{"id":15044855,"url":"https://github.com/aehrc/pathling","last_synced_at":"2026-05-09T09:56:18.758Z","repository":{"id":37093750,"uuid":"249342627","full_name":"aehrc/pathling","owner":"aehrc","description":"Tools that make it easier to use FHIR and clinical terminology within data analytics, built on Apache Spark.","archived":false,"fork":false,"pushed_at":"2026-02-13T10:03:02.000Z","size":215903,"stargazers_count":118,"open_issues_count":88,"forks_count":19,"subscribers_count":11,"default_branch":"main","last_synced_at":"2026-02-13T10:16:07.896Z","etag":null,"topics":["analytics","fhir","spark","standards","terminology"],"latest_commit_sha":null,"homepage":"https://pathling.csiro.au","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/aehrc.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-03-23T05:22:00.000Z","updated_at":"2026-02-06T18:52:46.000Z","dependencies_parsed_at":"2024-01-19T03:27:00.624Z","dependency_job_id":"62b638fe-a0a0-4d13-9f29-9af066135bb6","html_url":"https://github.com/aehrc/pathling","commit_stats":{"total_commits":2961,"total_committers":14,"mean_commits":211.5,"dds":0.270516717325228,"last_synced_commit":"c14dc6c27c638d72fd878a957d7b45ab925cffd3"},"previous_names":[],"tags_count":88,"template":false,"template_full_name":null,"purl":"pkg:github/aehrc/pathling","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aehrc%2Fpathling","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aehrc%2Fpathling/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aehrc%2Fpathling/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aehrc%2Fpathling/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aehrc","download_url":"https://codeload.github.com/aehrc/pathling/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aehrc%2Fpathling/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29475513,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-15T10:25:47.032Z","status":"ssl_error","status_checked_at":"2026-02-15T10:25:01.815Z","response_time":118,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["analytics","fhir","spark","standards","terminology"],"created_at":"2024-09-24T20:51:08.543Z","updated_at":"2026-02-15T10:26:26.021Z","avatar_url":"https://github.com/aehrc.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003ca href=\"https://pathling.csiro.au\"\u003e\n\u003cpicture\u003e\n  \u003csource srcset=\"https://raw.githubusercontent.com/aehrc/pathling/main/media/logo-colour-tight-dark.svg\" media=\"(prefers-color-scheme: dark)\"/\u003e\n  \u003cimg src=\"https://raw.githubusercontent.com/aehrc/pathling/main/media/logo-colour-detail-tight.svg\" alt=\"Pathling logo\" width=\"300\"/\u003e\n\u003c/picture\u003e\n\u003c/a\u003e\n\u003cbr/\u003e\n\u003cbr/\u003e\n\n[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=aehrc_pathling\u0026metric=alert_status)](https://sonarcloud.io/summary/new_code?id=aehrc_pathling)\n\nPathling is a set of tools that make it easier to\nuse [FHIR\u0026reg;](https://hl7.org/fhir) and clinical terminology within health\ndata analytics. It is built on [Apache Spark](https://spark.apache.org), and\nit implements the [SQL on FHIR](https://sql-on-fhir.org) view specification and\nthe [Bulk Data Access](https://hl7.org/fhir/uv/bulkdata/STU2/) implementation\nguide.\n\n[**Read the documentation \u0026rarr;**](https://pathling.csiro.au/docs)\n\n## What can it do?\n\n### Query and transformation of FHIR data\n\n[FHIR R4](https://hl7.org/fhir) is the dominant standard for exchanging health\ndata. It comes in both [JSON](https://hl7.org/fhir/json.html)\nor [XML](https://hl7.org/fhir/xml.html) formats, and can contain over 140\ndifferent types of resources, such\nas [Patient](https://hl7.org/fhir/patient.html),\n[Observation](https://hl7.org/fhir/observation.html),\n[Condition](https://hl7.org/fhir/condition.html),\n[Procedure](https://hl7.org/fhir/procedure.html), and many more.\n\nPathling is capable of reading all the different types of FHIR resources into a\nformat suitable for data analysis tasks. This makes the following things\npossible:\n\n- Creating SQL-friendly views from FHIR data\n- Transforming data into other formats, such as CSV\n  or [Parquet](https://parquet.apache.org/)\n- Performing terminology queries against coded fields within the FHIR data\n\nSee [Data in and out](https://pathling.csiro.au/docs/libraries/io) and\n[Running queries](https://pathling.csiro.au/docs/libraries/running-queries) for\nmore information.