fairstructure – structuring your data using spreadsheets

Create a data dictionary / schema for your data using simple spreadsheets – no coding required.

  • Author your schema as a google sheet or excel spreadsheet
  • Generate schemas:
    • LinkML
    • SHACL and ShEx
    • JSON-Schema
    • SQL DDL
    • OWL
  • Validate data automatically

See the test google sheets for examples

How it works

The following example shows a schema sheet for a schema that is focused around
the concept of a Person. The rows in the sheet describe either classes or slots (fields)

record field key multiplicity range desc schema.org
> class slot identifier cardinality range description exact_mappings: {curie_prefix: sdo}
id yes 1 string any identifier identifier
description no 0..1 string a textual description description
Person n/a n/a n/a a person,living or dead Person
Person id yes 1 string identifier for a person identifier
Person, Organization name no 1 string full name name
Person age no 0..1 decimal age in years
Person gender no 0..1 decimal age in years
Person has medical history no 0..* MedicalEvent medical history
MedicalEvent n/a n/a n/a

The sheet is structured as follows:

  • The first line is a header line. You get to decide the column headers
  • Subsequent lines starting with > are column descriptors
    • these provide a way to interpret the columns
    • descriptors can be drawn from the linkml vocabulary
  • Remaining rows are elements of your schema
    • Each element gets its own row
    • A row can represent a class (record, table), field (column), enumeration, or other element types

The most basic schema concepts are classes and slots

  • classes represent record types, similar to tables in a database or sheets in a spreadsheet
  • slots represent fields, similar to columns in a database or spreadsheet

These can be used in combination:

  • If a class is provided, but a slot is not, then the row represents a class.
  • If a slot is provided, but a class is not, then the row represents a slot (field)
  • If both class and slot are provided, then the row represents the usage of a slot in the context of a class

Generating schemas

Assuming your schema is arranged as a set of sheets (TSV files) in the src folder:

sheets2project -d . src/*.tsv

This will generate individual folders for jsonschema, shacl, … as well as
a website that can be easily hosted on github.

To create only LinkML yaml:

fairstructure -o my.yaml  src/*.tsv

Simple data dictionaries

This framework allows you to represent complex relation-style schemas
using spreadsheets/TSVs. But it also allows for representation of simple “data dictionaries” or “minimal information lists”.
These can be thought of as “wide tables”, e.g. representing individual observations or observable units such as persons or samples.



If you specify a column descriptor of prefix, then rows with that column
populated will represent prefixes. The prefix expansion is specified using prefix_reference


prefix URI
> prefix prefix_reference
sdo http://schema.org/
personinfo https://w3id.org/linkml/examples/personinfo/
famrel https://example.org/FamilialRelations
GSSO http://purl.obolibrary.org/obo/GSSO_

We recommend you specify prefixes in their own sheet.

If prefixes are not provided, and you do not specify --no-repair then prefixes
will be inferred using bioregistry

Schema-level metadata

If you specify a column descriptor of schema, then rows with that column
populated will represent schemas.


Schema uri Desc Schema Prefix
> schema id description default_prefix
PersonInfo https://w3id.org/linkml/examples/personinfo Information about people, based on schema.org personinfo

The list of potential descriptors for a schema can be found by consulting
SchemaDefinition in the LinkML metamodel.

Both id and name are required, these will be auto-filled if you don’t fill this in.

Populating the fields description and license is strongly encouraged.

Currently multiple schemas are not supported, we recommend providing a single-row sheet for
schema metadata


Two descriptors are provided for enumerations:

  • enum
  • permissible_value

These can be used in combination:

  • If enum is provided, and permissible_value is not, then the row represents an enumeration
  • If both enum and permissible_value are provided, the row represents a particular enum value

The following example includes two enums:

ValueSet Value Mapping Desc
> enum permissible_value meaning description
FamilialRelationshipType familial relationships
FamilialRelationshipType SIBLING_OF famrel:01 share the same parent
FamilialRelationshipType PARENT_OF famrel:02 biological parent
FamilialRelationshipType CHILD_OF famrel:03 inverse of parent
GenderType gender
GenderType nonbinary man GSSO:009254
GenderType nonbinary woman GSSO:009253

All other descriptors are optional, but we recommend you provide descriptions of
both the enumeration and the meaning descriptor which
maps the value to a vocabulary or ontology term.

For more on enumerations, see the linkml tutorial

Specifying cardinality

See configschema.yaml for all possible vocabularies, these include:

  • UML strings, e.g. ‘0..1’
  • text strings matching the cardinality vocabulary, e.g. ‘zero to one’
  • codes used in cardinality vocabulary, e.g. O, M, …

The vocabulary maps to underlying LinkML primitives:

Slot-class grids

If you have a large number of fields/columns, with varying applicability/cardinality
across different classes, it can be convenient to specify this as a grid.

