Updates to AMP-AD documentation, including adding general process ove…

…rview (#339)

* Add general process overview and a little more language

* Title case

* Remove html file and add this type of file to gitignore

* Add description of Instructions topic

.gitignore

@@ -9,3 +9,4 @@ restart.txt
 scratch.R
 inst/doc
 inst/*.md
+inst/*.html

inst/using-the-dccvalidator-app-amp-ad.Rmd

@@ -26,7 +26,7 @@ and shared more easily and quickly.
 
 The application can be found at https://shinypro.synapse.org/users/kwoo/dccvalidator-app/
 
-# Instructions
+# Requirements
 
 To use this application you must:
 
@@ -38,7 +38,26 @@ Some portions of the app submit data to Synapse. This allows curators at Sage to
 troubleshoot issues if needed; no one outside the Sage curation team will be
 able to download the data.
 
-## Documentation upload
+# Instructions
+
+This topic has a general overview of the data contribution process and
+detailed instructions for each step, including uploading documentation, metadata
+requirements, validating and reviewing the metadata, and uploading the dataset.
+
+## General Process Overview
+
+1. Contact the AMP-AD team to discuss the study and the expected data. Receive
+staging folder synIDs for each expected dataset.
+2. Upload documentation and validate metadata + manifest files in [dccvalidator](https://shinypro.synapse.org/users/kwoo/dccvalidator-app/).
+3. Contact the AMP-AD team when all files pass validation. The team will verify
+items not checked by the dccvalidator. Receive permissions to upload data to the
+staging folder.
+4. Use the validated manifest to upload the data with `syncToSynapse` (see
+[Synapse documentation](https://docs.synapse.org/articles/uploading_in_bulk.html) for uploading data in bulk).
+5. Contact the AMP-AD team. The team will do the final verifications before
+releasing the data.
+
+## Documentation Upload
 
 Each study in AMP-AD has accompanying [documentation in the portal](https://adknowledgeportal.synapse.org/#/Explore/Studies?Study=syn8391648).
 You can submit your documentation through the dccvalidator app on the
@@ -48,24 +67,25 @@ a single file, or you can upload multiple files to the assay description
 section.
 ![A screenshot of a website with instructions on how to provide documentation of a study, and a space to upload documentation files](../man/figures/amp-documentation.png)
 
-## Data validation
+## Data Validation
 
-### Metadata requirements
+### Metadata Requirements
 
 Each study should include metadata that would help a new researcher understand
 and reuse the data. In most cases, we will expect 4 files:
 
-1. **Individual metadata** describing each individual in the study
-2. **Biospecimen metadata** describing the specimens that were collected
-3. **Assay metadata** describing the assay that was performed. If multiple
+1. **Individual metadata** a csv file describing each individual in the study.
+2. **Biospecimen metadata** a csv file describing the specimens that were collected.
+3. **Assay metadata** a csv file describing the assay that was performed. If multiple
    assays were part of the study, there will be one assay file for each.
 4. A **manifest** listing each file that will be uploaded. You will use this
-   file to upload your data after it has been validated and approved.
+   file to upload your data after it has been validated and approved. The manifest
+   should be in tsv (tab-delimited text) format.
 
 We provide templates for all of the metadata files within the portal:
 https://www.synapse.org/#!Synapse:syn18512044
 
-You can download these files, fill out the first tab, and save it as a .csv
+You can download these files, fill out the first tab, and save it as a .csv or .tsv
 file. The other tabs exist to describe the variables and allowed values in the
 template. If you do not have any data for some of the columns, you can leave
 them blank (but do not remove the column header).
@@ -74,7 +94,7 @@ If you don't see a template for the assay(s) in your study, or if not all of the
 metadata types above seem relevant to your study, please get in touch with us at
 [email protected].
 
-### Validating metadata
+### Validating the Metadata and Manifest
 
 The data validation portion of the app allows you to upload metadata files (as
 .csv) and the manifest (as .tsv or .txt) and view the results of a series of
@@ -89,14 +109,16 @@ Examples of the types of checks we perform are:
 ![A screenshot showing three boxes on a webpage. Each box depicts successes, warnings, or failures that occurred when validating the data](../man/figures/amp-results.png)
 ![A screenshot showing three boxes on a webpage. Each box depicts successes, warnings, or failures that occurred when validating the data. Some of the failures have additional information describing the source of the problem.](../man/figures/amp-results-details.png)
 
-### Viewing data summary
+### Viewing Data Summary
 
 We also provide a summary of the files you have uploaded, showing the number of
 individuals, specimens, and files. We visualize the data in each column by its
 data type to help spot unexpected missing values.
+
 ![A screenshot showing a summary of several data files uploaded, including how many specimens, individuals, and data files were included, and a breakdown of the types of data in the file](../man/figures/amp-summary.png)
 
-## Uploading data
+
+## Uploading Data
 
 Once data has passed validation, and the AMP-AD data curators permit edit
 permissions to the staging folder for your study, you will use your newly