diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..75cb399 Binary files /dev/null and b/.DS_Store differ diff --git a/docs/.DS_Store b/docs/.DS_Store new file mode 100644 index 0000000..c032fa7 Binary files /dev/null and b/docs/.DS_Store differ diff --git a/docs/img/.DS_Store b/docs/img/.DS_Store new file mode 100644 index 0000000..ee45ddc Binary files /dev/null and b/docs/img/.DS_Store differ diff --git a/docs/img/userguide/annotate-fields-with-property-20230303.png b/docs/img/userguide/annotate-fields-with-property-20230303.png new file mode 100644 index 0000000..8e856ce Binary files /dev/null and b/docs/img/userguide/annotate-fields-with-property-20230303.png differ diff --git a/docs/img/userguide/annotate-metadata-with-ontolgy-class-20230303.png b/docs/img/userguide/annotate-metadata-with-ontolgy-class-20230303.png new file mode 100644 index 0000000..f2be72f Binary files /dev/null and b/docs/img/userguide/annotate-metadata-with-ontolgy-class-20230303.png differ diff --git a/docs/img/userguide/property-associated-with-field-20230303.png b/docs/img/userguide/property-associated-with-field-20230303.png new file mode 100644 index 0000000..52d0bcb Binary files /dev/null and b/docs/img/userguide/property-associated-with-field-20230303.png differ diff --git a/docs/img/userguide/property-search-dialog-20230303.png b/docs/img/userguide/property-search-dialog-20230303.png new file mode 100644 index 0000000..4f2a1b2 Binary files /dev/null and b/docs/img/userguide/property-search-dialog-20230303.png differ diff --git a/docs/user-guide/cadsr_users/1_building_templates.md b/docs/user-guide/cadsr_users/1_building_templates.md index 7cb9065..583476f 100644 --- a/docs/user-guide/cadsr_users/1_building_templates.md +++ b/docs/user-guide/cadsr_users/1_building_templates.md @@ -7,12 +7,12 @@ This page covers the basics of building templates in the {{ page.cedarw }}, with - [Introduction](#intro) - [Step-by-step guide: build a template](#step-by-step-guide) - - Step 1 - [Navigate to your workspace](#workspace) - - Step 2 - [Create a new template object](#create-template) - - Step 3 - [Add CDEs to your template](#add-cdes) - - Step 4 - [Configure CDE options](#configure-cdes) - - Step 5 - [Save your template](#save-template) - - Step 6 - [Share your template](#share-template) + - Step 1 - [Navigate to your workspace](#workspace) + - Step 2 - [Create a new template object](#create-template) + - Step 3 - [Add CDEs to your template](#add-cdes) + - Step 4 - [Configure CDE options](#configure-cdes) + - Step 5 - [Save your template](#save-template) + - Step 6 - [Share your template](#share-template) *** @@ -75,7 +75,7 @@ A section with instructions for making copies of CDEs is included later in this This page describes the process of adding individual CDEs to templates. One advantage to this approach is that you are allowed to make edits to CDE's common options, as well as edits to all other field types from within a template container. The {{ page.cedarw }} offers the ability to group CDEs together into "elements" so that multiple CDEs can be added to a template at once. The tradeoff for this approach is that the CDEs and other fields contained in elements are unmodifiable once the element has been added to a template. -More detail and instructions for creating elements with multiple CDEs are given on a [separate page](../building_elements). Understanding how to build templates in the {{ page.cedarw }} is not a prerequisite for creating elements. +More detail and instructions for creating elements with multiple CDEs are given on a [separate page](../3_building_elements). Understanding how to build templates in the {{ page.cedarw }} is not a prerequisite for creating elements.

