First OBOOK release (for archiving purposes)

What's Changed

• Added outline for week 2 by @matentzn in #1
• Update automation.md by @nicolevasilevsky in #2
• Update scientific-computing.md by @nicolevasilevsky in #3
• Some typos in scientific computing by @matentzn in #4
• minor typos by @nicolevasilevsky in #8
• Update linked-data.md by @nicolevasilevsky in #6
• minor typo by @nicolevasilevsky in #10
• minor typo by @nicolevasilevsky in #9
• fix apostrophe by @nicolevasilevsky in #11
• fix minor typos by @nicolevasilevsky in #12
• Update linked-data.md by @nicolevasilevsky in #7
• fix typos by @nicolevasilevsky in #13
• Kg phen dis by @matentzn in #17
• fix sourceforge->github for idobru by @cmungall in #19
• Update install_elk_0.5_protege.md by @emquardokus in #26
• Update contributing_to_obo_ontologies.md by @shawntanzk in #30
• Added link for Ontologies 101 Tutorial by @shawntanzk in #34
• Update ontology-curator.md by @nicolevasilevsky in #37
• Fix typo by @cthoyt in #39
• Small typo fix in doc navigation by @beckyjackson in #42
• Fix link to animals2.tsv by @caufieldjh in #46
• Fix a couple typos by @caufieldjh in #47
• New Lesson: How to manage an effective Ontology Project by @matentzn in #51
• Fix incorrect link for 'Install ELK 0.5' by @rays22 in #54
• Create git_faq.md by @shawntanzk in #55
• Update owl_formats_variants.md by @shawntanzk in #56
• Add repo_url to mkdocs by @cmungall in #57
• noctua is not a tool like the others by @cmungall in #59
• Adding note about ontobee difference, doesn't show hierarcjical relat… by @cmungall in #64
• Update dosdp_template.md by @shawntanzk in #67
• Fhkb formatting by @shawntanzk in #71
• FHKB Tutorial to Markdown by @matentzn in #69
• Adding FHKB by @matentzn in #72
• Small spelling fix by @joeflack4 in #73
• Fix issues with Markdown conversion by @kimrutherford in #74
• Add tip on how to filter text files by @rays22 in #76
• Update troubleshooting document by @sabrinatoro in #77
• updated format and image size by @sabrinatoro in #78
• Update contributing_to_obo_ontologies.md by @nicolevasilevsky in #80
• remove out of date section by @nicolevasilevsky in #85
• Update contributing_to_obo_ontologies.md by @nicolevasilevsky in #86
• add new example by @nicolevasilevsky in #87
• Update Ubergraph endpoint to new location by @balhoff in #102
• Create dosdp_on_ODK_quick_guide.md by @dosumis in #89
• Migration from odk docs by @matentzn in #96
• Adding link to Nomi's intro to github slides by @cmungall in #108
• Adding examples by @cmungall in #107
• GO-style make heavy use of equivalence axioms by @cmungall in #106
• Create edit-in-protege.md by @shawntanzk in #112
• added disjointness tutorial by @shawntanzk in #116
• Made changes to curator pathway by @shawntanzk in #111
• add dl query tutorial by @shawntanzk in #115
• added reference docs for annotations by @shawntanzk in #131
• Updated text to include some potential pitfalls by @Daniel-Olson in #132
• adding Bradley to editorial team by @shawntanzk in #134
• Intro to ontologies by @shawntanzk in #133
• proofreading edits in #135
• Update which-ontology-to-use.md by @henrietteharmse in #142
• Closes #137 Update fixing-conflicts.md in #139
• #143 fix link to getting-started by @chrisroederucdenver in #144
• added common errors in actions by @shawntanzk in #146
• Create github-intro.md in #148
• Create sparql-reference.md by @shawntanzk in #147
• Working on tutorial for building ontology from scratch by @matentzn in #141
• added link to recording of the last lesson by @sabrinatoro in #150
• Added logical axiomatization of classes & use of reasoning by @shawntanzk in #136
• Howto update ODK by @matentzn in #161
• Create new grouping in nav bar: Lessons Under Development by @nicolevasilevsky in #164
