Merge pull request #243 from cbielow/main

fix broken links & some menu rearrangements

docs/_data/menu.yml

@@ -4,41 +4,41 @@
 # LINKS ARE UNBROKEN AND ALL CONTENT IS REACHABLE!!! 
 - title: Home
   url: /
-- title: The Format
+- title: mzQC for Users
   url: /mzQC-intro/
   submenu:
-    - title: Specification
-      url: /spec-doc/
-    - title: '*omics'
+    - title: Introduction
+      url: /mzQC-intro/
+    - title: 'Use cases'
       url: /use-cases/
+    - title: QC Software with mzQC
+      url: /resource-guide/#qc-software
     - title: Examples
       url: /examples/
-    - title: Metrics
-      url: /metrics/
-    - title: The Format
-      url: /mzQC-intro/
-- title: Validator
-  url: /validator/
-  submenu:
-    - title: Validation Process
-      url: /validator/validation
-    - title: Local Validation
-      url: /validator/validation/#offline-validation
-    - title: Online Validator
-      url: /validator/
-- title: mzQC Resources
+- title: mzQC for Developers
   url: /resource-guide/
   submenu:
+    - title: Specification
+      url: /spec-doc/
+    - title: Metrics
+      url: /metrics/
     - title: mzQC Frameworks
       url: /resource-guide/#core-libraries
     - title: Tutorials
       url: /tutorials/
-    - title: QC Software with mzQC
-      url: /resource-guide/#qc-software
     - title: JSON Primer
       url: /tutorials/#json
     - title: Ontology Primer
       url: /tutorials/#ontologies
+- title: Validator
+  url: /validator/
+  submenu:
+    - title: Validation Process
+      url: /validator/validation
+    - title: Offline Validation
+      url: /validator/validation/#offline-validation
+    - title: Online Validator
+      url: /validator/
 - title: About
   url: /about/
   submenu:

docs/index.md

@@ -33,8 +33,7 @@ and analysts wanting a better insight to the data they analyse.
 
 * If you are familiar with JSON or have an understanding of PSI file formats, are however pressed for time, [mzQC at a glance](use-cases/at-a-glance/) will give you a brief overview of the essentials.
 
-* A in a nutshell exlanation is [here](mzQC-in-a-nutshell/)
-* Find out more about the format in general [here](mzQC-intro/)!
+* Find out more about the format in general [in our Introduction](mzQC-intro/)!
 
 ### Specification Document
 For the technical details on the mzQC format see either the [latest release static version](spec-doc/), or 

docs/pages/contribs.md

@@ -26,7 +26,7 @@ If you spot a problem, [search if an issue already exists](https://docs.github.c
 
 #### Request a new metric
 
-If you miss a specific metric, you can request it's addition via the issue system. It might be good if you'd familiarise yourself with [mzQC](https://hupo-psi.github.io/mzqc/) and [CV metric representation](https://hupo-psi.github.io/mzqc/metrics/) in particular. We have a dedicated issue template for the request of new QC terms in the PSI-MS-CV repository. 
+If you miss a specific metric, you can request it's addition via the issue system. It might be good if you'd familiarise yourself with [mzQC](https://hupo-psi.github.io/mzQC/) and [CV metric representation](https://hupo-psi.github.io/mzQC/metrics/) in particular. We have a dedicated issue template for the request of new QC terms in the PSI-MS-CV repository. 
 
 #### Solve an issue
 

docs/pages/tutorials.md

@@ -35,7 +35,7 @@ Here is a list of links and documents that should help you out in case you want
 * Ontologies are powerful tools, we mostly use them as [controlled vocabularies](https://en.wikipedia.org/w/index.php?title=Controlled_vocabulary&oldid=1092198296)
 * The W3C has a bit broader explanation of [ontologies](https://www.w3.org/standards/semanticweb/ontology)
 * Visit the [HUPO-PSI webpage](https://www.psidev.info/groups/controlled-vocabularies) for more information on CV use in different settings.
-* __Browse our controlled vocabulary terms on [OLS](https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_4000000&lang=en&viewMode=All&siblings=false)__
+* __Browse our controlled vocabulary terms on [OLS](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_4000000?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_4000000&lang=en&viewMode=All&siblings=false)__
 * If you want to start with the foundations and get ambitious here are the resources [from protege for ontology development](https://protege.stanford.edu/publications/ontology_development/ontology101.pdf)
 * Luckily, we have all the relevant metrics and terms in [PSI-MS CV](https://github.com/HUPO-PSI/psi-ms-CV) (<sub>so no [Ontology Dowsing](https://www.w3.org/wiki/Ontology_Dowsing) necessary</sub>)
 

docs/pages/use-cases.md

@@ -6,19 +6,25 @@ permalink: /use-cases/
 This page should give you a (non-exclusive) overview over the use cases covered by mzQC:
 
