Recommend submitting site to Bioschemas for inclusion on live deploy page

Originally identified in #30

Describe the bug
The link to the Jupyter Book Guide on this page is broken.

To Reproduce
Steps to reproduce the behavior:

1. Go to FAIR cookbook overview page
2. Search "the Jupyter Book Guide"
3. Click the hyperlink https://fairplus.github.io/the-fair-cookbook/guide/01_overview
4. See error 404

Stub recipe exists at https://github.com/FAIRplus/the-fair-cookbook/blob/identifiers/docs/content/recipes/findability/identifier-services/identifier-mapping.md

This recipe should cover the use of BridgeDb either through its public endpoint or by a local installation.

Describe the bug

1. The second image is not properly rendered. What I see now is a link to https://mermaid-js.github.io/mermaid-live-editor/#/edit/eyJjb2RlIjoiZ3JhcGggVERcbiAgQVtIVE1MIHBhZ2VdIC0tPnwgU2VhcmNoIEVuZ2luZSBPcHRpbWl6YXRpb258IEIoZmE6ZmEtc2VhcmNoIFNjaGVtYS5vcmcgYXVnbWVudGVkIEhUTUwgcGFnZSlcbiAgQiAtLT4gQ3t3aGljaCB0ZWNobmlxdWU_fVxuICBDIC0tPnxPbmV8IERbZmE6ZmEtc3RhciBmYTpmYS1zdGFyIGZhOmZhLXN0YXIgSlNPTi1MRF1cbiAgQyAtLT58VHdvfCBFW2ZhOmZhLXN0YXIgZmE6ZmEtc3RhciBSREZhXVxuICBDIC0tPnxUaHJlZXwgRltmYTpmYS1zdGFyIG1pY3JvZm9ybWF0XVxuICBEIC0tPiBHXG5cdEUgLS0-IEdcbiAgRlx0LS0-IEdbZmE6ZmEtc2VhcmNoIGZhOmZhLWNvZyBmYTpmYS1maWdodGVyLWpldCBpbXByb3ZlZCBkaXNjb3ZlcmFiaWxpdHldIiwibWVybWFpZCI6eyJ0aGVtZSI6Im5ldXRyYWwifX0
2. Bioschemas is misspelled on the subtitle "Bioschema: trying to address the coverage gap"

To Reproduce
Steps to reproduce the behavior:

1. Go to https://github.com/FAIRplus/the-fair-cookbook/blob/bioschemas-seo/docs/content/recipes/infrastructure/seo.md
2. Scroll down to the link right after the first image depicting the recipe objectives
3. See a link rather than an image displayed.
4. Now go to the subtitle "Bioschema: trying to address the coverage gap", it should be Bioschemas

Expected behavior

1. I expect to see the image rather than the link
2. I expect to see Bioschemas rather than Bioschema (missing 's' at the end)

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]: Windows 10
• Browser [e.g. chrome, safari]: Firefox
• Version [e.g. 22]: 75.0

Additional context
I suggest mentioning Bioschemas on the main objective together with schema.org as Bioschemas types are used in the recipe objectives graphic.
Page created by @AlasdairGray

Is your feature request related to a problem? Please describe.

Obtain information about how common the practice described in "https://fairtoolkit.pistoiaalliance.org/use-cases/adoption-and-impact-of-an-identifier-policy-astrazeneca/" actually is among Pharma/EFPIA partners

Describe the solution you'd like

based on the Pistoia Alliance document https://fairtoolkit.pistoiaalliance.org/use-cases/adoption-and-impact-of-an-identifier-policy-astrazeneca/, create a survey of what is used by EFPIA partners and contrast with infrastructure relied upon in open source projects.

pinging @robertgiessmann @karsten-quast @ereynrs @nsjuty (but not limited to) for initial discussion

Some ideas on recipes that can be generated from the raw recipes:

1. where to submit my data, a recommendation of hosting platform depending on datasets
2. how to perform ontology annotation
3. how to build an ETL
4. what is the community standards for different data types (Minimum information standard)
5. How to build a pipeline (Using KNIME to build reusable workflow) @Manfred might be more experienced in this work

It would be helpful if the dev branch (which holds the most up-to-date version of the cookbook, but is not officially released yet) would be visible somewhere in the internet.

