diff --git a/src/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/custom/demo_isa.study1.png b/src/docs/img/demo_isa.study1.png similarity index 100% rename from src/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/custom/demo_isa.study1.png rename to src/docs/img/demo_isa.study1.png diff --git a/src/docs/teaching-materials/disseminations/2023-06-28_ARC-Club_HHU/06-annotation.html b/src/docs/teaching-materials/disseminations/2023-06-28_ARC-Club_HHU/06-annotation.html index f6dc384c2..89334849f 100644 --- a/src/docs/teaching-materials/disseminations/2023-06-28_ARC-Club_HHU/06-annotation.html +++ b/src/docs/teaching-materials/disseminations/2023-06-28_ARC-Club_HHU/06-annotation.html @@ -225,7 +225,7 @@

Update ontology reference columns

Your ISA table is growing

At this point. Your table should look similar to this:

-

+

Hiding ontology reference columns

diff --git a/src/docs/teaching-materials/disseminations/2023-06-28_ARC-Club_HHU/06-annotation.md b/src/docs/teaching-materials/disseminations/2023-06-28_ARC-Club_HHU/06-annotation.md index 5e9554f59..62b2fbd8e 100644 --- a/src/docs/teaching-materials/disseminations/2023-06-28_ARC-Club_HHU/06-annotation.md +++ b/src/docs/teaching-materials/disseminations/2023-06-28_ARC-Club_HHU/06-annotation.md @@ -267,7 +267,7 @@ Click the Update Ontology Terms quick access buttons. At this point. Your table should look similar to this: -![w:1000](./../custom/demo_isa.study1.png) +![w:1000](./../../../img/demo_isa.study1.png) --- diff --git a/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block05-MetadataISA.html b/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block05-MetadataISA.html index fd8c08200..7e9627bf5 100644 --- a/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block05-MetadataISA.html +++ b/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block05-MetadataISA.html @@ -1,4 +1,4 @@ -Metadata and ISA
-

Block 5 – Metadata and ISA

+/* Styling page number */div#\:\$p>svg>foreignObject>section:after{font-family:Calibri,sans-serif;font-size:20px;color:#2D3E50}div#\:\$p>svg>foreignObject>section:after{--marpit-root-font-size:20px}div#\:\$p>svg>foreignObject>section .profile-picture{position:relative;overflow:hidden;border-radius:50%;border-color:black;height:75px;width:75px;margin:10px;display:block}div#\:\$p>svg>foreignObject>section .reference{font-size:20px;line-height:1.2em;position:fixed;left:50%;bottom:0px;transform:translate(-50%,-50%);margin:0 auto}div#\:\$p>svg>foreignObject>section section.reference{--marpit-root-font-size:20px}div#\:\$p>svg>foreignObject>section[data-marpit-scope-YRxwNF1R]{background:none;background-color:white}div#\:\$p>svg>foreignObject>section[data-marpit-scope-Sp4PGJC6]{text-align:center;background:#F9CD69}div#\:\$p>svg>foreignObject>section[data-marpit-scope-Sp4PGJC6]:after{display:none}div#\:\$p>svg>foreignObject>section[data-marpit-scope-Sp4PGJC6] footer{display:none}div#\:\$p>svg>foreignObject>section[data-marpit-scope-6dfT5d1S]{text-align:justify}div#\:\$p>svg>foreignObject>section[data-marpit-scope-z1UIFi9i]{text-align:justify}div#\:\$p>svg>foreignObject>section[data-marpit-scope-nrY5Hnxx] .columns{display:grid;grid-template-columns:repeat(3,minmax(0,1fr));gap:calc(var(--marpit-root-font-size, 1rem) * 1)}div#\:\$p>svg>foreignObject>section[data-marpit-scope-nrY5Hnxx] ul{margin:5;padding:0}div#\:\$p>svg>foreignObject>section[data-marpit-scope-sARIzq4u] .columns{display:grid;grid-template-columns:repeat(3,minmax(0,1fr));gap:calc(var(--marpit-root-font-size, 1rem) * 1)}div#\:\$p>svg>foreignObject>section[data-marpit-scope-sARIzq4u] ul{margin:5;padding:0}div#\:\$p>svg>foreignObject>section[data-marpit-scope-cozTGKhk] .columns{display:grid;grid-template-columns:repeat(2,minmax(0,1fr));gap:calc(var(--marpit-root-font-size, 1rem) * 4)}div#\:\$p>svg>foreignObject>section[data-marpit-scope-Fl5kfV3Z] code{display:inline-block;width:700px;font-size:18px}div#\:\$p>svg>foreignObject>section[data-marpit-scope-QNXwk9Fu] code{display:inline-block;width:700px}div#\:\$p>svg>foreignObject>section[data-marpit-scope-oB2KsyId] code{ + /*display: inline-block;*/font-size:12px}div#\:\$p>svg>foreignObject>section[data-marpit-scope-dwmWmumd]{font-size:25px}div#\:\$p>svg>foreignObject>section[data-marpit-scope-dwmWmumd]{--marpit-root-font-size:25px}div#\:\$p>svg>foreignObject>section[data-marpit-scope-i4zH27PQ] :is(h1,marp-h1){text-align:left}div#\:\$p>svg>foreignObject>section[data-marpit-scope-i4zH27PQ]{text-align:center}div#\:\$p>svg>foreignObject>section[data-marpit-scope-shRDC49u] :is(h1,marp-h1){text-align:left}div#\:\$p>svg>foreignObject>section[data-marpit-scope-shRDC49u]{text-align:center}div#\:\$p>svg>foreignObject>section[data-marpit-scope-lgBYfuz1] :is(h1,marp-h1){text-align:left}div#\:\$p>svg>foreignObject>section[data-marpit-scope-lgBYfuz1]{text-align:center}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background]{columns:initial!important;display:block!important;padding:0!important}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background]:after,div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background]:before,div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=content]:after,div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=content]:before{display:none!important}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background]>div[data-marpit-advanced-background-container]{all:initial;display:flex;flex-direction:row;height:100%;overflow:hidden;width:100%}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background]>div[data-marpit-advanced-background-container][data-marpit-advanced-background-direction=vertical]{flex-direction:column}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background][data-marpit-advanced-background-split]>div[data-marpit-advanced-background-container]{width:var(--marpit-advanced-background-split,50%)}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background][data-marpit-advanced-background-split=right]>div[data-marpit-advanced-background-container]{margin-left:calc(100% - 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+

