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icon: simple-icons:github + href: https://github.com/Etschbeijer diff --git a/src/content/docs/guides/annotate-in-excel.mdx b/src/content/docs/guides/annotate-in-excel.mdx index f49be957d..f15c7bef7 100644 --- a/src/content/docs/guides/annotate-in-excel.mdx +++ b/src/content/docs/guides/annotate-in-excel.mdx @@ -2,11 +2,58 @@ title: Annotate in Excel authors: - kevin-frey + - patrick-blume sidebar: + order: 1 badge: - text: beta + text: new variant: caution -draft: true --- -Lorem ipsum \ No newline at end of file +import { Steps } from '@astrojs/starlight/components'; +import { Tabs, TabItem } from '@astrojs/starlight/components'; + +## Installation + +With the help of an [Excel-Add-In](https://learn.microsoft.com/de-de/office/dev/add-ins/excel/excel-add-ins-overview) you can manage your data, utilizing the [ARC](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/core-concepts/arc/) standard, directly in excel, without the necessity to upload it anywhere. +The functionality the excel-add-in provides are similar to [Swate](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/swate/) and the differences will be explained in the different sections of swate. +The excel-add-in will soon be published in the official [Microsoft Excel-Add-Ins Store](https://appsource.microsoft.com/en-us/marketplace/apps?product=excel). +Currently, we recommend the installation using the [excel-browser version provided by microsoft](https://excel.cloud.microsoft/?wdOrigin=MARKETING.FREE.GO-TO-EXCEL) because the set up is much easier than with a local excel version. + + + + + + +1. In order to annotate your data in Excel, based on the DataPlant standard, you have to download the [Manifest File](https://github.com/nfdi4plants/Swate/tree/main/src/Client/public). +2. After downloading the manifest file, you have to upload it to Excel, by clicking on the Add-Ins button (a) in the start tab of Excel. +3. Then you click on the Additional Add-Ins button in the exanded widget + + ![Swate Excel Brwoser Installation Step 1](@images/swate/swate-browser-excel-add-in-basic.png) + +4. In the next step you select My Add-Ins (a) and Upload My Add-In. + + ![Swate Excel Brwoser Installation Step 2](@images/swate/swate-browser-excel-add-in-additional-ones.png) + +5. Then you select choose the folder where you have downloaded the [Manifest File](https://github.com/nfdi4plants/Swate/tree/main/src/Client/public) to and select it, in order to upload it. +6. When the installation was successful, the icon of [Swate](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/swate/), the Excel-Add-In for annotating data, should be available in the data tab. +7. When you click on the icon the sidebar of swate should appear. Its size is adaptable and when it is big enough, the quick icons of the navbar are visible. +8. When everything was successful, it should look similar to this: + + + + + + + + +1. Follow the installation guide for [Excel-Add-Ins](https://support.microsoft.com/en-us/office/add-or-remove-add-ins-in-excel-0af570c4-5cf3-4fa9-9b88-403625a0b460). +2. When the installation was successful, the icon of [Swate](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/swate/), the Excel-Add-In for annotating data, should be available in the data tab. +3. When you click on the icon the sidebar of swate should appear. Its size is adaptable and when it is big enough, the quick icons of the navbar are visible. +4. When everything was successful, it should look similar to this: + + + + + +![Swate Sidebar Overview](@images/swate/swate-excel-overview.png) diff --git a/src/content/docs/guides/vs-code-extension.mdx b/src/content/docs/guides/vs-code-extension.mdx index e6a847076..7462d8b82 100644 --- a/src/content/docs/guides/vs-code-extension.mdx +++ b/src/content/docs/guides/vs-code-extension.mdx @@ -19,8 +19,6 @@ Some features you know from [ARCitect](/nfdi4plants.knowledgebase/arcitect) are -## Local installation - 1. From the [GitHub release page](https://github.com/nfdi4plants/arc-vs-code/releases/latest) download the asset `arc-vs-code-x.x.x.vsix` @@ -66,7 +64,7 @@ You only have to do this once for your account. ## Using the extension -Once you open an ARC folder in VSCode, the functions become are available in