This was achieved by building in this repository by a Github Action, and pushing the result to another repo ( https://github.com/FAIRplus/cookbook-dev ), specifically to branch gh-pages there.

In this other repo (cookbook-dev), github pages is set up to serve from the branch gh-pages. This results in the dev branch of the-fair-cookbook being visible at https://fairplus.github.io/cookbook-dev .

I requested Francesco to break down the etox experience report into bite-size recipes.

No deadline agreed yet. Maybe during face-to-face?

Closes #40 .

Is your feature request related to a problem? Please describe.
As the author of a recipe, I don't know the official procedure for having it placed in the Book Table of Content.
Do I need to push both the Recipe and toc.yml` or just the recipe?

related to #1
to standardize self-reporting from software / recipe authors

Identifying the competency questions and use cases has been an important part in our work.
Is it possible to have a chapter about the FAIR background and identify the key challenges in FAIR?
The interviews and EFPIA requirements can be helpful to extract such info.

contact Chris, Alasdair.

Abstract of the recipe? "Assess the solutions available with respect to: identifier assignment, identifier resolution, identifier mapping and linking"?

Is your feature request related to a problem? Please describe.
some people find markdown & github too challenging and want to write in gdoc (collaborative editing). investigation how to convert from gdoc to markdown

• https://github.com/supreetpal/gdoc-markdown-converter

• https://gsuite.google.com/marketplace/app/docs_to_markdown/700168918607

Describe the solution you'd like
A clear and concise description of what you want to happen.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
conversion should match the github faircookbook recipe template
https://fairplus.github.io/the-fair-cookbook/recipes/recipe-template.html

Stub recipe exists at https://github.com/FAIRplus/the-fair-cookbook/blob/identifiers/docs/content/recipes/findability/identifier-services/id-resolution.md

This recipe should cover the use of Identifiers.org. In particular how to register your data source with the service.

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://github.com/FAIRplus/the-fair-cookbook/blob/dev/docs/content/recipes/help/how-to-create-recipe-with-hackmd.md'
2. Step 5 assumes that you have the Cookbook checked out somewhere but there are no instructions/links earlier in the recipe that tell you that you need to have done this.

proposed by Oya

Is your feature request related to a problem? Please describe.

Newly added recipes are added and need to be reviewed. We currently don't have an official process for this and we don't have an editorial board.

Describe the solution you'd like

• Identify and invite a group of up to 10 FAIR Cookbook editors; 50% EFPIA / 50% Academia

• Outline the duties of the said Editors

related to FAIRplus/FAIRPlus_squad2#72

-either use the markdown template included in this issue
-or use the gdoc templates

Table of Contents

1. Main FAIRification Objectives
2. Graphical Overview of the FAIRification Recipe Objectives
3. FAIRification Objectives, Inputs and Outputs
4. Capability & Maturity Table
5. Table of Data Standards
6. Executable Code in Notebook
7. How to create workflow figures
8. License

Main Objectives

The main purpose of this recipe is:

Making self describing tabular data using Frictionless tools instead of dumping Excel files.

Graphical Overview of the FAIRification Recipe Objectives

Capability & Maturity Table

FAIRification Objectives, Inputs and Outputs

Table of Data Standards

Executable Code in Notebook

import isatools
import json
import pandas as pd 
import holoview

How to create workflow figures

one may use the following mermaid syntax:

graph LR;
    A[Data Acquisition] -->B(Raw Data)
    B --> C{FAIR by Design}
    C -->|Yes| D[Standard Compliant Data]
    C -->|No| E[Vendor locked Data]

Authors:

License:

Table of Contents

1. Main FAIRification Objectives
2. Graphical Overview of the FAIRification Recipe Objectives
3. FAIRification Objectives, Inputs and Outputs
4. Capability & Maturity Table
5. Table of Data Standards
6. Executable Code in Notebook
7. How to create workflow figures
8. License

Main Objectives

The main purpose of this recipe is:

Making self describing tabular data using Frictionless tools instead of dumping Excel files.