Block 5 – Metadata and ISA

September 28th, 2023

@@ -42,28 +42,25 @@

Block 5 – Metadata and ISA

-
-

Metadata

+
+

What is
metadata?

-
-

What is
metadata?

-
-
-

Viola's PhD Project

+
+

Viola's PhD Project

Exercise: Take 5 minutes to note down the metadata

Viola investigates the effect of the plant circadian clock on sugar metabolism in W. mirabilis. For her PhD project, which is part of an EU-funded consortium in Prof. Beetroot's lab, she acquires seeds from a South-African botanical society. Viola grows the plants under different light regimes, harvests leaves from a two-day time series experiment, extracts polar metabolites as well as RNA and submits the samples to nearby core facilities for metabolomics and transcriptomics measurements, respectively. After a few weeks of iterative consultation with the facilities' heads as well as technicians and computational biologists involved, Viola receives back a wealth of raw and processed data. From the data she produces figures and wraps everything up to publish the results in the Journal of Wonderful Plant Sciences.

-
-

Metadata everywhere

+
+

Metadata everywhere

Viola investigates the effect of the plant circadian clock on sugar metabolism in W. mirabilis. For her PhD project, which is part of an EU-funded consortium in Prof. Beetroot's lab, she acquires seeds from a South-African botanical society. Viola grows the plants under different light regimes, harvests leaves from a two-day time series experiment, extracts polar metabolites as well as RNA and submits the samples to nearby core facilities for metabolomics and transcriptomics measurements, respectively. After a few weeks of iterative consultation with the facilities' heads as well as technicians and computational biologists involved, Viola receives back a wealth of raw and processed data. From the data she produces figures and wraps everything up to publish the results in the Journal of Wonderful Plant Sciences.

-
-

Project metadata

+
+

Project metadata

-

project design

+

project design

  • researcher
  • institute and project
    • @@ -74,7 +71,7 @@

    project design

-

experimental processes

+

experimental processes

  • origin and nature of the biological material
  • lab protocols
    • @@ -83,7 +80,7 @@

    experimental processes

-

data-analytical processes

+

data-analytical processes

  • algorithms
  • tools
    • @@ -93,11 +90,11 @@

    data-analytical processes

-
-

Other types of metadata

+
+

Other types of metadata

-

bibliographic

+

bibliographic

  • Title
  • Publication date and title
    • @@ -109,7 +106,7 @@

    bibliographic

-

legal or administrative

+
  • data origin, ownership, rovenance,
  • licensing
    • @@ -118,7 +115,7 @@

    legal or administrative

-

technical

+

technical

  • expected data volume
  • storage location
    • @@ -128,8 +125,8 @@

    technical

-
-

Metadata from a FAIR perspective

+
+

Metadata from a FAIR perspective

Findable

@@ -158,37 +155,37 @@

Metadata from a FAIR perspective

-
-

Metadata "Standards"

