Improved Home and Features page, add three new pages

_pages/api_and_programmatic_access.md

@@ -0,0 +1,12 @@
+---
+permalink: /api_and_programmatic_access.html
+title: "API and Programmatic Access"
+layout: single
+---
+
+FAIRDOM-SEEK includes a [JSON](https://www.json.org/) Application Programming Interface (API) that allows the searching, listing, reading, updating and creating of many items in your FAIRDOM-SEEK instance, along with their attributes.
+The API supports Basic Authentication, OAuth and API Tokens, and can also be used without any authentication.
+
+![Screenshot of the API in action](/assets/images/api-feature.png){: .screenshot}
+
+FAIRDOM-SEEK supports RDF export (in Turtle format) and can be configured with a SPARQL endpoint. RDF generation will include [Extended Metadata](extended_metadata.html) when present for the attributes that include an identifier, and similarly some basic RDF is generated for Samples.

_pages/explore.md

@@ -0,0 +1,14 @@
+---
+permalink: /explore.html
+title: "Explore spreadsheets"
+layout: single
+redirect_from: '/explore_and_annotate.html'
+---
+
+Excel spreadsheets can be explored without the need to download.
+
+The contents of spreadsheets are indexed and searchable - so data can be discovered by searching within their content.
+
+You can explore and view other types of documents in the browser, including PDF, Word, PowerPoint, CSV, text files, and models. 
+
+![Excel feature](/assets/images/Excel-feature.png){: .screenshot}

_pages/extended_metadata.md

@@ -0,0 +1,13 @@
+---
+permalink: /extended_metadata.html
+title: "Extended Metadata"
+layout: single
+---
+
+Extended Metadata is a feature added to FAIRDOM-SEEK as part of version 1.11, originally to support plant phenotyping [(MIAPPE)](https://github.com/MIAPPE/MIAPPE).
+It provides the ability to define additional metadata attributes for a particular type (such as Event, DataFile or Model). 
+This feature is useful in many other communities who adhere to a particular metadata standard, such as  [NFDI4Health](https://fair-dom.org/fairdom-in-use/nfdi4health).
+
+![Screenshot of Extended Metadata Type management](/assets/images/emt-management.png)
+
+[FAIR Data Station](https://fairds.fairbydesign.nl/) integration provides a lightweight approach to gathering, validating, and ingesting metadata through the use of spreadsheet templates and following FAIR principles. Current support includes the matching of metadata attributes configured in FAIR Data Station with those of pre-configured Extended Metadata Types which are then automatically applied. 

_pages/features.md

@@ -8,39 +8,50 @@ redirect_from: '/about.html'
 
 ## Key features
 
-**Data Catalogue** – The data catalogue in FAIRDOM-SEEK includes raw [Datasets](https://fairdomhub.org/data_files), [Documents](https://fairdomhub.org/documents), [Standard Operating Procedures(SOPs)](https://fairdomhub.org/sops), [Models](https://fairdomhub.org/models), [Publications](https://fairdomhub.org/publications) and [Presentations](https://fairdomhub.org/presentations). All data are grouped by projects, and associated with the researchers who produced them. Documents can be put into [collections](https://fairdomhub.org/collections). In order to encourage sharing of data we allow researchers flexibility in the formats they upload and share their data in. This means data formats in the FAIRDOM-SEEK catalogue can vary. We do offer a set of “best practice” guidelines for researchers who want to make their data available and usable to the widest possible audience.
-Most common formats allow viewing within the browser, without a download, with additional enhanced features for spreadsheets and SBML models.
-Multiple data files can be registered at once by uploading a zip file. 
+**Data Catalogue** – The data catalogue in FAIRDOM-SEEK includes raw [Datasets](https://fairdomhub.org/data_files), [Documents](https://fairdomhub.org/documents), [Standard Operating Procedures(SOPs)](https://fairdomhub.org/sops), [Models](https://fairdomhub.org/models), [Publications](https://fairdomhub.org/publications) and [Presentations](https://fairdomhub.org/presentations). All data are grouped by projects, and associated with the researchers who produced them. Documents can be put into [collections](https://fairdomhub.org/collections). 
+
+In order to encourage [sharing of data](flexible_sharing.html) we allow researchers flexibility in the formats they upload and share their data in. This means data formats in the FAIRDOM-SEEK catalogue can vary. We do offer a set of “best practice” guidelines for researchers who want to make their data available and usable to the widest possible audience.
+The sharing policy and permissions for assets can be changed in batch.
 
