Community

Code contribution

Repositories related to the PCORnet CDM:

• on github:

  • hms-dbmi/i2b2-to-PCORNET-CDM
    • not to be confused with SCILHS i2b2 PCORnet Common Data Model Ontology
  • OHDSI/OMOPV4_PCORNetV1_ETL
  • AppInformatics/SEDI_to_PCORnetCDM
  • PEDSnet/pedsnetcdm_to_pcornetcdm
  • https://github.com/chop-dbhi/ and more specifically
  • https://github.com/chop-dbhi/data-models-sqlalchemy
  • https://github.com/ufbmi/pcornet_cdm
  • [CDM v3.0 errata at https://github.com/CDMFORUM/CDM-ERRATA] (https://github.com/CDMFORUM/CDM-ERRATA)

• on bitbucket

  • gpcnetwork/gpc-pcornet-cdm

Related work:

• MCW_BMI/unstructured-notes-deidentification
• gpcnetwork/bc_qa - GPC Breast Cancer Data Quality Reporting
• portaquery -- migrate an query between i2b2 sites
• DECOY - Data Entrepreneur Clinical Observables Yardstick *toward a clinical equivalent to DeSYN PUF Files''

Clinical Informatics Research Division (GPC site at UT Health Science Center at San Antonio):

• on github:

  • Cohort characterization by finding over and under represented facts
  • Post-processing DataBuilder output to create a single, flat table representing visits as time-series-- i.e. one row per patient-date and one (or more) column/s per variable
  • Various methods for finding a control cohort given a disease cohort

• Semantic Processing of EHR data for Clinical Research. H. Sun, K. Depraetere, J. De Roo, G. Mels, B. De Vloed, M. Twagirumukiza, D. Colaert. Journal of Biomedical Informatics

  • "It is also possible to further convert data to application semantics and store the converted results in clinical research databases, e.g. i2b2, OMOP, to support different clinical research settings."
  • see also SALUS, Scalable, Standard based Interoperability Framework for Sustainable Proactive Post Market Safety Studies

Analytics

#Crossover with CTSA

Note efforts toward CIDR collaboration starting July 2012.

Misc (todo: organize)

• StoryTellingAndTestCases see also ModelMashUp

• liaisons?

  • NLM Value Set Authority Center?
    • UMLS?
  • CTSA, ACTS?
  • ODHSI?

• architecture: OWL? schema.org?

  • relevant research: Jos D. and co 2015 JBMI