Merge branch 'stable' into c2m2preview

nih-cfde · Sep 8, 2023 · 778777f · 778777f
2 parents 24f1d89 + 57b57b2
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diff --git a/.github/workflows/update_C2M2_stable.yml b/.github/workflows/update_C2M2_stable.yml
@@ -32,4 +32,4 @@ jobs:
               [1]: https://github.com/peter-evans/create-pull-request
             labels: proposedc2m2update
             branch: update-c2m2
-            reviewers: Acharbonneau, abradyIGS
+            reviewers: jonathancrabtree, raynamharris
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,25 +1,19 @@
-# .readthedocs.yml
-# Read the Docs configuration file
+# Read the Docs configuration file for MkDocs projects
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 # Required
 version: 2
 
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
 
-# Build documentation with MkDocs
 mkdocs:
   configuration: mkdocs.yml
 
-# Optionally build your docs in additional formats such as PDF
-formats:
-  - pdf
-
-# Optionally set the version of Python and requirements required to build your docs
+# Optionally declare the Python requirements required to build your docs
 python:
-  version: 3.7
   install:
-    - requirements: requirements.txt
-
-submodules:
-  include: all
-  recursive: true
+  - requirements: requirements.txt
diff --git a/docs/about/about.md b/docs/about/about.md
@@ -5,6 +5,6 @@ hide:
    - toc
 ---
 
-The Common Fund Data Ecosystem (CFDE) is developing an online portal that will allow researchers to access and work across multiple Common Fund (CF) program data sets within a digital cloud environment. CF programs generate a wide range of diverse and valuable data sets designed to be used by the research community to accelerate discovery. However, these data sets reside in different locations and it is challenging or even impossible to work with multiple data sets in an accessible and user-friendly way. The CFDE portal will help remedy this problem by creating a shared resource that helps make CF data sets FAIR (Findable, Accessible, Interoperable, and Reusable) and enables researchers to ask scientific and clinical questions from a single access point.
+The Common Fund Data Ecosystem (CFDE) is developing an online portal that allows researchers to access and work across multiple Common Fund (CF) program datasets within a digital cloud environment. CF programs generate a wide range of diverse and valuable datasets designed to be used by the research community to accelerate discovery. However, these datasets reside in different locations and it is challenging or even impossible to work with multiple datasets in an accessible and user-friendly way. The CFDE portal helps to remedy this problem by creating a shared resource that makes CF datasets FAIR (Findable, Accessible, Interoperable, and Reusable) and enables researchers to ask scientific and clinical questions from a single access point.
 
