Cm medit -> master (#110)

* new-test-hackmd-recipe

this is a test to push a recipe from HackMD to github FAIRplus/the-faircookbook repo

* adding  recipe

* First commit of new robot recipe

* UC3 R1.3

dfs

* 0.1

pushing initial draft to gihub dev branch

* first review

* new recipes, and more edits

* minor edits to gdoc recipe template

* Update how-to-create-recipe-with-gdoc.md

finalizing documentation

* more explaining about how to use HackMD

adding the missing bit about the browser extension

* edits to helper recipes

* adding the section about module extract

first pass

* First updates to extraction procedure

* Now with Karsten's competency questions included

* reorganizing the toc, clean up

* Update ontology-robot-recipe.md

Adding usage code for merge, annotate, convert,export robot commands
Adding mermaid figure
updating tables

* Added Karsten's dataset in Excel file

* R1.3 first cleaned up version

* Update recipe_template.md

* re-organizing toc, adding content stubs and drafts

* 1.0

initial draft for SEO and (Bio)Schema.org annotation

* ReviewCompleted

First review done

* 1.0

Initial draft - with introduction, user story (CMMI  group to review), table of standards.
TODO: add graphical overview, link to 'search engine optimization' recipe and 'ontology selection

* 1.01

minor edit to 'main objective section'

* toc reorganization, pushing several new recipes on datacatalog, seo, ...

* Add files via upload

* Delete UC3R1.3 recipe

* Various updates relating to Bioschemas #30

* Update roadmap.md - make ToC open and linked (#33)

* Update roadmap.md

* Update roadmap.md

* Update roadmap.md

* Stubs for bioschemas recipes

* Add direct links to the HackMD extensions (#43)

* added recipe 2.2.1 - request new term in public ontology (#38)

* added recipe 2.2.1 - request new term in public ontology

* incorporated feedback from Nick Juty from 21/04/20

Co-authored-by: Robert Giessmann <[email protected]>

* Update recipe-template.md

makes it clear where the main content goes

* Update recipe-template.md

* Updated authorship tables

* Reverted statement to CrediT ontology

* Update recipe-template.md

* Update recipe-template.md

* Flow diagram for marking up a data page

* Revised flow diagram

* Update how-to-create-recipe-with-hackmd.md

minor edits affecting rendering of images

* Update how-to-create-recipe-with-hackmd.md

Documenting how to pull and push file from and to github when using HackMD.
Following discussion with @petrospaps and @FuqiX

* Update data-catalog.md

* tests

* Updated steps in flow diagram

* Removed unnecessary instructions section

* Started method, added screenshot of tool

* Create _trigger_action

* tries to build dev to another github page repo

* tries to build dev to another github page repo

* tries to build dev to another github page repo

* tries to build dev to another github page repo

* tries to build dev to another github page repo

* Completed recipe steps

* tries to build dev to another github page repo

* fixed footnote formatting as github does not support it

* Fixed typo

* tries to build dev to another github page repo

* tries to build dev to another github page repo

* tries to build dev to another github page repo

* tries to build dev to another github page repo

* Refinements to methodology

* Removed unused Executable Code in Notebook section

* Changed to EDAM terms

* Updated FAIRification and Standards tables

* Added aim and flowchart

* Removed flowchart instructions

* Copied standard sections from data page recipe

* Fixed typo

* Written method for dataset markup

* Updated objective and flowchart

* Copied content over from Dataset recipe

* Added screenshot of Dataset form

* fixed typo

* Updated methodology for DataCatalog

* Update build-dev.yml

* Update build-dev.yml

* test

* tests transfer to other repo

* Update build-dev.yml

* corrects URLs; they have to start with trailing slash

* Fix #49 corrected markup formatting

* Fix #48

* Removed `[` missed in fix of #48

* Acknowledge external review of @ljgarcia

* Acknowledge external review of @ljgarcia

* Acknowledge external review of @ljgarcia

* Acknowledge external review of @ljgarcia

* Fix typos, internal links and styling

* Authors table update.

