V2.0.0 (#23)

* feat: ✨ make version 2.0.0 as current * feat: ✨ move assets folder into the docs * fix: 🐛 made modifications * fix: 🐛 move asssets and components to correct location * fix: 🐛 links * fix: 🐛 format and typo * fix: 🐛 broken links * fix: 🐛 path issue * fix: 🐛 restore path name * fix: 🐛 update healthsheet * fix: 🐛 add static files to global static * fix: 🐛 remove unnecessary files * fix: 🐛 update healthsheet * fix: 🐛 minor date * fix: 🐛 minor links * fix: 🐛 remove json and v2 files from components and static * fix: 🐛 relocate static files * fix: 🐛 remove version future * fix: 🐛 broken healthsheet files * chore: 🔨 lock docusaurus deps * fix: 🐛 reswizzle version dropdown component * fix: 🐛 move page feedback to client side * fix: 🐛 move page feedback to client side * fix: 🐛 move page feedback to client side * fix: 🐛 move page feedback to client side * fix: 🐛 remove page feedback * fix: 🐛 update changelog * fix: 🐛 typos * fix: 🐛 change doi in the fair principles page * fix: 🐛 change pdf name in questionnaries * chore: 🔨 update landing page details * chore: 🔨 update landing page details * fix: 🐛 link redirections * fix: 🐛 changelog headers * fix: 🐛 modify cognition moCA table view * fix: 🐛 modify hyperlink text in cognition moCA page * fix: 🐛 update doi in dataset distribution in healthsheet * fix: 🐛 CDS link * fix: 🐛 CDS links * feat: ✨ update version banner * feat: ✨ update version banner * fix: 🐛 banner text * chore: 🔨 update G30&G31 cells for the clinical data table * chore: 🔨 update alcaline and nt-proBNP table * chore: 🔨 update clinical table * chore: 🔨 update changelog * chore: 🔨 update omop table * fix: 🐛 update citation page * style: 🎨 format * chore: 🔨 update changelog * fix: 🐛 format of citation in training page * fix: 🐛 column header * fix: 🐛 column header * fix: 🐛 citation format * fix: 🐛 changelog * fix: 🐛 update landing page size and number of files * fix: 🐛 quotations * fix: 🐛 citation * fix: 🐛 update retinal photography page * fix: 🐛 landing page --------- Co-authored-by: Sanjay Soundarajan <[email protected]>
AI-READI · Nov 8, 2024 · f6d5c66 · f6d5c66
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diff --git a/docs/AI-readiness/ethical-practices.mdx b/docs/AI-readiness/ethical-practices.mdx
@@ -4,7 +4,3 @@ title: Ethical practices
 ---
 
