Create matrix of project deliverables and the software packages/repos that support those deliverables

[jshoughtaling]

In an effort to eliminate ambiguity regarding development efforts and the deliverables they support, we will catalog and align deliverables with the packages and display them on this site.

[jshoughtaling]

@del42 - I created a collapsible table structure below to capture items per team and per major deliverable.

Let me know if you think this is a reasonable way to represent the data and I'll do it for the other teams and then publish it on the developer site.

Data Acquisition

Expand Aims

1. Site startup

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 1.1\) Project Readiness | | | | | 1.2\) Ensure IRB readiness | | | |

2. Cohort Sampling and Size Justification

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 2.1\) Identify intellectual property concerns at each site | | | | | 2.2\) Ensure diversity in site data | | | | | 2.3\) Obtain population- representative inferences | JARED | container-apps \[atlas\] | |

3. Federation process to access data from all patients

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 3.1\) Ensure federated process to identify cohorts and request data | JARED | container-apps \[atlas\] | | | 3.2\) Document federated processes, with tooling module | | | | | 3.3\) Define and prepare meta dataset | JARED | container-apps \[atlas\] | |

4. Structured Data

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 4.1\) Prepare OMOP Data | JARED | container-apps \[etl\] | Central Processing SOP | | 4.1\) Prepare to query OMOP data | JARED | container-apps \[etl\] | |

5. Obtaining High-resolution physiological data

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 5.1\) Integrate OMOP vocabulary for physiological data | JARED | chorus-mapping \[vocab\] | SOP | | 5.2\) Standardize signal processing in waveforms | BRIAN | chorus\_waveform | | | 5.3\) Quality control | | | |

6. Collection and processing of image data

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 6.1\) Ensure collection of image data at all sites | | | | | 6.2\) Ensure generation of metadata from images | | | | | 6.3\) Ensure collection of image data at all sites | | | | | 6.4\) Ensure linkage to other data domain | JARED | container-apps \[registry\] | MM SOP |

7. Collection and Processing of Clinical notes

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 7.1\) Customize NLP algorithm | | | | | 7.2\) Validate the NLP tool using honest brokers | | | | | 7.3\) Unstructured EHR extraction | | | | | 7.4\) Implement NLP tool | | | |

8. Mining for socioeconomic status data

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 8.1\) Identify common data SDoH elements from collective experience of sites | | | | | 8.2\) Identify and resolve discrepancies in performance of SDoH elements | | | |

9. Collection of contextual SDoH data

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 9.1\) Review SDoH variables and data sources | | | | | 9.2\) Prepare geospatial crosswalk datasets | | | |

10. Linkage among EHR

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 10.0\)Design and communicate linkage SOP | JARED | | MM SOP | | 10.1\) Retrieve EHR data through MRNs at each site | JARED | container-apps \[registry\] | MM SOP | | 10.2\) Minimal EHR dataset elements created and communicated to all sites | | | | | 10.3\) EHR data extracted | JARED | | | | 10.4\) Site-specific EHR extracts validated | | | | | 10.5\) Implement tools to accurately link EHR and physiologic data | JARED | container-apps \[registry\] | | | 10.6\) Gap analysis of linkage performed | JARED | | |

11. Deidentification of data

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 11.1\) Prepare safe harboring approach | | | | | 11.2\) Apply SOP on safe harboring approach | | | | | 11.3\) Quality control of linked safe-harbor datasets | | | |

12. Event Annotation

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 12.1\) Develop semi-automatic predictive monitoring model to identify events | | | | | 12.2\) ndividual chart review of potential events by clinicians | | | | | 12.3\) Develop phenotype algorithm in OHDSI Phenotype repository | JARED | container-apps \[atlas\] | | | 12.4\) Implement phenotype algorithm in OHDSI Phenotype repository | JARED | container-apps \[atlas\] | | | 12.5\) Generate silver-standard labels at scale automatically | JARED | | | | 12.6\) Implement annotation pipeline to combine physiological data for resolved timeline | | | | | 12.7\) Store results both locally and centrally | | | | | 12.8\) Create datasheet describing each cohort | JARED | container-apps \[atlas\], CHoRUSReports | |

13. Site-specific metadata

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 13.1\) Encode de-identified hospital number on each data set | | | | | 13.2\) Report site-specific metadata from full patient dataset | | | |

14. Quality control

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 14.1\) Write protocols for quality controls checks at all sites | JARED | CHoRUSReports | Quality Central | | 14.2\) Quantify variability when it exists | JARED | CHoRUSReports | Quality Central | | 14.3\) Use the Data Quality Dashboard from OHSDI to evaluate datasets | JARED | container-apps \[ares, www-dgs\] | Quality Central |

15. Privacy Check

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 15.1\) Examine unique identifiability with combinations of attributes to check potential risk of linkability | | | | | 15.2\) Evaluate I-diversity and t-closeness | | | | | 15.3\) For unstructured data, extract concepts through whitelist mechanism and test for linkability | | | |

16. Generate synthetic data

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 16.1\) Use generative adversarial network \(GAN\) approaches to produce site-specific synthetic data sets | | | | | 16.2\) Post the data and the source code | | | |

17. Hold-out validation dataset

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 17.1\) Set aside 20% of patients for algorithm testing | | | | | 17.2\) Pursue qualification of reserved dataset for FDA's Medical Device Development Tool program | | | |

18. Data storage platform - CHoRUS

| SUBAIM | INVOLVED | SOFTWARE | DOCUMENTATION | | :--- | :--- | :--- | :--- | | 18.1\) Organize files by year/month, then Subject ID, data modalities | JARED | container-apps \[etl\] | Central Processing SOP | | 18.2\) Store dataset in in site-specific staging area | JARED | container-apps \[etl\] | Central Processing SOP | | 18.3\) Implement automated data integrity check; review error logs | JARED | CHoRUSReports | Quality Central | | 18.4\) Copy files to data lake using secure FTP | JARED | container-apps \[etl\] | Central Processing SOP |