• add recording to monarch tutorials by @sagehrke in #166
• Adding tutorial link for May 17, 2022 by @sagehrke in #170
• Add recording from May 17, 2022 Tutorial by @sagehrke in #172
• create annotation-properties by @sabrinatoro in #173
• Reformat, rename, reorganise Introduction to annotation properties by @matentzn in #174
• Add recording from May 31, 2022 by @sagehrke in #175
• Fix typo in shell command by @katiermullen in #179
• Update Protégé configuration for new metadata properties. by @gouttegd in #178
• updated the VBO section by @sabrinatoro in #151
• adding update import docs by @shawntanzk in #182
• Add recording from June 14, 2022 by @sagehrke in #186
• Minor grammatical updates by @joeflack4 in #190
• add an overview to this how to guide by @nicolevasilevsky in #192
• Very basic CLI tutorial by @matentzn in #193
• Cli tutorial by @matentzn in #194
• Intro cli 1 curl update by @ubyndr in #195
• Add recording from June 28, 2022 by @sagehrke in #196
• revisions to term request guide by @nicolevasilevsky in #198
• Small detail in https://oboacademy.github.io/obook/howto/installing-elk-in-protege/ by @manulera in #205
• How to be a "team open science" player by @matentzn in #204
• Update dosdp-overview.md by @dosumis in #209
• Create icbo2022.md by @nicolevasilevsky in #208
• Create pull-requests.md by @nicolevasilevsky in #202
• Add recording from July 12th, 2022 by @sagehrke in #211
• replace link to video with video on YouTube by @nicolevasilevsky in #214
• replace link to fix conflict video with link to YouTube video by @nicolevasilevsky in #215
• replace link to video by @nicolevasilevsky in #216
• remove iframe video because it is not working by @nicolevasilevsky in #217
• replace video link by @nicolevasilevsky in #218
• update video link by @nicolevasilevsky in #219
• embed video by @nicolevasilevsky in #221
• Create new page set-up-protege.md by @nicolevasilevsky in #222
• add protege instructions to nav bar by @nicolevasilevsky in #223
• fix typo by @nicolevasilevsky in #224
• Install Protege OBO plugin section by @manulera in #225
• Create how to guide on how to create screenshots (partial and full) and paste them into an issue by @nicolevasilevsky in #227
• Fixing formatting. See #233 by @cmungall in #234
• add protege-faq.md by @manulera in #229
• Update intro-to-ontologies.md by @dosumis in #169
• Fixing list formatting in multiple docs, #233 by @cmungall in #236
• Update merge and obsolete docs by @shawntanzk in #145
• WIP: Minor edits and formatting fixes by @cmungall in #235
• fix broken URL in Lessons learned from troubleshooting ROBOT by @nicolevasilevsky in #240
• fix dead link by @nicolevasilevsky in #241
• update obsoletion documentation by @nicolevasilevsky in #239
• update image of obsoleted term example by @nicolevasilevsky in #242
• fix formatting by @nicolevasilevsky in #245
• fix formatting by @nicolevasilevsky in #246
• add instructions to set up docker/use owltools by @nicolevasilevsky in #243
• add link to merge doc by @nicolevasilevsky in #244
• remove redundant text about fixing memory settings by @nicolevasilevsky in #248
• add instructions on how to increase memory on PC by @nicolevasilevsky in #251
• add text on how to be an open science ontologist by @nicolevasilevsky in #230
• add upcoming courses by @nicolevasilevsky in #250
• add link to How to be an open science ontologist by @nicolevasilevsky in #254
• change seeAlso to term tracker item by @nicolevasilevsky in #257
• close #237 and fix broken links by @manulera in #255
• Instructions to run the site locally added to readme.md by @manulera in #253
• extra notes for consider field in obsoletion by @manulera in #261
• Create ontology-overview.md by @nicolevasilevsky in #262
