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6 === About Annotations and Metadata Schemas ===
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8 Metadata annotations are pieces of code defined by a Dataset author to describe and represent what's inside the Dataset in a machine-readable structure that can be used by search and query engines to facilitate future discovery and reuse by the research community.  Adding metadata annotations does not change the actual content of the data itself.
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10 Certain research communities have launched initiatives to develop standard metadata annotation schemas for specific scientific research domains.  One example is the **open** **M**etadata **I**nitiative for **N**euroscience **D**ata **S**tructures ([[openMINDS>>https://github.com/HumanBrainProject/openMINDS]]// ) //schema supported by the Human Brain Project and EBRAINS.  Where no such domain-specific standards exist, generic metadata models can be used, such as the **DA**ta **T**ag **S**uite ([[DATS>>https://www.nature.com/articles/sdata201759]]) model. 
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12 Annotating your Dataset with a metadata schema enables Dataset findability in the VRE Knowledge Graph. The VRE provides several options for researchers to annotate their Datasets:
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14 1. [[VRE Default Schema>>||anchor="vre-default"]] is interoperable with OpenMINDS and DATS models and can represent a wide range of research domains.
15 1. [[VRE Custom Schemas>>||anchor="vre-custom"]] are flexible schemas whose elements are defined entirely by you.
16 1. [[Supported external schemas >>||anchor="vre-external"]]allow researchers to upload predefined supported* standard metadata schemas in JSON format. //*Currently, the [[EBRAINS openMINDS>>https://github.com/HumanBrainProject/openMINDS]] schema is supported.//
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18 Changes to your Dataset's metadata are tracked and can be viewed in the [[Activity Stream>>doc:Main.user_guide.Working with Datasets.Data Explorer.WebHome]].  When new versions of your Dataset are released, any metadata that has been defined for your Dataset at the time of release will be stored and will be available to download as part of that version.
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23 === VRE Schemas ===
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25 {{id name="vre-default"/}}
26
27 ==== VRE Schema ====
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29 The **VRE Schema **is a collection of metadata schema templates that a Dataset creator can use to annotate their Datasets and make them findable in the VRE Knowledge Graph.  The //Essential// schema stores the key mandatory information - title, code, authors, and description - collected during the [[creation of a new dataset>>doc:Main.user_guide.Working with Datasets.Dataset Creation.WebHome]].  If desired, you can use the additional metatadata fields in the VRE Schema to describe your dataset in greater detail.
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31 The metadata schema templates in the VRE Schema are listed below.  Complete field descriptions for these metadata schemas can be viewed in the [[VRE Schema Description>>doc:Main.user_guide.Working with Datasets.VRE Schema.WebHome]].
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33 * **Essential** - basic information about the Dataset, including the information collected at the time of Dataset creation.
34 ** Title
35 ** Dataset Code
36 ** Type
37 ** Authors
38 ** Description
39 ** Modality
40 ** Collection Method
41 ** License
42 ** Number of Subjects
43 ** Dataset Identifier
44 ** Dataset Identifier Source
45 * **Subjects** - information about each data subject in the Dataset (nested/repeating entries)
46 ** Subject ID
47 ** Subject Sex
48 ** Subject Species
49 ** Subject Age Category
50 * **Disease** - information about the disease condition
51 ** Disease Name
52 ** Disease Diagnosis Date
53 ** Disease Status
54 ** Identifier
55 ** Identifier Source
56 * **Distribution** - Information about the Dataset's distribution properties (format, web URL, authorization)
57 ** Dataset Distribution Access Landing Page
58 ** Dataset Distribution Technical Format
59 ** Dataset Distribution Access Authorization
60 * **Contributors - **Information about the persons or organizations who contributed to the dataset.
61 ** **Person: **Name/email address of Dataset creators
62 ** **Organization** - Name and abbreviation of a contributing organization
63 * **Grant **- Information about the grant that supported the work reported by the Dataset.
64 ** Grant Name
65 ** Grant Funder (Person or Organization), and applicable information about each.
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67 {{id name="vre-custom"/}}
68
69 ==== Custom Schema ====
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71 If you would like to annotate your Dataset with information that is not listed in the VRE Schemas, you can define a **Custom Schema **template.  You will be able to create your own unique fields, designate each field as required or optional, and then save the template for you to fill out with your annotations. 
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73 Field types that are available in the Custom Schema template include:
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75 * Text
76 * Multiple Choice
77 * Numeric
78 * Date
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80 How to create a Custom Schema template
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82 1. Open the Datasets feature from the top VRE menu bar, then navigate to your Dataset.
83 1. Click the **Metadata **tab. Under //Existing Schemas// click **VRE Schemas.**
84 1. In the Schemas section on the right panel, click in the **Select schema to complete **dropdown menu and select **+ Create Custom Schema.**
85 1. Enter a //Template Name//
86 1. Click **Add field** to create a new field:
87 1*. Select a //Type// (text, multiple choice, numeric, date)
88 1*. Enter a// Title// for the field
89 1*. If //Type// was Multiple Choice, define the accepted //Values// (hit Enter after each entry).
90 1*. Check the //Optional// box if the field is not a required annotation for your Dataset.
91 1. Click the green checkmark to save the new field, or the red X to remove the field.