\n\n### Terminology queries\n\nHealth data often contains codes from systems such\nas [SNOMED CT](https://www.snomed.org/snomed-ct/five-step-briefing), [LOINC](https://loinc.org/)\nor [ICD](https://www.who.int/standards/classifications/classification-of-diseases).\nThese codes contain a great deal of information about diagnoses, procedures,\nobservations and many other aspects of a patient's clinical record.\n\nIt is common to group these codes based upon their properties, relationships to\nother codes, or membership within a pre-defined set. Pathling can automate the\ntask of calling out to\na [FHIR terminology server](https://hl7.org/fhir/terminology-service.html) to\nask questions about the codes within your data.\n\nExamples of the types of questions that can be answered include:\n\n- Is this SNOMED CT procedure code a type of endoscopy?\n- Does this LOINC test result code have an analyte of bilirubin?\n- Is this ICD-10 code within the pre-defined list of codes within my cohort\n  definition?\n\nSee [Terminology functions](https://pathling.csiro.au/docs/libraries/terminology)\nfor more information.\n\n### Server\n\nPathling Server is a FHIR R4 analytics server that exposes a range of\nfunctionality for use by applications and implements:\n\n- **SQL on FHIR**:\n  [Run](https://pathling.csiro.au/docs/server/operations/view-run) view\n  definitions to\n  preview tabular projections of FHIR data,\n  then [export](https://pathling.csiro.au/docs/server/operations/view-export) to\n  NDJSON, CSV, or Parquet\n- **Bulk Data Access\n  **: [Export data](https://pathling.csiro.au/docs/server/operations/export) at\n  system,\n  patient, or group level using the FHIR Bulk Data Access specification\n- **Bulk Import\n  **: [Import data](https://pathling.csiro.au/docs/server/operations/import)\n  from NDJSON,\n  Parquet, or Delta Lake sources,\n  or [sync with another FHIR server](https://pathling.csiro.au/docs/server/deployment/synchronization)\n  that supports bulk export\n- **[Bulk Submit](https://pathling.csiro.au/docs/server/operations/bulk-submit)\n  **: An experimental\n  implementation of the new Bulk Submit proposal\n- **[FHIRPath Search](https://pathling.csiro.au/docs/server/operations/search)\n  **: Query resources using\n  FHIRPath expressions\n- **[CRUD Operations](https://pathling.csiro.au/docs/server/operations/crud)**:\n  Create, read, update, and\n  delete resources\n\nThe server is distributed as a Docker image. It\nsupports [authentication](https://pathling.csiro.au/docs/server/authorization)\nand also can be scaled\nover a cluster\non [Kubernetes](https://pathling.csiro.au/docs/server/deployment/kubernetes) or\nother\nApache Spark clustering solutions.\n\nSee [Server](https://pathling.csiro.au/docs/server) for installation and\nconfiguration details.\n\n## Artifact signing\n\nPublished Maven artifacts and Helm charts are signed with the following GPG key:\n\n- **Key ID**: `ED48678D`\n- **Fingerprint**: `F814 751C 64B5 F5E7 08A8 C73F C3C6 291F ED48 678D`\n- **User ID**: `Pathling Developers \u003cpathling@csiro.au\u003e`\n\nThe public key is available\non [keys.openpgp.org](https://keys.openpgp.org/search?q=F814751C64B5F5E708A8C73FC3C6291FED48678D).\n\n## Licensing and attribution\n\nPathling is copyright © 2018-2025, Commonwealth Scientific and Industrial\nResearch Organisation\n(CSIRO) ABN 41 687 119 230. Licensed under\nthe [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0).\n\nThis means that you are free to use, modify and redistribute the software as\nyou wish, even for commercial purposes.\n\nIf you use this software in your research, please consider citing our paper,\n[Pathling: analytics on FHIR](https://doi.org/10.1186/s13326-022-00277-1).\n\n**Pathling is experimental software, use it at your own risk!** You can get a\nfull description of the current set of known issues\n[here](https://github.com/aehrc/pathling/issues).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faehrc%2Fpathling","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faehrc%2Fpathling","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faehrc%2Fpathling/lists"}