Skip to content

Commit

Permalink
updating collections doc
Browse files Browse the repository at this point in the history
  • Loading branch information
@crisaless
crisaless committed Jun 24, 2024
1 parent 3137658 commit 1c65ccb
Show file tree
Hide file tree
Showing 3 changed files with 166 additions and 23 deletions.
185 changes: 164 additions & 21 deletions docs/_docs/3_submitting_data/Submitting-Data-Collections.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,22 @@ We also have the following training materials available:

## Table of Contents

TBD
## Table of Contents

- [1. Joining the Globus Group](#1-joining-the-globus-group)
- [2. What is a Collection?](#2-what-is-a-collection)
- [2.1 Overview for creating a Collection](#21-overview-for-creating-a-collection)
- [3. Submit Metadata Fields](#3-submit-metadata-fields)
- [3.1 Fields for Collection Metadata](#31-fields-for-collection-metadata)
- [4. Link to Publications](#4-link-to-publications)
- [4.1 Fields for Publication Records](#41-fields-for-publication-records)
- [5. Provide Protocols and Contributors](#5-provide-protocols-and-contributors)
- [5.1 Link to Protocols](#51-link-to-protocols)
- [5.2 Add Contributors](#52-add-contributors)
- [6. Link to your data records](#6-link-to-your-data-records)
- [7. Reviewing and Submitting Data Collections](#7-reviewing-and-submitting-data-collections)
- [8. Deleting Data Collections](#8-deleting-data-collections)


## 1. Joining the Globus Group

Expand Down Expand Up @@ -53,39 +68,76 @@ Some common use cases include:

Adding data Collections involves the following steps:

* [**Submit metadata**](#). When you first create a Collection record, you will fill out a form to submit metadata about the data described by this Collection.
* [**Submit metadata**](#3-submit-metadata-fields). When you first create a Collection record, you will fill out a form to submit metadata about the data described by this Collection.

* [**Link to your publication**](#).
* [**Link to your publication**](#4-link-to-publications). Link to the publication related to the data in this collection. If this collection is for other sharing purposes, this is not required.

* [**Link to protocols and contributors**](#). To provide more complete transparency, reproducibility and provenance, you will link to the protocols used to capture the data in this collection and document the people who handled the data.
* [**Provide protocols and contributors**](#5-provide-protocols-and-contributors). To provide more complete transparency, reproducibility and provenance, you will link to the protocols used to capture the data in this collection and document the people who handled the data.

* [**Link the data records**](#). This is where you connect the Collection to the data records you are organizing.
* [**Link toy our data records**](#6-link-to-your-data-records). This is where you connect this Collection to the data records you are organizing.


## 3. Submit Metadata Fields

* [Use this link to log in and create a Collection](https://staging.atlas-d2k.org/chaise/recordedit/#2/Common:Collection?pcid=navbar/recordedit&ppid=22tx2me522k42d4f1ung2rpx). Alternatively, from atlas-d2k.org,:
- In the top-level menu, click *Internal*, then *Data Collections*.
* [Use this link to log in and create a Collection](https://www.atlas-d2k.org/chaise/recordedit/#2/Common:Collection). Alternatively, from atlas-d2k.org,:
- In the top-level menu, click *Internal*, then *Data Collections*, OR
- From a "Collection" page, you can also click the `Create` button (you must be logged in to see this button).

* At a minimum, fill out the essential fields marked with a red asterisk (*). However, filling out more fields enhances data discoverability.

* Upon completion, click `Save`.

![Screenshot of the Create Collection form]({{ "/assets/wiki_images/submitting-data/TBD.png" | relative_url }})
![Screenshot of the Create Collection form]({{ "/assets/wiki_images/submitting-data/create-collections-record-form.png" | relative_url }})

### 3.1. Fields for Collection Metadata

| Field | Description | Required or Optional |
|------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------|
| Title | Provide the title of the Collection (this could be the title of your publication) | Required |
| Description | Provide a useful description of the Collection (for example this could be the abstract of your publication) | Required |
| Details | Use this field if there are other details you'd like to include. | Optional |
| Require DOI? | This indicates to the Hub to generate a DOI for this Collection. Highly recommended for citing in your publication. | Optional |
| Curation Status | Indicates if this record is still being worked on, is being reviewed, is embargoed until publication or has been released to the public. For a complete description of the Curation Process, click here.](../curation-workflow/) | Required |
| Principal Investigator | Use the primary Principal Investigator for this collection of data. You may only indicate one PI. | Required |
| Data Provider | Use the institution of the Principle Investigator. | Required |
| Consortium | Indicate the Consortium (GUDMAP, RBK, etc). | Required |
<table>
<tr>
<th>Field</th>
<th>Description</th>
<th>Required or Optional</th>
</tr>
<tr>
<td class="required">Title</td>
<td>Provide the title of the Collection (this could be the title of your publication)</td>
<td class="required">Required</td>
</tr>
<tr>
<td class="required">Description</td>
<td>Provide a useful description of the Collection (for example this could be the abstract of your publication)</td>
<td class="required">Required</td>
</tr>
<tr>
<td>Details</td>
<td>Use this field if there are other details you'd like to include.</td>
<td>Optional</td>
</tr>
<tr>
<td>Require DOI?</td>
<td>This indicates to the Hub to generate a DOI for this Collection. Highly recommended for citing in your publication.</td>
<td>Optional</td>
</tr>
<tr>
<td class="required">Curation Status</td>
<td>Indicates if this record is still being worked on, is being reviewed, is embargoed until publication or has been released to the public. For a complete description of the curation process, see <a href="../curation-workflow/">Curation Workflow</a></td>
<td class="required">Required</td>
</tr>
<tr>
<td class="required">Principal Investigator</td>
<td>Use the primary Principal Investigator for this collection of data. You may only indicate one PI.</td>
<td class="required">Required</td>
</tr>
<tr>
<td class="required">Data Provider</td>
<td>Use the institution of the Principle Investigator.</td>
<td class="required">Required</td>
</tr>
<tr>
<td class="required">Consortium</td>
<td>Indicate the Consortium (GUDMAP, RBK, etc).</td>
<td class="required">Required</td>
</tr>
</table>

