John Grimes (@john-grimes.bsky.social)

John Grimes

@john-grimes.bsky.social

Health tech, health data analytics. I make Pathling 🔥✨

@john-grimes.bsky.social

I'm bringing this poster along to the SNOMED CT Expo in Sydney on Wednesday. The QR code is a SMART Health Link to a FHIR Questionnaire. A token in the link sends your answers back to a FHIR server, with no login. Fill it in in your browser, or in Platypus (see Kyle Pettigrew) with your own data.

John Grimes

@john-grimes.bsky.social

The app behind it is Smart Forms Health Links, written by Clinton Gillespie: formlinks.fhirapp.net It's a SMART on FHIR app that a clinic launches from its clinical system to send out forms as SMART Health Links, and to review the answers that come back.

formlinks.fhirapp.netSmart Forms Health Links

John Grimes

@john-grimes.bsky.social

Webinar this Thursday: getting analytical value out of FHIR data. Turning clinical text into FHIR, enriching it with SNOMED CT-AU and the AMT, then querying with SQL on FHIR and Pathling. Thu 15 Oct, 10-11am AEST, online www.eventbrite.com.au/e/2000536052...

eventbrite.com.auText, Terminology and Treasure: Finding Value in FHIR DataThis webinar explores how terminology services and SQL-on-FHIR can unlock analytical value from FHIR data.

John Grimes

@john-grimes.bsky.social

Two #FHIR webinars ahead of the Qld Health FHIR Connectathon: FHIR Questionnaires for preoperative anaemia - Thu 8 Oct, register by 4pm today www.eventbrite.com.au/e/2000951604... Terminology and SQL on FHIR for analytics - Thu 15 Oct www.eventbrite.com.au/e/2000536052...

eventbrite.com.auFHIR Questionnaires and SMART apps for Preoperative Anaemia ManagementThis webinar explores how The Prince Charles Hospital's Preoperative Anaemia Management service uses REDCap, Power BI and FHIR.

John Grimes

@john-grimes.bsky.social

21 Sept

The R port of fhir-tx-encoder is out: turn SNOMED CT codes into ML features via a FHIR terminology server. Multi-hot sparse matrix, subsumption ancestors, a tidymodels recipes step, same output as the Python lib. github.com/aehrc/fhir-t...

github.comGitHub - aehrc/fhir-tx-encoder: A tool for encoding FHIR terminology concepts for machine learning applications.A tool for encoding FHIR terminology concepts for machine learning applications. - aehrc/fhir-tx-encoder

John Grimes

@john-grimes.bsky.social

19 Sept

Data Golf 2026, 10 days to go. Where it stands: 🥇 @marcusbaw.com 0.968 (73 entries) 🥈 FullySpecifiedNoName 0.950 (22) 🥉 Womp Ratter 0.948 (10) 10 teams, 156 submissions. The public board is scored on half the test data, so the final one may differ. www.kaggle.com/competitions...

John Grimes

@john-grimes.bsky.social

14 Sept

Signet is now open source, Apache 2.0. Multi-tenant SMART App Launch 2.2.0 authorisation server that sits in front of an existing FHIR server. Simulated EHR launch with seeded personas, configurable scope-to-claim mapping. github.com/aehrc/signet

github.comGitHub - aehrc/signet: A SMART authorisation server.A SMART authorisation server. Contribute to aehrc/signet development by creating an account on GitHub.

John Grimes reposted

Marcus Baw

@marcusbaw.com

10 Sept

Replying to @john-grimes.bsky.social

UPDATE: I'm now in the lead! Sorry Shane! I'm not used to the AU edition, and am based in UK so there's been a serious learning curve on many of the questions... but the `sct` toolkit coped with its first non-UK SNOMED edition test without any problems. github.com/pacharanero/...

