Updates to documentation (#51)

src/Web/WebUI/GlobalPollenProject.Web/Docs/1.QuickStart.md

@@ -8,10 +8,6 @@ Icon:        bolt
 Intro:       Discover the data and features of the Global Pollen Project
 ---
 
-<div class="alert alert-info">
-    <strong>Welcome to the Global Pollen Project (GPP) v1.5.</strong> After a positive reception for the original release, we are happy to welcome you to the new Global Pollen Project (1.5). Please note that data is currently being migrated from the original dataset into a new format. While this is in progress, some data may not be available. <a href="https://v1.globalpollenproject.org" target="_blank">You can still access the original Global Pollen Project dataset in our temporary archive here.</a>
-</div>
-
 The Global Pollen Project is an online platform that facilitates the storage and organisation of pollen images which can be accessed freely and globally. Its framework has been specifically designed to encompass: access, transparency and uniformity going forward through time. 
 
 There are two main concepts for which the Global Pollen Project can be used for: (1) the identification of unknown grains, and (2) as a morphological reference collection. 

src/Web/WebUI/GlobalPollenProject.Web/Docs/3.Digitisation.md

@@ -3,22 +3,23 @@ Title:       Digitising Your Reference Material
 ShortTitle:  Digitise
 Author:      Andrew Martin
 Affiliation: University of Oxford
-Date:        October 27, 2017
+Date:        3rd February, 2023
 Icon:        camera-retro
 Intro:       Learn how to use our online digitisation tools. 
 ---
 
-<div class="alert alert-warning">
-    <strong>Welcome to the Global Pollen Project (GPP) v1.5. The digitisation tools are currently in a preview release.</strong> The tools are functional but with some rough edges. Please report any bugs or problems on our GitHub issues page.
-</div>
-
 The Global Pollen Project aims to provide a home for digital pollen reference collections.
 
 We provide tools for easy digitisation of reference collection slides. These have the following advantages:
 - *Taxonomy*. We provide a taxonomic backbone to verify taxonomic information, and provide quick data entry.
 - *Focus Images*. Images can be stacked and presented as focusable images, just like using a microscope.
 - *Integration*. Your slides will appear alongside slides from other collections, and user uploaded grains.
 
+<div class="alert alert-info">
+   We are working on providing DOIs and archival downloads of digitised pollen collections in the next release. Please contact us for more information.
+</div>
+
+
 ### The Digitisation Process
 
 Digitisation is completed using the online Digitisation Dashboard.
@@ -100,11 +101,17 @@ Publication is irreversable: any errors must be corrected by issuing a new versi
 
 ### Microscope Calibration
 
-Documentation coming soon.
+To support *focus images*, microscopes may be calibrated using images of a scale bar at each magnification level. The key requirement for this is that your microscope is set up with a fixed camera that does not move. 
+
+The digitisation tools include a 'click-click' measurement to save the measurement of a scale bar image as pixel units in the image.
+
+For a compound microscope, you must configure the magnification of the ocular lens and objectives. You may then calibrate each objective individually, allowing images to be submitted at varying magnification levels from a single microscope. 
+
+The digitisation tools also support digital microscopes that only have a single fixed magnification.
 
 ### Crediting Contributions
 
-The Global Pollen Project contains comprehensive tracking of contributions within reference collections. The information captured for each slide includes:
+The Global Pollen Project contains tracking of contributions within reference collections. The information captured for each slide includes:
 
 - If field-based plant identification was conducted, who the identifier was
 - Who collected the pollen residue used to create the slide
@@ -127,4 +134,4 @@ The GPP's master reference collection will always reflect the most recent publis
 
 Ready to add your own reference material?
 
-<a class="btn btn-secondary" href="/Digitise">Start the digitisation process.</a>
+<a class="btn btn-outline-secondary" href="/Digitise">Start the digitisation process.</a>

src/Web/WebUI/GlobalPollenProject.Web/Docs/4. MakingReferenceMaterial.md → src/Web/WebUI/GlobalPollenProject.Web/Docs/4.MakingReferenceMaterial.md

@@ -8,3 +8,4 @@ Icon:        eraser
 Intro:       Advice and sources for pollen identification and preperation
 ---
 
+Documentation coming soon

src/Web/WebUI/GlobalPollenProject.Web/Docs/5.ProgramaticAccess.md

@@ -3,19 +3,23 @@ Title:       Access our data programatically
 ShortTitle:  API
 Author:      Andrew Martin
 Affiliation: University of Oxford
-Date:        October 27, 2017
+Date:        29th January, 2023
 Icon:        terminal
 Intro:       Use your favourite language
 ---
 
-You can access data in the Global Pollen Project using your programming language of choice.
+<div class="alert alert-info">
+    <strong>Welcome to the Global Pollen Project (GPP) v2.</strong> As part of this release, we have included a preview of the public Application Programming Interface (API). While in preview, the specification and endpoints are subject to change.
+</div>
 
-We currently provide keyless access to the API, but this may change in future. Version one of the API will only be updated with non-breaking changes. 
+You can access data within the Global Pollen Project database using our Application Programming Interface (API) and your programming language of choice.
 