Once you have saved the form, you will see a new Collection record much like the following example:

Expand All @@ -103,7 +155,98 @@ Otherwise, click the `Create new` button and fill out the fields with informatio

### 4.1 Fields for Publication Records:

TBD
<table>
<tr>
<th>Field</th>
<th>Description</th>
<th>Required/Optional</th>
</tr>
<tr>
<td class="required">Title</td>
<td>Title of the publication</td>
<td class="required">Required</td>
</tr>
<tr>
<td>Authors list</td>
<td>List of authors, as they appear in the publication.</td>
<td>Optional</td>
</tr>
<tr>
<td>Abstract</td>
<td>Abstract of the publication</td>
<td>Optional</td>
</tr>
<tr>
<td class="required">Publication venue</td>
<td>Name of the journal or publication venue. If this is not available, you may click <code class="language-plaintext highlighter-rouge">Create new</code> to add an entry for the venue.</td>
<td class="required">Required</td>
</tr>
<tr>
<td>Month</td>
<td>Publication month</td>
<td>Optional</td>
</tr>
<tr>
<td class="required">Year</td>
<td>Publication year.</td>
<td class="required">Required</td>
</tr>
<tr>
<td>Volume</td>
<td>Journal volume.</td>
<td>Optional</td>
</tr>
<tr>
<td>Issue</td>
<td>Journal issue.</td>
<td>Optional</td>
</tr>
<tr>
<td>Pages</td>
<td>The pages where the publication appears.</td>
<td>Optional</td>
</tr>
<tr>
<td>PubMed ID</td>
<td>The PubMed ID of the publication.</td>
<td>Optional</td>
</tr>
<tr>
<td>DOI</td>
<td>The DOI reference.</td>
<td>Optional</td>
</tr>
<tr>
<td>URI</td>
<td>Link from which the publication may be downloaded.</td>
<td>Optional</td>
</tr>
<tr>
<td>Publisher Item Identifier</td>
<td>A unique identifier, used by scientific journal publishers, to identify documents.</td>
<td>Optional</td>
</tr>
<tr>
<td>File URL</td>
<td>Use this field to upload a PDF of the publication.</td>
<td>Optional</td>
</tr>
<tr>
<td class="required">Curation Status</td>
<td>Keep the default value of Submitted.</td>
<td class="required">Required</td>
</tr>
<tr>
<td class="required">Principal Investigator</td>
<td>The lead principal investigator of the publication.</td>
<td class="required">Required</td>
</tr>
<tr>
<td class="required">Consortium</td>
<td>Indicate GUDMAP or RBK.</td>
<td class="required">Required</td>
</tr>
</table>

## 5. Provide Protocols and Contributors

Expand Down Expand Up @@ -135,7 +278,7 @@ Once the base Collection record is created, now you can add the related data. To
-->
* Click _Save_ to add them to the Collection record.

## 3. Reviewing and Submitting Data Collections
## 7. Reviewing and Submitting Data Collections

Here is how to find your project's data with a Curation Status of "In Preparation":

Expand All @@ -149,7 +292,7 @@ Here is how to find your project's data with a Curation Status of "In Preparatio

* When your record is approved internally, change _Curation Status_ to _Submitted_ to send it to the Hub (click here for the full [Curation Workflow](/docs/curation-workflow)).

## 4. Deleting Data Collections
## 8. Deleting Data Collections

Before you can delete the base Collection record, you need to unlink any data records associated with it.

Expand Down
4 changes: 2 additions & 2 deletions docs/_docs/3_submitting_data/Submitting-Specimen-Data.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -161,7 +161,7 @@ An example of such a hierarchy is if an original tissue sample (Specimen A) is d
</tr>
<tr>
<td class="required">Curation Status</td>
<td>The default value is In Preparation which means this record is in draft mode and will only be viewable by other Consortium members who are logged in. For more information, see Curation Workflow.</td>
<td>The default value is In Preparation which means this record is in draft mode and will only be viewable by other Consortium members who are logged in. For more information, see <a href="../curation-workflow/">Curation Workflow</a>.</td>
<td class="required">Required</td>
</tr>
<tr>
Expand Down Expand Up @@ -243,7 +243,7 @@ Otherwise, click the `Create new` button and fill out the fields with informatio
</tr>
<tr>
<td class="required">Publication venue</td>
<td>Name of the journal or publication venue. If this is not available, you may click `Create new` to add an entry for the venue.</td>
<td>Name of the journal or publication venue. If this is not available, you may click <code class="language-plaintext highlighter-rouge">Create new</code> to add an entry for the venue.</td>
<td class="required">Required</td>
</tr>
<tr>
Expand Down
Binary file added docs/assets/wiki_images/submitting-data/create-collections-record-form.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.

0 comments on commit 1c65ccb

Please sign in to comment.