added recipe 2.2.1 - request new term in public ontology #38
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This was referenced Apr 21, 2020
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@proccaserra , you are invited to review this recipe. See Pull request #38 . Please post your evaluation checklist here. |
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I just added some changes based on the feedback from Nick, see: FAIRplus/FAIRPlus_squad1#7 |
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Jul 9, 2020
* 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 <57750026+robertgiessmann@users.noreply.github.com> * 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 <57750026+robertgiessmann@users.noreply.github.com> * 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 <philippe@ecsgadminsmbp3.home> * . * Cm medit (#106) * Update recipe_template.md * Add files via upload Co-authored-by: Oya Beyan <oyadeniz@yahoo.com> * Cm medit (#107) * Update recipe_template.md * Add files via upload Co-authored-by: Oya Beyan <oyadeniz@yahoo.com> * Revert "Cm medit (#104)" This reverts commit 31c4d54. * . * . Co-authored-by: HackMD <no-reply@hackmd.io> Co-authored-by: Philippe Rocca-Serra <philippe@ecsgadminsmbp3.home> Co-authored-by: daniwelter <danielle.welter@uni.lu> Co-authored-by: Philippe Rocca-Serra <proccaserra@gmail.com> Co-authored-by: Oya Beyan <oyadeniz@yahoo.com> Co-authored-by: Fuqi Xu <54043294+FuqiX@users.noreply.github.com> Co-authored-by: Alasdair Gray <A.J.G.Gray@hw.ac.uk> Co-authored-by: Robert Giessmann <57750026+robertgiessmann@users.noreply.github.com> Co-authored-by: Ulrich Goldmann <ulo@users.noreply.github.com> Co-authored-by: mrwolf on behalf of Robert Giessmann <robert.giessmann@bayer.com> Co-authored-by: Garcia-Castro <ljgarcia@zbmed.org> Co-authored-by: Emiliano Reynares <32556146+ereynrs@users.noreply.github.com> Co-authored-by: Petros Papadopoulos <petros.papadopoulos@gmail.com> Co-authored-by: fuqiX <fuqi@ebi.ac.uk> Co-authored-by: Philippe Rocca-Serra <philippe@ecsgadmins-MacBook-Pro-3.local>
github-actions bot
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Jul 9, 2020
* 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 <57750026+robertgiessmann@users.noreply.github.com> * 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 <57750026+robertgiessmann@users.noreply.github.com> * 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 <philippe@ecsgadminsmbp3.home> * . * Cm medit (#106) * Update recipe_template.md * Add files via upload Co-authored-by: Oya Beyan <oyadeniz@yahoo.com> * Cm medit (#107) * Update recipe_template.md * Add files via upload Co-authored-by: Oya Beyan <oyadeniz@yahoo.com> * Revert "Cm medit (#104)" This reverts commit 31c4d54. * . * . Co-authored-by: HackMD <no-reply@hackmd.io> Co-authored-by: Philippe Rocca-Serra <philippe@ecsgadminsmbp3.home> Co-authored-by: daniwelter <danielle.welter@uni.lu> Co-authored-by: Philippe Rocca-Serra <proccaserra@gmail.com> Co-authored-by: Oya Beyan <oyadeniz@yahoo.com> Co-authored-by: Fuqi Xu <54043294+FuqiX@users.noreply.github.com> Co-authored-by: Alasdair Gray <A.J.G.Gray@hw.ac.uk> Co-authored-by: Robert Giessmann <57750026+robertgiessmann@users.noreply.github.com> Co-authored-by: Ulrich Goldmann <ulo@users.noreply.github.com> Co-authored-by: mrwolf on behalf of Robert Giessmann <robert.giessmann@bayer.com> Co-authored-by: Garcia-Castro <ljgarcia@zbmed.org> Co-authored-by: Emiliano Reynares <32556146+ereynrs@users.noreply.github.com> Co-authored-by: Petros Papadopoulos <petros.papadopoulos@gmail.com> Co-authored-by: fuqiX <fuqi@ebi.ac.uk> Co-authored-by: Philippe Rocca-Serra <philippe@ecsgadmins-MacBook-Pro-3.local>
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