General Help
- Brief Overview: How to use PheKB
- How to Create Phenotypes on PheKB: Creating a Phenotype Page and Uploading Documentation
- How to Share Phenotypes on PheKB: Public, Private, and Collaborative Accessibility
- How to Share Data on PheKB: Creating an Implementation and Uploading Data
- Data Dictionary Validation Tool User Guide
- Sample Data Dictionary with errors and Sample Corrected Data Dictionary
- Sample Data File with errors and Sample Corrected Data File
Cite PheKB.org
Kirby JC, Speltz P, Rasmussen LV, Basford M, Gottesman O, Peissig PL, Pacheco JA, Tromp G, Pathak J, Carrell DS, Ellis SB, Lingren T, Thompson WK, Savova G, Haines J, Roden DM, Harris PA, Denny JC. PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J Am Med Inform Assoc. 2016 Mar 28; PMID: 27026615
Other Phenotype Resources
Phenotype Design
- MEDI - MEDication Indication Resource - data-derived tables of medications and their indications
- Natural Language Processing Survey of Tools and Resources
- Phenome-wide association studies (PheWAS) - grouping of ICD9 codes for clinical and genetic analysis
Data Dictionary Creation
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eleMAP - Allows researchers to harmonize their local phenotype data dictionaries to existing metadata and terminology standards such as the caDSR (Cancer Data Standards Registry and Repository), NCIT (NCI Thesaurus) and SNOMED-CT (Systematized Nomenclature of Medicine-Clinical Terms). Use this tool to search/browse metadata related to different studies, create new study & its related metadata, users can also export metadata in excel format.
Validation Methods
- Validation of electronic Medical record-based phenotyping algorithms: Results and Lessons Learned from the eMERGE Network. JAMIA 2013;20(e1):e147-54.
- Chapter 13: Mining Electronic Health Records in the Genomics Era. PLoS Comput Biol 8(12): e1002823.