diff --git a/docs/user-guide/cadsr_users/2_importing_templates.md b/docs/user-guide/cadsr_users/2_importing_templates.md index 340f96b..b2618b2 100644 --- a/docs/user-guide/cadsr_users/2_importing_templates.md +++ b/docs/user-guide/cadsr_users/2_importing_templates.md @@ -7,12 +7,12 @@ This page covers the basics of importing caDSR Form Builder forms into the {{ pa - [Introduction](#intro) - [Step-by-step guide: import a template](#step-by-step-guide) - - Step 1 - [Export form(s) to XML format](#export-forms) - - Step 2 - [Navigate to your workspace](#workspace) - - Step 3 - [Select XML files for import](#select-xml-files) - - Step 4 - [Perform an import](#import) - - Step 5 - [Look over the import report](#import-report) - - Step 6 - [View the imported template](#view-template) + - Step 1 - [Export form(s) to XML format](#export-forms) + - Step 2 - [Navigate to your workspace](#workspace) + - Step 3 - [Select XML files for import](#select-xml-files) + - Step 4 - [Perform an import](#import) + - Step 5 - [Look over the import report](#import-report) + - Step 6 - [View the imported template](#view-template) - [Editing imported templates](#edit-template) --- diff --git a/docs/user-guide/cadsr_users/3_building_elements.md b/docs/user-guide/cadsr_users/3_building_elements.md index d5a522a..ea3710d 100644 --- a/docs/user-guide/cadsr_users/3_building_elements.md +++ b/docs/user-guide/cadsr_users/3_building_elements.md @@ -7,16 +7,16 @@ This page covers the basics of building elements in the {{ page.cedarw }}, with - [Introduction](#intro) - [Step-by-step guide: build an element](#step-by-step-guide) - - Step 1 - [Navigate to your workspace](#workspace) - - Step 2 - [Create a new element](#create-element) - - Step 3 - [Add CDEs to your element](#add-cdes) - - Step 4 - [Configure CDE options](#configure-cdes) - - [Preferred labels](#opts-labels) - - [Cardinality](#opts-cardinality) - - [Required vs. optional](#opts-required) - - [Suggestions](#opts-suggest) - - [Hidden](#opts-hide) - - [Permissible values](#opts-values) + - Step 1 - [Navigate to your workspace](#workspace) + - Step 2 - [Create a new element](#create-element) + - Step 3 - [Add CDEs to your element](#add-cdes) + - Step 4 - [Configure CDE options](#configure-cdes) + - [Preferred labels](#opts-labels) + - [Cardinality](#opts-cardinality) + - [Required vs. optional](#opts-required) + - [Suggestions](#opts-suggest) + - [Hidden](#opts-hide) + - [Permissible values](#opts-values) - [Arranging CDEs in elements](#arrange-cdes) - [Deleteing CDEs from elements](#delete-cdes) - [Nesting elements](#nesting) @@ -91,7 +91,7 @@ This will launch a modal dialog where you can use the search bar across the top You can select items in the list of search results to display a details pane on the right hand side of the dialog for viewing informaton such as the CDE owner, storage location, version number, etc. -If you need more information about how to efficiently search for CDEs in the {{ page.cedarw }}, please refer to the ["Finding CDEs"](../finding_cdes) page. +If you need more information about how to efficiently search for CDEs in the {{ page.cedarw }}, please refer to the ["Finding CDEs"](../4_finding_cdes) page. Once you locate the desired CDE, select it in the middle pane of the search dialog and click the "SELECT" button. This will insert the CDE into your element and return to the element designer. @@ -146,7 +146,7 @@ The REQUIRED link allows you to specify whether or not the CDE needs to be fille ### Suggestions -Setting SUGGESTIONS to YES enables the {{ page.cedarw }} intelligent authoring suggestion system for the field. For a detailed explanation of this functionality, see [Understanding the Suggestion System](../../sections/c4/understanding_the_suggestion_system/). +Setting SUGGESTIONS to YES enables the {{ page.cedarw }} intelligent authoring suggestion system for the field. For a detailed explanation of this functionality, see [Understanding the Suggestion System](../../sections/c4/3_understanding_the_suggestion_system/). ### Hidden diff --git a/docs/user-guide/cadsr_users/4_finding_cdes.md b/docs/user-guide/cadsr_users/4_finding_cdes.md index a1c869c..e79abe3 100644 --- a/docs/user-guide/cadsr_users/4_finding_cdes.md +++ b/docs/user-guide/cadsr_users/4_finding_cdes.md @@ -83,7 +83,7 @@ as the "Desktop". One way to make sure the Desktop view is displayed is to click on the Workspace link in the upper-left portion of the window. For a more in-depth explanation of the Desktop and other components displayed in the Workspace, refer to the section entitled -"[Your CEDAR Workspace](../../sections/a4/your_cedar_workspace)" in the +"[Your CEDAR Workspace](../../sections/a4/3_your_cedar_workspace)" in the "[Desktop and Navigation](../../basic_topics/a4_desktop_and_navigation)" chapter. When CDEs are imported into the {{ page.cedarw }}, they are named by diff --git a/docs/user-guide/pages/cedar-for-cadsr.md b/docs/user-guide/pages/cedar-for-cadsr.md index 114e8a2..ecc8ab0 100644 --- a/docs/user-guide/pages/cedar-for-cadsr.md +++ b/docs/user-guide/pages/cedar-for-cadsr.md @@ -24,4 +24,4 @@ The {{ page.fb }} and {{ page.cedarw }} use different naming conventions to desc |module|element| |permissible values|values| -To get started with any of the following topics, navigate to the [CEDAR Workbench](http://cedar.metadatacenter.org/){:target="_blank"} and log in to your account. If you need instructions for creating an account, please refer to the "[Accounts and Logging In](basic_topics/a1_accounts_and_logging_in "Accounts and Logging In")" section of the user guide. +To get started with any of the following topics, navigate to the [CEDAR Workbench](http://cedar.metadatacenter.org/){:target="_blank"} and log in to your account. If you need instructions for creating an account, please refer to the "[Accounts and Logging In](../../basic_topics/a1_accounts_and_logging_in "Accounts and Logging In")" section of the user guide. diff --git a/docs/user-guide/pages/faq.md b/docs/user-guide/pages/faq.md index 2bdffe5..cfcecb6 100644 --- a/docs/user-guide/pages/faq.md +++ b/docs/user-guide/pages/faq.md @@ -17,17 +17,17 @@ If you want to submit your metadata (even including data) to a particular domain **How do I get an account on CEDAR?** Detailed instructions are available in our -CEDAR User Manual's [Accounts and Logging In chapter](https://metadatacenter.github.io/cedar-manual/basic_topics/a1_accounts_and_logging_in/). +CEDAR User Manual's [Accounts and Logging In chapter](../../basic_topics/a1_accounts_and_logging_in/). Just go to [the CEDAR application](https://cedar.metadatacenter.org), where you will see a login screen. You can register for the system using the Register link on that screen (just above the red Google icon), using your social media account or email address. That's it—you can start using CEDAR now! **I can't figure out what to do! How do I create a template or fill one out?** -**[Quick reference for template creation](https://metadatacenter.github.io/cedar-manual/cedar_templates/c2_building_basic_templates/)** If you want to create a template that people can then use, go to your home directory (using the Home button at upper left). To create a new template (or anything else) move the mouse pointer to the New button in the upper left, wait for the options to pop up, and select what you want to create. +**[Quick reference for template creation](../../cedar_templates/c2_building_basic_templates/)** If you want to create a template that people can then use, go to your home directory (using the Home button at upper left). To create a new template (or anything else) move the mouse pointer to the New button in the upper left, wait for the options to pop up, and select what you want to create. -**[Quick reference for filling out metadata](https://metadatacenter.github.io/cedar-manual/basic_topics/a5_filling_out_creating_metadata/)** To fill out some metadata for a template, you'll need to find the template you're providing metadata for (hint: you can [search for it](https://metadatacenter.github.io/cedar-manual/basic_topics/a2_finding_resources/)), then control-click or right-click on the template and select "Populate" to generate a form to fill out. (If someone else has given you a link to fill out a CEDAR template, just go to that link in your browser.) Once you're logged in you'll be in the Metadata Editor, ready to start filling out metadata. +**[Quick reference for filling out metadata](../../basic_topics/a5_filling_out_creating_metadata/)** To fill out some metadata for a template, you'll need to find the template you're providing metadata for (hint: you can [search for it](../../basic_topics/a2_finding_resources/)), then control-click or right-click on the template and select "Populate" to generate a form to fill out. (If someone else has given you a link to fill out a CEDAR template, just go to that link in your browser.) Once you're logged in you'll be in the Metadata Editor, ready to start filling out metadata. -For more startup information, go to our [CEDAR User Manual](https://metadatacenter.github.io/cedar-manual/), or to our [CEDAR training page](https://more.metadatacenter.org/tools-training/training-cedar), +For more startup information, go to our [CEDAR User Manual](../../../user-overview/), or to our [CEDAR training page](https://more.metadatacenter.org/tools-training/training-cedar), which each have a variety of introductory content. **What makes CEDAR forms so special? Google forms/SurveyMonkey surveys can do most of this.** @@ -51,7 +51,7 @@ Over time CEDAR developers will be adding more time savers, like pulling in meta **What format is the metadata saved in? How can I access it?** We save the metadata as JSON-LD (in a Mongo database). We make it available (to those with access privileges) via the user interface, in both JSON-LD and the equivalent RDF. Click on the format (at the bottom of the screen) to choose how you want to view it -[detailed information in CEDAR's User Manual](https://metadatacenter.github.io/cedar-manual/sections/a3/4_viewing_resource_as_raw_metadata/) +[detailed information in CEDAR's User Manual](../../sections/a3/4_viewing_resource_as_raw_json/) You can also access the metadata via the CEDAR API, in both of these formats, and in a "condensed JSON" format. That last format gets rid of lots of the links in the metadata (including much of the rich semantics). @@ -76,8 +76,8 @@ Our example repository on GitHub shows how to generate Java classes that produce **What is the 'link' field type for?** -This is appropriate when you know the result has to be a URL, or some other type of IRI (the internationalized, generalized form of a URL). Unlike text fields, this field type validates the metadata entry to make sure it’s an IRI, and it produces appropriately typed RDF in the resulting metadata. Please reference the [Adding Fields section](https://metadatacenter.github.io/cedar-manual/sections/c2/2_adding_fields/) -and the [Field Type Reference](https://metadatacenter.github.io/cedar-manual/sections/c2/field_type_reference/) +This is appropriate when you know the result has to be a URL, or some other type of IRI (the internationalized, generalized form of a URL). Unlike text fields, this field type validates the metadata entry to make sure it’s an IRI, and it produces appropriately typed RDF in the resulting metadata. Please reference the [Adding Fields section](../../sections/c2/2_adding_fields/) +and the [Field Type Reference](../../sections/c2/field_type_reference/) for more information on field types. **What do you use for your identifiers?** @@ -90,14 +90,14 @@ you will see the first identifier string, like `https://repo.metadatacenter.net/ Note that the template identifier will not (yet) resolve in your browser if you do not prefix it with the appropriate CEDAR context, e.g., in this case `https://cedar.metadatacenter.net/templates/edit/`. -Detailed information on our identifiers is available at [How CEDAR Defines and Applies IRIs (URIs, URLs)](https://metadatacenter.github.io/cedar-manual/sections/c4/how_cedar_defines_and_accesses_identifiers/) +Detailed information on our identifiers is available at [How CEDAR Defines and Applies IRIs (URIs, URLs)](../../sections/b1/3_how_cedar_defines_and_accesses_identifiers/) **How do I look up all instances of a template?** If you have read access to the template, you can look in the metadata for the template to see all the instances -to which you have read or write access. See [Viewing Resource Metadata](https://metadatacenter.github.io/cedar-manual/a3/5_viewing_resource_metadata/) +to which you have read or write access. See [Viewing Resource Metadata](../../sections/a3/5_viewing_resource_metadata/) to learn how to find the metadata for an artifact in the CEDAR Desktop. Use the API search feature with the identifier of the template to find all the related instances. See the [API search documentation](https://resource.metadatacenter.org/api/#!/Template32Instances/get_search) for the details. @@ -113,7 +113,7 @@ Please tell us if there is a CEDAR field that does not handle them correctly. **Can I deploy CEDAR in my own computing environment?** Yes, though CEDAR has not been thoroughly tested in remote deployments. -We have [detailed instructions about deploying CEDAR](https://metadatacenter.readthedocs.io/en/latest/install-developer/intro.html). +We have [detailed instructions about deploying CEDAR](../../../install-overview/). There are several caveats: * We don't have a good way to upgrade metadata instances to match a new metadata schema. (We do this manually when our schema has a breaking change.) * You will need to continue using BioPortal or another OntoPortal-based ontology repository for your vocabularies. diff --git a/docs/user-guide/sections/a1/logging_in_with_cedar.md b/docs/user-guide/sections/a1/logging_in_with_cedar.md index 6b57a82..332ab63 100644 --- a/docs/user-guide/sections/a1/logging_in_with_cedar.md +++ b/docs/user-guide/sections/a1/logging_in_with_cedar.md @@ -6,6 +6,6 @@ status: Ready To log in, go to [https://cedar.metadatacenter.org](https://cedar.metadatacenter.org "CEDAR Workbench"), and enter the account name and your password as shown in the screenshot below. If you have forgotten your password, you can use the "Forgot Password?" link just below the Password line. Once you have logged in, you will see the CEDAR Workspace. -In the next section, we provide important information about the visibility of your account, your content, and your user information. Or if you prefer, you may skip to the CEDAR Workspace [Desktop and Navigation](https://metadatacenter.github.io/cedar-manual/basic_topics/a4_desktop_and_navigation/) section, or the [Finding Resources](https://metadatacenter.github.io/cedar-manual/basic_topics/a2_finding_resources/) section. +In the next section, we provide important information about the visibility of your account, your content, and your user information. Or if you prefer, you may skip to the CEDAR Workspace [Desktop and Navigation](../../../basic_topics/a4_desktop_and_navigation/) section, or the [Finding Resources](../../../basic_topics/a2_finding_resources/) section. ![](../../../img/userguide/login.png){:width="50%" class="centered"} diff --git a/docs/user-guide/sections/a2/1_simple_searching.md b/docs/user-guide/sections/a2/1_simple_searching.md index 913c32d..faeb5c2 100644 --- a/docs/user-guide/sections/a2/1_simple_searching.md +++ b/docs/user-guide/sections/a2/1_simple_searching.md @@ -4,7 +4,7 @@ status: Ready --- # Simple Searching -*To learn about simple navigation in the Desktop, visit [Navigating Within CEDAR](https://metadatacenter.github.io/cedar-manual/sections/a4/navigating_within_cedar/).* +*To learn about simple navigation in the Desktop, visit [Navigating Within CEDAR](../../a4/2_navigating_within_cedar/).*