* reorganizing table of content, adding placeholders for new recipes for integration and release, testing

* update to the mermaid overview + typo fixes

* Update README.md (#51)

* Update README.md

Updates to the Github README file for the project to clarify status of the project and address feedback received from @Chris-Evelo 
@robertgiessmann please have a look

* Update README.md

Co-authored-by: Robert Giessmann <[email protected]>

* Update build-dev.yml

* Update build-dev.yml

* Update build-dev.yml

* Update build-dev.yml

* Update build-dev.yml

* Update build-dev.yml

* Update build-dev.yml

* Update build-dev.yml

* Update build-dev.yml

* Update build-dev.yml

* Update build-dev.yml

* restyling of mermaid diagrams and testing image resizing

* Update _config.yml

* Update _config.yml

* reloads mermaid in the footer

* minor fixes

* adding jupyter notebook for MSIO build process

* netlify testing

* MONDO seed list

* tissue uberon seeds list

* Add seed extraction and term relationships sections.

* Minor typos fixed, authors table updated

* Step 1.1 Source ontologies updated

* V1

Recipe notes on branch extraction task.

* Branch extraction task's notes added.

* Final version

* Recipe 1.2

* modify reference

* add review CMMI and userStory

* r1.3

a recipe comparing 4 publicly available vocabulary services

* Update UC3_R1.3_local_ontology_services.md

* improvement to css to deal with bad rendering of markdown checkbox, integration of recipes from squads, adding a section for recipe difficulty, target audience and type

* further testing and content addition for liaising sections - head of chapters - adding under construction banners

* V2

Ontology branch merging added.

* V2

Ontology branch merging added.

* V2

Ontology branch merging added.

* V2.0.1

Minor changes to branch merging task description.

* Update how-to-create-recipe-with-hackmd.md

updating the help on hackMD and how to create a recipe

* 2020.05.25

updating layout, adding  difficulty level, intended audience, conclusion sections

* 2020-05-26

Creation of a recipe showing how to deposit to zenodo (web and rest)

* enhancing help documentations, adding new zenodo recipe, updating toc

* 2020-26-05

adding a new recipe about how to choose an ontology

* 2020-05-26

adding MarkDown, Mermaid tips and tricks recipe to assist contributors

* fix to toc

* adding tips and tricks recipe as part of help, fixing toc

* Updated to new TOC of FAIR Cookbook

* update source selection

* Updated ROBOT templates for the development of app ontologies

* First draft of the catalog deployment recipe

* Update data-catalog-deployment.md

* Update data-catalog-deployment.md

* Update data-catalog-deployment.md

* Update data-catalog-deployment.md

* Update data-catalog-deployment.md

* Update data-catalog-deployment.md

* Update data-catalog-deployment.md

* Update data-catalog-deployment.md

* Update data-catalog-deployment.md

* 20200529_draft

* Update data-catalog-deployment.md

edits (minor reformatting) + adding `what to read next` section in the conclusion

* adding imi-data-catalogue-deployment recipe, fixing toc accordingly

* Competency questions proposed by Karsten

* cleaned up version

* 20200603

* Update ontology-robot-recipe.md

* Update ontology-robot-recipe.md

* Update ontology-robot-recipe.md

* Reviewd and revised version, ready to push

* Reviewd and revised version, ready to push

* Reviewed and revised version. Minor typo fixed. Ready to push

* Reviewed and revised. Minor typo fixed. Ready to push.

