data, datetime].

description

Free text documentation describing the attribute

description-{languageCode}

Description for specified language (can be multiple languages, example: description-nl)

rangeMin

Used to set range in case of int or long attributes

rangeMax

Used to set range in case of int or long attributes

lookupAttribute

true/false, default false

Indicates if this attribute should appear in the xref/mref search dropdown in the dataexplorer. A lookupAttribute must be visible. An entity inherits the lookupAttributes from the entity it extends.

If an entity has no lookupAttributes, the labelAttribute is used in the dropdown.

label

optional human readable name of the attribute

label-{languageCode}

label for specified language (can be multiple languages, example: label-nl)

aggregateable

true/false to indicate if the user can use this atrribute in an aggregate query

labelAttribute

true/false to indicate that the value of this attribute should be used as label for the entity (in the dataexplorer when used in xref/mref). Default: false. A labelAttribute must be visible. If an entity's idAttribute is not visible, it should have a labelAttribute.

readOnly

true/false to indicate a readOnly attribute

tags

ability to tag the data referring to the tags sections, described below

validationExpression

Magma JavaScript validation expression that must return a bool. Must return true if valid and false if invalid. See the Expressions section for a syntax description.

visible

true/false to indicate whether the attribute can be seen by users. Can also contain a Magma JavaScript expression to dynamically decide if the attribute should be shown or not. See the Expressions section for a syntax description.

defaultValue

value that will be filled in in the forms when a new entity instance is created. For mref and categorical_mref, this should be a comma separated list of ids. For categorical and xref this should be the id of the refEntity. For bool should be true or false. For datetime should be a string in the format YYYY-MM-DDTHH:mm:ssZZ. For date should be a string in the format YYYY-MM-DD.

partOfAttribute

is used to group attributes into a compound attribute. Put here the name of the compound attribute.

expression

is used to create computed attributes.

Computed object example: "computed myXref" (config attributes table)

  1. Create a two new target attributes (attr1, attr2) in a new entity (newEntity).

  2. Create a xref attribute (myXref) to contain the computed entity.

  3. Add in the expression column of new xref attribute (myXref) the next script: "{attr1: myAttr1, attr2: myAttr2}"

  4. The name of the attributes to convert from should be in the same entity as the new xref attribute (myEntity).

name

entity

label

dataType

idAttribute

refEntity

nillable

visible

labelAttribute

expression

id

myEntity

Id

int

TRUE

FALSE

FALSE

FALSE

myXref

myEntity

New Entity

xref

FALSE

newEntity

TRUE

TRUE

FALSE

{attr1: myAttr1, attr2: myAttr2}

myAttr1

myEntity

My Attr 1

date

FALSE

TRUE

FALSE

TRUE

myAttr2

myEntity

My Attr 2

int

FALSE

TRUE

FALSE

TRUE

attr1

newEntity

Attr 1

string

FALSE

TRUE

FALSE

TRUE

attr2

newEntity

Attr 2

string

TRUE

TRUE

FALSE

TRUE

Template

In addition to basic 'computed strings' and 'computed' objects a template can be used as expression. The template expression format is: {"template":"..."} with the value a Mustache template. Tags must refer to attribute identifiers (e.g.

). For attributes referencing another entity type the attribute in the referencing entity type needs to be specified as well (e.g.

).

Example:

name

entity

dataType

refEntity

expression

id

MyEntityType

string

xref0

MyEntityType

xref

MyReference

xref1

MyEntityType

xref

MyReference

computedXref

MyEntityType

string

{% raw %}{"template":"lorum ipsum "}{% endraw %}

mref0

MyEntityType

mref

MyReference

mref1

MyEntityType

mref

MyReference

computedMref

MyEntityType

string

{% raw %}{"template":"my text "}{% endraw %}

string0

MyEntityType

string

string1

MyEntityType

string

computedString

MyEntityType

string

{% raw %}{"template":" and "}{% endraw %}

id

MyReference

string

label

MyReference

string

Entities options

Required columns

entity

unique name of the entity. If packages are provided, name must be unique within a package.

Optional columns

extends

reference to another entity that is extended

package

name of the group this entity is part of

abstract

indicate if data can be provided for this entity (abstract entities are only used for data modeling purposes but cannot accept data)

description

free text description of the entity

description-{languageCode}

description for specified language (can be multiple languages, example: description-nl)

backend

the backend (database) to store the entities in (currently only PostgreSQL)

tags

ability to tag the data referring to the tags sections, described below

Packages options

Required columns

name

unique name of the package. If parent package is provided the name is unique within the parent.

Optional columns

description

free text description of the package

parent

use when packages is a sub-package of another package

tags

mechanism to add flexible meta data such as ontology references, hyperlinks

Tags options (BETA)

Optionally, additional information can be provided beyond the standard meta data described above. Therefore all meta-data elements can be tagged in simple or advanced ways (equivalent to using RDF triples). For example, above in the packages example there is a 'homepage' tag provided. For example:

identifier

label

objectIRI

relationLabel

codeSystem

relationIRI

like

like

homepage

http://www.molgenis.org

http://www.molgenis.org

homepage

docs

http://some.url

http://www.molgenis.org

Documentation and Help

EDAM

http://edamontology.org/topic_3061

Required columns

identifier

unique name of this tag, such that it can be referenced

label

the human readable label of the tag (e.g. the 'like' tag as shown above).

Optional columns

objectIRI

url to the value object (will become an hyperlink in the user interface)

relationLabel

human readible label of the relation, e.g. 'Documentation and Help'

relationIRI

url to the relation definition, e.g. http://edamontology.org/topic_3061

codeSystem

name of the code system used, e.g. EDAM

Internationalization

You can internationalize attribute labels and descriptions, entity labels and descriptions and you can define internationalized versions of entity attributes.

entities

description-{languageCode} : description for specified language (can be multiple languages) label-{languageCode} : label for specified language (can be multiple languages)

Example:

name

package

description-en

description-nl

label-en

label-nl

cities

hospital

list of cities

lijst van steden

Cities

Steden

persons

hospital

list of persons

lijst van personen

Persons

Personen

attributes

description-{languageCode} : description for specified language (can be multiple languages) label-{languageCode} : label for specified language (can be multiple languages)

Example:

name

entity

idAttribute

description-en

description-nl

label-en

label-nl

displayName

patients

TRUE

Patient name

Naam van de patient

name

naam

firstName

patients

Patient first name

Voornaam van de patient

first name

voornaam

lastName

patients

Patient family name

Achternaam van de patient

family name

achternaam

Language depended entity attributes

You can internationalize attributes by postfixing the name with -{countryCode}.

If this is the label attribute, you must set all city-xx labelAttribute values to 'TRUE' on the 'entities' tab.

Example:

entities:

name

entity

idAttribute

label-nl

label-de

labelAttribute

name

gender

TRUE

genderlabel-nl

gender

Label (nl)

Etikette (nl)

TRUE

genderlabel-de

gender

Label (de)

Etikette (de)

TRUE

gender:

name

genderlabel-nl

genderlabel-de

Male

Man

Man

Female

Vrouw

Frau

Unknown

Onbekend

Unbekannt