the context menus of relevant files and folders in your ARC (e.g. studies and assays) via right-click: +Once you open an ARC folder in VSCode, the functions are available in the context menus of relevant files and folders in your ARC (e.g. studies and assays) via right-click: - In the VSCode file tree, right-click on a study or assay name or the isa.investigation.xlsx to delete or edit the respective ISA metadata. - Right-click on the folders `studies` or `assays` to add a new study or assay. diff --git a/src/content/docs/swate/add-building-blocks.mdx b/src/content/docs/swate/add-building-blocks.mdx index 44bc2b1cf..adf695b6e 100644 --- a/src/content/docs/swate/add-building-blocks.mdx +++ b/src/content/docs/swate/add-building-blocks.mdx @@ -4,11 +4,24 @@ lastUpdated: 2024-04-26 authors: - kevin-frey - stella-eggels + - patrick-blume --- +import { Steps } from '@astrojs/starlight/components'; +import { Tabs, TabItem } from '@astrojs/starlight/components'; + + + + ![](@images/swate/swate-alpha-add-building-block.png) -import { Steps } from '@astrojs/starlight/components'; + + + +![](@images/swate/swate-excel-add-building-block.png) + + + @@ -40,9 +53,37 @@ import { Steps } from '@astrojs/starlight/components';

+ :::note If you cannot find a fitting term, you can write an issue to request an ontology term [here](https://github.com/nfdi4plants/nfdi4plants_ontology/issues/new/choose) **OR** use free text input. + ::: + + + + + + -4. Click "Add column" to insert the building block into an existing [Annotation Table](/nfdi4plants.knowledgebase/swate/annotation-table). The new building block will be added to the right side of the table. To change the position you can use the [context menu](/nfdi4plants.knowledgebase/swate/context-menu). +4. Click "Add column" to insert the building block into an existing [Annotation Table](/nfdi4plants.knowledgebase/swate/annotation-table). +The new building block will be added to the right side of the table. +To change the position you can use the [context menu](/nfdi4plants.knowledgebase/swate/context-menu). + + + + + + + + +4. Click "Add column" to insert the building block into an existing [Annotation Table](/nfdi4plants.knowledgebase/swate/annotation-table). +The new building block will be added at your selected column of the table. +When you have selected a column outside the table or the worksheet contains no annotation table, "Add column" fails. + + + + + + + 5. Depending on the [building block type](/nfdi4plants.knowledgebase/swate/building-blocks), multiple columns might be created. diff --git a/src/content/docs/swate/annotation-table.mdx b/src/content/docs/swate/annotation-table.mdx index 023ecdf24..cd8a0f380 100644 --- a/src/content/docs/swate/annotation-table.mdx +++ b/src/content/docs/swate/annotation-table.mdx @@ -1,27 +1,44 @@ --- title: Annotation Table -lastUpdated: 2024-04-25 +lastUpdated: 2024-11-14 authors: - kevin-frey - stella-eggels + - patrick-blume --- +import { Tabs, TabItem } from '@astrojs/starlight/components'; + :::tip Consider reading about [Swate](/nfdi4plants.knowledgebase/swate) ::: -## Open or create an assay or study file + + + +## Add an annotation table -To create an annotation table file with the [Swate standalone](https://swate-alpha.nfdi4plants.org/) in your browser, click "New File" and select which kind of file (investigation, study, assay) you want to create. If you already created a `isa.study.xlsx` or `isa.assay.xlsx` file, you can select "Import File" to modify and add to it. +In the "New Table" sheet, you can create your annotation table by adding [building blocks](/nfdi4plants.knowledgebase/swate/building-blocks). +Your annotation table should consist of an "Input", multiple descriptive building blocks ("Characteristics", "Parameters", "Components") and an "Output". -![Image showing add new file option in Swate](@images/swate/swate-alpha-new-file.png) +To create an annotation table within ARCitect, add a new table to your assay or study by clicking the plus (+) symbol next to your metadata sheet. +Here, you can build your annotation table by adding [building blocks](/nfdi4plants.knowledgebase/swate/building-blocks) the same way as in the Swate standalone. -In the "Metadata" sheet, you can fill in general metadata about your investigation, study