• Added prerequisite by @sabrinatoro in #263
• prettify files by @nicolevasilevsky in #267
• Create prettify.md by @nicolevasilevsky in #268
• Add Pull Request Part 2 Video Recording by @sagehrke in #269
• add specific examples to How to be an open science ontologist by @nicolevasilevsky in #270
• Update icbo2022.md by @nicolevasilevsky in #271
• Use canonical form for true in yaml by @cmungall in #258
• Open science edits by @nicolevasilevsky in #273
• Update icbo2022.md by @nicolevasilevsky in #274
• Add recording How to be an open science ontologist by @sagehrke in #275
• Mac heap memory size instructions update by @turbomam in #276
• when to changes to Protege config files take effect? by @turbomam in #277
• Update odk.md by @shawntanzk in #278
• create outreach materials by @nicolevasilevsky in #280
• Add a sparql example by @shawntanzk in #282
• add another sparql example by @shawntanzk in #285
• Add MAxO recording from Oct 18, 2022 by @sagehrke in #286
• Update Schedule: Move Contributing to Ontologies Part 1 by @sagehrke in #287
• Update Taxon restriction documents by @shawntanzk in #283
• Updating OBO Academy schedule by @sagehrke in #290
• Glossary of terms by @shawntanzk in #259
• create doc for our hackthon on 11/29 by @nicolevasilevsky in #291
• Add Contributing to OBO Ontologies Recordings. by @sagehrke in #294
• embed video of contributing to ontologies by Sabrina by @nicolevasilevsky in #296
• Create embed-video.md by @nicolevasilevsky in #297
• fix link by @nicolevasilevsky in #298
• Update embed-video.md by @nicolevasilevsky in #299
• Update hackathon.md by @nicolevasilevsky in #300
• Fixed typos in the disease-phenotype tutorial by @LCCarmody in #309
• Update: Developing an OBO Ontology lesson by @sagehrke in #312
• Created documentation on how to revert a commit using GitHub Desktop by @ar-ibrahim in #314
• fix broken links by @nicolevasilevsky in #310
• fix broken links by @nicolevasilevsky in #305
• Update ontology-design.md by @laurenechan in #319
• Review Ontology Pipelines with ROBOT lesson by @anitacaron in #316
• correct protege spelling by @yaseminbridges in #317
• Change my affiliation on frontpage by @matentzn in #302
• Update ontology-term-use.md by @laurenechan in #308
• updated a broken link by @sabrinatoro in #311
• Update mkdocs.yml by @nicolevasilevsky in #318
• Add 404 page and fix some broken links by @caufieldjh in #306
• Updating Schedule for December 2022 by @sagehrke in #323
• Update instructions for configuring Protege memory in MS Windows by @turbomam in #320
• Ontology mappings tutorials by @matentzn in #66
• Create getting-hands-on.md by @nicolevasilevsky in #321
• updates to getting hands on... by @nicolevasilevsky in #330
• create exercise by @nicolevasilevsky in #331
• add hyperlink by @nicolevasilevsky in #332
• Taxon constraints update by @balhoff in #329
• fixes mermaid graphs are not rendering #333 by @souzadevinicius in #334
• Add a tutorial on how to use the tools from the ODK. by @gouttegd in #336
• Add Guide to Taxon Restrictions link to schedule by @sagehrke in #348
• Use 4 spaces for sub-lists by @balhoff in #347
• Update schedule and add recording by @sagehrke in #350
• Add a subsection on how to setup Docker in Lubuntu VM by @StroemPhi in #351
• update affiliation by @nicolevasilevsky in #352
• Update set-up-protege.md by @nicolevasilevsky in #353
• Edit button gone in OBOOK? by @souzadevinicius in #356
• Tutorial - How to add custom quality checks with ODK by @anitacaron in #335
• Update link to slides in ontology-summit-2023.md by @StroemPhi in #358
• improve readability and fix typos by @slobentanzer in #359
• try to fix rendering of indentation using 4 spaces by @slobentanzer in #360
• Update Custom OBO Dashboard creation workflow by @anitacaron in #361