 The Bridge2AI program aspires to create four datasets that are ethically sourced. The Bridge2AI Center is working to define and characterize what “ethically source” means with respect to the use of machine learning and artificial intelligence technologies applied to health data. In the meantime, AI READI and other grand challenge programs apply accepted regulatory practices including, for example, the involvement of an institutional review board to evaluate compliance with human research protections. In addition, a license has been developed to state the terms of use for those accessing the data available to the public. For data that are deemed more sensitive, a data use agreement will be negotiated.
-
-import PageFeedback from '@site/src/components/PageFeedback';
-
-<PageFeedback />
diff --git a/docs/AI-readiness/fair-principles.mdx b/docs/AI-readiness/fair-principles.mdx
@@ -27,7 +27,7 @@ The [FAIR Principles](https://doi.org/10.1038/sdata.2016.18) published in 2016 a
     </td>
     <td className="align-top">
       The AI-READI dataset is shared on fairhub.io, which provides a DOI for the dataset
-        ([https://doi.org/10.60775/fairhub.1](https://doi.org/10.60775/fairhub.1))
+        ([https://doi.org/10.60775/fairhub.2](https://doi.org/10.60775/fairhub.2))
     </td>
   </tr>
   <tr>
@@ -228,7 +228,7 @@ The [FAIR Principles](https://doi.org/10.1038/sdata.2016.18) published in 2016 a
       The AI-READI dataset includes a dataset_description.json metadata file as per the
       CDS which has a field to include qualified reference to other (meta)data. More
       details are provided in the
-      [CDS specification documentation](https://cds-specification.readthedocs.io/en/v0.1.0/).
+      [CDS specification documentation](https://cds-specification.readthedocs.io/en/v0.1.1/).
     </td>
   </tr>
   <tr>
@@ -311,7 +311,7 @@ The [FAIR Principles](https://doi.org/10.1038/sdata.2016.18) published in 2016 a
     <td className="align-top">
       The AI-READI dataset is structured according to the CDS, which imposes a standard
       folder structure, naming convention for directories, and metadata files that follow
-      community standards. More details are provided in the [CDS specification documentation](https://cds-specification.readthedocs.io/en/v0.1.0/).
+      community standards. More details are provided in the [CDS specification documentation](https://cds-specification.readthedocs.io/en/v0.1.1/).
       <p>
         All the data files in the AI-READI dataset are in format that meet domain-relevant
         community standards (e.g., DICOM for images). This is described in detail in the
@@ -320,7 +320,3 @@ The [FAIR Principles](https://doi.org/10.1038/sdata.2016.18) published in 2016 a
     </td>
   </tr>
 </table>
-
-import PageFeedback from '@site/src/components/PageFeedback';
-
-<PageFeedback />
diff --git a/docs/about.mdx b/docs/about.mdx
@@ -23,7 +23,3 @@ This documentation is associated with v1.0 of the dataset, which contains data f
 - The `Dataset Documentation` section includes an overall description of the dataset using the Healthsheet template, and this section also provides details about each of the data domains included in the dataset. For each data domain, we have provided a general overview of the clinical context and how the data were acquired in the study, relevant individual variables, and data processing details including file formats, data standards, metadata, and example outputs.
 - The `AI-readiness` section describes additional considerations that were integrated into the study design, including consideration of FAIR principles and Ethical practices.
 - The [`Additional resources`](additional-resources) section provides a list of resources related to the dataset that could be useful for understanding and using the dataset.
-
-import PageFeedback from '@site/src/components/PageFeedback';
-
-<PageFeedback />
diff --git a/docs/additional-resources.mdx b/docs/additional-resources.mdx
@@ -26,7 +26,3 @@ We are pleased to present several abstracts concerning work from AI-READI at the
 ## Resources citing the dataset
 
 We will add resources that cite the dataset as they become available.
-
-import PageFeedback from '@site/src/components/PageFeedback';
-
-<PageFeedback />
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -5,14 +5,48 @@ title: Changelog
 
 All notable changes to this documentation will be documented in this file.
 
-The format is based on [Keep a Changelog v1.0.0](https://keepachangelog.com/en/1.0.0/).
+## [2.0.0] - 2024-11-08
 
-## 1.0.0 (2024-04-01)
+### Identifier/Link
+
+https://doi.org/10.60775/fairhub.2
 
 ### Added
 
-- First version of the documentation associated with the AI-READI dataset v1.0
+- Data from additional 863 participants has been added.
+- OCT and OCTA scans from the Zeiss Cirrus device have been added.
+
+### Changed
+
+- v1.0.0 (pilot) data environmental sensor processing was performed manually. When upgrading to a consistent, automated process, the number of removed rows of data changed for 22 cases. More lines were removed in 18 cases comprising less than .1% of the data in each case. In 4 cases, up to 2% more rows were recovered and added to the dataset.
+- Garmin:
+  - Sleep:
+    - We have applied a standardized extension to incorporate sleep stages (awake, light, rem, deep) in the data.
+    - We updated the calories data tag from “duration” to “calories_value”:
+      - `"calories_value": { "value": X, "unit": "kcal"}`
+  - Manifest [needs to be updated in the documentations/website]:
+    - The “physical_activity_num_records” field has been renamed to “physical_activity_num_days” and the values also update respectively.
+    - Values for the “sleep_record_count” field have been updated to reflect the number of individual sleep stage records instead of the number of days.
+    - Values for the “average_sleep_hours” field have been updated with respect to the following formula:
+      - average_sleep_duration = total_sleep_duration / number_of_records
+- CGM: To ensure consistency in the body format across all wearable data files, we have updated the structure of the JSON files as follows:
+  - The "body" field now includes a section for continuous glucose monitoring (CGM) data:
+    - "body": `{ "cgm": [ ...list of observations ] }`
+- Labs OMOP mapping table replaced with updated version
+  - 2 mapping rows updated (units changed to mg/DL for Urine creatinine and Urine Albumin)
+  - 9 mapping rows added to add UCUM codes for units
+- MOCA OMOP mapping table replaced with updated version
+  - 7 mapping rows updated
+- REDCap OMOP mapping table replaced with updated version
+  - 344 mapping rows updated
+  - “value_as_concept_id,” “qualifier_concept_id,” and “qualifier_source_value” columns added to mapping table
+
+## [1.0.0] - 2024-05-03
 