-The CFDE Coordinating Center oversees CFDE activities and works closely with participating CF data coordinating centers to include an initial subset of CF data sets, with plans to expand to additional data sets in the future. The CFDE portal will also develop and deploy a number of resources and tools, including training materials that will be created to empower the research community to use CF data sets for novel scientific research that was not possible before. This may include hypothesis generation, discovery, or validation that leads to new insights in health and disease.
+The CFDE Coordinating Center oversees CFDE activities and works closely with participating CF data coordinating centers (DCCs) to include an initial set of CF datasets, with plans to expand to additional datasets in the future. The CFDE portal will also develop and deploy a number of resources and tools, including training materials that will be created to empower the research community to use CF datasets for novel scientific research that was not possible before. This may include hypothesis generation, discovery, or validation that leads to new insights in health and disease.
diff --git a/docs/about/portalguide.md b/docs/about/portalguide.md
diff --git a/docs/cfde-submit b/docs/cfde-submit
diff --git a/docs/images/Biosample_Data_Browser_v3.png b/docs/images/Biosample_Data_Browser_v3.png
diff --git a/docs/images/Collection_Data_Browser_v2.png b/docs/images/Collection_Data_Browser_v2.png
diff --git a/docs/images/Data_Type_Facet_v2.png b/docs/images/Data_Type_Facet_v2.png
diff --git a/docs/images/Export_Options_v2.png b/docs/images/Export_Options_v2.png
diff --git a/docs/images/File_Count_by_CF_Program_Chart_v2.png b/docs/images/File_Count_by_CF_Program_Chart_v2.png
diff --git a/docs/images/File_Data_Browser_v3.png b/docs/images/File_Data_Browser_v3.png
diff --git a/docs/images/Generic_Dashboard_v2.png b/docs/images/Generic_Dashboard_v2.png
diff --git a/docs/images/ID_Namespace_Data_Browser_v3.png b/docs/images/ID_Namespace_Data_Browser_v3.png
diff --git a/docs/images/Login.png b/docs/images/Login.png
diff --git a/docs/images/Login_CFDE.png b/docs/images/Login_CFDE.png
diff --git a/docs/images/My_Profile.png b/docs/images/My_Profile.png
diff --git a/docs/images/Personal_Collection_Add_File.png b/docs/images/Personal_Collection_Add_File.png
diff --git a/docs/images/Personal_Collection_Data_Browser.png b/docs/images/Personal_Collection_Data_Browser.png
diff --git a/docs/images/Personal_Collection_Data_Browser_Add.png b/docs/images/Personal_Collection_Data_Browser_Add.png
diff --git a/docs/images/Personal_Collection_Home.png b/docs/images/Personal_Collection_Home.png
diff --git a/docs/images/Personal_Collection_Update.png b/docs/images/Personal_Collection_Update.png
diff --git a/docs/images/Personalized_Dashboard_Chart_v2.png b/docs/images/Personalized_Dashboard_Chart_v2.png
diff --git a/docs/images/Portal_Home_1_2023.png b/docs/images/Portal_Home_1_2023.png
diff --git a/docs/images/Primary_DCC_Contact.png b/docs/images/Primary_DCC_Contact.png
diff --git a/docs/images/Project_Data_Browser_v3.png b/docs/images/Project_Data_Browser_v3.png
diff --git a/docs/images/Samples_by_Anatomy_Chart_v2.png b/docs/images/Samples_by_Anatomy_Chart_v2.png
diff --git a/docs/images/Saved_Search_Button.png b/docs/images/Saved_Search_Button.png
diff --git a/docs/images/Search_by_Data_Type_v2.png b/docs/images/Search_by_Data_Type_v2.png
diff --git a/docs/images/Subject_Data_Browser_v3.png b/docs/images/Subject_Data_Browser_v3.png
diff --git a/docs/images/Subjects_by_Assay_Chart_v2.png b/docs/images/Subjects_by_Assay_Chart_v2.png
diff --git a/docs/images/Summary_View_Chart.png b/docs/images/Summary_View_Chart.png
diff --git a/docs/images/View_Details_v2.png b/docs/images/View_Details_v2.png
diff --git a/docs/index.md b/docs/index.md
@@ -3,11 +3,11 @@ layout: default
 title: Home
 ---
 
-# Welcome to the Documentation for the CFDE
+# Welcome to the CFDE Documentation
 
-The goal of Common Fund Data Ecosystem (CFDE) is to federate data from Common Fund Data Coordinating Centers (DCCs) to improve access to data derived from hundreds of studies and samples collected from thousands of human subjects. This project involves a diversity of datatypes has been generated at the genomic, expression, proteomic, metagenomic, and imaging levels, and the DCCs support a tremendous range of scientific discovery efforts.
-To facilitate this task, the CFDE has developed and refined software tools. To view documentation for these tools, please select from the following:
+The goal of the Common Fund Data Ecosystem (CFDE) is to federate data from Common Fund Data Coordinating Centers (DCCs) to improve access to data derived from hundreds of studies and samples collected from thousands of human subjects. This project involves diverse datatypes that have been generated at the genomic, expression, proteomic, metagenomic, and imaging levels, and the contributing DCCs support a tremendous range of scientific discovery efforts.
+To facilitate the task of federating the DCCs' data, the CFDE has developed and refined software tools. To view documentation for these tools, please select from the following:
 
-- The [Crosscut Metadata Model](./c2m2/draft-C2M2_specification/README.md) (C2M2) documentation provides a flexible standard for describing biomedical experimental data.
+- The [Crosscut Metadata Model](./c2m2/draft-C2M2_specification/README.md) (C2M2) provides a flexible standard for describing biomedical experimental data.
 - The [Datapackage Submission System](./cfde-submit/docs/index.md) documentation describes how Common Fund metadata is submitted to the [CFDE Search Portal](https://app.nih-cfde.org/). For help with submissions, you can also check the [wiki](https://github.com/nih-cfde/published-documentation/wiki), search common errors in the [discussion board](https://github.com/nih-cfde/published-documentation/discussions), or read the [CFDE Portal User Guide](./about/portalguide/). 
-- The [FAIR cookbook](./the-fair-cookbook/intro.md) provides introductory materials about various aspects of FAIRness, including practical guides that show how to enhance digital objects by adhering them to community accepted standards.
+- The [FAIR cookbook](./the-fair-cookbook/intro.md) provides introductory materials about various aspects of FAIRness, including practical guides that show how to enhance digital objects by adhering to community accepted standards.