-All data and information added to FAIRDOM-SEEK is searchable using key-words.
+Most common formats allow viewing within the browser, without a download, with additional enhanced features for spreadsheets and SBML models. The contents of [Excel spreadsheets can be explored](explore.html) in the browser.
+Multiple data files can be registered at once by uploading a zip file. 
+All data and information added to FAIRDOM-SEEK is searchable using key-words. 
 
 **Versioning** – All data is stored using versioning, selectable privacy, and static URLs. Versioning and privacy settings ensure that you can share your most recent data, with who you choose. Static URLs ensure that you can be credited directly for all shared work.
 Individual versions can have their visibility controlled, allowing past versions to be completely hidden if desired.
 
-**Model simulation and annotation** – if models follow the [SBML standard](http://sbml.org/), they can be simulated from within FAIRDOM-SEEK with [JWS Online](http://jjj.mib.ac.uk/).
+**Model simulation and annotation** – if models follow the [SBML standard](http://sbml.org/), they can be [simulated from within FAIRDOM-SEEK](simulate_sbml.html) with [JWS Online](http://jjj.mib.ac.uk/).
 [COPASI](http://copasi.org/) models can be interpreted and manipulated directly from the browser. 
 [Morpheus](https://morpheus.gitlab.io/) models can be simulated directly from the browser.
 
 **Access Control** – Data will go through a research lifecycle between collection and publication. In a competitive academic environment it is important that the data can be shared with collaborators, and then the wider community at appropriate points within the life-cycle. FAIRDOM-SEEK allows users to keep their uploaded data entirely private, to share between individuals, then across entire projects, until eventually making it public upon publication.
+A gatekeeper role can be assigned to manage sharing of a project's assets.
 
-**People index** – FAIRDOM-SEEK contains an [index of people](https://fairdomhub.org/people) where users can browse, or keyword-search, profiles of the projects, groups and people that contribute to the data on the site. People can describe their areas of expertise, which allows other users to quickly identify the right people to approach regarding specialist enquiries and collaboration proposals.
+**People index** – FAIRDOM-SEEK contains an [index of people](yellow_pages.html) where users can browse, or keyword-search, profiles of the projects, groups and people that contribute to the data on the site. People can describe their areas of expertise, which allows other users to quickly identify the right people to approach regarding specialist enquiries and collaboration proposals.
 Extra identifying information, such ORCID and affiliation, can be added for each creator, even if they are not registered in FAIRDOM-SEEK.
 
 **Samples** – FAIRDOM-SEEK has a flexible samples framework that allows users to generate templates for sample metadata. Samples can be data, or laboratory samples. The framework integrates with Rightfield sheets, so that semantically-enhanced title sheets can be included with the data. The default Rightfield sheet uses the JERM and allows automatic generation and linking of the data files to an assay.
 Sample attributes can be limited to controlled vocabularies backed by an ontology.
 
-**Extended Metadata** – FAIRDOM-SEEK allows items to be customized with additional typed metadata, similar to samples, and was used to support [MIAPPE](https://www.miappe.org/).
+**Extended Metadata** – FAIRDOM-SEEK allows items to be customized with [additional typed metadata](extended_metadata.html), similar to samples, and was used to support [MIAPPE](https://www.miappe.org/).
 Extended Metadata can be nested, i.e one Extended Metadata type definition can include a reference to another, and these will be nested together in a single form.
 
 **ISA and Interlinking** – Data in FAIRDOM-SEEK gain increased value and usability when they are described within the context of an experimental process. 
 Multiple experiments will be carried out as part of a single Study, and that study may be part of a wider overall funded Investigation. 
-In FAIRDOM-SEEK we adopt the [ISATAB structure (Investigation, Studies, Assays)](https://isa-tools.org/) which is a community standard for describing links between Omics experiments. 
+In FAIRDOM-SEEK we adopt the [ISATAB structure (Investigation, Studies, Assays)](organise.html) which is a community standard for describing links between Omics experiments. 
 We believe that many aspects of the ISA framework are equally appropriate for describing experiments beyond Omics and Biology, so allow this framework to be applied to all data.
 