-import PageFeedback from '@site/src/components/PageFeedback';
+### Identifier/Link
+
+https://doi.org/10.60775/fairhub.1
+
+### Added
 
-<PageFeedback />
+- Added data from pilot study (204 participants)
diff --git a/docs/citation.mdx b/docs/citation.mdx
@@ -5,12 +5,13 @@ title: Citation
 
 As per the [license terms](preliminary/license), if you use the AI-READI dataset or any subset of it, you must cite the following references:
 
-```
-AI-READI Consortium. (2024). Flagship Dataset of Type 2 Diabetes from the
-AI-READI Project (1.0.0) [Data set]. FAIRhub.
-https://doi.org/10.60775/fairhub.1
-```
-
-import PageFeedback from '@site/src/components/PageFeedback';
-
-<PageFeedback />
+1. ```
+   AI-READI Consortium. (2024). "AI-READI: rethinking data collection, preparation and
+   sharing for propelling AI-based discoveries in diabetes research and beyond."
+   Nature metabolism. https://doi.org/10.1038/s42255-024-01165-x
+   ```
+2. ```
+   AI-READI Consortium. (2024). Flagship Dataset of Type 2 Diabetes from the
+   AI-READI Project (2.0.0) [Data set]. FAIRhub.
+   https://doi.org/10.60775/fairhub.2
+   ```
diff --git a/docs/dataset/cardiac-ecg/cardiac-ecg.mdx b/docs/dataset/cardiac-ecg/cardiac-ecg.mdx
@@ -113,7 +113,3 @@ There is more than one protocol for obtaining and reporting ECG information. Thi
 
 - [General information on the ECG protocols and reading an ECG](https://en.wikipedia.org/wiki/Electrocardiography)
 - [Philips DXL ECG Algorithm Physician’s Guide](<https://www.documents.philips.com/doclib/enc/fetch/2000/4504/577242/577243/577246/581601/711562/DXL_ECG_Algorithm_Physician_s_Guide_(ENG)_Ed.2.pdf>) with information on the fields that are printed on an ECG report. Please note that while the guide offers insights into ECG interpretation, it does not replace medical expertise. Always consult with a physician for accurate diagnosis and treatment recommendations.
-
-import PageFeedback from '@site/src/components/PageFeedback';
-
-<PageFeedback />
diff --git a/...set/clinical-data/OMOP-Clinical-Data-Structure/OMOP-Clinical-Data-Structure.mdx b/...set/clinical-data/OMOP-Clinical-Data-Structure/OMOP-Clinical-Data-Structure.mdx
@@ -135,15 +135,10 @@ Resources to learn more about SSSOM:
 
 ### OMOP Mapping Table
 
-import StructureTable from '@site/src/components/StructureTable';
-
-<a href="/omopTable" target="_blank">See the table here</a>
+<a href="/v2-omopTable" target="_blank">
+  See the table here
+</a>
 