or assay. +![Image showing Swate integration in ARCitect with focus on "add new annotation table"-button.](@images/swate/swate-alpha-arcitect-newtable.png) + + + ## Add an annotation table -In the "New Table" sheet, you can create your annotation table by adding [building blocks](/nfdi4plants.knowledgebase/swate/building-blocks). Your annotation table should consist of an "Input", multiple descriptive building blocks ("Characteristics", "Parameters", "Components") and an "Output". +When you have an empty excel sheet or one hat already contains an annotation table, you can click on the "Create Annotation Table" icon of the navbar of the sidebar. +When the excel sheet contains no annotation table, a new annotation table will be created in the active excel sheet. +When an annotation table already exists in the active excel sheet, a new excel sheet will be created, become active and a new annotation table will be created in that sheet. -To create an annotation table within ARCitect, add a new table to your assay or study by clicking the plus (+) symbol next to your metadata sheet. Here, you can build your annotation table by adding [building blocks](/nfdi4plants.knowledgebase/swate/building-blocks) the same way as in the Swate standalone. +The new annotation table will be created in the cell that was selected, when you the "Create Annotation Table" icon was clicked. +The newly created annotation table has a size of 1 Input [Source Name] column and row. -![Image showing Swate integration in ARCitect with focus on "add new annotation table"-button.](@images/swate/swate-alpha-arcitect-newtable.png) +![Image showing add new file option in Swate](@images/swate/swate-excel-add-annotation-table.png) + + + diff --git a/src/content/docs/swate/building-blocks.mdx b/src/content/docs/swate/building-blocks.mdx index 3130f9c53..77e48a2e3 100644 --- a/src/content/docs/swate/building-blocks.mdx +++ b/src/content/docs/swate/building-blocks.mdx @@ -16,7 +16,7 @@ Check out the ISA-XLSX specification to find out more about the individual build ISA-XLSX specification ::: -import SwateOverview from '@images/swate/overview.png' +import SwateOverview from '@images/swate/swate-alpha-overview.png' ## Usage in Swate diff --git a/src/content/docs/swate/file-picker.mdx b/src/content/docs/swate/file-picker.mdx index 2763e6aa4..12994f2db 100644 --- a/src/content/docs/swate/file-picker.mdx +++ b/src/content/docs/swate/file-picker.mdx @@ -4,8 +4,11 @@ lastUpdated: 2024-04-26 authors: - kevin-frey - stella-eggels + - patrick-blume --- +import { Tabs, TabItem } from '@astrojs/starlight/components'; + You might want to add file names to a column, "Input" or "Output". Since typing them in name by name could get quite tedious, you can copy the file names with the file picker instead. For this, click on the 'File Picker' tab in the sidebar and select "Pick file names". The file names will appear in the sidebar and you can modify their order. Once your files are listed in the correct order, click on "Insert File Names" to directly paste their names into the selected column. {/* reduce size of all images on this page */} @@ -18,4 +21,20 @@ You might want to add file names to a column, "Input" or "Output". Since typing `} -![](@images/swate/swate-alpha-filepicker.png) \ No newline at end of file + + + + + +![](@images/swate/swate-alpha-filepicker.png) + + + + + + +![](@images/swate/swate-excel-filepicker.png) + + + + diff --git a/src/content/docs/swate/index.mdx b/src/content/docs/swate/index.mdx index 07a289068..59be8a4b5 100644 --- a/src/content/docs/swate/index.mdx +++ b/src/content/docs/swate/index.mdx @@ -4,10 +4,13 @@ lastUpdated: 2024-09-04 authors: - martin-kuhl - stella-eggels + - patrick-blume sidebar: order: 1 --- +import { Tabs, TabItem } from '@astrojs/starlight/components'; + Welcome to the Swate Manual. Here you can find documentation about Swate features and best practices. @@ -16,7 +19,7 @@ Please explore the sections on the left to find guides on: - adding building blocks to your annotation table - filling cells with ontology terms - using and creating templates - +- handling top level metadata in excel Swate (Swate workflow annotation tool for Excel) is one of three central DataPLANT tools designed for convenient interaction with your [ARC](/nfdi4plants.knowledgebase/core-concepts/arc) (the other ones being [ARCitect](/nfdi4plants.knowledgebase/arcitect) and [ARC Commander](/nfdi4plants.knowledgebase/arc-commander)). Swate simplifies adding standardized metadata for your experimental workflows by leveraging a simple use of [ontologies](/nfdi4plants.knowledgebase/fundamentals/ontologies). Swate is integrated into ARCitect and will automatically be used when adding metadata to your studies and assays from within ARCitect, but it can also be used as a [standalone tool](https://swate-alpha.nfdi4plants.org/) in your browser. @@ -35,7 +38,22 @@ Users can add and delete building blocks to their ISA compliant annotation table Combination of ISA terms (Characteristic, Parameter, Factor, Component) and biological or technological ontology terms (e.g. temperature, strain, instrument model) gives the flexibility to display an ontology term, e.g. temperature, as a regular process parameter or as the factor your study is based on within your annotation table (Parameter [temperature] or Factor [temperature]). For more information on these building blocks, please check our [annotation principles](https://nfdi4plants.github.io/AnnotationPrinciples/). -![Building Blocks](@images/swate/building-block-categories.png) + + + + +![Building Blocks](@images/swate/swate-alpha-building-block-categories.png) + + + + + + +![Building Blocks](@images/swate/swate-excel-building-block-categories.png) + + + + Ontology terms within the Swate database can not only be used to standardize the headers of your annotation table, but also for standardization of the respective values. When filling in metadata via the "ontology term search", which can be activated by clicking the magnifying glass symbol, Swate will suggest matching metadata terms for the respective building block. Of course, users are not forced to use this feature in case they opt for more flexibility. @@ -44,7 +62,23 @@ Ontology terms within the Swate database can not only be used to standardize the Metadata annotation as part of the data submission routine to public repositories is often bothersome due to a high variability between repository requirements. This can become particularly inconvenient when the same metadata is submitted repeatedly, e.g. to unrelated public repositories. To assist researchers in this process, DataPLANT provides a growing collection of templates as a starting point for their annotation tables. The template design process is initiated “backwards”, starting from the requirements of public repositories and thereby, compliance with metadata standards. Our Data stewards supervise the metadata harmonization between template and target repository and simultaneously contribute to the development of the DataPLANT biology ontology [(DPBO)](https://github.com/nfdi4plants/nfdi4plants_ontology). From a technical perspective, these templates are ISA Protocols containing various Characteristics, Parameters, and the Study specific Factor. DataPLANT provides checklists and requirements of public repositories as templates that are considered useful for various technologies and common standards, e.g. MIAPPE. For finding metadata checklists and Swate templates that are suitable for your data, you might want to use the [Metadata recommendation quiz](/nfdi4plants.knowledgebase/resources/metadata-quiz). Swate templates can directly be integrated to the isa.study.xlsx and isa.assay.xlsx files using Swate. Once loaded into the table, they still can be modified to special needs in the sense of adding or deleting annotation building blocks. The modularity of the system also gives labs and institutions the possibility to create their own lab specific templates for experiments that are frequently run in the lab, e.g. a metabolomics experiment of a measurement facility. High flexibility is fostered by offering a manual or Swate-supported template customization, distribution, and use. -![Templates](@images/swate/swate-add-template.png) + + + + + +![Templates](@images/swate/swate-alpha-add-template.png) + + + + + + +![Templates](@images/swate/swate-excel-add-template.png) + + + + ## There is no wrong or right diff --git a/src/content/docs/swate/json.mdx b/src/content/docs/swate/json.mdx index 31038f5bf..3e97da281 100644 --- a/src/content/docs/swate/json.mdx +++ b/src/content/docs/swate/json.mdx @@ -3,9 +3,11 @@ title: JSON import and export lastUpdated: 2024-04-30 authors: - kevin-frey + - patrick-blume --- -import SwateOverview from '@images/swate/overview.png' +import SwateOverview from '@images/swate/swate-alpha-overview.png' +import { Tabs, TabItem } from '@astrojs/starlight/components'; Utilizing [ARCtrl](https://github.com/nfdi4plants/ARCtrl) all json formats Swate supports multiple different import and export formats for json. @@ -13,6 +15,20 @@ Utilizing [ARCtrl](https://github.com/nfdi4plants/ARCtrl) all json formats Swate The "File Export" function can be found in the Sidebar. + + + +You can export your data sheet simply by clicking on "Download". + + + + +In contrast to the web version of swate, you cannot simply download your annotation tables. +In order to do so, you have to create a [top level metadata sheet](http://localhost:4321/nfdi4plants.knowledgebase/swate/annotation-table/). + + + + ![](@images/swate/json-export.png) ## Import diff --git a/src/content/docs/swate/swate-template-contribution.mdx b/src/content/docs/swate/swate-template-contribution.mdx index 2d6bb4224..8e3ec5f48 100644 --- a/src/content/docs/swate/swate-template-contribution.mdx +++ b/src/content/docs/swate/swate-template-contribution.mdx @@ -5,9 +5,11 @@ authors: - dominik-brilhaus - kevin-frey - stella-eggels + - patrick-blume --- import { Steps } from '@astrojs/starlight/components'; +import { Tabs, TabItem } from '@astrojs/starlight/components'; :::note[About this guide] This tutorial guides you how to create Swate metadata templates with [Swate-alpha](https://swate-alpha.nfdi4plants.org/). @@ -49,8 +51,19 @@ Before contributing Swate templates you ideally have Open [Swate-alpha](https://swate-alpha.nfdi4plants.org/). To create a new template click "New File" and select "Template". If you want to edit an existing template, click "Import" and select the respective file. + + + ![](@images/swate/swate-alpha-template-new.png) + + + +![](@images/swate/swate-excel-template-new.png) + + + + ### Add Template Metadata Once you open a new template, you will see a "Metadata" sheet. Here you will enter a name for the template as well as further information describing the template. You can find explanations of the necessary information in the table below. @@ -76,10 +89,27 @@ Here is an example for filled out template metadata and how it helps in Swate's ### Add building blocks + + + To add the building blocks of your actual template, you need to switch from the "Metadata" sheet to the "New Table" sheet on the bottom left. Using the "Add Building Block" button, you can add your desired building blocks with or without a unit. ![](@images/swate/swate-alpha-building-block.png) + + + +To add the building blocks of your actual template, you have to create an annotation table with the "Create an Annotation table" icon (a) in the navbar. +Then you can select the desired building blocks in the "Building Block" tab (b) in the sidebar. +You can add building blocks with or without a unit at your selected column in the table by clicking the "Add Column" button. + +![](@images/swate/swate-excel-building-block.png) + + + + + + #### Recommendations for template design - Keep the template as concise as possible diff --git a/src/content/docs/swate/templates.mdx b/src/content/docs/swate/templates.mdx index ffa835aef..9cf6387c2 100644 --- a/src/content/docs/swate/templates.mdx +++ b/src/content/docs/swate/templates.mdx @@ -4,15 +4,29 @@ lastUpdated: 2024-04-26 authors: - kevin-frey - stella-eggels + - patrick-blume --- +import { Tabs, TabItem } from '@astrojs/starlight/components'; + A good starting point for your data annotation is using a predefined template. You can find them by clicking the "Add Template" widget at the top or under the "Templates" tab in the sidebar. Here, click on the "Browse database" to explore all currently available templates. :::note[Get in contact] If you have any problems in using the templates please contact us [via Swate issues](https://github.com/nfdi4plants/Swate/issues/new/choose) or if you want to discuss existing templates or request new ones, please contact us [via templates