-

Examples from Minimum Information for Biological and Biomedical Investigations (MIBBI):

+
+

Metadata "Standards"

+

Examples from Minimum Information for Biological and Biomedical Investigations (MIBBI):

-

💡 Check out https://fairsharing.org/ for more examples

+

💡 Check out https://fairsharing.org/ for more examples

-
-

Metadata standards ≈ Checklists

+
+

Metadata standards ≈ Checklists

  • Determine (minimal) required information
  • Usually do not determine the format (i.e. shape or file type)
-
-

A small Interactive detour

+
+

A small Interactive detour

-> favorite Movie

-
-

How does google "know"?!

+
+

How does google "know"?!

-
-

Schemas and machine-readability

+
+

Schemas and machine-readability

-
-

Structured data and the internet

+
+

Structured data and the internet

Schema.org

  • create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, ...
    • @@ -199,45 +196,37 @@

    Structured data and the internet

  • Metadata interoperability and standardization across all website using schema.org
-
-

Structured data and the internet: Schema.org

+
+

Structured data and the internet: Schema.org

https://schema.org/Person

-
    <script type="application/ld+json">
-    {
-      "@context": "https://schema.org",
-      "@type": "VisualArtwork",
-      "name": "La trahison des images",
-      "alternateName": "The Treachery of Images",
-      "image": "http://upload.wikimedia.org/wikipedia/en/b/b9/MagrittePipe.jpg",
-      "description": "The painting shows a pipe. Below it, Magritte...",
-      "creator": [
-        {
-          "@type": "Person",
-          "name": "René Magritte",
-          "sameAs": "https://www.freebase.com/m/06h88"
-        }
-      ],
-      "width": [
-        {
-          "@type": "Distance",
-          "name": "940 mm"
-        }
-      ],
-      "height": [
-        {
-          "@type": "Distance",
-          "name": "635 mm"
-        }
-      ],
-      "artMedium": "oil",
-      "artworkSurface": "canvas"
-    }
-    </script>
+
<script type="application/ld+json">
+{
+  "@context": "https://schema.org",
+  "@type": "Person",
+  "address": {
+    "@type": "PostalAddress",
+    "addressLocality": "Seattle",
+    "addressRegion": "WA",
+    "postalCode": "98052",
+    "streetAddress": "20341 Whitworth Institute 405 N. Whitworth"
+  },
+  "colleague": [
+    "http://www.xyz.edu/students/alicejones.html",
+    "http://www.xyz.edu/students/bobsmith.html"
+  ],
+  "email": "mailto:jane-doe@xyz.edu",
+  "image": "janedoe.jpg",
+  "jobTitle": "Professor",
+  "name": "Jane Doe",
+  "telephone": "(425) 123-4567",
+  "url": "http://www.janedoe.com"
+}
+</script>
-
-

JSON-LD

+
+

JSON-LD

JSON-LD = JavaScript Object Notation for Linked Data

<script type="application/ld+json">
@@ -259,8 +248,8 @@ 
JSON-LD

 </script>
-
-

RDFa

+
+

RDFa

RDFa = Resource Description Framework in Attributes

<div vocab="http://schema.org/" typeof="SportsTeam">
   <span property="name">San Francisco 49ers</span>
@@ -275,18 +264,18 @@ 
RDFa

 </div>
-
-

Standards

-

Dublin Core

+
+

Standards

+

Dublin Core

https://www.dublincore.org/schemas/

-

DataCite Schema

+

DataCite Schema

-
-

DataCite Schema: Simple Example

+
+

DataCite Schema: Simple Example

...
   <identifier identifierType="DOI">10.5072/D3P26Q35R-Test</identifier>
   <creators>
@@ -325,8 +314,8 @@ 
DataCite Schema: Simple Example

https://schema.datacite.org/meta/kernel-4.3/example/datacite-example-dataset-v4.xml

-
-

Ontology

+
+

Ontology

(Sometimes also referred to "semantic model")