John Grimes

@john-grimes.bsky.social

7 Sept

One week into Data Golf, our SNOMED CT analysis competition on Kaggle: 26 entrants, 31 submissions, 4 teams on the board. Shane Byrnes leads on 0.916; Marcus Baw is at 0.872 after 25 entries. Results at SNOMED CT Expo in October. Still time to enter: www.kaggle.com/competitions...

kaggle.comkaggle.com

John Grimes

@john-grimes.bsky.social

7 Sept

Pathling can now answer SNOMED CT and FHIR terminology queries with no terminology server and no network connection. Release files import once into Delta tables; the same seven functions run against them. A full SNOMED CT UK edition fits in 536 MB of heap. pathling.csiro.au/blog/local-terminology

pathling.csiro.auLocal terminology mode | PathlingPathling 9.9.0 adds a local terminology mode. SNOMED CT and FHIR terminology

John Grimes

@john-grimes.bsky.social

2 Sept

Pathling server v3 is out. It implements the two SQL on FHIR 3.0.0 operations that just went to HL7 ballot, `$sql-run` and `$sql-export`, and lets you build SQL queries out of other SQL queries. pathling.csiro.au/blog/pathlin...

pathling.csiro.auPathling server 3.0.0 | PathlingPathling server 3.0.0 is now available. It lets you build SQL queries out of

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John Grimes

@john-grimes.bsky.social

2 Sept

`$jobs` lists the asynchronous jobs on the server: the operation that started each one, its status, progress, and the URL to poll or cancel it. With authorisation on, a caller sees only their own. The admin UI has a matching page, so an operator can stop a runaway query.

John Grimes

@john-grimes.bsky.social

2 Sept

The three SQL on FHIR operations inherited from the continuous build are retired in favour of `$sql-run` and `$sql-export`. Renamed config properties, authorities and upgrade notes are all in the post. pathling.csiro.au/blog/pathlin...

pathling.csiro.auPathling server 3.0.0 | PathlingPathling server 3.0.0 is now available. It lets you build SQL queries out of

John Grimes

@john-grimes.bsky.social

2 Sept

pathling.csiro.auPathling server 3.0.0 | PathlingPathling server 3.0.0 is now available. It lets you build SQL queries out of

John Grimes

@john-grimes.bsky.social

2 Sept

SQLView Libraries are named SQL table sources, stored on the server and referenced by canonical URL. A cohort filter or a derived column is written once, then read by any number of queries and views. Change the definition and every dependent query picks it up on its next run.

John Grimes

@john-grimes.bsky.social

2 Sept

`$sql-export` carries any number of subjects in one job, in any mixture of ViewDefinitions, SQLQueries and SQLViews. Each reads the Delta table versions pinned when the job began, so a write that lands mid-job is invisible to all of them. NDJSON, CSV or Parquet, one file per subject.

John Grimes

@john-grimes.bsky.social

28 Aug

We have just launched a new Kaggle competition called "Data Golf"! ⛳️ This is your opportunity to test your #SNOMEDCT analysis skills in the lead up to #SCTExpo26 in October! 🥸 go.csiro.au/FwLink/data-... You have 1 month! 🏃 We'll be presenting the results back at the Expo!

go.csiro.auData Golf 2026SNOMED CT data analytics

John Grimes

@john-grimes.bsky.social

11 May

Co-leading the SQL on FHIR track at HL7 Connectathon in Rotterdam this Sat + Sun, with Nikolai Ryzhikov, Adam Culbertson and Arjun Sanyal. Portable, tabular views over #FHIR data, run anywhere. Come help us improve the standard. confluence.hl7.org/spaces/FHIR/...

John Grimes

@john-grimes.bsky.social

24 Jan

🚀 We've just released a fresh new Pathling server! Rebuilt from the ground up with #SQLonFHIR support ✨ #FHIR REST API, FHIRPath search, bulk data ops, auth, web admin UI, and Helm charts for K8s. Check out the blog post: pathling.csiro.au/blog/new-pat...

pathling.csiro.auIntroducing the new Pathling server | PathlingWe're excited to announce the release of a new Pathling server. This is a

John Grimes

@john-grimes.bsky.social

24 Jan

Hi all, happy to join you here on BlueSky! I've heard good things, looking forward to sharing some of my work.

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