Green Team - Spring 2019

ICEES: Scientific Use Cases

[ ] Validate integrated feature tables #136, #122
[ ] Evaluate ICEES API output
[ ] ICEES API usability with respect to Gamma Reasoner - BioLink, Workflows 4 and 5
[ ] Expand temporally to include additional years of patient data (2012-2017), #146
[X] Expand feature variables to include additional clinical variables (e.g., pulmonary function tests, FA-relevant measures [metformin, HCT, PLT, WBC]), CMAQ airborne pollutants data, DOT roadway data, and ACS Socioenvironmental data, #146
[ ] Develop plans for expanding to include new cohorts (e.g., pain, DILI, diabetes), #146
[ ] Publish approach and preliminary findings, #145

Present a proof of concept translating EHRs across CTSAs into a single de-identified format sharable as a smartAPI. Publish a pipeline from i2b2 to FHIR to ICEES:
- [ ] Publish a unified ICEES repo https://github.com/NCATS-Tangerine/icees-api preprocessing https://github.com/xu-hao/datatrans/tree/master/spark #138
- [ ] Generate FHIR from i2b2 #137
- [ ] Document and share across Translator/CTSAs, #140
- [ ] Publish software R&D manuscript

[x] Document and share, including an architecture diagram #139
[x] Create new CMAQ airborne pollutants exposures API #141
[X] Create ACS socioenvironmental exposures API #142
- [ ] Expand service
[X] Create DOT roadway exposures API #143
[ ] Document exposures services
[ ] Develop integrated exposures service with visualization capabilities for a nation-wide map of 'environmental profiles' #166

Reasoner Development Toolkit
- [ ] BioNames
- [ ] Onto
- [ ] CTD
[ ] OmniCorp
- [ ] #158 Labels
- [ ] #159 Information Content
- [ ] #160 Article Similarity
[x] Ros Project
- [x] Develop a Ros CWLTool
- [x] Develop a CWL workflow for Workflow 5
- [x] Build a prototype facade for ICEES to (a) implement wf5 modules and (b) map biolink concepts.
[ ] UberGraph
[ ] Collaborate on development of NIEHS Tox21 API
[ ] Develop a link prediction API working with Weifan and Changsung.