An ontology combines features of

    @@ -335,81 +324,81 @@

    Ontology

  • a thesaurus
-
-

Dictionary

+
+

Dictionary

Alphabetically lists terms and their definitions

Pizza: "a dish made typically of flattened bread dough spread with a savory mixture usually including tomatoes and cheese and often other toppings and baked"

-
-

Taxonomy

+
+

Taxonomy

Hierarchy or classification

-
-

Thesaurus

+
+

Thesaurus

Dictionary of synonyms and relations

Pizza ≈ Lahmacun ≈ Focaccia ≈ Flammkuchen

-
-

Ontology

+
+

Ontology

  • Structures a set of concepts in a particular area and the relations between them in a graph-like manner
  • Can be used in disambiguation, defining hierarchies, a standard to define terms
  • Define a common vocabulary of concepts and their relationships to model a particular domain while making it machine understandable
-
-

The semantic triple

+
+

The semantic triple

-
-

Modeling a pizza menu

+
+

Modeling a pizza menu

-
-

Modeling a pizza menu

+
+

Modeling a pizza menu

-
-

Modeling a pizza menu

+
+

Modeling a pizza menu

-
-

Predicates have two directions

+
+

Predicates have two directions

-
-

Looking at the menu from a different perspective

+
+

Looking at the menu from a different perspective

An object of one triplet can be the subject to another

-
-

(Towards) a knowledge graph

+
+

(Towards) a knowledge graph

-
-

Searching the menu

+
+

Searching the menu

An ontology can be queried:

  • "name all pizzas with topping mushrooms"
-
-

The Pizza Ontology

+
+

The Pizza Ontology

-
-

Example ontologies

-

EDAM ontology

+
+

Example ontologies

+

EDAM ontology

-

PECO ontology

+

PECO ontology

-
-

ARC builds on ISA

+
+

ARC builds on ISA

https://isa-tools.org/format/specification.html

-
-

ARC builds on ISA

+
+

ARC builds on ISA

-
-

isa.<>.xlsx files within ARCs

+
+

isa.<>.xlsx files within ARCs

-
-

Study and assay files are registered in the investigation file

+
+

Study and assay files are registered in the investigation file

-
-

The output of a study or assay file can function as input for a new isa.assay.xlsx

+
+

The output of a study or assay file can function as input for a new isa.assay.xlsx

Output building blocks:

  • Sample Name
    • @@ -448,22 +437,22 @@

    The output of a study or assay file can function as input for a new isa.assa
  • Derived Data File

-
-

+
+

-
-

Swate

+
+

Swate

-
-

Annotation by flattening the knowledge graph

+
+

Annotation by flattening the knowledge graph

  • Low-friction metadata annotation
  • Familiar spreadsheet, row/column-based environment
-
-

Annotation principle

+
+

Annotation principle

    @@ -471,15 +460,15 @@

    Annotation principle

  • Familiar spreadsheet, row/column-based environment
-
-

Adding new building blocks (columns)

+
+

Adding new building blocks (columns)

  • Swate can be used for the annotation of isa.study.xlsx and isa.assay.xlsx files
-
-

Annotation Building Block types

+
+

Annotation Building Block types

  • Source Name (Input)
    • @@ -500,43 +489,43 @@

    Annotation Building Block types

Let's take a detour on Annotation Principles | slides

-
-

Ontology term search

+
+

Ontology term search

Enable related term directed search to directly fill cells with child terms

-
-

Fill your table with ontology terms

+
+

Fill your table with ontology terms

-
-

Hierarchical combination of ontologies

+
+

Hierarchical combination of ontologies

-
-

Swate templates

+
+

Swate templates

-
-

Checklists and Templates

+
+

Checklists and Templates

Metadata standards or repository requirements can be represented as templates

-
-

Realization of lab-specific metadata templates

-

+
+

Realization of lab-specific metadata templates

+

Facilities can define their most common workflows as templates

-
-

Directly import templates via Swate

+
+

Directly import templates via Swate

  • DataPLANT curated
  • Community templates
-
-
-

Contributors

+
+
+

Contributors

Slides presented here include contributions by

Exercise: Association map +

Exercise: Association map Online: Let participants annotate (via video conference tool) -Presence: Draw map on (white) board

- let participant name a movie +Presence: Draw map on (white) board

- let participant name a movie - how do you find out the actors, director, release year, etc.? - => google.com - google movie - see knowledge graph to the right - how does google know all that?! -- ===> schema.org

TODO: -- This is actually not a proper ontology(!), but rather a knowledge graph (= ontology + data)