Graphical Overview of the FAIRification Recipe Objectives

Capability & Maturity Table

FAIRification Objectives, Inputs and Outputs

Table of Data Standards

Executable Code in Notebook

import isatools
import json
import pandas as pd 
import holoview

How to create workflow figures

one may use the following mermaid syntax:

graph LR;
    A[Data Acquisition] -->B(Raw Data)
    B --> C{FAIR by Design}
    C -->|Yes| D[Standard Compliant Data]
    C -->|No| E[Vendor locked Data]

Authors:

License:

Recipe1: Deploying and hosting a terminology service

identifier:

authors:

Tony Burdett
Fuqi Xu

maintainers:

version:

license

Ingredients:

Identifier Schema:

1. Metadata Model:
    - 
    - 
    -
2. Vocabularies and Terminologies:
    -
    -
    -
3. Data Format:
    -
    -
    -
4. Tools and  Software:
    - OLS
    -
    -

Objectives:

Deployment and Maintaining a vocabulary service

Step by Step Process:

 ### Step1:
 
 ### Step2:
 
 ### Step3:
 
 ### Step4:
 
 ### Step5: ...

Is your feature request related to a problem? Please describe.
relates to #15

Describe the solution you'd like

allow operational linking to mybinder.org

Is your feature request related to a problem? Please describe.
I want to contribute content but need guidance ? Is there a template ?

Describe the solution you'd like
A clear and concise description of what you want to happen.

Describe alternatives you've considered
current template is ok but possible too shallow and lacks guidance.

Additional context
Request made following FAIRplus face 2 face meeting January 2020 at the Wellcome Trust Genome campus. @JolandaS @tburdett @nsjuty as per our discussion.

As @ereynrs suggested in R1.3, "the assumption of the recipe be explicitly stated among a ingredients/dependencies/requirements section. "

When reading a recipe, I want to know what are the requirements to understand and test it, so that I can decide whether to continue with the recipe or not.

The requirements can be

• technical requirements (Bash knowledge needed)
• recipe dependency (read Recipe 1 before Recipe 2)
• knowledge requirement (OBO foundry knowledge needed)
• ...

Shall we create a new Requirements section in the recipe template? Or shall we provide such info in the Ingredients section?

Discuss the current model and contrast with a dual model

Link to recipe: https://hackmd.io/@7GH6ArIbRnm_7fgcv8mmWw/HJVQ7nHKL

To do for this recipe:

• finish writing @daniwelter
• test/review recipe (Peter and Rudi)
• write user story
• publish in cookbook

investigate if there are easy options available in github to transfer recipe related tickets created in the squad repositories to the FAIR cookbook gh repo

I had problems with mermaid parsing the diagrams only after refreshing, i.e.:

Clicking on the page -> content appears, but no diagram; click "refresh" in browser -> diagram appears.

I fixed this by telling mermaid to parse everything in the footer ; it appeared that there was some change in mermaid specs, and they would desire mermaid to be loaded in the body now (before: load in head).

Hi @nsjuty ,

I hope I don't find you too stressed out (I bet on the "stressed out", though...) .

I would like to invite you to submit an 100-150 word abstract regarding a contribution on identifiers.org . It would be great if you have a look at the ToC draft (https://docs.google.com/spreadsheets/d/13B2aLm5ZXFUwAu6DlcL7soWL8yzX6juR4ijgUpzIsv4/edit#gid=818333385), to find out where a recipe of yours might fit best.

Can you confirm a deadline to submit this abstract until Friday 2020-04-24 (or make an alternative suggestion)?

Thank you so much in advance!
Robert

• Enable a graphical overview of the overall process described in the the recipes, for instance as flowcharts .