Searching use the search bar

@@ -19,7 +19,7 @@ The CEDAR Workbench organizes resources in three different categories, depending Searching for a resource in a particular set is very simple. Just click on the given set (e.g., "Shared with everybody") and input the search string as free text in the search bar, as described above. All the resources in the selected set that have the string listed in their labels, version, or description are shown. -You can also constrain the resulting resources by their type, as described in [Constraining the Results by Type](https://metadatacenter.github.io/cedar-manual/sections/a2/3_constraining_the_results_by_type/). +You can also constrain the resulting resources by their type, as described in [Constraining the Results by Type](../../a2/3_constraining_the_results_by_type/). The search results are illustrated in the Figure below. In later sections, we will demonstrate how to organize and constrain these search results, and perform advanced searches. diff --git a/docs/user-guide/sections/a3/1_viewing_resources_overview.md b/docs/user-guide/sections/a3/1_viewing_resources_overview.md index 863e1aa..15f67a4 100644 --- a/docs/user-guide/sections/a3/1_viewing_resources_overview.md +++ b/docs/user-guide/sections/a3/1_viewing_resources_overview.md @@ -8,7 +8,7 @@ status: Ready There are four types of resources in CEDAR: folders, metadata templates, metadata elements, metadata fields, and metadata instances. In this section we will drop the term 'metadata' from these names and refer to each resource by its shorter form. -CEDAR folders are used to organize CEDAR content and the sharing settings for that content. To view folder resources you navigate into the folders. This is described in [Navigating Within CEDAR](https://metadatacenter.github.io/cedar-manual/sections/a4/navigating_within_cedar/), under Browsing Within the Desktop. +CEDAR folders are used to organize CEDAR content and the sharing settings for that content. To view folder resources you navigate into the folders. This is described in [Navigating Within CEDAR](../../a4/2_navigating_within_cedar/), under Browsing Within the Desktop. The rest of this section emphasizes CEDAR artifacts: templates, elements, fields, and instances. @@ -31,7 +31,7 @@ make changes to the document. This is also the view which enables seeing the raw artifact content inside CEDAR. -For more details about this viewing mode, visit [Viewing Resource Content](https://metadatacenter.github.io/cedar-manual/sections/a3/2_viewing_resource_content_in_cedar/). +For more details about this viewing mode, visit [Viewing Resource Content](../2_viewing_resource_content_in_cedar/).

On the Web with OpenView

@@ -45,7 +45,7 @@ to the web page for this artifact that supports navigation and viewing features. You can also see artifact metadata and raw artifact content from the OpenView format. -For more details about this viewing mode, visit [Viewing Resource Content on the Web](https://metadatacenter.github.io/cedar-manual/sections/a3/3_viewing_resource_content_on_the_web/). +For more details about this viewing mode, visit [Viewing Resource Content on the Web](../../a3/3_viewing_resource_content_on_the_web/).

Viewing Resources in Raw Formats

@@ -60,7 +60,7 @@ Whichever format applies, the information is accessible at the bottom of the artifact's view in CEDAR by clicking on the appropriate link. (Raw formats can also be accessed via the web when OpenView is enabled for the artifact.) -For more details about this viewing mode, visit [Viewing Resource as Raw JSON](https://metadatacenter.github.io/cedar-manual/sections/a3/4_viewing_resource_as_raw_json/). +For more details about this viewing mode, visit [Viewing Resource as Raw JSON](../../a3/4_viewing_resource_as_raw_json/).

Viewing Resource Metadata

@@ -71,7 +71,7 @@ side of the Desktop, click on the 'i' information icon to open it. Another metadata panel is available from the top part of the OpenView format, with a different metadata collection appropriate to OpenView users. -For more details about viewing resource , visit [Viewing Resource Metadata](https://metadatacenter.github.io/cedar-manual/sections/a3/5_viewing_resource_metadata/). +For more details about viewing resource , visit [Viewing Resource Metadata](../../a3/5_viewing_resource_metadata/). diff --git a/docs/user-guide/sections/a3/2_viewing_resource_content_in_cedar.md b/docs/user-guide/sections/a3/2_viewing_resource_content_in_cedar.md index 789a46f..4d871d9 100644 --- a/docs/user-guide/sections/a3/2_viewing_resource_content_in_cedar.md +++ b/docs/user-guide/sections/a3/2_viewing_resource_content_in_cedar.md @@ -55,7 +55,7 @@ the template model specifications.)

Artifact Footers

-At the foot of every artifact one or two horizontal bars let you view the raw format of the artifact. See [Viewing Resource as Raw JSON](https://metadatacenter.github.io/cedar-manual/sections/a3/4_viewing_resource_as_raw_json/) for more information. +At the foot of every artifact one or two horizontal bars let you view the raw format of the artifact. See [Viewing Resource as Raw JSON](../4_viewing_resource_as_raw_json/) for more information.

Template Designer View

@@ -67,7 +67,7 @@ with visual indentation to show the organization of the elements within the temp There is also an identifier field, which can be used to provide an external identifier for the template. (This is not the same as the artifact's identifier, which is always a CEDAR-generated IRI.) The external identifier does not have to be an IRI, and does not have to be unique across different artifacts, though both are highly recommended. -More information about using the Template Designer can be found in the CEDAR Templates chapter, starting with [Description of a Template](https://metadatacenter.github.io/cedar-manual/cedar_templates/c1_description_of_a_template/). +More information about using the Template Designer can be found in the CEDAR Templates chapter, starting with [Description of a Template](../../../cedar_templates/c1_description_of_a_template/).