LIVE-Demo +- ===> schema.org

TODO: +- This is actually not a proper ontology(!), but rather a knowledge graph (= ontology + data)

LIVE-Demo - Search an "interesting" term from PECO in browser (EBI OLS) - Example: - plant exposure @@ -569,9 +556,9 @@

Contributors

drought environment exposure - Show the graph view (and expand it interactively) - Mention that terms (subjects, objects) and properties (predicates) have "URIs", "PIDs" -- Show that terms can have alternative / external IDs and link to "outdated" ontologies

<style scoped> +- Show that terms can have alternative / external IDs and link to "outdated" ontologies

<style scoped> section p img{ /* padding-left: 230px */ } -</style>

combination of ISA (Characteristics, Parameter, Factor) and a biological or technological ontology (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 (Parameter \[temperature\] or Factor \[temperature\]).

\ No newline at end of file +</style>

combination of ISA (Characteristics, Parameter, Factor) and a biological or technological ontology (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 (Parameter \[temperature\] or Factor \[temperature\]).

\ No newline at end of file diff --git a/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block05-MetadataISA.md b/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block05-MetadataISA.md index c64690426..0255173e0 100644 --- a/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block05-MetadataISA.md +++ b/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block05-MetadataISA.md @@ -11,8 +11,6 @@ author: - name: Martin Kuhl github: https://github.com/Martin-Kuhl orcid: https://orcid.org/0000-0002-8493-1077 -- name: Sabrina Zander - orcid: https://orcid.org/0009-0000-4569-6126 --- # Block 5 – Metadata and ISA @@ -48,10 +46,6 @@ September 28th, 2023 --- -# Metadata - ---- - # What is
**metadata**?
-

Block 6 – Swate hands-on

+/* Styling page number */div#\:\$p>svg>foreignObject>section:after{font-family:Calibri,sans-serif;font-size:20px;color:#2D3E50}div#\:\$p>svg>foreignObject>section:after{--marpit-root-font-size:20px}div#\:\$p>svg>foreignObject>section .profile-picture{position:relative;overflow:hidden;border-radius:50%;border-color:black;height:75px;width:75px;margin:10px;display:block}div#\:\$p>svg>foreignObject>section .reference{font-size:20px;line-height:1.2em;position:fixed;left:50%;bottom:0px;transform:translate(-50%,-50%);margin:0 auto}div#\:\$p>svg>foreignObject>section section.reference{--marpit-root-font-size:20px}div#\:\$p>svg>foreignObject>section[data-marpit-scope-WFwZBx9U]{background:none;background-color:white}div#\:\$p>svg>foreignObject>section[data-marpit-scope-mDtitS9k] .columns{ + /* grid-template-columns: repeat(2, minmax(0, 1fr)); */grid-template-columns:500px 500px;gap:30px;display:flex;justify-content:center}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background]{columns:initial!important;display:block!important;padding:0!important}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background]:after,div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background]:before,div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=content]:after,div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=content]:before{display:none!important}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background]>div[data-marpit-advanced-background-container]{all:initial;display:flex;flex-direction:row;height:100%;overflow:hidden;width:100%}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background]>div[data-marpit-advanced-background-container][data-marpit-advanced-background-direction=vertical]{flex-direction:column}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background][data-marpit-advanced-background-split]>div[data-marpit-advanced-background-container]{width:var(--marpit-advanced-background-split,50%)}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background][data-marpit-advanced-background-split=right]>div[data-marpit-advanced-background-container]{margin-left:calc(100% - var(--marpit-advanced-background-split, 50%))}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=background]>div[data-marpit-advanced-background-container]>figure{all:initial;background-position:center;background-repeat:no-repeat;background-size:cover;flex:auto;margin:0}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=content],div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=pseudo]{background:transparent!important}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background=pseudo],div#\:\$p>svg[data-marpit-svg]>foreignObject[data-marpit-advanced-background=pseudo]{pointer-events:none!important}div#\:\$p>svg>foreignObject>section[data-marpit-advanced-background-split]{width:100%;height:100%}
+

Block 6 – Swate hands-on

September 28th, 2023

@@ -43,25 +43,25 @@

Block 6 – Swate hands-on

-

Goals

+

Goals

  • Get familiar with ISA metadata and Swate
  • Annotate data in your ARC
-

Check Swate installation

-

☑️ Make sure Swate is installed:

+

Check Swate installation

+

☑️ Make sure Swate is installed:

