healthcare resources

Best of healthcare resources, data, engineering, etc...for health informaticists

Maps / interactive

• Interactive US News:
  • https://www.usnews.com/news/healthiest-communities/oregon/lane-county#food-nutrition
    • https://careshq.org
    • https://www.usnews.com/news/healthiest-communities/oregon/lane-county#food-nutrition

Standards

ICD

• ICD Mappings (cost, risk): https://www.cms.gov/medicare/health-plans/medicareadvtgspecratestats/risk-adjustors/2023-model-software/icd-10-mappings
• ICD-CM: https://www.cdc.gov/nchs/icd/comprehensive-listing-of-icd-10-cm-files.htm

LOINC

FHIR

• https://www.hl7.org/fhir/index.html
• https://medium.com/@jaideeppahwa1/list/fhir-for-developers-ea551cc4840c
• Most popular FHIR server: HAPI FHIR - Java based -> https://hapi.fhir.org/ - demo client; https://github.com/hapifhir/hapi-fhir
• Interesting client: https://samply.github.io/blaze/ - FHIR server with CQL, where you can connect it to a HAPI FHIR server as a example
• Interesting client: python: SMART - https://github.com/smart-on-fhir/client-py
• FHIR Vendor Sandboxes
  • Allscripts https://developer.allscripts.com/
  • athenahealth - athenaOne https://docs.athenahealth.com/api/
  • Cerner - Provider and Patient Facing Apps https://fhir.cerner.com/millennium/dstu2/
  • Epic Provider Facing Apps https://uscdi.epic.com/
  • Epic Patient Facing Apps https://open.epic.com/
  • Intersystems https://www.intersystems.com/fhir/
  • Meditech https://ehr.meditech.com/meditech-greenfield

Quality Measures

• CQL
  • Example of FHIR + CQL for colorectal screening: https://github.com/cqframework/cqf-ccc/blob/master/WALKTHROUGH.md / CMS 113
  • https://www.youtube.com/watch?v=PlAbNxgG2xo
  • https://ecqi.healthit.gov/fhir
    • Built on top of:  Quality Data Model (QDM), Clinical Quality Language (CQL), Health Quality Measure Format (HQMF), and Quality Reporting Document Architecture (QRDA)
  • CQL runner: https://cql-runner.dataphoria.org/

OMOP Common Data Model

Tools / searchable engines

• Drug (ATC - NDC), genomic, diseases (ICD-9:ICD-11), genomic, and more
  • KEGG: https://www.kegg.jp/ AND https://www.kegg.jp/kegg/brite.html
  • MONDO: Disease mappings: https://github.com/monarch-initiative/mondo
• Biome
  • https://disbiome.ugent.be/disease/61
• Government Data US (focuses on open source government datasets (healthdata.gov, cdc.gov, etc...): https://www.find.nhit.org
• SNOWMED searchable: https://browser.ihtsdotools.org/?
• Relational search tool (athena - via ohdsi.org - / 'Odyssey': https://athena.ohdsi.org/search-terms/start AND https://www.ohdsi.org
• Tools from US government agencies (HHS, CDC, etc...): https://code.gov/agencies
• Other health data / aggregator: https://ghdx.healthdata.org/
• H-CUP tools -> CCS, CCI, ECI, and more --> python package: https://github.com/yubin-park/hcuppy

Synthetic / Fake Data

• For FHIR - Synthea: https://github.com/synthetichealth/synthea
• Synthetia Module Builder: https://synthetichealth.github.io/module-builder/
  • https://synthetichealth.github.io/spt/#/customizer
• For HL7v2 messages - Google SIM Hospital - - https://github.com/google/simhospital
• FHIR with Genetics: https://registry.opendata.aws/synthea-coherent-data/

Open source tools

• Symptom to condition check - https://github.com/hantswilliams/medical-symptom-checker

Services

• Particle Health - https://www.particlehealth.com/ - https://docs.particlehealth.com/reference/
• Better Platform - Build healthcare apps - https://platform.better.care/sandbox
• DrChrono API Platform - https://www.drchrono.com/api/
• Bluebutton CMS - https://bluebutton.cms.gov/developers/
• Humana Data Exchange - https://developers.humana.com/apis/registerapp
• Redux API - https://www.redoxengine.com/product/fhir-api/
• Morf (dr.P clone) - https://www.morf.health/