Metadata Editor View

@@ -80,7 +80,7 @@ again with visual indentation to show the organization of the elements within th If there is an arrow to the left of a given line, clicking on the arrow will expand or collapse the content under that entity. -Information about using the Metadata Editor can be found in the Filling Out (Creating) Metadata chapter, starting with [Filling Out Metadata](https://metadatacenter.github.io/cedar-manual/sections/a5/2_filling_out_metadata/). +Information about using the Metadata Editor can be found in the Filling Out (Creating) Metadata chapter, starting with [Filling Out Metadata](../../a5/2_filling_out_metadata/). diff --git a/docs/user-guide/sections/a3/3_viewing_resource_content_on_the_web.md b/docs/user-guide/sections/a3/3_viewing_resource_content_on_the_web.md index 6d10a9b..51baf97 100644 --- a/docs/user-guide/sections/a3/3_viewing_resource_content_on_the_web.md +++ b/docs/user-guide/sections/a3/3_viewing_resource_content_on_the_web.md @@ -6,7 +6,7 @@ status: Ready We use the phrase 'viewing resource content' to mean looking at the resource in human-friendly form, in this case viewing it on the web using CEDAR OpenView. -OpenView is a CEDAR feature that allows you to publish CEDAR artifacts to the web, where anyone with the IRI can view them. The details of this process are described in [Sharing Via the Web](https://metadatacenter.github.io/cedar-manual/sections/a6/4_sharing_via_the_web/). +OpenView is a CEDAR feature that allows you to publish CEDAR artifacts to the web, where anyone with the IRI can view them. The details of this process are described in [Sharing Via the Web](../../a6/4_sharing_via_the_web/). Under the heading Viewing the Shared Content on the Web, that page also describes how to access an OpenView page, what content is visible on the page, and how to view additional hidden information. An added feature of the web-based view of instance artifacts is that you can view not just the raw JSON-LD or RDF for the instance, but also the JSON Schema for that instance. Simply click on the appropriate viewing link at the bottom of the form on the web. diff --git a/docs/user-guide/sections/a3/4_viewing_resource_as_raw_json.md b/docs/user-guide/sections/a3/4_viewing_resource_as_raw_json.md index 96a194a..ba4ef1b 100644 --- a/docs/user-guide/sections/a3/4_viewing_resource_as_raw_json.md +++ b/docs/user-guide/sections/a3/4_viewing_resource_as_raw_json.md @@ -4,7 +4,7 @@ status: Ready --- # Viewing Resource as Raw JSON -As noted in the [Viewing Resources Overview](https://metadatacenter.github.io/cedar-manual/sections/a3/1_viewing_resources_overview/), +As noted in the [Viewing Resources Overview](../../a3/1_viewing_resources_overview/), all CEDAR artifacts are maintained internally in JSON. The three CEDAR templating artifacts—templates, elements, and fields—are maintained diff --git a/docs/user-guide/sections/a3/5_viewing_resource_metadata.md b/docs/user-guide/sections/a3/5_viewing_resource_metadata.md index 11a61aa..d336a2a 100644 --- a/docs/user-guide/sections/a3/5_viewing_resource_metadata.md +++ b/docs/user-guide/sections/a3/5_viewing_resource_metadata.md @@ -17,7 +17,7 @@ if it is not already visible. If no resource is selected, the 'i' icon presents metadata about the folder (B) shown in the Resources box. The right-hand smaller image below shows the information panel for one of these artifacts. -The information panel displays 3 types of metadata in the corresponding tabs: metadata about the resource's general characteristics; metadata about an artifact's version history (for templating resources only, not instances); and metadata about the categories into which the resource has been classified (artifacts only, not folders). +The information panel displays 3 types of metadata in the corresponding tabs: metadata about the resource's general characteristics; metadata about an [artifact's version history](../../c4/4_updating_and_versioning/) (for templating resources only, not instances); and metadata about the categories into which the resource has been classified (artifacts only, not folders). In the main window, most of the metadata is self-explanatory, but there are two features of special interest. The Description field is the same content as the description at the top of the artifact when it is open, and this field is editable in the information panel. Also, for metadata templates the panel shows all the metadata instances that are visible to you; clicking on any of the instances in the list will open it. The count at the top of that metadata instances sub-panel is the count of instances you can see, and the total count of instances. @@ -27,12 +27,12 @@ In the main window, most of the metadata is self-explanatory, but there are two If an artifact has OpenView enabled, you can navigate to the OpenView either with the direct IRI (if you have it), or by navigating to the artifact in CEDAR (if you have access to that) and clicking on the Visit in OpenView resource menu item. -In either case, the top line of the artifact in OpenView has a metadata block with the title in the middle. By clicking on this metadata block, you will unfold a metadata view, as shown in [Viewing Resource Content on the Web](https://metadatacenter.github.io/cedar-manual/sections/a3/3_viewing_resource_content_on_the_web/) +In either case, the top line of the artifact in OpenView has a metadata block with the title in the middle. By clicking on this metadata block, you will unfold a metadata view, as shown in [Viewing Resource Content on the Web](../../a3/3_viewing_resource_content_on_the_web/)