-### Taxonomic Backbone
+#### Authentication
 
-The taxonomic backbone...
+The API is currently keyless, meaning that you do not have to log in to access it. However, this is planned to change. The reason for the planned change is to optimise running costs of the Global Pollen Project.
 
-### Master Reference Collection
+#### Available Endpoints
 
-Coming soon...
+The available endpoints allow accessing our taxonomic backbone, individual reference collections, and the master reference collection.
+
+[You can find the latest documentation for the API here](https://api.globalpollenproject.org)

src/Web/WebUI/GlobalPollenProject.Web/Docs/6.VersionUpdates.md

@@ -4,12 +4,22 @@ ShortTitle:  Changelog
 Author:      Andrew Martin
 Affiliation: University of Oxford
 Date:        October 22, 2017
-Icon:        code-fork
+Icon:        code-branch
 Intro:       Changelog of feature updates and bug fixes
 ---
 
 The Global Pollen Project was launched as a preview in Feburary 2015. 
 
+### Release 2.0.1 (February 2023)
+
+This release includes bug fixes and enhancements to the digitisation tools. It does not include any new functionality.
+
+### Release 2.0 (February 2022)
+
+Release 2.0 included mainly under-the-hood changes that enable new functionality to be built in future releases and modernise the platform. It also updated connections to third-party services to the latest APIs.
+
+A preview of our own API was included in this release, with documentation accessible at [https://api.globalpollenproject.org](https://api.globalpollenproject.org).
+
 ### Release 1.5 (October 2017)
 
 The Global Pollen Project has been revised from the ground-up, to include more robust data models, a significantly more performant web interface, and new features. New features include:
@@ -30,3 +40,7 @@ General improvements include:
 | --- | --- |
 | Speed  | The project has been rewritten using a fuctional approach. All user-facing features are powered by a Redis in-memory database, for near-instant querying.  |
 | Temporal Dataset  | Rather than storing state, all changes to the taxonomy, pollen reference material, and crowdsourced elements are captured as events. This allows us to keep a full history of changes in taxonomy as they occur in the future. |
+
+### Release 1.0
+
+This release of the Global Pollen Project is detailed in: [Martin A.C., and Harvey, W. J. (2017). The Global Pollen Project: A New Tool for Pollen Identification and the Dissemination of Physical Reference Collections. *Methods in Ecology and Evolution*](http://dx.doi.org/10.1111/2041-210X.12752)

src/Web/WebUI/GlobalPollenProject.Web/Docs/9.0.FAQs.md

@@ -0,0 +1,11 @@
+---
+Title:       FAQs
+ShortTitle:  FAQ
+Author:      Andrew Martin
+Affiliation: University of Oxford
+Date:        October 27, 2017
+Icon:        life-ring
+Intro:       Learn how to use our online digitisation tools. 
+---
+
+FAQ coming soon

src/Web/WebUI/GlobalPollenProject.Web/Docs/11.Cite.md → src/Web/WebUI/GlobalPollenProject.Web/Docs/9.1.Cite.md

@@ -1,26 +1,26 @@
 ---
 Title:       How to Cite
 ShortTitle:  Cite
-Author:      Global Pollen Project
+Author:      Global Pollen Project Team
 Affiliation: Global Pollen Project
 Date:        21st July 2020
-Icon:        pen-fancy
+Icon:        pencil-alt
 Intro:       Reference us in your publication
 ---
 
 The Global Pollen Project was designed to encourage good tracability of data sources and contributors.
 
-### To cite the Global Pollen Project itself
+### To cite the Global Pollen Project itself (the database)
 The Global Pollen Project is described in the following paper, which can be cited directly:
 
 > Martin, A. C. and Harvey, W. J. (2017), The Global Pollen Project: a new tool for pollen identification and the dissemination of physical reference collections. Methods Ecol Evol, 8: 892–897. doi:10.1111/2041-210X.12752.
 
-#### To cite an individual reference collection
+### To cite an individual reference collection or item
 Example citations are provided on individual reference collection and slide pages in APA format. An example is shown below:
 
 > Willis, Kathy J (2017). Picea abies (26.4.1 - 1). Digitised palynological slide. In: European Reference Collection (Version 1). Retrieved from globalpollenproject.org on 10/22/2017.
 
