GA4GH Session · April 16, 2026

Andra Waagmeester · Amsterdam UMC · a.s.waagmeester@amsterdamumc.nl · ORCID: 0000-0001-9773-4008

Bring Your Own
Disease — as FAIR Data

Capture what you know about a rare disease — phenotypes, timelines, patient organisations, literature, expert panels — and make it machine-readable.

A candid note. This is the first time this system runs with real contributors. We have built a complete FAIR Data Point backend and a form-to-RDF pipeline, but this is the inaugural run — expect some start-up friction. There are no prior examples to show, because you are the first.

How to participate

Sign in with your ORCID and fill in one of the web forms. Your submission is converted to RDF and published as a FAIR dataset within about 60 seconds.

Open the session page

Practical recommendation

Also keep a document or running notes — unstructured is fine. If the system has a hiccup we add them later. The goal is to not lose the knowledge you bring today.

Scan for slides

What is in this system

Five contribution forms · a FAIR Data Point · per-disease datasets · a live SPARQL endpoint

Contribution forms

Five ways to contribute

Submit a disease case — narrative, timeline, ontology IDs
Submit a disease resource — paper, patient org, expert panel
Report an ontology gap — ORDO, HPO, ICD, SNOMED
Report a data model gap — Phenopackets, FHIR, OMOP
Feedback and new form proposals

Sign in with ORCID to contribute

FAIR Data Point

Machine-readable output

Submission becomes RDF Turtle in ~60 seconds
Each disease gets its own versioned DCAT Dataset
Published as Turtle and JSON-LD
Cases, ontology gaps, and data gaps linked together
Registered in the StaticFDP global index

Disease dataset index

Live query

SPARQL in the browser

Powered by Comunica — fully client-side
Query all registered FAIR Data Points at once
Pre-loaded queries: list diseases, find by ORDO/OMIM
Works on any DCAT-compliant FDP
Your submissions appear here within the session

Open SPARQL demo

ORCID login → Web form → GitHub Issue → GitHub Actions (~60 s) → RDF Turtle → FAIR Data Point → SPARQL queryable

Session page and forms Live SPARQL demo Disease dataset index

What is a BioHackathon?

"A special kind of unconference in which people come together to state, discuss, and solve problems by means of collaborative brainstorming, modeling, design, coding, testing, and documenting." — Garcia et al., 2020

What it is

Collaborative problem-solving sprint

Not a conference — the goal is outputs, not presentations
Not only for developers — clinicians, ontologists, patient advocates, and informaticians all contribute
Participants self-organise around problems they care about
Open-source outputs hosted in public repositories from day one
Collaborations formed here often outlast the event itself

What comes out

Tangible, lasting outputs

Working code, prototypes, and pipelines
Standards proposals and ontology improvements
FAIR datasets and interoperability bridges
Preprints on BioHackrXiv — a dedicated preprint server launched in 2019
New professional networks across disciplines and institutions

2002 First BioHackathon — Open Bioinformatics Foundation

2008+ DBCLS BioHackathon series — annual, Japan

2014+ ELIXIR BioHackathon — annual, Europe

2019 BioHackrXiv launched — dedicated preprint server

Today This GA4GH session — FAIR rare disease data sprint

Garcia L, Antezana E, Garcia A, et al. (2020) Ten simple rules to run a successful BioHackathon. PLoS Comput Biol 16(5): e1007808. doi:10.1371/journal.pcbi.1007808 · biohackathon.org

BioHackathons around the world

Two decades of collaborative bioinformatics sprints — from Tokyo to Berlin, and Toronto today

O|B|F BioHackathon (2002–)

NESCent Hackathon (2006–)

DBCLS/NBDC BioHackathon (Japan, 2008–)

BOSC Codefest (2010–)

EU Codefest (2012–)

ELIXIR BioHackathon Europe (2018–)

This session — Toronto, 2026

Sources: biohackathon.org · elixir-europe.org · Garcia et al. 2020

Ready to contribute?

Bring Your Own Disease

Sign in with ORCID and fill in a form — your submission becomes FAIR data in 60 seconds.

Scan or click below

Open session page →

https://fdp.semscape.org/ga4gh-rare-disease-trajectories/