 ## Race, ethnicity, gender, and date/month of birth
 
 Note that the fields for race, ethnicity, gender, and date/month of birth are all coded as '0' in the person.csv file because this information is omitted from the data. Birthday has to be released with birth year only per the HIPAA law for Safe Harbor. Additionally, we have decided to remove race, ethnicity, and gender information from this public set of the AI-READI dataset to prevent stigmatizing findings. More details are available in the [healthsheet](https://docs.aireadi.org/docs/1/dataset/healthsheet) regarding which variables were removed.
-
-import PageFeedback from '@site/src/components/PageFeedback';
-
-<PageFeedback />
-
diff --git a/docs/dataset/clinical-data/OMOP-Clinical-Data-Structure/OMOP-Mapping-Table.mdx b/docs/dataset/clinical-data/OMOP-Clinical-Data-Structure/OMOP-Mapping-Table.mdx
@@ -8,6 +8,5 @@ import {Redirect} from '@docusaurus/router';
 import DirectOmopTable from '@site/src/components/DirectOmopTable';
 
 
-<!-- {/* <Redirect to="/omopTable"/>; */} -->
 <DirectOmopTable />
 
diff --git a/docs/dataset/clinical-data/clinical-lab-tests/clinical-lab-tests.mdx b/docs/dataset/clinical-data/clinical-lab-tests/clinical-lab-tests.mdx
@@ -2,7 +2,6 @@
 sidebar_position: 2
 title: Clinical Lab Tests
 ---
-import ClinicalLabTable from '@site/src/components/ClinicalLabTable';
 
 ## Overview of Data Domain
 
@@ -20,43 +19,69 @@ Clinical lab tests are a fundamental component of medical diagnostics and patien
 
 ## Variables included in Data Domain
 
-<a href="/dataDomainTable" target="_blank">See the table here</a>
+<a href="/v2-dataDomainTable" target="_blank">
+  See the table here
+</a>
 
 {/* <ClinicalLabTable /> */}
 
 #### NT-proBNP Reference Intervals
-| Age | Female Range        | Male Range      |
-| ------ | --------------- | ------------------ |
-|  0-2d  |  321-11987 | 321-11987  |
-|  3d-10d  |  263-5918 | 263-5918  |
-|  11d-1m  |  263-5918 | 263-5918  |
-| 2m-1y   | 37-646  |37-646   |
-|  2y  |  39-413 | 39-413  |
-|  3y-6y  |  23-289 | 23-289  |
-| 7y-14y   | 0-157  |0-157   |
-|  15y-18y  |  0-158 | 0-158  |
-|   19y-39y |   0-160|  0-79 |
-| 40y-44y   | 0-162  |0-72   |
-| 45y-54y   | 0-141  |0-87   |
-|  55y-64y  |  0-226 | 0-88  |
-|   65y- |   0-540|  0-540 |
 
+| Sex | Age_Low | Age_High | Range_Low | Range_High |
+|-----|---------|----------|-----------|-------------|
+| F   | 0d      | 2d       | 321       | 11987       |
+| F   | 3d      | 10d      | 263       | 5918        |
+| F   | 11d     | 1m       | 263       | 5918        |
+| F   | 2m      | 1y       | 37        | 646         |
+| F   | 2y      | 2y       | 39        | 413         |
+| F   | 3y      | 6y       | 23        | 289         |
+| F   | 7y      | 14y      | 0         | 157         |
+| F   | 15y     | 18y      | 0         | 158         |
+| F   | 19y     | 38y      | 0         | 160         |
+| F   | 40y     | 44y      | 0         | 162         |
+| F   | 45y     | 54y      | 0         | 141         |
+| F   | 55y     | 64y      | 0         | 226         |
+| F   | 65y     | 200y     | 0         | 540         |
+| M   | 0d      | 2d       | 321       | 11987       |
+| M   | 3d      | 10d      | 263       | 5918        |
+| M   | 11d     | 1m       | 263       | 5918        |
+| M   | 2m      | 1y       | 37        | 646         |
+| M   | 2y      | 2y       | 39        | 413         |
+| M   | 3y      | 6y       | 23        | 289         |
+| M   | 7y      | 14y      | 0         | 157         |
+| M   | 15y     | 18y      | 0         | 158         |
+| M   | 19y     | 38y      | 0         | 79          |
+| M   | 40y     | 44y      | 0         | 72          |
+| M   | 45y     | 54y      | 0         | 87          |
+| M   | 55y     | 64y      | 0         | 88          |
+| M   | 65y     | 200y     | 0         | 540         |
 