Metadata in the raw artifact views

-By looking in any [raw artifact view](https://metadatacenter.github.io/cedar-manual/sections/a3/4_viewing_resource_as_raw_json/), +By looking in any [raw artifact view](../../a3/4_viewing_resource_as_raw_json/), you can see the metadata that CEDAR maintains as part of that artifact. To understand the metadata in more detail, -you will need to understand the CEDAR Template Model, as described in the [Description of a Template](https://metadatacenter.github.io/cedar-manual/cedar_templates/c1_description_of_a_template/). +you will need to understand the CEDAR Template Model, as described in the [Description of a Template](../../../cedar_templates/c1_description_of_a_template/). diff --git a/docs/user-guide/sections/a4/1_managing_cedar_resources.md b/docs/user-guide/sections/a4/1_managing_cedar_resources.md index cdacff9..d41a88c 100644 --- a/docs/user-guide/sections/a4/1_managing_cedar_resources.md +++ b/docs/user-guide/sections/a4/1_managing_cedar_resources.md @@ -7,7 +7,7 @@ status: Ready ## **Introduction** This section describes how to manage CEDAR resources. In CEDAR, resources include the various artifact types (templates, elements, fields, metadata instances) and folders. These are all managed through the CEDAR Desktop, -typically through your [workspace view](https://metadatacenter.github.io/cedar-manual/sections/a4/your_cedar_workspace/). +typically through your [workspace view](../../a4/3_your_cedar_workspace/). Management operations include copying, moving, renaming, and deleting resources, and setting sharing permissions on resources. @@ -69,7 +69,7 @@ After selecting the Rename… command, you will be asked for the new name. This The Share… command opens a sharing configuration window. In this window you can perform all sharing and group management operations needed to control resource access in CEDAR. -See the [Sharing Your Content](https://metadatacenter.github.io/cedar-manual/basic_topics/sharing_your_content/) +See the [Sharing Your Content](../../../basic_topics/a6_sharing_your_content/) section for detailed information about sharing resources in CEDAR. ### ***Delete*** Command diff --git a/docs/user-guide/sections/a4/2_navigating_within_cedar.md b/docs/user-guide/sections/a4/2_navigating_within_cedar.md index 9c9a04b..940244c 100644 --- a/docs/user-guide/sections/a4/2_navigating_within_cedar.md +++ b/docs/user-guide/sections/a4/2_navigating_within_cedar.md @@ -10,7 +10,7 @@ Navigating around CEDAR is pretty easy, but it helps to understand a few basics. CEDAR (the "CEDAR Workbench") has 3 tools: -* the Desktop (which includes [your workspace](https://metadatacenter.github.io/cedar-manual/sections/a4/your_cedar_workspace/)), +* the Desktop (which includes [your workspace](../../sections/a4/3_your_cedar_workspace/)), * the Template Editor, and * the Metadata Creator. @@ -34,7 +34,7 @@ double-click on the folder. (You can also use the resource menu (*⋮*) and click on Open.) This works in either search or browse mode to display the contents of folder in the Desktop. -Note that when My Workspace is the selected viewing mode (see [Your CEDAR Workspace](https://metadatacenter.github.io/cedar-manual/sections/a4/your_cedar_workspace/) for more details on viewing modes), you only see resources at the current folder level. In either of the Shared views you will see all the folders and artifacts that explicitly satisfy the chosen criteria. +Note that when My Workspace is the selected viewing mode (see [Your CEDAR Workspace](../../a4/3_your_cedar_workspace/) for more details on viewing modes), you only see resources at the current folder level. In either of the Shared views you will see all the folders and artifacts that explicitly satisfy the chosen criteria. ## **Moving Back and Forth** diff --git a/docs/user-guide/sections/a5/1_creating_the_metadata_form_instance_for_filling.md b/docs/user-guide/sections/a5/1_creating_the_metadata_form_instance_for_filling.md index 7d8964e..2b85d86 100644 --- a/docs/user-guide/sections/a5/1_creating_the_metadata_form_instance_for_filling.md +++ b/docs/user-guide/sections/a5/1_creating_the_metadata_form_instance_for_filling.md @@ -49,7 +49,7 @@ click on the dropdown menu (Item 2a, the kebab, `:`) and select Populate Templat In this scenario, the template creator has obtained a web link (an IRI) that, when entered into a browser or included clicked on as a link in a web page, will create a metadata instance for that template. (To create such a link -for a template, see [Building Shareable Metadata Creation IRIs](https://metadatacenter.github.io/cedar-manual/sections/b1/building-sharable-metadata-creation-iris/). +for a template, see [Building Shareable Metadata Creation IRIs](../../b1/2_building_sharable_metadata_creation_iris/). For example, clicking on the following link will start the process of creating an instance to be filled out for the Adaptive Immune Receptor Repertoire community's minimum information model (MiAIRR). @@ -89,7 +89,7 @@ make a copy of the instance profile and replace 'name' and 'date' in the title w the name of the author and the date of this copy (or a short instance sequence number), or any other appropriate unique labeling. (Note that the intended location to receive the filled-out instances must be -writable by all the people who are creating metadata.) See [Sharing Your Content](https://metadatacenter.github.io/cedar-manual/basic_topics/a6_sharing_your_content/) for more information on creating writable folders. +writable by all the people who are creating metadata.) See [Sharing Your Content](../../../basic_topics/a6_sharing_your_content/) for more information on creating writable folders. The copied instance will have all the information that was in the instance profile, and can be filled out and saved normally. diff --git a/docs/user-guide/sections/a5/2_filling_out_metadata.md b/docs/user-guide/sections/a5/2_filling_out_metadata.md index 378fe1f..5ac5c08 100644 --- a/docs/user-guide/sections/a5/2_filling_out_metadata.md +++ b/docs/user-guide/sections/a5/2_filling_out_metadata.md @@ -15,11 +15,11 @@ In some cases (see the image below), the metadata instance may show elements as ![](../../../img/userguide/entering-metadata-folded-elements-20191124.png){:width="80%" class="centered"} Your metadata is not saved until you hit the SAVE button, visible in the image above. -You may have to scroll to the end of a long template to see the Save button in the lower right corner. We recommend you save your metadata often, so that little is lost if your browser window is accidentally closed. See [Saving and Validating](https://metadatacenter.github.io/cedar-manual/sections/a5/3_saving_and_validating/) for more details. +You may have to scroll to the end of a long template to see the Save button in the lower right corner. We recommend you save your metadata often, so that little is lost if your browser window is accidentally closed. See [Saving and Validating](../../a5/3_saving_and_validating/) for more details. ## **Viewing JSON-LD and RDF** -You can see the JSON-LD and RDF versions of your metadata by clicking on the appropriate controls at the bottom of your metadata instance. For more information see [Viewing Resource as Raw JSON](https://metadatacenter.github.io/cedar-manual/sections/a3/4_viewing_resource_as_raw_json/). +You can see the JSON-LD and RDF versions of your metadata by clicking on the appropriate controls at the bottom of your metadata instance. For more information see [Viewing Resource as Raw JSON](../../a3/4_viewing_resource_as_raw_json/). ## **Multiple Fields** @@ -58,7 +58,7 @@ with one exception. The format control that enables filling out arrays ("spreadsheet view") is only visible if the element just contains simple fields. If the element contains other elements or fields that allow MULTIPLE entries, viewing and editing it as an array is not possible. -See the **Spreadsheet-compatible Elements** subsection of [Adding Elements](https://metadatacenter.github.io/cedar-manual/sections/c2/3_adding_elements) +See the **Spreadsheet-compatible Elements** subsection of [Adding Elements](../../c2/3_adding_elements) to learn how to set up this feature. CEDAR's spreadsheet view of arrays automatically performs @@ -124,7 +124,7 @@ CEDAR will make the most likely answers visible to you as the suggested values we describe here (and show below). More details about the suggestion system in CEDAR may be found at -[Understanding the Suggestion System](https://metadatacenter.github.io/cedar-manual/sections/c4/understanding_the_suggestion_system/). +[Understanding the Suggestion System](../../c4/3_understanding_the_suggestion_system/). ### Attribute-value fields diff --git a/docs/user-guide/sections/b2/1_api_about_swagger_documentation.md b/docs/user-guide/sections/b2/1_api_about_swagger_documentation.md index 16cbe7a..7ad2192 100644 --- a/docs/user-guide/sections/b2/1_api_about_swagger_documentation.md +++ b/docs/user-guide/sections/b2/1_api_about_swagger_documentation.md @@ -47,7 +47,7 @@ and no useful information will be returned. To use CEDAR's API resource documentation to make CEDAR requests as we describe in this Guide, you must enter your API key to the documentation interface. -To obtain your