  1. Open Excel (online or Desktop)
  2. Go to the Insert tab: Click the arrow next to "My Add-ins". There you should be able to select Swate.
  3. Go to the Data tab: you should see the Swate (Core) add-in.
-

💡 Alternatively, you can use Swate standalone
-(⚠️ this is however work in progress and likely to change)

+

💡 Alternatively, you can use Swate standalone
+(⚠️ this is however work in progress and likely to change)

-

Have a simple text editor ready

+

Have a simple text editor ready

  • Windows Notepad
  • MacOS TextEdit
    • @@ -74,46 +74,46 @@

    Have a simple text editor ready

-

Download the demo data

+

Download the demo data

git clone "https://demo-user:5ehDYeHcqP2MqVXsNNPu@git.nfdi4plants.org/teaching/demo-arc_level1.git"
-

Where we left off last time

-

👩‍💻 Initiated an ARC
-📂 Structured and ...
-🌐 Shared with collaborators

+

Where we left off last time

+

👩‍💻 Initiated an ARC
+📂 Structured and ...
+🌐 Shared with collaborators


Today we want to

... annotate the experimental data

-

Swate hands-on with demo data

+

Swate hands-on with demo data

-

Swate Overview

+

Swate Overview

-

Let's annotate the plant samples first

+

Let's annotate the plant samples first

  1. Navigate to the demo ARC.
  2. Open the lab notes studies/talinum_drought/protocols/plant_material.txt in a text editor.
  3. Open the empty studies/talinum_drought/isa.study.xlsx workbook in Excel.
-
-

Create an annotation table

+
+

Create an annotation table


Create a Swate annotation table via the create annotation table button in the yellow pop-up box OR click the Create Annotation Table quick access button.


-

💡 Each table is by default created with one input (Source Name) and one output (Sample Name) column

+

💡 Each table is by default created with one input (Source Name) and one output (Sample Name) column

-

💡 Only one annotation table can be added per Excel sheet

+

💡 Only one annotation table can be added per Excel sheet

@@ -122,7 +122,7 @@

Create an annotation table

-

Add a building block

+

Add a building block

  1. Navigate to the Building Blocks tab via the navbar. Here you can add Building Blocks to the table.
  2. Instead of Parameter select Characteristic from the drop-down menu (A)
    3. @@ -131,19 +131,19 @@

    Add a building block

  3. Click Add building block.
-

💡 This adds three columns to your table, one visible and two hidden.

+

💡 This adds three columns to your table, one visible and two hidden.

-

Insert values to annotate your data

+

Insert values to annotate your data

  1. Navigate to the Terms tab in the Navbar
  2. In the annotation table, select any number of cells below Characteristic [organism]
  3. Click into the search field in Swate.
-

💡 You should see organism showing in a field in front of the search field
-💡 The search will now yield results related to organism

+

💡 You should see organism showing in a field in front of the search field
+💡 The search will now yield results related to organism

  1. In the search field, search for "Talinum fruticosum"
    2. @@ -151,7 +151,7 @@

    Insert values to annotate your data

-

Add a building block with a unit

+

Add a building block with a unit

  1. In the Building Blocks tab, select Parameter, search for light intensity exposure and select the term with id PECO:0007224.
  2. Check the box for This Parameter has a unit and search for microeinstein per square meter per second in the adjacent search bar.
    3. @@ -159,46 +159,46 @@

    Add a building block with a unit

  3. Click Add building block.
-

💡 This adds four columns to your table, one visible and three hidden.

+

💡 This adds four columns to your table, one visible and three hidden.

-

Insert unit-values to annotate your data

+

Insert unit-values to annotate your data

In the annotation table, select any cell below Parameter [light intensity exposure] and add "425" as light intensity.

-

💡 You can see the numbers being complemented with the chosen unit, e.g. 425.00 microeinstein per square meter per second

+

💡 You can see the numbers being complemented with the chosen unit, e.g. 425.00 microeinstein per square meter per second

-

Showing ontology reference columns

+

Showing ontology reference columns

Hold Ctrl and click the Autoformat Table quick access button to adjust column widths and un-hide all hidden columns.

-

💡 You can see that your organism of choice was added with id and source Ontology in the reference (hidden) columns.
-⚠️ This feature is currently not supported on MacOS

+

💡 You can see that your organism of choice was added with id and source Ontology in the reference (hidden) columns.
+⚠️ This feature is currently not supported on MacOS

-

Update ontology reference columns

+

Update ontology reference columns

Click the Update Ontology Terms quick access buttons.