 #### Alkaline Phosphatase reference ranges
-| Age | Female Range        | Male Range      |
-| ------ | --------------- | ------------------ |
-|  0-9y  | 111-281 | 115-324|
-|  10y-11y  | 132-366 | 115-324|
-|  12y-13y |  89-285 | 119-426|
-| 14y-17y  | 43-226  |72-400|
-|  18y-24y  | 26-98 | 42-136|
-| 25y-34y  | 25-100 | 35-109|
-| 35y-44y   |25-112  |36-122|
-|  45y-54y  | 34-121 | 39-139|
-|   55y-64y |  31-132|  37-159|
-| 65y-74y  | 38-172  |36-161|
-| 75y-   |49-199  |52-227|
 
+| Sex | Age_Low | Age_High | Range_Low | Range_High |
+|-----|---------|----------|-----------|-------------|
+| F   | 0y      | 9y       | 111       | 281         |
+| F   | 10y     | 11y      | 132       | 366         |
+| F   | 12y     | 13y      | 89        | 285         |
+| F   | 14y     | 17y      | 43        | 226         |
+| F   | 18y     | 24y      | 26        | 98          |
+| F   | 25y     | 34y      | 25        | 100         |
+| F   | 35y     | 44y      | 25        | 112         |
+| F   | 45y     | 54y      | 34        | 121         |
+| F   | 55y     | 64y      | 31        | 132         |
+| F   | 65y     | 74y      | 38        | 172         |
+| F   | 75y     | 200y     | 49        | 199         |
+| M   | 0y      | 9y       | 115       | 324         |
+| M   | 10y     | 11y      | 115       | 324         |
+| M   | 12y     | 13y      | 119       | 426         |
+| M   | 14y     | 17y      | 72        | 400         |
+| M   | 18y     | 24y      | 42        | 136         |
+| M   | 25y     | 34y      | 35        | 109         |
+| M   | 35y     | 44y      | 36        | 122         |
+| M   | 45y     | 54y      | 39        | 139         |
+| M   | 55y     | 64y      | 37        | 159         |
+| M   | 65y     | 74y      | 36        | 161         |
+| M   | 75y     | 200y     | 52        | 227         |
 
 ## Data Processing
 
@@ -138,7 +163,3 @@ print(‘ Data saved to hba1c.csv')
 | value_source_value            | Source value for the measurement value      | 65                          | 5.7                 |
 | measurement_event_id          | Unique identifier for the measurement event | 0                           | 0                   |
 | meas_event_field_concept_id   | Concept ID for the measurement event field  | 0                           | 0                   |
-
-import PageFeedback from '@site/src/components/PageFeedback';
-
-<PageFeedback />
diff --git a/docs/dataset/clinical-data/cognition-MoCA/Cognition-MoCA-Table.mdx b/docs/dataset/clinical-data/cognition-MoCA/Cognition-MoCA-Table.mdx
@@ -0,0 +1,11 @@
+---
+sidebar_position: 2
+title: MoCA Table
+---
+
+
+import {Redirect} from '@docusaurus/router';
+import DirectCognitionMoCA from '@site/src/components/DirectCognitionMoCA';
+
+<DirectCognitionMoCA />
+
diff --git a/docs/dataset/clinical-data/cognition-MoCA/_category_.json b/docs/dataset/clinical-data/cognition-MoCA/_category_.json
@@ -0,0 +1,4 @@
+{
+  "label": "Cognition MoCA",
+  "position": 6
+}
Original file line number	Diff line number	Diff line change
Expand Up		@@ -8,6 +8,5 @@ import {Redirect} from '@docusaurus/router';
		import DirectOmopTable from '@site/src/components/DirectOmopTable';


		<!-- {/* <Redirect to="/omopTable"/>; */} -->
		<DirectOmopTable />