Assessments

• SDoH, mental health, substance use disorders, etc... -> https://www.phenxtoolkit.org/
• CMS quality measure inventory -> https://cmit.cms.gov/cmit/#/
• AHRQ - Health Tech Assessments -> https://digital.ahrq.gov/health-it-tools-and-resources/evaluation-resources/health-it-survey-compendium-search
• AHRQ time motion - https://digital.ahrq.gov/time-and-motion-studies-database

Unique open source datasets

• Gun Violence: https://www.gunviolencearchive.org/
• SDoH - https://socialcapital.org
• PhysioNet - physionet: models, databases, software - https://physionet.org/content/
• University Pittsburg Library - https://hsls.libguides.com/health-data-sources/data-sets
• NY related SDoH list of resources, data -> https://journals.sagepub.com/doi/full/10.1177/00469580231152318
• All of Us (NIH) - genetric, PRO, environmental, social, etc... - https://databrowser.researchallofus.org/
• Mimic - ICU-like data - https://physionet.org/content/mimiciii-demo/1.4/
• CMS - open payments - https://www.cms.gov/OpenPayments/Data/Dataset-Downloads
• CMS - medicare claims public use files (PUF) - https://www.cms.gov/Research-Statistics-Data-and-Systems/Downloadable-Public-Use-Files/BSAPUFS
• Text examples for NLP: https://www.mtsamples.com/
• Healthdata.gov -> DATAJAM Curated Datasets -> SDoH, Care Access, Lyme Disease, COVID-19 equity; https://healthdata.gov/stories/s/6usb-uzrp

APIs

• FDA open APIs
  • Open FDA: https://open.fda.gov/apis/
  • FDA: Drug Side effects, product labeling
    • https://open.fda.gov/apis/drug/event/
    • https://dailymed.nlm.nih.gov/dailymed/
  • National Library Medicine (clinicaltables - ICD, LOINC, NPI, RXnorm, and many more)
    • https://clinicaltables.nlm.nih.gov/
    • For more NLM, go here and filter for APIs: https://eresources.nlm.nih.gov/nlm_eresources/
• Drug Classes (NLM)
  • NLM RxNav - https://lhncbc.nlm.nih.gov/RxNav/APIs/RxClassAPIs.html
• Nutrition
  • nutritionix: https://www.nutritionix.com/

Building Cerner/Epic Tools

• Cerner Mellenium - Secure Sandbox
  • https://docs.particlehealth.com/reference/getting-started

Open Source HIEs/TEFA related

• OpenHIE https://ohie.org/
  • https://openhie.github.io/instant/docs/introduction/vision/
  • https://wiki.ohie.org/
• Sequia Project - QHINS / TEFCA
  • https://rce.sequoiaproject.org/designated-qhins/
• Global / WHO version:
  • https://www.ihe.net/resources/profiles/
• SDoH Related: GRAVITY Project
  • Terminology sets: https://confluence.hl7.org/display/GRAV/Social+Risk+Terminology+Value+Sets

Open sourced ML

• Python Packages
  • https://github.com/sunlabuiuc/PyHealth
• LLM
  • https://github.com/shibing624/MedicalGPT/blob/main/README_EN.md
  • FHIR LLM with LangChain - Flask - - FHIR LangChain LLM - Connecting GPT LLM to FHIR resources - https://github.com/sumeetkh/fhir_record_gpt
  • FHIR LLM with open LLM model - FLask - Answers questions r/t patient records - https://github.com/John-64/Botor-for-FHIR
• Radiology related
  • Arcrdsi: https://www.acrdsi.org
  • MONAI project: https://github.com/Project-MONAI/MONAI
• Generic
  • The-algorithms: https://the-algorithms.com/category/machinelearning
• Pose/body estimation
  • Movement - https://github.com/akshaybahadur21/GymLytics
  • Bed Position - https://web.northeastern.edu/ostadabbas/2019/06/27/multimodal-in-bed-pose-estimation/
  • Instructional - https://www.analyticsvidhya.com/blog/2022/01/a-comprehensive-guide-on-human-pose-estimation/
  • Summary of librarires - https://medium.datadriveninvestor.com/top-and-best-computer-vision-human-pose-estimation-projects-186d04204dde
• NLP - GTP for Pubmed
  • https://www.mosaicml.com/blog/introducing-pubmed-gpt

