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

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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

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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, a character string.	A string of characters
text	A long character string, when editing the user will be presented with a textarea.	A string of characters
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
script	A piece of code, typically edited in a text editor	A string of characters
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 Can also contain an expression to dynamically decide if the attribute may be left empty or not. See the Expressions section for a syntax description. If visible is an expression that does not evaluate to true, the attribute may be left empty.

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)

maxLength

The maximum number of characters.

• For string, email, enum and hyperlink, the default is 255.

• For text and script, the default is 64 KiB.

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

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 an 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.

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

Example:

name	entity	dataType	refEntity	expression
id	MyEntityType	string
xref0	MyEntityType	xref	MyReference
xref1	MyEntityType	xref	MyReference
computedXref	MyEntityType	string		{"template":"lorum {{xref0.id}} ipsum {{xref1.label}}"}
mref0	MyEntityType	mref	MyReference
mref1	MyEntityType	mref	MyReference
computedMref	MyEntityType	string		{"template":"my {{mref0.id}} text {{mref1.label}}"}
string0	MyEntityType	string
string1	MyEntityType	string
computedString	MyEntityType	string		{"template":"{{string0}} and {{string1}}"}
id	MyReference	string
label	MyReference	string

Math helper

Use a math helper to do some simple arithmetics. {"template":"{{molgenis-math myIntValue '+' mySecondIntValue}}"} Will add the 2 attributes.

It's possible to nest multiple math helpers like this: {"template":"{{molgenis-math myIntValue '+' (molgenis-math mySecondIntValue '-' myThirdDecimalValue)}}"}

Valid operators are: '+', '-', '*', '/' and the modulo operator '%'

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