-

💡 This updates all reference columns according to the main column. In this case the reference columns for Parameter [light intensity exposure] are updated with the id and source ontology of the microeinstein per square meter per second unit.

+

💡 This updates all reference columns according to the main column. In this case the reference columns for Parameter [light intensity exposure] are updated with the id and source ontology of the microeinstein per square meter per second unit.

-

Your ISA table is growing

+

Your ISA table is growing

At this point. Your table should look similar to this:

-

+

-

Hiding ontology reference columns

+

Hiding ontology reference columns

Click the Autoformat Table quick access button without holding Ctrl to hide all reference columns.

-

Exercise 📝

+

Exercise 📝

Try to add suitable building blocks for other pieces of metadata from the plant growth protocol (studies/talinum_drought/protocols/plant_material.txt).

-

Let's annotate the RNA Seq data

+

Let's annotate the RNA Seq data

  1. Navigate to the demo ARC.
  2. Open the lab notes assays/rnaseq/protocols/RNA_extraction.txt in a text editor.
    3. @@ -206,12 +206,12 @@

    Let's annotate the RNA Seq data

-

Use a template

+

Use a template

  1. Navigate to Templates in the Navbar and click Browse database in the first function block.
-

💡 Here you can find community created workflow annotation templates

+

💡 Here you can find community created workflow annotation templates

  1. Search for RNA extraction and click select @@ -223,30 +223,30 @@

    Use a template

-

Adding / Updating unit references

+

Adding / Updating unit references

Sometimes you need to add or update the unit of an existing building block.

  1. Select any number of rows of the Parameter [biosource amount] building block to mark it for the next steps.
  2. Open the Building Blocks tab
  3. In the bottom panel "Add/Update unit reference to existing building block", search for the unit "milligram". Select the unit term and click Update unit for cells.
    -💡 If you already had values in the main column they will be updated automatically.
    4. +💡 If you already had values in the main column they will be updated automatically.
  4. Click the Update Ontology Terms quick access button, to update the reference columns.
-

Remove building blocks

+

Remove building blocks

If there are any Building Blocks which do not fit your experiment you can use the Remove Building Block quick access button to remove it including all related (hidden) reference columns.

-

⚠️ Due to the hidden reference columns, we recommend not to delete table columns via usual Excel functions.

+

⚠️ Due to the hidden reference columns, we recommend not to delete table columns via usual Excel functions.

-

New process, new worksheet

+

New process, new worksheet

  1. Add a new sheet to the assays/rnaseq/isa.assay.xlsx) workbook.
  2. Add the template "RNASeq Assay"
-

Exercise 📝

+

Exercise 📝

Try to fill the two sheets with the protocol details:

  • assays/rnaseq/protocols/RNA_extraction.txt and
    • @@ -254,12 +254,12 @@

    Exercise 📝
    -

    Your ISA table is ready 🎉

    +

    Your ISA table is ready 🎉

    Go ahead, adjust the Building Blocks you want to use to describe your experiment as you see fit.
    Insert values using Swate Term search and add input and output.

    -

    A small detour on "Excel Tables"

    +

    A small detour on "Excel Tables"

    Swate uses Excel's "table" feature to annotate workflows. Each table represents one process from input (e.g. plant leaf material) to output (e.g. leaf extract).

    Example workflows with three processes each:

      @@ -267,7 +267,7 @@

      A small detour on "Excel Tables"

    • Measured data files → statistical analysis → result files
    -

    💡 Excel tables allow to group data that belongs together inside one sheet. This is not to be confused with a (work)sheet or workbook.

    +

    💡 Excel tables allow to group data that belongs together inside one sheet. This is not to be confused with a (work)sheet or workbook.

    workbook              (e.g. "isa.assay.xlsx")
  └─── worksheet       (e.g. "plant_growth")
           └─── table  (e.g. "annotationTable")
@@ -275,15 +275,15 @@ 
    A small detour on "Excel Tables"
    -

    Annotation with ARCitect

    +

    Annotation with ARCitect

    -

    Process Information

    +

    Process Information

    -

    Contributors

    +

    Contributors

    Slides presented here include contributions by

    • name: Dominik Brilhaus
      @@ -301,5 +301,5 @@

      Contributors

    TODO Update ARCitect Annotation -Examples, Excelsheet...

    \ No newline at end of file +Examples, Excelsheet...