Describe the solution you'd like
During F2F meeting in January 2020, @CaroleGoble and @proccaserra discussed how to express the recipes as flowcharts. Currently, working with mermaid javascript library working with Jekyll for deployment via gh-pages.

Describe alternatives you've considered
suggestion by @CaroleGoble:

• https://draw.io
  • good for flowcharts and has various integration (like google drive)
  • works with jupyter - https://blog.jupyter.org/a-diagram-editor-for-jupyterlab-a254121ff919

hi Franceso / Laura , we found this fork -- do you want to make this a recipe within this cookbook? https://github.com/fra82/the-fair-cookbook

Is your feature request related to a problem? Please describe.
people with no experience with github and markdown feel the learning curve is too steep
googledoc provides nice collaborative editing, low barrier to entry but Markdown export not available and conversion tool are wanting.

Describe the solution you'd like
allows push and pull to github
allows use of template
allows collaborative editing
allows comments in a markdown document
allows view of markdown and rendered version
allows multi users.

https://hackmd.io/c/tutorials/%2Fs%2Finvite

Related to this GH issue #74. Document with overview of the tools and their functionalities can be found here.

Is your feature request related to a problem? Please describe.
We are missing an overview of what tools are available on the market or as OS to perform some FAIRification steps.

Describe the solution you'd like
We can just have a section for that, kept dynamic and we can invite contributions for interested parties (tools developers). We will need to add a review process from FAIRplus.

Describe alternatives you've considered
Go to other resources (FAIR matrix? Pistoia? bu there is nothing comprehensive enough and FAIRplus is in a good spot to try to be a reference.

Additional context
It's difficult, as being up2data and reasonably complete is hard. But as this is an open document, it may work. If it works, this would be very useful.

Is your feature request related to a problem? Please describe.

Current organisation does not necessarily help potential users , seems more geared to recipe developers.

Describe the solution you'd like
It would be nice to include the middle out approached as presented in the following: https://zenodo.org/record/3822219#.Xrqo8hNKh24
by AZ.

Additional context
Build on FAIRification 'snake' presented by @tburdett

Is your feature request related to a problem? Please describe.

Allow users to report how useful/helpful the FAIR recipe/protocol has been

Describe the solution you'd like
link the GitHub issue tracker to each recipe.
find a widget that would integrate with jupyter-book to allow users to rate.

Is your feature request related to a problem? Please describe.
Discussion with @egonw @nsjuty about the need to perform an Audit over any code included in the recipes to ensure the EFPIA partners (and others ?) that no data is leaked publicly or send to public services (e.g. sending a private/proprietary Inchi key to public REST service)

Describe the solution you'd like
A service that would raise warnings over any API call hitting a public service
A declarative document from the developer listing all the potential risks associated with using a service for an EFPIA partners

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

Is your feature request related to a problem? Please describe.
@FuqiX reported during dedicated FAIRcookbook call (2020.05.27) the Reusability aspects were absent from the current outline

Describe the solution you'd like

• Need to demonstrate a case of reuse / integration challenge

tagging @FuqiX @proccaserra @JolandaS @nsjuty for first round of discussions

Relates to #67

Would document the implementation aspect (e.g. testing a set of SPARQL queries against a knowledge graph, evaluating query results in the lights of the 'competency questions: scientific question')

discussion with @karsten-quast @FuqiX @daniwelter @ereynrs

Recipe1: Anonymizing Patient Data

identifier:

authors:
Wei Gu
Venkata Satagopam
Philippe Rocca-Serra

maintainers:

version:

license

Ingredients:

1. Identifier Schema:
    - DOI
    - ARK

2. Metadata Model:
    - DATS
    - DCAT 1.0
    - DCAT 2.0
    - ISA

3. Vocabularies and Terminologies:
    - EFO
    - OBI
    
4. Data Format:
    - JSON
    - JSON-LD

5. Tools and Software:
    - GRAPHQL

Objectives:

Findability

Allow dataset discovery

Step by Step Process:

 ### Step1:
 
 ### Step2:
 
 ### Step3:
 
 ### Step4:
 
 ### Step5: ...

Discussions with @daniwelter @karsten-quast @ereynrs @FuqiX during discussions with R4.