ML test data healthcare

• Medical Imaging

  • Stanford: https://aimi.stanford.edu/shared-datasets
  • NYU Langone Health: https://fastmri.med.nyu.edu/
    • Facebooks code for NYU langone data: https://github.com/facebookresearch/fastMRI
  • COVID data - big ML
    • https://www.kaggle.com/datasets/andyczhao/covidx-cxr2
    • https://alexswong.github.io/COVID-Net/

• EMRs/EHRs

  • Open Source
    • MedPlum (2023-; built on FHIR); has different portals: https://github.com/medplum/medplum
  • Behavioral health specific:
    • valant emr (https://www.valant.io)
    • eleos health - https://eleos.health
    • blue print health - https://www.blueprint-health.com
    • luminello - https://luminello.com
    • kipu health -https://kipuhealth.com
    • opus health - https://www.opusbehavioral.com/ehr
    • alleva - https://helloalleva.com (know these guys, somewhat competitor to inrecovery platform which I have access to)
    • sessionshealth - https://www.sessionshealth.com/pricing - interesting thing here -> free level that we could use
    • therapy notes (https://www.therapynotes.com)
    • non-EMR/complementary for mental health:
      • patient success - https://www.lumahealth.io
  • next-gent EMR/headless:
    • canvas EMR (
  • generic / for SMBs
    • elationhealth https://www.elationhealth.com/ehr/
    • drchrono https://www.drchrono.com
    • kareo emr (https://www.kareo.com)
  • other, younger/new that are still startup phase:
    • https://www.akutehealth.com

• Healthcare Icons

  • https://healthicons.org/

To organize:

Healthcare:

• https://www.nature.com/articles/s41746-022-00557-1
• https://www.nature.com/articles/s41587-021-01145-6
• https://jamanetwork.com/journals/jama/article-abstract/2788483
• Brain imaging tools:
  • https://github.com/fepegar/torchio
  • Zip code better then genetics -> https://medcitynews.com/2021/08/zip-codes-have-become-a-better-predictor-of-health-outcomes-than-genetic-codes-technology-may-be-ready-to-fix-that/
• Statistical tests
  • https://link.springer.com/article/10.1007/s10654-016-0149-3
• ML best practices
  • FDA
  • https://www.fda.gov/medical-devices/software-medical-device-samd/good-machine-learning-practice-medical-device-development-guiding-principles
  • https://www.fda.gov/medical-devices/software-medical-device-samd/artificial-intelligence-and-machine-learning-aiml-enabled-medical-devices
  • Action plan - > https://www.fda.gov/media/145022/download
  • Digital health reports -> https://www.fda.gov/medical-devices/digital-health-center-excellence/digital-health-reports
• Conceptual framework for investigating mental disorders
  • https://www.nimh.nih.gov/research/research-funded-by-nimh/rdoc/about-rdoc
• Clinical Knowledge graph (contains tons of APIs/open data to capture) - https://github.com/MannLabs/CKG
• Interoperability: - https://smarthealthit.org/ - USCDI: https://www.healthit.gov/isa/united-states-core-data-interoperability-uscdi - SAFER - https://www.healthit.gov/topic/safety/safer-guides
• Case Studies: - https://www.healthit.gov/case-studies - https://www.ahrq.gov/news/newsroom/case-studies/index.html
• Enrichment of geographic data: - General data by zipcode - https://censusreporter.org/ - https://github.com/censusreporter/census-api/blob/master/API.md - Demographics - Economics - Families - Housing - Social - Health insurance - Poverty (food stamps / SNAP) - Disparities -> - https://www.neighborhoodatlas.medicine.wisc.edu/ - https://www.countyhealthrankings.org/