diff --git a/docs/_docs/3_submitting_data/Submitting-Data-Collections.md b/docs/_docs/3_submitting_data/Submitting-Data-Collections.md index 56ff92a..e1a5abb 100644 --- a/docs/_docs/3_submitting_data/Submitting-Data-Collections.md +++ b/docs/_docs/3_submitting_data/Submitting-Data-Collections.md @@ -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 @@ -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 | + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldDescriptionRequired or Optional
TitleProvide the title of the Collection (this could be the title of your publication)Required
DescriptionProvide a useful description of the Collection (for example this could be the abstract of your publication)Required
DetailsUse 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 StatusIndicates 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 Curation WorkflowRequired
Principal InvestigatorUse the primary Principal Investigator for this collection of data. You may only indicate one PI.Required
Data ProviderUse the institution of the Principle Investigator.Required
ConsortiumIndicate the Consortium (GUDMAP, RBK, etc).Required
Once you have saved the form, you will see a new Collection record much like the following example: @@ -103,7 +155,98 @@ Otherwise, click the `Create new` button and fill out the fields with informatio ### 4.1 Fields for Publication Records: -TBD + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldDescriptionRequired/Optional
TitleTitle of the publicationRequired
Authors listList of authors, as they appear in the publication.Optional
AbstractAbstract of the publicationOptional
Publication venueName of the journal or publication venue. If this is not available, you may click Create new to add an entry for the venue.Required
MonthPublication monthOptional
YearPublication year.Required
VolumeJournal volume.Optional
IssueJournal issue.Optional
PagesThe pages where the publication appears.Optional
PubMed IDThe PubMed ID of the publication.Optional
DOIThe DOI reference.Optional
URILink from which the publication may be downloaded.Optional
Publisher Item IdentifierA unique identifier, used by scientific journal publishers, to identify documents.Optional
File URLUse this field to upload a PDF of the publication.Optional
Curation StatusKeep the default value of Submitted.Required
Principal InvestigatorThe lead principal investigator of the publication.Required
ConsortiumIndicate GUDMAP or RBK.Required
## 5. Provide Protocols and Contributors @@ -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": @@ -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. diff --git a/docs/_docs/3_submitting_data/Submitting-Specimen-Data.md b/docs/_docs/3_submitting_data/Submitting-Specimen-Data.md index a964719..a992d89 100644 --- a/docs/_docs/3_submitting_data/Submitting-Specimen-Data.md +++ b/docs/_docs/3_submitting_data/Submitting-Specimen-Data.md @@ -161,7 +161,7 @@ An example of such a hierarchy is if an original tissue sample (Specimen A) is d Curation Status - 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. + 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. Required @@ -243,7 +243,7 @@ Otherwise, click the `Create new` button and fill out the fields with informatio Publication venue - Name of the journal or publication venue. If this is not available, you may click `Create new` to add an entry for the venue. + Name of the journal or publication venue. If this is not available, you may click Create new to add an entry for the venue. Required diff --git a/docs/assets/wiki_images/submitting-data/create-collections-record-form.png b/docs/assets/wiki_images/submitting-data/create-collections-record-form.png new file mode 100644 index 0000000..96df1a8 Binary files /dev/null and b/docs/assets/wiki_images/submitting-data/create-collections-record-form.png differ