* adding R4 ontology-robot-recipe

* pinning jupyterbook version as building with latest 0.7 version fails

* switching baseurl value in config.yml to allow run on dev server

* another fix on _config.yml for dev

* Refine competency questions and add link

* sync with dev to support review

* creation of FAIRplus cookbook CSS + adding cards to recipes throughout + testing FAIRification representation process

* adding favicon, tweak toc by adding section on reusability and associated stub page, clarify personas on intro page

* addressing all typos and errors reported Hannah, fixing intro text, fixing favicon, fixing table of developers

* correction to people.md as per request

* fix to github handle on people page

* adding shex validation metadata profile recipe

* edits and fixes to shex recipe

* fixing email address in help document

* Update technical-and-architectural-selection-criteria-of-ontology-lookup-services.md (#69)

REVIEW: following a request from @petrospaps, I carried out a review. Many corrections around style and grammar but more edits are needed to address content and differentiate more clearly from the recipe about functional requirements.
Please [REVIEWER QUESTION] tag in the text for additional comments/questions
@karsten-quast @ereynrs @petrospaps

* adding new recipe corresponding to issue #91 (#92)

Co-authored-by: Philippe Rocca-Serra <[email protected]>

* .

* Cm medit (#106)

* Update recipe_template.md

* Add files via upload

Co-authored-by: Oya Beyan <[email protected]>

* Cm medit (#107)

* Update recipe_template.md

* Add files via upload

Co-authored-by: Oya Beyan <[email protected]>

* Revert "Cm medit (#104)"

This reverts commit 31c4d54.

* .

* .

Co-authored-by: HackMD <[email protected]>
Co-authored-by: Philippe Rocca-Serra <[email protected]>
Co-authored-by: daniwelter <[email protected]>
Co-authored-by: Philippe Rocca-Serra <[email protected]>
Co-authored-by: Oya Beyan <[email protected]>
Co-authored-by: Fuqi Xu <[email protected]>
Co-authored-by: Alasdair Gray <[email protected]>
Co-authored-by: Robert Giessmann <[email protected]>
Co-authored-by: Ulrich Goldmann <[email protected]>
Co-authored-by: mrwolf on behalf of Robert Giessmann <[email protected]>
Co-authored-by: Garcia-Castro <[email protected]>
Co-authored-by: Emiliano Reynares <[email protected]>
Co-authored-by: Petros Papadopoulos <[email protected]>
Co-authored-by: fuqiX <[email protected]>
Co-authored-by: Philippe Rocca-Serra <[email protected]>

.github/ISSUE_TEMPLATE/recipe_template.md

@@ -34,7 +34,6 @@ ___
 ___
 ## User Stories
 
-
 ## Capability & Maturity Table
 
 | Capability  | Initial Maturity Level | Final Maturity Level  |

.github/workflows/build-dev.yml

@@ -0,0 +1,33 @@
+name: transfer-dev-to-external-repo
+on:
+  push:
+    branches:
+      - dev
+
+jobs:
+  copy-to-other-repo:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout dev branch 🛎️
+      uses: actions/checkout@v2 # If you're using actions/checkout@v2 you must set persist-credentials to false in most cases for the deployment to work correctly.
+      with:
+        persist-credentials: false
+        ref: dev
+    - name: Setup Python
+      uses: actions/[email protected]
+    - name: Install and Build 🔧 
+      run: pip install jupyter-book==0.6.3 && jupyter-book build ./docs --overwrite
+    - run: ls -alhR 
+    - name: Install SSH Client 🔑
+      uses: webfactory/[email protected]
+      with:
+        ssh-private-key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
+    - name: Deploy 🚀
+      uses: JamesIves/github-pages-deploy-action@releases/v3
+      with:
+        SSH: true
+        BASE_BRANCH: dev #The branch of this repository which should be transfered from.
+        REPOSITORY_NAME: FAIRplus/cookbook-dev # The repository on github.com to which will be deployed = pushed.
+        BRANCH: gh-pages # The branch the action should deploy to.
+        FOLDER: docs # The folder the action should deploy.
+

.gitignore

@@ -1,5 +1,7 @@
 .DS_Store
-docs/_site
+docs/_site/
 docs/.sass-cache
 docs/Gemfile.lock
-.gitignore~
+.gitignore~
+docs/_config_netlify.yml
+docs/_build/

README.md

@@ -1,4 +1,4 @@
-# The FAIR cookbook
+# The FAIR Cookbook :construction: 
 
 FAIR data is **F**indable, **A**ccessible, **I**nteroperable and **R**eusable. 
 