API key, reference the [CEDAR's API](../) documentation. +To obtain your API key, reference the [CEDAR's API](../../advanced_topics/b2_cedars_api.md) documentation. In the upper right section of any API's documentation, just under the summary description of the API method, diff --git a/docs/user-guide/sections/c1/1_template_overview.md b/docs/user-guide/sections/c1/1_template_overview.md index 3a27e33..b0d3505 100644 --- a/docs/user-guide/sections/c1/1_template_overview.md +++ b/docs/user-guide/sections/c1/1_template_overview.md @@ -23,7 +23,7 @@ The template is in JSON Schema format, and conforms to a higher-level JSON Schem specification. The higher-level JSON Schema can be used to validate the syntax of any CEDAR template at any time; errors in this validation are displayed in the Template Designer user interface, -as described in [Filling Out (Creating) Metadata: Saving and Validating](https://metadatacenter.github.io/cedar-manual/sections/a5/3_saving_and_validating/). +as described in [Filling Out (Creating) Metadata: Saving and Validating](../../a5/3_saving_and_validating/). The JSON Schema of a given metadata template similarly validates any Metadata Instance that CEDAR users create with that template, @@ -33,10 +33,10 @@ can be easily checked inside or outside the CEDAR system. You can specify the content and order of questions in the template using the Template Designer. You make up a template from Template Fields and Template Elements. The Template Elements are made up of other Template Elements and Template Fields. -The [Building Basic Templates](https://metadatacenter.github.io/cedar-manual/cedar_templates/c2_building_basic_templates/) +The [Building Basic Templates](../../../cedar_templates/c2_building_basic_templates/) chapter describes the template specification process using the Template Designer. -Before reading about the specification process, you may want to review the [next section](https://metadatacenter.github.io/cedar-manual/sections/c1/2_template_organization/), +Before reading about the specification process, you may want to review the [next section](../../c1/2_template_organization/), which more explicitly addresses the organization of the template. diff --git a/docs/user-guide/sections/c1/2_template_organization.md b/docs/user-guide/sections/c1/2_template_organization.md index aadb4dd..fe3e518 100644 --- a/docs/user-guide/sections/c1/2_template_organization.md +++ b/docs/user-guide/sections/c1/2_template_organization.md @@ -8,7 +8,7 @@ status: Ready All information for the Metadata Template is stored internally in the JSON Schema format. CEDAR lets you view the template in this format at any time during template creation. -See [Viewing Resource as Raw JSON](https://metadatacenter.github.io/cedar-manual/basic_topics/a3_viewing_resource_information/) +See [Viewing Resource as Raw JSON](../../a3/4_viewing_resource_as_raw_json/) to learn how to view the template in its raw form. The three Metadata Template functions (define questions, order the questions, and @@ -20,7 +20,7 @@ The details of the template artifact's format is described in more detail in the As a CEDAR user you will compose Metadata Templates from Template Elements and Template Fields. These three CEDAR resources, which we call templating resources, together establish the questions for the metadata user to fill out. The actual process is described in -the [Building Basic Templates](https://metadatacenter.github.io/cedar-manual/cedar_templates/c2_building_basic_templates/) +the [Building Basic Templates](../../../cedar_templates/c2_building_basic_templates/) chapter. As you reuse elements that you or others have created, CEDAR copies those elements diff --git a/docs/user-guide/sections/c2/1_first_steps.md b/docs/user-guide/sections/c2/1_first_steps.md index 490d475..8663581 100644 --- a/docs/user-guide/sections/c2/1_first_steps.md +++ b/docs/user-guide/sections/c2/1_first_steps.md @@ -21,7 +21,7 @@ and can be changed from the Desktop view. ![](../../../img/userguide/creating-new-template-20191216.png){:width="80%" class="centered"} -You can [save and close your Template](https://metadatacenter.github.io/cedar-manual/sections/c2/4-saving-and-closing/) at any time and return to it later. You can open it for viewing or editing +You can [save and close your Template](../../c2/4_saving_and_closing/) at any time and return to it later. You can open it for viewing or editing (or any other Template for which you have those access privileges) by double-clicking on its icon in the Desktop. @@ -66,7 +66,7 @@ information you want to be able to search on to find this field. ## **Next Steps** -Now, you can fill in the content of your template by [Adding Fields](https://metadatacenter.github.io/cedar-manual/sections/c2/2_adding_fields/) -and [Adding Elements](https://metadatacenter.github.io/cedar-manual/sections/c2/3_adding_elements/), -or [save and close it](https://metadatacenter.github.io/cedar-manual/sections/c2/4-saving-and-closing/) +Now, you can fill in the content of your template by [Adding Fields](../../c2/2_adding_fields/) +and [Adding Elements](../../c2/3_adding_elements/), +or [save and close it](../../c2/4_saving_and_closing/) to return to it later. diff --git a/docs/user-guide/sections/c2/2_adding_fields.md b/docs/user-guide/sections/c2/2_adding_fields.md index 5bec6c6..3240d3b 100644 --- a/docs/user-guide/sections/c2/2_adding_fields.md +++ b/docs/user-guide/sections/c2/2_adding_fields.md @@ -49,7 +49,7 @@ to customize presentation of the template to the metadata creator. The search (magnifying glass) icon brings up a window to find other CEDAR templating resources—Elements or Fields— that can be imported into the resource you are editing. -Use of this window is described in [Adding Elements](https://metadatacenter.github.io/cedar-manual/sections/c2/3_adding_elements/) +Use of this window is described in [Adding Elements](../../c2/3_adding_elements/) ### Choosing and Configuring the Field Definition @@ -57,7 +57,7 @@ For each data-entry field type, CEDAR supports certain options. For example, the Required option is offered on every data-entry field type. You can find simple information about a few key field types below, and detailed information about field types and their customizations -in the [Field Type Reference](https://metadatacenter.github.io/cedar-manual/sections/c2/field_type_reference/). +in the [Field Type Reference](../../c2/field_type_reference/). ### Common Options @@ -133,14 +133,14 @@ from which legal values may be chosen by the metadata author. You can repeat this process as often as you want to select additional terms, branches, or ontologies. -Advice about finding and choosing controlled values is available in the [Choosing Controlled Terms](https://metadatacenter.github.io/cedar-manual/sections/c3/3_choosing_controlled_terms/) section. +Advice about finding and choosing controlled values is available in the [Choosing Controlled Terms](../../c3/3_choosing_controlled_terms/) section. #### Suggestions Set the Suggestions tab to Yes to enable intelligent authoring suggestions for this field from CEDAR. You can read a detailed explanation of the suggestions system -at [Understanding the Suggestion System](https://metadatacenter.github.io/cedar-manual/sections/c4/understanding_the_suggestion_system/). +at [Understanding the Suggestion System](../../c4/3_understanding_the_suggestion_system/). ### Options for Numeric Fields @@ -178,7 +178,7 @@ entered by the metadata author. ## **Creating a Stand-Alone Field** This process begins by creating the Field artifact, -which is almost exactly like creating the Template artifact in [First Steps](https://metadatacenter.github.io/cedar-manual/sections/c2/1_first_steps/). +which is almost exactly like creating the Template artifact in [First Steps](../../c2/1_first_steps/). After that, the content of the Field artifact—the field definition— is created following the Adding a Field Definition subsection above. @@ -208,7 +208,7 @@ you can save the artifact and use the Template Designer's left-arrow to return to the Desktop. From there, you can modify the name, access permissions, and public visibility of the Field artifact, as described in -[Managing CEDAR Resources](https://metadatacenter.github.io/cedar-manual/sections/a4/managing_cedar_resources/). +[Managing CEDAR Resources](../../a4/1_managing_cedar_resources/). ## **Importing a Stand-Alone Field** @@ -219,13 +219,13 @@ when you are editing a Template or Element, the search (magnifying glass) icon in the Template Designer's field addition menu brings up a window to find other CEDAR templating resources—Elements or Fields— that can be imported into the Element or Field you are editing. -Use of this window is described in [Adding Elements](https://metadatacenter.github.io/cedar-manual/sections/c2/3_adding_elements/). +Use of this window is described in [Adding Elements](../../c2/3_adding_elements/). ![](../../../img/userguide/artifact-import-window-20200101.png){:width="60%" class="centered"} ## **Next Steps** -You can fill in more content of your template by [Adding Elements](https://metadatacenter.github.io/cedar-manual/sections/c2/3_adding_elements/), -or [save and close