-#### Using Images and Metadata in Your Own Work
+### Using Images and Metadata in Your Own Work
 The data available in the Global Pollen Project has been kindly contributed by individuals and organisations around the world.
 The image library and metadata is available under a Creative Commons License (<a href="/Terms">see terms</a>). When using this data in your work, please
 attribute both the contributors of the information you use and the Global Pollen Project itself. Please acknowledge any digitised reference collections that you use heavily.

src/Web/WebUI/GlobalPollenProject.Web/Docs/9.2.Contact.md

@@ -0,0 +1,33 @@
+---
+Title:       Contact Us
+ShortTitle:  Contact
+Author:      Global Pollen Project Team
+Affiliation: Global Pollen Project
+Date:        3rd February, 2023
+Icon:        address-card
+Intro:       Please find contacts below
+---
+
+For general enquiries, you can email the Global Pollen Project Team at [[email protected]](mailto:[email protected]). The project is currently led by Andrew Martin, School of Geography and Environment, University of Oxford. 
+
+For more specific enquiries, please see the best contacts below.
+
+#### I am interested in digitising a pollen reference collection that I curate
+
+Thank you for your interest. If you have queries about our digitisation tools and digitisation process, or would like a demonstration of the process, please contact Dr Andrew Martin at [[email protected]](mailto:[email protected]).
+
+#### I've found a bug or have encountered an issue
+
+We keep track of bugs on our [GitHub issues page](https://github.com/AndrewIOM/gpp-cqrs/issues). If you are familiar with GitHub, you may open a new issue and we will address it when able. If you're not a GitHub user, you can also email us at [[email protected]](mailto:[email protected]) to report bugs or problems.
+
+#### I would like to collaborate or contribute financially
+
+Please have a look at [our current roadmap here](https://github.com/AndrewIOM/gpp-cqrs/milestones). If you have ideas or would like to collaborate further, please [send us an email](mailto:[email protected]).
+
+As part of ensuring the long-term provision of the Global Pollen Project, we are considering establishing a stewardship group. If you are interested this, please [send us an email](mailto:[email protected]).
+
+The Global Pollen Project has some maintainance costs that are currently unmet from grant funding. If you can help, let us know.
+
+#### I wish to use the whole database for a project
+
+You can use [the API](/Guide/API) to access the contents of our database, including images. Please be mindful of our [citation guidelines and attribution requirements of the licenses used](/Guide/Cite). If you are intending to make substantial use of the whole database, please let us know so we can track project impact at [this email](mailto:[email protected]).

src/Web/WebUI/GlobalPollenProject.Web/Docs/10.Terms.md → src/Web/WebUI/GlobalPollenProject.Web/Docs/9.3.Terms.md

@@ -1,10 +1,10 @@
 ---
 Title:       Terms of Service
 ShortTitle:  Terms
-Author:      Global Pollen Project
+Author:      Global Pollen Project Team
 Affiliation: Global Pollen Project
 Date:        1st March, 2017
-Icon:        terms
+Icon:        file-alt
 Intro:       Our terms of use
 ---
 

src/Web/WebUI/GlobalPollenProject.Web/Docs/12.Privacy.md → src/Web/WebUI/GlobalPollenProject.Web/Docs/9.4.Privacy.md

@@ -4,7 +4,7 @@ ShortTitle:  Privacy
 Author:      Andrew Martin
 Affiliation: University of Oxford
 Date:        24th May, 2018
-Icon:        terms
+Icon:        eye
 Intro:       Our privacy policy
 ---
 
@@ -76,10 +76,10 @@ You can 'opt out' of communications from us in your account settings.
 
 #### Further information and requests
 
-The Data Controller is the Gloabl Pollen Project Research Team. For a copy of the information we hold on you please contact us at the address below:
+The Data Controller is the Global Pollen Project Research Team. For a copy of the information we hold on you please contact us at the address below:
 
 Andrew Martin
-Department of Zoology
+School of Geography and Environment
 South Parks Road
-Oxford, OX1 3PS
+Oxford, OX1 3QY
 United Kingdom

src/Web/WebUI/GlobalPollenProject.Web/Urls.fs

@@ -20,6 +20,7 @@ let api = "/Guide/API"
 let tools = "/Tools"
 let cite = "/Cite"
 let terms = "/Terms"
+let contactUs = "/Contact"
 let notFound = "/NotFound"
 
 module MasterReference =

src/Web/WebUI/GlobalPollenProject.Web/View.fs

@@ -234,9 +234,10 @@ module Layout =
                         h4 [] [ encodedText "Information" ]
                         ul [] [
                             li [] [ a [ _href Urls.guide ] [ encodedText "About"] ]
-                            li [] [ a [ _href Urls.api ] [ encodedText "Public API"; span [ _style "font-weight: normal;margin-left: 0.5em;"; _class "badge badge-info" ] [ encodedText "Beta" ] ] ]
+                            li [] [ a [ _href Urls.api ] [ encodedText "Public API"; span [ _style "font-weight: normal;margin-left: 0.5em;"; _class "badge badge-info" ] [ encodedText "Preview" ] ] ]
                             li [] [ a [ _href Urls.terms ] [ encodedText "Terms and Licensing"] ]
                             li [] [ a [ _href Urls.cite ] [ encodedText "How to Cite"] ]
+                            li [] [ a [ _href Urls.contactUs ] [ encodedText "Contact Us"] ]
                         ]
                     ]
                     div [ _class "col-md-5"; _style "padding-right:4em" ] [