_trigger_action

@@ -0,0 +1,2 @@
+## change this file to trigger a build-and-deploy action.
+## 2

docs/_build/1/frictionless.html

@@ -1,20 +1,27 @@
 ---
 title: |-
+<<<<<<< HEAD
   frictionless
+pagenum: 22
 prev_page:
   url: /features/notebooks.html
+=======
+  frictionless data example
+prev_page:
+  url: /1/mermaidsetup.html
   title: |-
-    Jupyter notebooks
+    mermaidsetup
+>>>>>>> dev
 next_page:
   url: /1/testnb/0-rose-metabolites-Python-data-handling.html
-  title: |-
-    1
 suffix: .md
+search: data fairsharing org c objectives b edamontology table fairification mermaid d maturity div operation import stroke main recipe capability license graph lr acquisition input output structure file sdf ewv annotation orcid frictionless tabular graphical overview inputs outputs standards executable code notebook create workflow figures class raw fair design yes standard compliant e vendor locked level calculation text human phenotype ontology kbttf conversion open format automatic style fill width px university oxford readiness group writing creativecommons png package contents mainfairificationobjectives graphicaloverviewofthefairificationrecipeobjectives fairificationobjectives inputsandoutputs capabilitymaturitytable tableofdatastandards executablecodeinnotebook howtocreateworkflowfigures purpose making self describing using tools instead dumping excel files initial final interoperability minimal
 
 comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
 ---
 
     <main class="jupyter-page">
+    <div id="page-info"></div>
     <div class="jb_cell">
 
 <div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
@@ -111,7 +118,7 @@ <h2 id="Table-of-Data-Standards">Table of Data Standards<a class="anchor-link" h
 <hr>
 <h2 id="Executable-Code-in-Notebook">Executable Code in Notebook<a class="anchor-link" href="#Executable-Code-in-Notebook"> </a></h2><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">isatools</span>
 <span class="kn">import</span> <span class="nn">json</span>
-<span class="kn">import</span> <span class="nn">pandas</span> <span class="kn">as</span> <span class="nn">pd</span> 
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span> 
 <span class="kn">import</span> <span class="nn">holoview</span>
 </pre></div>
 <hr>

docs/_build/1/mermaidsetup.html

@@ -1,20 +1,29 @@
 ---
 title: |-
   mermaidsetup
+pagenum: 27
 prev_page:
+<<<<<<< HEAD
   url: /1/testnb/2-rose-metabolites-Python-RDF-querying-analysis.html
-  title: |-
-    4
 next_page:
   url: /People.html
+=======
+  url: /recipes/help/recipe-template.html
+  title: |-
+    Recipe Template
+next_page:
+  url: /1/frictionless.html
   title: |-
-    People
+    frictionless data example
+>>>>>>> dev
 suffix: .md
+search: mermaid js jekyll github com library d following div diagrams file unpkg dist pages javascript plugin config distribution section diagram still gantt task data stroke flow core open ruby path min curl o chart script does class moving another enable served jekyllrb docs graphical overview processes since recipes via documentation here gem need install bash edit yml add files default jsurl src work site head html template include state crash display input b conversion format c automatic annotation output style fill width px gh information found document sequence popular mean provide fairification strong requirement enhance such allowing generate charts graphs
 
 comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
 ---
 
     <main class="jupyter-page">
+    <div id="page-info"></div>
     <div class="jb_cell">
 
 <div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
@@ -87,17 +96,19 @@ <h1 id="How-to-enable-flow-diagrams-in-Github-from-gh-pages:">How to enable flow
 