it](https://metadatacenter.github.io/cedar-manual/sections/c2/4-saving-and-closing/) +You can fill in more content of your template by [Adding Elements](../../c2/3_adding_elements/), +or [save and close it](../../c2/4_saving_and_closing/) to return to it later. diff --git a/docs/user-guide/sections/c2/3_adding_elements.md b/docs/user-guide/sections/c2/3_adding_elements.md index c594957..ec4ae27 100644 --- a/docs/user-guide/sections/c2/3_adding_elements.md +++ b/docs/user-guide/sections/c2/3_adding_elements.md @@ -30,7 +30,7 @@ and can also be changed from the Desktop. Now the content of the Element artifact can be created. Field definitions can be added directly, or by importing Field artifacts; -instructions for both operations are found in the [Adding Fields](https://metadatacenter.github.io/cedar-manual/sections/c2/2_adding_fields/) section. +instructions for both operations are found in the [Adding Fields](../../c2/2_adding_fields/) section. Element content can also be created by importing existing elements, as described below. @@ -40,7 +40,7 @@ you can save the artifact and use the Template Designer's left-arrow to return to the Desktop. From there, you can modify the name, access permissions, and public visibility of the Field artifact, as described in -[Managing CEDAR Resources](https://metadatacenter.github.io/cedar-manual/sections/a4/managing_cedar_resources/). +[Managing CEDAR Resources](../../a4/1_managing_cedar_resources/). ### **Spreadsheet-compatible Elements** @@ -55,7 +55,7 @@ will prevent the user from displaying the element in spreadsheet mode. Also, the MULTIPLE attribute of the element must be defined to allow multiple entries. The process of filling out the metadata using spreadsheet mode -is described in [Spreadsheet entry](https://metadatacenter.github.io/cedar-manual/sections/a5/2_filling_out_metadata/). +is described in [Spreadsheet entry](../../a5/2_filling_out_metadata/). ## **Embedding the Element Resource** diff --git a/docs/user-guide/sections/c2/field_type_reference.md b/docs/user-guide/sections/c2/field_type_reference.md index fc976c6..526f827 100644 --- a/docs/user-guide/sections/c2/field_type_reference.md +++ b/docs/user-guide/sections/c2/field_type_reference.md @@ -143,7 +143,7 @@ even though the required field is not completed. Set the Suggestions tab to Yes to enable intelligent authoring suggestions for this field from CEDAR. You can read a detailed explanation of the suggestions system -at [Understanding the Suggestion System](https://metadatacenter.github.io/cedar-manual/sections/c4/understanding_the_suggestion_system/). +at [Understanding the Suggestion System](../../c4/3_understanding_the_suggestion_system/). #### Unit of Measure (Numeric field Option) @@ -198,5 +198,5 @@ terms, branches, or ontologies. You can remove any of the selected terms, branches, or ontologies by clicking on the X to the right of the row you want to delete. -Advice about finding and choosing controlled values is available in the [Choosing Controlled Terms](https://metadatacenter.github.io/cedar-manual/sections/c2/choosing_controlled_terms/) +Advice about finding and choosing controlled values is available in the [Choosing Controlled Terms](../../c3/3_choosing_controlled_terms/) section. diff --git a/docs/user-guide/sections/c3/2_defining_your_answers_with_term_lists.md b/docs/user-guide/sections/c3/2_defining_your_answers_with_term_lists.md index eee9ec5..21665b6 100644 --- a/docs/user-guide/sections/c3/2_defining_your_answers_with_term_lists.md +++ b/docs/user-guide/sections/c3/2_defining_your_answers_with_term_lists.md @@ -8,17 +8,17 @@ To go to a particular topic, click on that link. * [Introduction](#introduction) * [Basic Interactions](#basic-interactions) - * [Searching for Terms](#searching-for-terms) - * [Reviewing Found Terms](#reviewing-found-terms) - * [Selecting Terms, Branches, or Ontologies](#selecting-terms-branches-or-ontologies) - * [Searching for Ontologies and Value Sets](#searching-for-ontologies-and-value-sets) + * [Searching for Terms](#searching-for-terms) + * [Reviewing Found Terms](#reviewing-found-terms) + * [Selecting Terms, Branches, or Ontologies](#selecting-terms-branches-or-ontologies) + * [Searching for Ontologies and Value Sets](#searching-for-ontologies-and-value-sets) * [Adding Your Own Terms](#adding-your-own-terms) - * [About Provisional Terms](#about-provisional-terms) - * [Adding your Own Single Term(s)](#adding-your-own-single-terms) - * [Adding a New List of Terms](#adding-a-new-list-of-terms) + * [About Provisional Terms](#about-provisional-terms) + * [Adding your Own Single Term(s)](#adding-your-own-single-terms) + * [Adding a New List of Terms](#adding-a-new-list-of-terms) * [Customizing What You Have](#customizing-what-you-have) - * [Rejecting Terms](#rejecting-terms) - * [Putting Favorites First](#putting-favorites-first) + * [Rejecting Terms](#rejecting-terms) + * [Putting Favorites First](#putting-favorites-first) ## Introduction @@ -26,12 +26,12 @@ To go to a particular topic, click on that link. Now we will show you exactly how to create questions that have very precise answers, using CEDAR's semantic tools. You don't have to know semantics to use these tools— -we'll give you some tips (in [Choosing Controlled Terms](https://metadatacenter.github.io/cedar-manual/sections/c3/3_choosing_controlled_terms/) that help you find good answers for your questions, +we'll give you some tips (in [Choosing Controlled Terms](../../c3/3_choosing_controlled_terms/) that help you find good answers for your questions, and know they are good enough for your needs. For you semantic experts, we provide advanced details elsewhere in this User Manual: -* [Tips for Template Creation: Term Discovery/Selection](https://metadatacenter.github.io/cedar-manual/sections/c5/term_discovery_selection/) -* [Advanced Template Topics: More Semantics](https://metadatacenter.github.io/cedar-manual/sections/c4/more_semantics/) +* [Tips for Template Creation: Term Discovery/Selection](../../c5/4_term_discovery_selection/) +* [Advanced Template Topics: More Semantics](../../c4/2_more_semantics/) In this section we outline the mechanical steps to find, select, and even create terms. The next section will tell how to figure out which terms are good ones to use. @@ -42,12 +42,12 @@ walks you through CEDAR interfaces that work hand-in-hand with the This repository contains over 800 public terminologies that offer precise semantic content you can use for your metadata collection process. But if BioPortal does not contain a terminology that you want to use, you can add it! -See the subsection called "Adding Content to BioPortal" in the [More Semantics](https://metadatacenter.github.io/cedar-manual/sections/c4/more_semantics/) section for more information on this process. +See the subsection called "Adding Content to BioPortal" in the [More Semantics](../../c4/2_more_semantics/) section for more information on this process. All the following sub-sections assume you have created a basic text field, clicked on the Values tab for your field, and clicked on the Add button to bring up the term search dialog box, -as described in [Adding Fields](https://metadatacenter.github.io/cedar-manual/sections/c2/2_adding_fields/). +as described in [Adding Fields](../../c2/2_adding_fields/). ## Basic Interactions diff --git a/docs/user-guide/sections/c3/3_choosing_controlled_terms.md b/docs/user-guide/sections/c3/3_choosing_controlled_terms.md index ea94950..b9a6e86 100644 --- a/docs/user-guide/sections/c3/3_choosing_controlled_terms.md +++ b/docs/user-guide/sections/c3/3_choosing_controlled_terms.md @@ -259,7 +259,7 @@ For example, if instead of looking for 'location' or 'city' as an ontology name you search for a typical location with an uncommon name (say "Sacramento"), you can see ontologies containing items with that name. In this case, you may quickly see that BioPortal has only one good location ontology -(GAZ) and that it is flat, so you might [create your own vocabulary](../3_defining_your_answers_with_term_lists) for these purposes. +(GAZ) and that it is flat, so you might [create your own vocabulary](../2_defining_your_answers_with_term_lists) for these purposes. ### Serendipity and Reuse diff --git a/docs/user-guide/sections/c3/4_creating_lists_in_the_metadata_entry_forms_for_users.md b/docs/user-guide/sections/c3/4_creating_lists_in_the_metadata_entry_forms_for_users.md index 62bcaf1..dfa1811 100644 --- a/docs/user-guide/sections/c3/4_creating_lists_in_the_metadata_entry_forms_for_users.md +++ b/docs/user-guide/sections/c3/4_creating_lists_in_the_metadata_entry_forms_for_users.md @@ -12,7 +12,7 @@ Unfortunately, only one of these (described in previous chapters) is truly seman This section serves as a relatively simple review of the types of lists CEDAR supports. In each list type we'll discuss pros and cons unique to that list type. -In the [Field Type Reference](https://metadatacenter.github.io/cedar-manual/sections/c2/field_type_reference/), you can +In the [Field Type Reference](../../c2/field_type_reference/), you can find listed the 4 field types that can generate lists of answers: Basic Text; Multi-Choice; Checkbox; and Pick From List. diff --git a/docs/user-guide/sections/c4/1_extending_a_template_adding_fields.md