 Beyond the ISA framework, FAIRDOM-SEEK allows data to be interlinked within the site itself in order to describe their relationship.
 
-If research resulted in a publication, this can also be registered with FAIRDOM-SEEK (including accreditation to relevant people) using a [PUBMED](http://www.ncbi.nlm.nih.gov/pubmed) identifier or [DOI](http://www.doi.org/), 
+**Publishing and licensing** – If research resulted in a [publication](publishing_and_doi.html), this can also be registered with FAIRDOM-SEEK (including accreditation to relevant people) using a [PUBMED](http://www.ncbi.nlm.nih.gov/pubmed) identifier or [DOI](http://www.doi.org/), 
 and linked to the assets involved in that research – allowing other researchers access to use, examine, or validate the data that would otherwise be unavailable through the publication alone.
+FAIRDOM-SEEK can be set up as [registration hub](publishing_and_doi.html) for your publications and issue DOIs.
+
+We recommended giving a license to public resources in FAIRDOM-SEEK to clarify under what terms they may be used. A Project administrator may specify the default license for their project which is automatically selected when creating a new item, but can be changed by the user if necessary.
+
+**API and programmatic access** – The [JSON API](api_and_programmatic_access.html) allows the searching, listing, reading, updating and creating of many items in your FAIRDOM-SEEK instance, along with their attributes. FAIRDOM-SEEK supports RDF export (in Turtle format) and can be configured with a SPARQL endpoint.
+
+**Bioschemas support** – A **sitemap.xml** is generated for all public content, improving indexing by the main search engines, and supports [Bioschemas](https://bioschemas.org/) scraping. Bioschemas (and therefore [schema.org](https://schema.org/)) metadata is generated for each asset type in FAIRDOM-SEEK, using the common Bioschemas profiles such as Project, Sample and DataSet.
 
 ## Bespoke Development
 

_pages/index.md

@@ -12,14 +12,14 @@ row1:
     excerpt: "FAIRDOM-SEEK has adopted an ISATAB style structure for organising experiments and data."
     url: "/organise.html"    
   - image_path: /assets/images/Excel-feature.png
-    alt: "Explore and annotate"
-    title: "Explore and annotate data"
-    excerpt: "Excel spreadsheets can be explored and annotated without the need to download."
-    url: "/explore_and_annotate.html"    
+    alt: "Explore spreadsheets"
+    title: "Explore spreadsheets"
+    excerpt: "Excel spreadsheets and other documents can be explored without the need to download."
+    url: "/explore.html"    
   - image_path: /assets/images/Model-simulation-feature.png
     alt: "Simulate SBML"
     title: "Simulate SBML models"
-    excerpt: "Most models that conforms to the SBML format can be simulated within FAIRDOM-SEEK."
+    excerpt: "Most models that conforms to the SBML, COPASI or Morpheus formats can be simulated within FAIRDOM-SEEK."
     url: "/simulate_sbml.html"
 
 row2:
@@ -39,7 +39,22 @@ row2:
     excerpt: "RightField enabled sheets allow rich semantic descriptions of data. Our Just Enough Results Model can be used with Rightfield."
     url: "/rightfield_templates.html"    
 
-
+row3:
+  - image_path: /assets/images/emt-management.png
+    alt: "Extended Metadata Types management"
+    title: "Extended Metadata"
+    excerpt: "Define additional metadata attributes for a particular type, adhere to standards."
+    url: "/extended_metadata.html"
+  - image_path: /assets/images/DOI_logo.svg
+    alt: "DOI logo"
+    title: "Publishing and DOI"
+    excerpt: "Set up a registration hub for your publications, manage DOIs."
+    url: "/publishing_and_doi.html"
+  - image_path: /assets/images/api-feature.png
+    alt: "API feature"
+    title: "API and programmatic access"
+    excerpt: "The JSON API allows the searching, listing, reading, updating and creating. FAIRDOM-SEEK supports RDF export."
+    url: "/api_and_programmatic_access.html"   
 ---
 
 
@@ -73,3 +88,5 @@ A publicly available instance of a FAIRDOM-SEEK commons is available - as the [F
 {% include feature_row id="row1" %}
 
 {% include feature_row id="row2" %}
+
+{% include feature_row id="row3" %}

_pages/organise.md

@@ -6,7 +6,7 @@ layout: single
 
 FAIRDOM-SEEK has adopted an ISATAB style structure for organising experiments and data.
 