     - Does this state diagram work?
 </code></pre>
-<div class="mermaid">
+<p><div class="mermaid">
 stateDiagram
     [*] --> Still
     Still --> [*]
     Still --> Moving
     Moving --> Still
     Moving --> Crash
     Crash --> [*]
-</div>        
-        - Does this Gantt chart display?  
-<div class="mermaid">
+</div></p>
+
+<pre><code>    - Does this Gantt chart display?  
+</code></pre>
+<p><div class="mermaid">
 gantt
     title A Gantt Diagram
     dateFormat  YYYY-MM-DD
@@ -107,17 +118,21 @@ <h1 id="How-to-enable-flow-diagrams-in-Github-from-gh-pages:">How to enable flow
     section Another
     Task in sec      :2014-01-12  , 12d
     another task      : 24d
-</div>
-        - Does this flowchart display?
-<div class="mermaid">
+</div></p>
+
+<pre><code>    - Does this flowchart display?
+</code></pre>
+<p><div class="mermaid">
 graph LR;
     A["input data"]-->B["conversion to open format"];
-    A["input data"]-->C["automatic annotation"];
+    A["input data"]-->C["automatic annotation"]:::box;
     B["conversion to open format"]-->D(("output data"));
     C["automatic annotation"]-->D(("output data"));  
     style A fill:#FF5733,stroke:#333,stroke-width:2px
     style D fill:#0A749B,stroke:#333,stroke-width:2px
-</div><p>if you cannot view the Gantt chart or the State Diagram, it means you  are running an outdated version of the mermaid distribution.
+    classDef box fill:#2a9fc9,color:#fff;
+</div>
+if you cannot view the Gantt chart or the State Diagram, it means you  are running an outdated version of the mermaid distribution.
 try upgrading by download the files from <a href="https://unpkg.com/browse/[email protected]/dist/">here</a></p>
 
 </div>

docs/_build/1/testnb/0-rose-metabolites-Python-data-handling.html

@@ -3,23 +3,28 @@
   - "/1/testnb/0-rose-metabolites-python-data-handling"
 interact_link: content/1/testnb/0-rose-metabolites-Python-data-handling.ipynb
 kernel_name: venv372
+kernel_path: content/1/testnb
 has_widgets: false
 title: |-
   1
+pagenum: 23
 prev_page:
   url: /1/frictionless.html
+<<<<<<< HEAD
+=======
   title: |-
-    frictionless
+    frictionless data example
+>>>>>>> dev
 next_page:
   url: /1/testnb/1-rose-metabolites-Python-analysis.html
-  title: |-
-    2
 suffix: .ipynb
+search: data pandas package file p m rose python dataframe s tabular table r metabolites analysis ipynb values j json information doi org function field new notebooks l f c frictionless using packages set excel chebi reading row fields chemical not libchebi retrieve layout step bendahmane fair scent supplementary philippe rocca serra e results such metabolite profiling easily libraries show create validate against definition allow descriptors independent variables easy zenodo following manual start take extract axis columns index name match api does transformation library widetolong reference position solve writing setting empty uri requires order also output convert dataset plot rdf querying
 
 comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
 ---
 
     <main class="jupyter-page">
+    <div id="page-info"></div>
     <div class="jb_cell">
 
 <div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
@@ -67,8 +72,8 @@ <h2 id="Background:">Background:<a class="anchor-link" href="#Background:"> </a>
 <span class="kn">import</span> <span class="nn">libchebipy</span>
 <span class="kn">import</span> <span class="nn">re</span>
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
-<span class="kn">from</span> <span class="nn">datapackage</span> <span class="k">import</span> <span class="n">Package</span>
-<span class="kn">from</span> <span class="nn">goodtables</span> <span class="k">import</span> <span class="n">validate</span>
+<span class="kn">from</span> <span class="nn">datapackage</span> <span class="kn">import</span> <span class="n">Package</span>
+<span class="kn">from</span> <span class="nn">goodtables</span> <span class="kn">import</span> <span class="n">validate</span>
 </pre></div>
 