An example is a minimal information standard that includes different packages or checklists, e.g. MIxS.

For example:

term title desc mi_patient mi_mod mi_terrestrial mi_marine mi_extraterrestrial
> slot title description cardinality cardinality cardinality cardinality cardinality
> applies_to_class: MI patient applies_to_class: MI model organism applies_to_class: MI terrestrial sample applies_to_class: MI marine sample applies_to_class: MI extraterrestrial sample
id unique identifier a unique id M M M M M
alt_ids other identifiers any other identifiers O O O O O
body_site body site location where sample is taken from M R
disease disease status disease the patient had M O
age age age M R
depth depth depth in ground or water R R R
alt altitude height above sea level R R R
salinity salinity salinity R R R
porosity porosity porosity
location location location on earth
astronomical_body astronomical body planet or other astronomical object where sample was collected M

Here the applies_to_class descriptor indicates that the column value for the slot indicated in the row
is interpreted as slot usage for that class.

Metatype fields

In all of the examples above, distinct descriptors are used for class names, slot names, type names, enum names, etc

An alternative pattern is to mix element types in a single sheet, indicate the name of the element using name and the type using metatype.

For example:

type item applies to key multiplicity range parents desc schema.org wikidata belongs status notes
> metatype name class identifier cardinality range is_a description exact_mappings: {curie_prefix: sdo} exact_mappings: {curie_prefix: wikidata} in_subset status ignore
> vmap: {C: class, F: slot}
> curie_prefix: wikidata vmap: {T: testing, R: release}
F id yes 1 string any identifier identifier
F name Person, Organization no 1 string full name name
F description no 0..1 string a textual description description
F age Person no 0..1 decimal age in years
F gender Person no 0..1 decimal age in years
F has medical history Person no 0..* MedicalEvent medical history T
C Person a person,living or dead Person Q215627 R
C Event grouping class for events Q1656682 a R
C MedicalEvent Event a medical encounter b T
C ForProfit Organization
C NonProfit Organization Q163740 foo

Formal specification

In progress. The following is a sketch. Please refer to the above examples for elucidation.

  • The first line is a HEADER line.
    • Each column must be non-null and unique
    • In future grouping columns may be possible
  • Subsequent lines starting with > are column configurations
    • A column configuration can be split over multiple lines
    • Each line must be a valid yaml string (note that a single token is valid yaml for that token)
    • The first config line must include a descriptor
    • Subsequent lines are settings for that descriptor
    • A descriptor can be one of:
      • Any LinkML metamodel slot (e.g. description, comments, required, recommended, multivalued)
      • The keyword cardinality
      • An element metatype (schema, prefix, class, enum, slot, type, subset, permissible_value)
    • Setting can be taken from configschema.yaml
      • vmap provides a mapping used to translate column values. E.g. a custom “yes” or “no” to “true” or “false”
      • various keys provide ways to auto-prefix or manipulate strings
  • Remaining rows are elements of your schema
    • Each element gets its own row
    • A row can represent a class (record, table), field (column), enumeration, or other element types
    • The type of the row is indicated by whether columns with metatype descriptors are filled
      • E.g. if a column header “field” has a descriptor “slot” then any row with a non-null value is interpreted as a slot
    • If a metatype descriptor is present then this is used
    • A row must represent exactly one element type
    • If both class and slot descriptors are present then the row is interpreted as a slot in the context of that class (see slot_usage)
  • All sheets/TSVs are combined together into a single LinkML schema as YAML
  • This LinkML schema can be translated to other formats as per the LinkML generators

Working with files / google sheets

This tool takes as input a collection of sheets, which are
stored as TSV files.

You can make use of various ways of managing/organizing these:

  • TSVs files maintained in GitHub
  • Google sheets
  • Excel spreadsheets
  • SQLite databases

Tips for each of these and for organizing your information are provided below

Multiple sheets vs single sheets

It is up to you whether you represent your schema as a single sheet or as multiple sheets

However, if your schema includes a mixture of different element types, you may end up with
a lot of null values if you have a single sheet. It can be more intuitive to “normalize” your schema
description into different sheets:

  • sheets for classes/slots
  • sheets for enums
  • sheets for types

Currently fairstructure has no built in facilities for interacting directly with google sheets – it is up to you to both download and upload these

TODO: scripts for merging/splitting sheets

Manual upload/download

Note that you can create a URL from a google sheet to the TSV download – TODO


We recommend the COGS framework for working with google sheets

A common pattern is a single sheet document for a schema, with
different sheets/tabs for different parts of the schema

TODO: example

Working with Excel spreadsheets

Currently no direct support, it is up to you to load/save as individual TSVs

Working with SQLite


View Github