-The ISA format (Investigations, Studies and Assays) is a community standardisation activity to allow the association of multiple 'Omics datasets, in the context of the experiments that created them, in order to make it easier to compare and combine different data sets. It also provides the possibility of exporting or importing data from other sources in ISA-TAB format and therefore allows data exchange with a wider community.
+The [ISATAB format (Investigation, Studies, Assays)](https://isa-tools.org/) is a community standardisation activity to allow the association of multiple 'Omics datasets, in the context of the experiments that created them, in order to make it easier to compare and combine different data sets. It also provides the possibility of exporting or importing data from other sources in ISA-TAB format and therefore allows data exchange with a wider community.
 
 
 ![ISA Graph](/assets/images/ISA-feature.png){: .screenshot}      

_pages/publishing_and_doi.md

@@ -0,0 +1,17 @@
+---
+permalink: /publishing_and_doi.html
+title: "Publishing and DOI"
+layout: single
+---
+
+If research resulted in a publication, this can also be registered with FAIRDOM-SEEK (including accreditation to relevant people) using a [PUBMED](http://www.ncbi.nlm.nih.gov/pubmed) identifier or [DOI](http://www.doi.org/),
+and linked to the assets involved in that research – allowing other researchers access to use, examine, or validate the data that would otherwise be unavailable through the publication alone.
+
+FAIRDOM-SEEK can be set up as registration hub for your publications. 
+Research outputs can be assigned a persistent identifier, making them findable by a unique URL. 
+For example, materials shared on [FAIRDOMHub](https://fair-dom.org/fairdom-in-use/fairdomhub) (a public hub) can be issued with a DOI. 
+
+![DOI logo](/assets/images/DOI_logo.svg)
+
+If you set up your own hub and wish to issue DOIs, you will need to [become a member of DataCite](https://datacite.org/become-a-member/) (see their [fee model](https://datacite.org/fee-model/)).
+

_pages/simulate_sbml.md

@@ -1,6 +1,6 @@
 ---
 permalink: /simulate_sbml.html
-title: "Simulate SBML models"
+title: "Simulate SBML, COPASI and Morpheus models"
 layout: single
 ---
 
@@ -10,4 +10,10 @@ The [JWS Online](http://jjj.mib.ac.uk/) model simulator presents a schematic dia
 
 
 
-![Simulate_SBML feature](/assets/images/Model-simulation-feature.png){: .screenshot}
+![Simulate_SBML feature](/assets/images/Model-simulation-feature.png){: .screenshot}
+
+[COPASI](http://copasi.org/) models can be interpreted and manipulated directly from the browser or using your local installation of COPASI.
+
+![Simulate COPASI model](/assets/images/copasi-model-browser.png){: .screenshot}
+
+[Morpheus](https://morpheus.gitlab.io/) models can be simulated directly from the browser.

_pages/yellow_pages.md

@@ -6,12 +6,15 @@ layout: single
 
 We recognise that people, and their knowledge, are important.
 
-You can find out what people using, and have expertise in, and how to get in contact with them.
+You can find out [what people are using](https://fairdomhub.org/people), and have expertise in, and how to get in contact with them.
 
 The Yellow Pages is a directory of who is on which project, where they are located, and what they specialise in. This allows researchers to identify people with similar interests, or to find people with the relevant experience when troubleshooting new techniques.
 
-With a quick glance it also is possible to see what items they have been involved with producing, what experiments they have been doing, and what registered publications they are an author of.
+With a quick glance it also is possible to see what items they have been involved with producing, what experiments they have been doing, and what registered publications they are an author of. For people who have provided their [ORCID](https://info.orcid.org/what-is-orcid/), you can click through to view their wider publishing record.
 
 
 
-![Yellow_pages feature](/assets/images/Who-feature.png){: .screenshot}
+![Yellow_pages feature](/assets/images/Who-feature.png){: .screenshot}
+
+We recognise that the institutions people work for are important too. For each person, you can assign an [ROR](https://ror.org/about/), a persistent identifier for research institutions. 
+ROR makes it easier to disambiguate institution names and connect research organisations to researchers and research outputs.