     </div>

docs/_build/1/testnb/1-rose-metabolites-Python-analysis.html

@@ -3,23 +3,23 @@
   - "/1/testnb/1-rose-metabolites-python-analysis"
 interact_link: content/1/testnb/1-rose-metabolites-Python-analysis.ipynb
 kernel_name: venv372
+kernel_path: content/1/testnb
 has_widgets: false
 title: |-
   2
+pagenum: 24
 prev_page:
   url: /1/testnb/0-rose-metabolites-Python-data-handling.html
-  title: |-
-    1
 next_page:
   url: /1/testnb/3-rose-metabolites-R-analysis.html
-  title: |-
-    3
 suffix: .ipynb
+search: data p m package s tabular r j python ggplot such dataset same l f c scent packages using org datasets simply file generated bendahmane plotnine philippe rocca serra profiling libraries graphical lets read relevant generate barplot similar both rosa structure another shows studies compounds x y caissard jc vergne dubois raymond o baudino roses science doi h exploring comparing rose profiles stored port oerc ox ac uk university oxford e research centre background experimental results metabolite published straightfowardly reported okfn frictionlessdata io specs components easily parsed frames exploiting visualization purpose implementing grammar concepts here show equivalent rich tidyverse few
 
 comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
 ---
 
     <main class="jupyter-page">
+    <div id="page-info"></div>
     <div class="jb_cell">
 
 <div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
@@ -65,7 +65,7 @@ <h2 id="Background:">Background:<a class="anchor-link" href="#Background:"> </a>
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-<span class="kn">from</span> <span class="nn">plotnine</span> <span class="k">import</span> <span class="o">*</span>
+<span class="kn">from</span> <span class="nn">plotnine</span> <span class="kn">import</span> <span class="o">*</span>
 </pre></div>
 
     </div>

docs/_build/1/testnb/2-rose-metabolites-Python-RDF-querying-analysis.html

@@ -3,23 +3,29 @@
   - "/1/testnb/2-rose-metabolites-python-rdf-querying-analysis"
 interact_link: content/1/testnb/2-rose-metabolites-Python-RDF-querying-analysis.ipynb
 kernel_name: venv372
+kernel_path: content/1/testnb
 has_widgets: false
 title: |-
   4
+pagenum: 26
 prev_page:
   url: /1/testnb/3-rose-metabolites-R-analysis.html
-  title: |-
-    3
 next_page:
+<<<<<<< HEAD
   url: /1/mermaidsetup.html
+=======
+  url: /project_information.html
   title: |-
-    mermaidsetup
+    Project Information
+>>>>>>> dev
 suffix: .ipynb
+search: rose sparql function lets using philippe rocca serra following ask query exploring garden oerc ox ac uk university oxford e research centre credits bob du charme www snee com bobdc blog jupyter aka ipytho html read rdf graph generated dtpkgrdf py python script saved disk turtle file independent variables levels display results declared earlier biological technical replicates used compute mean concentration chemical compounds detected forming signature fragrance once invoked pretty printing
 
 comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
 ---
 
     <main class="jupyter-page">
+    <div id="page-info"></div>
     <div class="jb_cell">
 
 <div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
@@ -49,19 +55,19 @@ <h1 id="Exploring-a-rose-garden-with-SPARQL">Exploring a rose garden with SPARQL
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">rdflib</span>
-<span class="kn">from</span> <span class="nn">rdflib</span> <span class="k">import</span> <span class="n">Graph</span><span class="p">,</span> <span class="n">RDF</span>
-<span class="kn">from</span> <span class="nn">IPython.core.display</span> <span class="k">import</span> <span class="n">display</span><span class="p">,</span> <span class="n">HTML</span>
+<span class="kn">from</span> <span class="nn">rdflib</span> <span class="kn">import</span> <span class="n">Graph</span><span class="p">,</span> <span class="n">RDF</span>
+<span class="kn">from</span> <span class="nn">IPython.core.display</span> <span class="kn">import</span> <span class="n">display</span><span class="p">,</span> <span class="n">HTML</span>
 <span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">import</span> <span class="nn">json</span>
 <span class="kn">import</span> <span class="nn">csv</span>
 <span class="kn">import</span> <span class="nn">uuid</span>
 