 ## Handover Format
-It is easy with **mzQC** to get relevant QC info, easy to put your data into context (of measurement realities). That makes it a preferred medium to handover quality information. Read more about it in [mzQC at a glance](at-a-glance/) and explore [a small mzQC example](../examples/intro_run/).
+It is easy with **mzQC** to get relevant QC info, easy to put your data into context (of measurement realities). That makes it a preferred medium to handover quality information. 
+Read more about it in [mzQC at a glance](at-a-glance/) and explore [a small mzQC example](../examples/intro_run/).
 
 ## Quality Reports
-With JSON at its core, mzQC follows a '_works online, works everywhere_' approach. Even for single spectra, as we show with the [universal spectrum identifier example](../examples/USI-example/).
+With JSON at its core, mzQC follows a '_works online, works everywhere_' approach. Even for single spectra, as we show with the [universal spectrum identifier example](../examples/adv_mzqc_usi/).
 
 ## Archival
-The format is an optimal QC tool for the analytical chemist and instrument operators keeping track (and archive) instrument performance. Read on with an [introduction to mzQC for anlytical chemists](analytical-chemists/) or explore our [QC sample example](../examples/QC2-sample-example/). You can even embed mzQC in mzML, should you choose to. [View an example here](../examples/mzml-mzqc-example/).
+The format is an optimal QC tool for the analytical chemist and instrument operators keeping track (and archive) instrument performance.
+Read on with an [introduction to mzQC for anlytical chemists](analytical-chemists/) or explore our [QC sample example](../examples/intro_qc2/).
+You can even embed mzQC in mzML, should you choose to. [View an example here](../examples/adv_mzqc_in_mzml/).
 
 ## Common currency
 With mzQC for archival, quality reports, and as handover format, [mzQC can serve as a common currency](mzQC-common-currency/) for data repositories, journals, and collaborators.
 
 ## Bridge the *omics Gap: Metabolomics
-A technology agnostic design makes QC with mzQC easy in other fields as well! Assuming you make per sample measurements (runs in mzQC parlance) and multiple groups of runs in a study (sets), then all you need is to define your metrics to open up the mzQC 'ecosystem' to your field. Explore in [this example](../examples/metabo-batches/), how easy you can include QC data from quite different instruments, employ advanced QC concepts like batch correction, and use metrics on expansive datasets. 
+A technology agnostic design makes QC with mzQC easy in other fields as well! Assuming you make per sample measurements (runs in mzQC parlance) and multiple groups of runs in a study (sets),
+then all you need is to define your metrics to open up the mzQC 'ecosystem' to your field. Explore in [this example](../examples/metabo-batches/), 
+how easy you can include QC data from quite different instruments, employ advanced QC concepts like batch correction, and use metrics on expansive datasets. 
 
 ## Keep track of your study's runs as a whole
-With mzQC you can keep track of the quality of all your study's runs. We show in [this example](../examples/set-of-runs/) how you can apply metrics to a whole set of runs. There are of course more scenarios in which you want to consider the quality of multiple runs, and you can read [more here](mzqc-multi/).
+With mzQC you can keep track of the quality of all your study's runs. We show in [this example](../examples/intro_set/) how you can apply metrics to a whole set of runs. 
+There are of course more scenarios in which you want to consider the quality of multiple runs, and you can read [more here](mzqc-multi/).

docs/pages/worked-examples/adv_mzqc_in_mzml.md

@@ -7,7 +7,7 @@ permalink: /examples/adv_mzqc_in_mzml/
 While QC metrics in the PSI-MS controlled vocabulary are primarily intended for use in mzQC files, they can also be embedded directly within other file formats developed by the Proteomics Standards Initiative, such as [mzML](https://github.com/HUPO-PSI/mzML) and [mzIdentML](https://github.com/HUPO-PSI/mzIdentML) files.
 This integration is particularly useful when it's preferred to store a limited set of QC metrics alongside the data they describe, thereby enhancing data integrity and accessibility.
 
-You can view a comprehensive example of an mzML file incorporating QC metrics [here](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/adv_mzqc_in_mzml.mzml).
+You can view a comprehensive example of an mzML file incorporating QC metrics [here](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/adv_mzqc_in_mzml.mzML).
 Below, we detail the steps and elements involved in this process.
 
 1. **Source file specification**