FAQ: General#

Why does this project exist?#

LinkML originally grew out of the needs of the Biolink-Model project, which needed a flexible schema representation for biological knowledge graphs that was independent of particular database systems (relational, triplestore, graph database) and serialization format (TSV, JSON, RDF, RDFStar).

Recognizing similar needs elsewhere, Harold Solbrig took the original Biolink metamodel and generalized it to create the original BiolinkML framework. This was later named LinkML.

Is LinkML stable?#

The features of the core LinkML model are stable, you can use this to describe your data model without fear of breaking changes.

The language is being continually extended to meet the needs of a growing community. New language features are always added to be backwards compatible with existing schemas.

Similarly, the LinkML toolchain is also growing. The core toolchain is in Python, but efforts are underway to build tooling in Java, Typescript, and Go. Some language features may be unsupported in some toolchains.

How is LinkML licensed?#

All aspects of LinkML, from the core language itself to the toolchain are in the public domain through a CC-0 waiver.

Who uses LinkML?#

A subset of groups using LinkML can be found via the linkml-registry. However, we do not have the resources to track all uses, and the registry only scratches the surface of current usage.

LinkML is used in a number of major database resource projects. Many of these are centered around genomics and managing complex biological or environmental data, but the framework is completely domain neutral.

Users include:

  • The National Microbiome Data Collaborative

  • The Center for Cancer Data Harmonization

  • The Alliance of Genome Resources

  • The Biomedical Data Translator project

  • The iSamples project

  • The NIH INCLUDE project

See Examples of use for more info on current uses.

Is LinkML only for Python developers?#

Definitely not! While the core framework is written in Python, and there is strong support for Python developers in the form of generation of Python dataclasses from a model, uses are not restricted to Python developers.

For example, some users of LinkML compile their schema down to JSON-Schema and then use JSON-Schema toolchains in their language of choice.

And note that there is increasing support for generating object models in other languages, with java generators under active development!

Do I need to be a developer to use LinkML?#

You don’t need to be a developer to use LinkML. You can create schemas without writing any code.

For now it helps to have some basic familiarity with core data modeling concepts, and the basics of object-oriented design. In future we will add additional training material for non-modelers giving a gentle introduction to these topics.

LinkML schemas are maintained as YAML files, so it helps to have some basic understanding of YAML syntax. Many developers will use IDEs for editing YAML, which helps avoid a lot of common pitfalls. You may want the advice of a local friendly developer on what a good YAML editing environment is for your workflow.

schemasheets is a tool that allows schemas to be edited as google sheets or excel files. Currently it still takes a little bit of technical expertise to get up and running though.

We recommend managing all of your schema products using GitHub. If you have not used GitHub or version control systems before, this may be a little daunting. You may need some assistance from someone technical to get you set up with a workflow here. There is a lot of expertise here in the OBO Foundry community, where many non-technical curators autonomously manage their ontologies in GitHub.

We aim to make this whole process easier for curators, data modelers, and inexperienced developers. See the getting help section for info on how to get assistance.

Is LinkML just for metadata?#

LinkML doesn’t draw any hard and fast distinction between data and metadata, recognizing that “metadata” is often defined in relative terms.

Our position is nicely summarized by this paper on the Immune Epitope Database (IEDB):

Several of the FAIR principles make a distinction between data and metadata. This distinction makes immediate sense for knowledge repositories that store raw data in a standardized format, such as sequence reads in FASTQ format in the Sequence Read Archive (SRA) or Flow Cytometry Standard files in FlowRepository. Such ‘data’ must be accompanied with ‘metadata’ on how the data were generated. For example, in the case of an SRA deposition, information on what sample was being sequenced would be considered ‘metadata’, and specific sequence reads would be considered ‘data’. However, in the case of the information stored in the IEDB, there is no separation between data and metadata. Arguably, the IEDB stores only metadata, and the raw data can be found in the original journal article, typically in the form of figures or tables that follow no specific convention.

Full reference:

Vita R, et al. FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. Database (Oxford). 2018 Jan 1;2018:bax105. doi: 10.1093/database/bax105. PMID: 29688354; PMC5819722

Is LinkML suitable for high volume datasets?#

The current main serialization formats for LinkML are JSON, YAML, RDF, as relational databases. These may not be the most appropriate serializations for high volume data such as brain imaging data, high throughput instrumentation readouts, satellite data, etc.

If your use case falls into this scenario, one option is to separate “data” and “metadata” (but see the previous question) and use LinkML for the descriptive aspects.

You may also be interested in using metadata-aware high-volume frameworks such as HDMF or NetCDF.

The LinkML N-Dimensional Array (NDArr) working group, consisting of developers from LinkML and HDMF teams are currently actively working towards a solution that enables LinkML to be used in conjunction with serializations such as HDF5 and Zarr.

How do I cite LinkML?#

A paper is in progress, for now, cite the GitHub repo