issues](https://github.com/nfdi4plants/SWATE_templates/issues/new/choose). ::: -![](@images/swate/swate-add-template.png) + + + +![](@images/swate/swate-alpha-add-template.png) + + + + +![](@images/swate/swate-excel-add-template.png) + + + ## Template search diff --git a/src/content/docs/swate/term-search.mdx b/src/content/docs/swate/term-search.mdx index f2cb19d72..ee05c05cb 100644 --- a/src/content/docs/swate/term-search.mdx +++ b/src/content/docs/swate/term-search.mdx @@ -4,9 +4,12 @@ lastUpdated: 2024-04-26 authors: - kevin-frey - stella-eggels + - patrick-blume --- -import SwateOverview from '@images/swate/overview.png' +import { Tabs, TabItem } from '@astrojs/starlight/components'; + +import SwateOverview from '@images/swate/swate-alpha-overview.png' While this page will focus on the ontology term search, it will also feature useful information about term search related to the [Building Blocks](/nfdi4plants.knowledgebase/swate/add-building-blocks) page. @@ -20,6 +23,9 @@ You can find ontology term search fields on the *Building Blocks* and on the *On ## Usage + + + ![Image highlighting important components of the swate in-table term search](@images/swate/swate-alpha-ontology-termsearch4.png) *When you start typing a word to search for a specific term, both child terms and unrelated terms will be suggested. You can recognize the terms that are related to your building block header (parent term, b) by the symbol in front of the terms ( c ).* @@ -31,6 +37,25 @@ Type in the search field to trigger the auto-complete function and find terms. S You can toggle the auto complete search by clicking on the magnifying glass ( a ) or pressing Tab with the search field active! ::: +:::tip[Search all Children] +Double click into a empty search field to return up to 500 children of a given [parent term](#relationship-directed-search). +::: + + + + +![Image highlighting important components of the swate in-table term search](@images/swate/swate-excel-ontology-termsearch4.png) +*When you start typing a word to search for a specific term, several terms will be suggested, independent of a parent term. +Upon clicking the small arrow on the side (a) additional information of the ontology will be shown, its name, description and source (b).* + +The term search function of the sidebar enables you to find and insert ontology terms in an [ISA-Tab conform way](https://isa-specs.readthedocs.io/en/latest/isatab.html#ontology-annotations). + +Type in the search field to trigger the auto-complete function and find terms. +Select the term you want and add it to the selected building blocks of your table by clicking "Fill celected cells with this term". + + + + Terms will be added to the selected rows in the format: ``` @@ -49,10 +74,6 @@ To trigger this search the input must match the [Swate Regex pattern](http://reg To execute the search query on any search text again after closing the dropdown with the search results, double click into the search field. ::: -:::tip[Search all Children] -Double click into a empty search field to return up to 500 children of a given [parent term](#relationship-directed-search). -::: - ## SwateDB Access to the SwateDB with a list of established, [external ontologies](/nfdi4plants.knowledgebase/fundamentals/ontology-service-landscape) deemed fit for use in plant science. In addition we feature our very own ontology [DPBO](https://github.com/nfdi4plants/nfdi4plants_ontology/blob/main/nfdi4plants_ontology.obo), which we extend with missing but necessary terms. @@ -77,6 +98,6 @@ Let's look at this with an example: |-------------|------------------------------|------------------------------|------------------------------------|-------------| | | | | | | -import SwateRelationshipGraph from '@images/swate/swate-relationship-graph-exp.jpg' +import SwateRelationshipGraph from '@images/swate/swate-relationship-graph-exp.png' If a user wants to fill in cells of the column `Component [instrument model]`, they are most likely looking for the instrument model used in their experimental workflow. In this example the instrument model series and the exact instrument models are so-called child terms of `instrument model (MS:1000031)` because they are connected to `instrument model (MS:1000031)` via `is_a` relationships. When a cell of the column `Component [instrument model]` is selected, the