    \ No newline at end of file diff --git a/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block06-Swate-HandsOn.md b/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block06-Swate-HandsOn.md index 741006ebf..c04931e6f 100644 --- a/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block06-Swate-HandsOn.md +++ b/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block06-Swate-HandsOn.md @@ -235,7 +235,7 @@ Click the Update Ontology Terms quick access buttons. At this point. Your table should look similar to this: -![w:1000](./../custom/demo_isa.study1.png) +![w:1000](./../../../img/demo_isa.study1.png) --- diff --git a/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/index.md b/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/index.md index 1d5c4f51c..92ecf4aed 100644 --- a/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/index.md +++ b/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/index.md @@ -25,8 +25,8 @@ Here you can find the slides prepared for the September 2023 MibiNet/CEPLAS *Sta - Block 3a – ARCCommander-HandsOn - Block 3b – ARCitect-HandsOn - - +- Block 5 – MetadataISA +- Block 6 – Swate-HandsOn :warning: Links are not permanent. Slides may move elsewhere or be updated. We do our best to keep the knowledge base up-to-date – so you will find all relevant information here. diff --git a/src/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-14_CEPLAS-Session03/2023-06-14_CEPLAS-Session03.html b/src/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-14_CEPLAS-Session03/2023-06-14_CEPLAS-Session03.html index 44e1fe51b..823b26714 100644 --- a/src/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-14_CEPLAS-Session03/2023-06-14_CEPLAS-Session03.html +++ b/src/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-14_CEPLAS-Session03/2023-06-14_CEPLAS-Session03.html @@ -1,4 +1,4 @@ -Start-Your-ARC Workshop Series - Session 03
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    Start Your ARC Workshop Series

    Session 03 - Annotate your data
    @@ -27,7 +29,7 @@

    Start Your ARC Workshop Series


    Dominik Brilhaus - CEPLAS Data Science

    -
    +

    Goals

    • Get familiar with ISA metadata and Swate
      • @@ -141,7 +143,7 @@

      Annotati

    -

    💡 For details, check out the annotation principles.

    +

    💡 For details, check out the Annotation Principles.

    Part 2: Swate hands-on with demo data

    @@ -161,7 +163,7 @@

    Let's annotate the plant samples
  • Open the empty studies/talinum_drought/isa.study.xlsx workbook in Excel.

    • -
    +

    Create an annotation table


    @@ -246,7 +248,7 @@

    Update ontology reference columns

    Your ISA table is growing

    At this point. Your table should look similar to this:

    -

    +

    Hiding ontology reference columns

    @@ -343,5 +345,5 @@

    Contributors

    Title slide to class

    Source to slide(s)

    ../../bricks/ARC_ISAmodel.md

    Source to slide(s)

    ../../bricks/ARC_ISA-tab.md

    Source to slide(s)

    ../../bricks/ARC_ISAxlsx01.md

    Source to slide(s)

    ../../bricks/ARC_ISAxlsx02.md

    Source to slide(s)

    ../../bricks/ARC_ISAxlsx03.md

    Source to slide(s)

    ../../bricks/ARC_ISAxlsx04.md

    Source to slide(s)

    ../../bricks/lesson_Swate_DataPLANT-Annotation_Building_Block_types.md

    Title slide to class

    Source to slide(s)

    ../../bricks/ARC_ISAmodel.md

    Source to slide(s)

    ../../bricks/ARC_ISA-tab.md

    Source to slide(s)

    ../../bricks/ARC_ISAxlsx01.md

    Source to slide(s)

    ../../bricks/ARC_ISAxlsx02.md

    Source to slide(s)

    ../../bricks/ARC_ISAxlsx03.md

    Source to slide(s)

    ../../bricks/ARC_ISAxlsx04.md

    Source to slide(s)

    ../../bricks/lesson_Swate_DataPLANT-Annotation_Building_Block_types.md

    \ No newline at end of file diff --git a/src/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-14_CEPLAS-Session03/2023-06-14_CEPLAS-Session03.md b/src/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-14_CEPLAS-Session03/2023-06-14_CEPLAS-Session03.md index e2a36b6f8..991bd830c 100644 --- a/src/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-14_CEPLAS-Session03/2023-06-14_CEPLAS-Session03.md +++ b/src/docs/teaching-materials/disseminations/CEPLAS-StartYourARC-Series/2023-06-14_CEPLAS-Session03/2023-06-14_CEPLAS-Session03.md @@ -346,7 +346,7 @@ Click the Update Ontology Terms quick access buttons. At this point. Your table should look similar to this: -![w:1000](./../custom/demo_isa.study1.png) +![w:1000](./../../../../img/demo_isa.study1.png) ---