-<span class="kn">from</span> <span class="nn">SPARQLWrapper</span> <span class="k">import</span> <span class="n">SPARQLWrapper</span><span class="p">,</span> <span class="n">SPARQLWrapper2</span><span class="p">,</span> <span class="n">JSON</span><span class="p">,</span> <span class="n">JSONLD</span><span class="p">,</span> <span class="n">CSV</span><span class="p">,</span> <span class="n">TSV</span><span class="p">,</span> <span class="n">N3</span><span class="p">,</span> <span class="n">RDF</span><span class="p">,</span> <span class="n">RDFXML</span><span class="p">,</span> <span class="n">TURTLE</span>
+<span class="kn">from</span> <span class="nn">SPARQLWrapper</span> <span class="kn">import</span> <span class="n">SPARQLWrapper</span><span class="p">,</span> <span class="n">SPARQLWrapper2</span><span class="p">,</span> <span class="n">JSON</span><span class="p">,</span> <span class="n">JSONLD</span><span class="p">,</span> <span class="n">CSV</span><span class="p">,</span> <span class="n">TSV</span><span class="p">,</span> <span class="n">N3</span><span class="p">,</span> <span class="n">RDF</span><span class="p">,</span> <span class="n">RDFXML</span><span class="p">,</span> <span class="n">TURTLE</span>
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pds</span>
 <span class="kn">import</span> <span class="nn">itertools</span>
 
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-<span class="kn">from</span> <span class="nn">plotnine</span> <span class="k">import</span> <span class="o">*</span>
+<span class="kn">from</span> <span class="nn">plotnine</span> <span class="kn">import</span> <span class="o">*</span>
 </pre></div>
 
     </div>

docs/_build/1/testnb/3-rose-metabolites-R-analysis.html

@@ -3,23 +3,23 @@
   - "/1/testnb/3-rose-metabolites-r-analysis"
 interact_link: content/1/testnb/3-rose-metabolites-R-analysis.ipynb
 kernel_name: ir
+kernel_path: content/1/testnb
 has_widgets: false
 title: |-
   3
+pagenum: 25
 prev_page:
   url: /1/testnb/1-rose-metabolites-Python-analysis.html
-  title: |-
-    2
 next_page:
   url: /1/testnb/2-rose-metabolites-Python-RDF-querying-analysis.html
-  title: |-
-    4
 suffix: .ipynb
+search: data p m s tabular package r such j ggplot same l f c scent packages library org datasets simply dataset generated bendahmane philippe rocca serra profiling using into lets additional file generate barplot both rosa structure another shows studies compounds x y caissard jc vergne dubois raymond o baudino roses science doi h exploring comparing rose profiles stored oerc ox ac uk university oxford e research centre background experimental results metabolite published straightfowardly reported okfn frictionlessdata io specs components easily parsed exploited rich graphical libraries well tidyverse few line codes allow query rapidly explore information importantly rapid exploration possible
 
 comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
 ---
 
     <main class="jupyter-page">
+    <div id="page-info"></div>
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docs/_build/Contributing.html

@@ -1,22 +1,21 @@
 ---
 redirect_from:
-  - "contributing"
+  - "/contributing"
 title: |-
   Contributing
+pagenum: 29
 prev_page:
   url: /People.html
-  title: |-
-    People
 next_page:
   url: /Governance.html
-  title: |-
-    Governance
 suffix: .md
+search: github cookbook fair com issues pull project please issue request help requests changes contributors work labels new articles markdown io contributing youre code img shields badge svg team documentation repository here linkissues following understanding contributions bug enhancement question jupyter development fork master any opening need linkgithub already joining conversation through milestones boards making change recognizing open conduct git working think formatting page linkhelpwanted member thats similar existing book keep review doc www html welcome excited contribute guidelines possible involved questions arent discussed below before youll account linksignupinstructions guide place linkcoc linkgit useful text example bold italics link rickroll dqwwwgxcq getting
 
 comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
 ---
 
     <main class="jupyter-page">
+    <div id="page-info"></div>
     <div class="jb_cell">
 
 <div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">