The recipe as it stands now needs to be generalised to reflect the process that we adopted (proposed and discussed during the Berlin squad meeting) and separate the specifics on implementation in a separate subsection

Describe the bug
Search function from Side menu returns a 404

To Reproduce
Steps to reproduce the behavior:

1. Go to Side Menu on the left hand side of the screen
2. Look for the Search menu item
3. Click the 'Link'
4. which brings up a github 404 page not found error from Github

Expected behavior
The page should be the same as the one display when hitting the magnifying glass on the top right hand corner.
https://fairplus.github.io/the-fair-cookbook/search.html

When I browse a recipe in the Cookbook website, I want to find all recipes related to the current recipe, so that I can be easily directed to other recipes and better decide which recipe to read first.

Example:
Recipe 1.3 is dependent on Recipe 1.2
Recipe 1.3 is related to Recipe 1.1 and [Recipe 3.1]

Possible solutions

1. Add a "related recipe" side panel in the recipe page. This might takes some work
2. Add a "related recipe" section in the recipe template. So that authors can link the recipes manually using hyperlinks.

One problem I had linking recipes manually is that some recipe links are not available yet.
Can we 'pre-register' the recipe, so that other recipes can point to the unfinished recipe? Or is it the editors' job to link the recipes manually?

Describe the bug
It looks like the code block was not properly used on Step 6. Make adjustments for any bits that could not be properly entered through the form.

To Reproduce
Steps to reproduce the behavior:

1. Go to https://github.com/FAIRplus/the-fair-cookbook/blob/bioschemas-seo/docs/content/recipes/infrastructure/bioschemas-datacatalog.md
2. Scroll down to Step 6. Make adjustments for any bits that could not be properly entered through the form. under subtitle Method
3. See error
   "provider": { "@type": "Organization", "@id": "https://fairsharing.org/communities" } ],
   rendered as regular text rather than code and then step 7 rendered as code rather than text

Expected behavior
I expect to see a code rendered as code

"provider": { "@type": "Organization", "@id": "https://fairsharing.org/communities" } ],

and then text, tables and so normally rendered, not as code as it happens now.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]: Windows 10
• Browser [e.g. chrome, safari]: Firefox
• Version [e.g. 22]: 75.0

Additional context
Add any other context about the problem here.
Page contributed by @AlasdairGray

@proccaserra , you are invited to review this recipe. See Pull request #38 .

Please post your evaluation checklist here.

Need to include a statement about sitemaps in

• seo recipe
• data page recipe

Is your feature request related to a problem? Please describe.

Suggestion by Oya Beyan to possibly move it earlier to highlight how the CMMI model can be used to define a FAIRification process in terms of goals to achieve for a given set of capabilities

When searching in the cookbook, the links in the search results are invalid.

For example: when searching for "eTox" in this page ,
It redirects me to page "https://fairplus.github.io/the-fair-cookbook/YOUR%20URL/the-fair-cookbook/recipes/etox_raw/FAIRplus_Recipe_Ontology_mapping_the_eTox_dataset_scenario.html"

The correct link shall be https://fairplus.github.io/the-fair-cookbook/recipes/etox_raw/FAIRplus_Recipe_Ontology_mapping_the_eTox_dataset_scenario.html

Describe the bug
Unable to run the code provided on the HTML page. Running the code got stuck on waiting for kernel....

To Reproduce

1. Go to any recipe, e.g. https://fairplus.github.io/the-fair-cookbook/recipes/fair-data-matrix/0-rose-metabolites-Python-data-handling.html

2. Click on the code cell -> interactive mode - > run

3. Running the code got stuck on "waiting for kernel"

Additional context

• I am able to run ThebeLab example code, though it also took some time to connect to the kernel.
• Downloading the .ipynb file and running locally it work for me.

Screenshot
The code got stuck on Waiting for kernel

needs to be further processed, e.g. check on ToC position, identify reviewer, ...