b/docs/user-guide/sections/c4/1_extending_a_template_adding_fields.md index d2160f8..65bb3f3 100644 --- a/docs/user-guide/sections/c4/1_extending_a_template_adding_fields.md +++ b/docs/user-guide/sections/c4/1_extending_a_template_adding_fields.md @@ -29,7 +29,7 @@ doesn't really create a new specification many specifications are extended for additional uses (sometimes called profiling, alas) -after basic steps, add your desired field, at end or (for eximple templates) inline +after basic steps, add your desired field, at end or (for example templates) inline if you want inline but inside an element are used, they would have to be extended themselves diff --git a/docs/user-guide/sections/c4/2_more_semantics.md b/docs/user-guide/sections/c4/2_more_semantics.md index d368c8c..9115de4 100644 --- a/docs/user-guide/sections/c4/2_more_semantics.md +++ b/docs/user-guide/sections/c4/2_more_semantics.md @@ -8,6 +8,32 @@ chapter_title: Advanced Template Topics We're sorry, this resource has not yet been developed. You are welcome to contribute to its development at the link below. +## Annotating Metadata and Fields + +CEDAR allows metadata to be of a particular type like an ontology class. This can be easily achieved by few clicks. For example, say we have a simple template named "Study" with a single field named "Study Title". + +We can indicate that the metadata is of a particular type by selecting the top right ontology icon and searching for study class in BioPortal. Image below shows selected Study class from NCIT. + +![](../../../img/userguide/annotate-metadata-with-ontolgy-class-20230303.png){:width="90%" class="centered"} + +Fields can also be annotated with properties in a similar way. For example, to select property for the "Study Title" field, you can select the ontology icon near the top right of the field: + +![](../../../img/userguide/annotate-fields-with-property-20230303.png){:width="90%" class="centered"} + +This will bring up a property search dialog, which can be used to search for an appropriate property in BioPortal. Here, we show that we are about to select the “Study Title” datatype property form the NGSONTO ontology. + +![](../../../img/userguide/property-search-dialog-20230303.png){:width="90%" class="centered"} + +Once selected, it is associated with the field. + +![](../../../img/userguide/property-associated-with-field-20230303.png){:width="90%" class="centered"} + +Now, when metadata are generated using that template the generated JSON-LD and RDF will contain the selected classes and properties. + +``` +_:b0 "My study title" . +_:b0 . +``` ## Characterizing your templating artifact diff --git a/docs/user-guide/sections/c4/4_updating_and_versioning.md b/docs/user-guide/sections/c4/4_updating_and_versioning.md index e02772e..2885658 100644 --- a/docs/user-guide/sections/c4/4_updating_and_versioning.md +++ b/docs/user-guide/sections/c4/4_updating_and_versioning.md @@ -23,7 +23,7 @@ First, you must update the element that needs to be changed. (If it is a versioned resource, follow the instructions in the Creating and Managing Versions topic below.) After saving your updated element, go to the template that contains it. -Import the updated element as described in [Adding Elements](https://metadatacenter.github.io/cedar-manual/sections/c2/3_adding_elements/); the updated element will appear at the bottom of your form. +Import the updated element as described in [Adding Elements](../../c2/3_adding_elements/); the updated element will appear at the bottom of your form. Move the element to the correct location in your form, and delete the element that is already there. @@ -134,7 +134,7 @@ Now, all versions will be shown in any search or folder display that contains th The version history for any artifact is shown in the Version tab of the metadata panel (see image on the right). (Click on the 'i' icon to make this panel visible; see -Viewing Resource Details for more information.) +[Viewing Resource Details](../../a3/5_viewing_resource_metadata/) for more information.) In the metadata panel example, you can see the three versions of the Version Test artifact. diff --git a/docs/user-guide/sections/c4/5_working_with_cdes.md b/docs/user-guide/sections/c4/5_working_with_cdes.md index f504db7..70f2f90 100644 --- a/docs/user-guide/sections/c4/5_working_with_cdes.md +++ b/docs/user-guide/sections/c4/5_working_with_cdes.md @@ -16,13 +16,13 @@ we can offer some tips for working with them efficiently in the CEDAR system. ## **Finding and Browsing CDEs** -The same practices used for [finding other CEDAR resources](https://metadatacenter.github.io/cedar-manual/basic_topics/a2_finding_resources/) will work with CDEs as well. +The same practices used for [finding other CEDAR resources](../../../basic_topics/a2_finding_resources/) will work with CDEs as well. However, there are a few additional strategies that may be particular helpful for those working with CDEs in CEDAR on a regular basis. ### Searching from the CEDAR Desktop -As described in the section [Finding Resources](https://metadatacenter.github.io/cedar-manual/basic_topics/a2_finding_resources/) +As described in the section [Finding Resources](../../../basic_topics/a2_finding_resources/) you can search for resources by name or description. In the case of CDEs, it is also possible to search by their CDE identifier. This number is shown at the top middle of the CEDAR field in the Template Editor @@ -71,7 +71,7 @@ in the left-hand navigation panel. Selecting an item at any level of the categor hierarchy will show all the CDEs contained within that level, and all lower levels. You can view the Category or Categories for any CDE you see in the Desktop by clicking on -the CDE, [bringing up the information metadata tab](https://metadatacenter.github.io/cedar-manual/cedar_templates/basic_topics/a3_viewing_resource_metadatda/), and selecting the Categories tab. +the CDE, [bringing up the information metadata tab](../../../basic_topics/a3_viewing_resource_information/), and selecting the Categories tab. CEDAR lists all the Categories to which the selected CDE belongs. ### When Creating a Template @@ -84,7 +84,7 @@ so searching using the identifier is the best approach. If you are trying to find all the templates (or instances) that are using a particular CDE, you could try using the field name of the CDE if it is relatively uncommon. -By using the [Advanced Searching—Field Names](https://metadatacenter.github.io/cedar-manual/sections/a2/4_advanced_searching_search_fields/) +By using the [Advanced Searching—Field Names](../../a2/4_advanced_searching_search_fields/) strategies, you can search by the name of the field for templates and/or instances containing that field. (You must use the actual name of the field, not the displayed label.) @@ -108,7 +108,7 @@ We do not manage the entire content of the CDE specification. CDEs in caDSR cont These references provide more information about performing CDE-related activities. -* [CEDAR for caDSR Users](https://metadatacenter.github.io/cedar-manual/cedar-for-cadsr)—a separate section of this manual targeting users of caDSR systems +* [CEDAR for caDSR Users](../../../pages/cedar-for-cadsr/)—a separate section of this manual targeting users of caDSR systems * [CEDAR Announcement of CDE Support](https://metadatacenter.org/happenings/news/cedar-announces-cde-support/)—Blog post describing CEDAR's support for CDEs * [Unleashing the value of Common Data Elements through the CEDAR Workbench](hhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153094/). Published in [Proceedings of AMIA 2019 Annual Symposium](https://knowledge.amia.org/69862-amia-1.4570936), 681-690. diff --git a/docs/user-guide/sections/c5/4_term_discovery_selection.md b/docs/user-guide/sections/c5/4_term_discovery_selection.md index fc23dcc..f7dd421 100644 --- a/docs/user-guide/sections/c5/4_term_discovery_selection.md +++ b/docs/user-guide/sections/c5/4_term_discovery_selection.md @@ -11,11 +11,11 @@ We're sorry, this resource has not yet been developed. You are welcome to contribute to its development at the link below. Will be just tips, in addition to those already provided in the detailed guide -[Choosing Controlled Terms](https://metadatacenter.github.io/cedar-manual/sections/c3/3_choosing_controlled_terms/) +[Choosing Controlled Terms](../../c3/3_choosing_controlled_terms/) * prefill the label effectively * look up related terms in BioPortal -* use tree to explore \ No newline at end of file +* use tree to explore diff --git a/docs/user-overview.md b/docs/user-overview.md index 1c14e54..14e55b4 100755 --- a/docs/user-overview.md +++ b/docs/user-overview.md @@ -6,6 +6,6 @@ Please send us your feedback -
  • Getting Started: CEDAR Workbench Orientation: If you want to understand just a little about the CEDAR Workbench tool before diving in, start here!
    • -
  • CEDAR Frequently Asked Questions: The most common questions we get about CEDAR and the CEDAR Workbench
    • +
  • Getting Started: CEDAR Workbench Orientation: If you want to understand just a little about the CEDAR Workbench tool before diving in, start here!
    • +
  • CEDAR Frequently Asked Questions: The most common questions we get about CEDAR and the CEDAR Workbench