92 1. Repeat steps 5-6 until all fields have been added.
93 1. Click **Submit **to save your new custom schema template.
94 1. To add more fields to your VRE Custom Schema Template after it has been saved and annotated, navigate to //Existing Schema //(left panel of the Metadata tab) and select your Custom schema from the //Existing Schema //list. Click the "eye" icon to view the Schema In the right //Schemas //panel, then click **Manage Template.**
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96 {{warning}}
97 **Note: **Once a custom schema template has been saved, new fields may be added to the template but existing fields cannot be edited or removed. 
98 {{/warning}}
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103 ==== How to annotate your dataset using VRE Default or Custom Schema templates ====
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105 1. Open the Datasets feature from the top VRE menu bar, then navigate to your Dataset.
106 1. Click the **Metadata **tab. Under //Existing Schemas// click **VRE Schemas**
107 1. In the Schemas section on the right panel, click in the **Select schema to fill **dropdown menu and select one of the VRE default schema templates or a Custom Schema created by you.
108 1. Enter the requested fields. For complete field descriptions of the VRE Schema, see [[VRE Schema Description>>doc:Main.user_guide.Working with Datasets.6\.6 VRE Metadata Fields Description.WebHome]].
109 1. Click **Save as Draft **to save the annotations and return later (this option can be used if not all required fields have been filled out).
110 1. Cick **Submit **to save the schema to your Dataset. 
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112 To view the metadata entries on your Dataset:
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114 * navigate to //Existing Schema //(left panel of the Metadata tab)
115 * select **VRE Schemas**.
116 * Click the schema name, then click the "eye" icon.
117 * The entries can be viewed in //Schemas// (right panel or metadata tab). You can make changes to any schema's metadata entries by selecting the schema from the dropdown list and clicking **Edit**.
118 * //Note: T//he metadata viewing function in the Existing Schema panel is unavailable while a Custom Schema Template is being created or edited in the Schemas panel, and the "eye" icon turns grey.
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120 To make changes to the existing metadata entries on your Dataset:
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122 * You can make changes to a VRE Default or Custom Schema's metadata entries by selecting the schema from the dropdown list and clicking **Edit**.
123 * Make the desired changes, then click **Update** to save.
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127 {{id name="vre-external"/}}
128
129 === Supported External Schemas ===
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131
132 ==== openMINDS Schema ====
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135 [[image:openMINDS_logo.png||height="50" width="100"]]
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138 The[[ open Metadata Initiative for Neuroscience Data Structures (openMINDS)>>https://github.com/HumanBrainProject/openMINDS]] is an open-source, community-driven research infrastructure initiative powered by EBRAINS and the Human Brain Project.  The openMINDS schema gathers a set of metadata models that can be used for describing heterogeneous neuroscience data. The data can originate from human, animal or simulated studies, computational models, and software tools, as well as metadata or data models. Metadata stored in the openMINDS configuration can be uploaded directly to your Dataset in the Metadata tab of the [[Dataset Explorer>>doc:Main.user_guide.Working with Datasets.Dataset Explorer.WebHome]].
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140 {{info}}
141 **NOTE**: Before starting, you must have one or more JSON files in openMINDS format.
142 {{/info}}
143
144 ===== How to annotate your Dataset in the openMINDS format =====
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146
147 1. Open the Datasets feature from the top VRE menu bar, then navigate to your Dataset.
148 1. Click the **Metadata **tab.
149 1. Under //Existing Schemas// click **openMINDS Schemas.**
150 1. Click **Upload Schema.**
151 1. Click **Select Schema**.
152 1. Select the json file(s) that contain your metadata in the openMINDS format and click **Open.**
153 1. Click **Upload.**
154 1. Your schemas will appear in the //Existing Schemas// list.  Click the eye icon to view your schema, click the trash icon to delete a schema.
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158 === Contributing Metadata Annotations into the Knowledge Graph ===
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160 After annotating your VRE Dataset with a schema template, the metadata annotations can be ingested in the VRE Knowledge Graph in order to make your Dataset searchable and discoverable by other researchers. At present, this is possible by importing the annotations in JSON format into the VRE Knowledge Graph.  For more information, see:[[Importing Dataset schemas into a Knowledge Graph with the Guacamole VM and VRE Command Line Tool>>doc:Main.user_guide.Analyzing Data.Guacamole.Importing Dataset schemas into a Knowledge Graph with the Guacamole VM and VRE Command Line Tool.WebHome]].
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166 **See Also: **
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168 [[Dataset Creation>>doc:Main.user_guide.Working with Datasets.Dataset Creation.WebHome]]
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170 [[Dataset Versioning>>doc:Main.user_guide.Working with Datasets.Dataset Versioning.WebHome]]
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172 [[Importing Dataset schemas into a Knowledge Graph with the Guacamole VM and VRE Command Line Tool>>doc:Main.user_guide.Analyzing Data.Guacamole.Importing Dataset schemas into a Knowledge Graph with the Guacamole VM and VRE Command Line Tool.WebHome]]
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181 Copyright © 2022, Indoc Research. This work is licensed under a [[Creative Commons Attribution-ShareAlike 4.0>>http://creativecommons.org/licenses/by-sa/4.0/ ||rel="noopener noreferrer" target="blank"]] International License.
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