Metroline Step: Select identifier scheme

Status: Future work

Short description 

FAIR (meta)data requires globally unique and persistent identifiers (principle F1). Such identifiers remove ambiguity in the meaning of your data by assigning a unique identifier to every element of metadata and every concept/measurement in your dataset [GOFAIR_F1]. In this context, an identifier consists of an internet link, such as a URL, which can be resolved. Identifiers can help both humans and computers interpreting your data.  

Existing identifiers can be reused, or new identifiers can be created (minted) if necessary. Often locally unique identifiers are used, which can be transformed into globally unique identifiers using namespaces [FCB016].  

Equivalence between identifiers are presented in mappings. Such a mapping can, for example, be a tsv file with two columns, one per dataset, with each row representing two equivalent concepts, or can adhere to the Simple Standard for Sharing Ontology Mapping standard [SSSOM]. 

Furthermore, many specialised identifier services exist, which can help map from one identifier to another. BridgeDB, for example, is a framework to map identifiers between various biological databases and related resources [BRIDGEDB]. It provides mappings for genes, proteins, metabolites, metabolic reactions, diseases, complexes and publications. 

How to 

[FAIRInAction]: Select the identifier scheme 

• Identifier Minting: How to create unique, persistent and resolvable identifiers  

  • FCB006: Unique, persistent identifiers 

  • FCB007: InChI and SMILES identifiers for chemical structures 

  • FCB008: Minting identifiers with Minid 

  • FCB077: Creating resolvable identifiers 

• Reusing community identifiers: How to reuse existing identifiers in a dataset 

  • FCB016: Interlinking data from different sources 

  • FCB017: Identifier mapping with BridgeDb 

BridgeDB (API, Tutorials and Workflows, Documentation): https://www.bridgedb.org/  

[GOFAIR_F1] Example services that supply globally unique and persistent identifiers: 

• Identifiers.org provides resolvable identifiers in the form of URIs and CURIEs: http://identifiers.org 

• Universally unique identifier: https://en.wikipedia.org/wiki/Universally_unique_identifier 

• Persistent URLs: http://www.purlz.org 

• Digital Object Identifier: http://www.doi.org 

• Archival Resource Key: https://escholarship.org/uc/item/9p9863nc 

• Research Resource Identifiers: https://scicrunch.org/resources 

• Identifiers for funding organisations (see F3 & R1): https://www.crossref.org/services/funder-registry/ 

• Identifiers for the world’s research organisations (see F3 & R1): https://www.grid.ac 

The How to section should:

• be split into easy to follow steps;

  • Step 1 - Title of the step

  • Step 2 - Title of the step

  • etc.

• help the reader to complete the step;

• aspire to be readable for everyone, but, depending on the topic, may require specialised knowledge;

• be a general, widely applicable approach;

• if possible / applicable, add (links to) the solution necessary for onboarding in the Health-RI National Catalogue;

• aim to be practical and simple, while keeping in mind: if I would come to this page looking for a solution to this problem, would this How-to actually help me solve this problem;

• contain references to solutions such as those provided by FAIR Cookbook, RMDkit, Turing way and FAIR Sharing;

• contain custom recipes/best-practices written by/together with experts from the field if necessary. 

Expertise requirements for this step 

Describes the expertise that may be necessary for this step. Should be based on the expertise described in the Metroline: Build the team step.

Practical examples from the community 

Examples of how this step is applied in a project (link to demonstrator projects).  

Training

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