respective child terms can be shown by double clicking into the empty search field. diff --git a/src/content/docs/swate/top-level-metadata.mdx b/src/content/docs/swate/top-level-metadata.mdx new file mode 100644 index 000000000..340988a70 --- /dev/null +++ b/src/content/docs/swate/top-level-metadata.mdx @@ -0,0 +1,49 @@ +--- +title: Top Level Metadata +lastUpdated: 2024-11-14 +authors: + - kevin-frey + - stella-eggels + - patrick-blume +--- + +import { Tabs, TabItem } from '@astrojs/starlight/components'; + +:::tip +Consider reading about [Swate](/nfdi4plants.knowledgebase/swate) +::: + + + + +## Open or create an assay or study file + +To create an annotation table file with the [Swate standalone](https://swate-alpha.nfdi4plants.org/) in your browser, click "New File" and select which kind of file (investigation, study, assay) you want to create. +If you already created a `isa.study.xlsx` or `isa.assay.xlsx` file, you can select "Import File" to modify and add to it. + +![Image showing add new file option in Swate](@images/swate/swate-alpha-new-file.png) + +In the "Metadata" sheet, you can fill in general metadata about your investigation, study or assay. + + + + +## Top level metadata handling + +In contrast to [Swate standalone](https://swate-alpha.nfdi4plants.org/) in your browser, swate in excel doesn't need a metadata sheet and can be used to just store your data without any additional information. + +In order to export your data as [JSON](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/swate/json/) a top level metadata file is needed but it can be added afterwards and be changed any time, without affecting the rest of your data. + +You create by clicking the "Create Metadata" icon in the nabar of the sidebar. When a top level metadatasheet is available, the different properties of it will be loaded, enabling you to manipulate the data outside the sheet itself or delete it. +When no top level meta data sheet is available, you can determine its [Type](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/arc-commander/isa/). + +![Image showing add new file option in Swate](@images/swate/swate-excel-create-top-level-metadata.png) + +After you decided its type, the sheet with the basic information of the top level metadata will be created. While the dialogue is open in the sidebar, changes in the sheet will not be recognized. +When you reopen the dialogue to adapt your top level metadata, the changes in the sheet will be present now. + +![Image showing add new file option in Swate](@images/swate/swate-excel-update-top-level-metadata.png) + + + + diff --git a/src/content/docs/vault/swate-quickstart.md b/src/content/docs/vault/swate-quickstart.md index 2de70f62e..1d71a2f43 100644 --- a/src/content/docs/vault/swate-quickstart.md +++ b/src/content/docs/vault/swate-quickstart.md @@ -62,7 +62,7 @@ Briefly: Alternatively, you can also use one of DataPLANT’s [Swate templates](/nfdi4plants.knowledgebase/swate/templates). You can find them via the "add template" button, next to the "add building block" button. -![](@images/swate/swate-add-template.png) +![](@images/swate/swate-alpha-add-template.png) ## Annotate your samples and data diff --git a/src/content/docs/vault/swate-walkthrough.md b/src/content/docs/vault/swate-walkthrough.md index d0761d12e..4d3e66e7d 100644 --- a/src/content/docs/vault/swate-walkthrough.md +++ b/src/content/docs/vault/swate-walkthrough.md @@ -24,13 +24,13 @@ Create and/or open an annotation table as described in the [Swate QuickStart](/n ## Swate Overview -![](@images/swate/overview.png) +![](@images/swate/swate-alpha-overview.png) ## Add building blocks to create your annotation table Each annotation should start with an *Input* and end with an *Output* column. To add and specify your *Input* building block, click either the "Add Building Block" widget on the top (A) or use the "Building Blocks" function in the sidebar (B). Select *Input* from the drop-down menu instead of *Parameter* and select *Source Name* as input type. Then click Add column. Add *Output [Sample Name]* analogously. -![](@images/swate/building-block-categories.png) +![](@images/swate/swate-alpha-building-block-categories.png) > 💡 Only one *Input*, one *Output* and one of each *Protocol* columns can be added per table.