• Update change-files-pull-request.md by @nicolevasilevsky in #362
• Add new document on how to install Protege by @rays22 in #364
• Update editor information by @nicolevasilevsky in #366
• Fix some typos and formatting (take 2) by @clnsmth in #369
• Monarch-kg neo4j basics tutorial by @kevinschaper in #357
• add section on How to interpret an 'and' or an 'or' by @nicolevasilevsky in #367
• Update links to tutorials by @sagehrke in #371
• Embed Taxon Constraint video by @sagehrke in #372
• Embed Neo4J OBO Academy Video by @sagehrke in #373
• Embed video in Semantic Entity Matching Tutorial by @sagehrke in #374
• Embed How to be an open science ontologist video by @sagehrke in #375
• Embed Intro to CL Part 2 video by @sagehrke in #378
• Embed CL Part 1 Youtube video by @sagehrke in #377
• Update merge-terms.md by @dosumis in #379
• Update set-up-protege.md by @nicolevasilevsky in #381
• Update schedule with OAK tutorial by @sagehrke in #383
• Update set-up-protege.md by @nicolevasilevsky in #385
• Add Description Logic video link to explanation by @anitacaron in #388
• Add OAK tutorial YouTube video by @sagehrke in #389
• Add How-to add an ORCIDIO module by @matentzn in #390
• Add YouTube video of Wikidata session by @sagehrke in #393
• Create wikidata.md by @andrawaag in #394
• Embed Pull Request tutorial videos by @sagehrke in #376
• Update set-up-protege.md by @dosumis in #392
• Exomiser tutorial by @iQuxLE in #396
• Add Exomiser tutorial by @yaseminbridges in #397
• Updating Exomiser Tutorial by @yaseminbridges in #399
• Update add-new-slim.md in #398
• Add link to the Protégé 5.6 tutorial slides. by @gouttegd in #404
• fixes Edit button gone in OBOOK? #349 by @souzadevinicius in #407
• Add Exomiser and Protege Youtube video links by @sagehrke in #408
• Add OBO Academy Exomiser Tutorial Recording to Exomiser OBOOK page by @sagehrke in #409
• Add correct title for May 30, 2023 tutorial by @sagehrke in #410
• Create a basic tutorial for leveraging ChatGPT for ontology curation by @matentzn in #400
• Chatgpt by @matentzn in #411
• Updated Schedule Table for 30 May 2023 Tutorial by @sagehrke in #412
• Subclass vs equivalence and existential restriction tutorials by @henrietteharmse in #418
• Update OBO Academy Schedule by @sagehrke in #420
• fixed typo, made some phrasing parallel by @nlharris in #422
• Improvements to documentation about how to review PRs by @nlharris in #423
• Create early-career-data-scientist.md by @nicolevasilevsky in #425
• Removed tutorial listed for August 8, 2023 by @sagehrke in #426
• update docs for new Protege version by @nicolevasilevsky in #427
• Update early-career-data-scientist.md by @JoyeuseMuj in #428
• create Ontology User pathway by @nicolevasilevsky in #429
• add ontology user pathway by @nicolevasilevsky in #430
• Fix list of topics in DO video library by @nlharris in #431
• Create review-disease-mappings.md by @nicolevasilevsky in #293
• Update mapping predicate cheatsheet by @matentzn in #433
• Add presentation links to icbo2023.md by @matentzn in #436
• move ontology user pathway to ontology user reference by @nicolevasilevsky in #439
• Add August and September OBO Academy recordings to Schedule by @sagehrke in #442
• Add CITATION.cff to OBOOK by @matentzn in #441
• First draft of units tutorial by @jamesaoverton in #443
• Update schedule for 2023/10/03 with correct link by @sagehrke in #444
• Minor updates to unit tutorial by @jamesaoverton in #445
• Linking Data fixes by @jamesaoverton in #447
• Add several Biopragmatics tutorials by @cthoyt in #446
• Add youtube recordings for Sept & Oct 2023 by @sagehrke in #452
• Try to fix formatting issue in curies.md by @lubianat in #453
• Add citation instructions to the README by @cthoyt in #454
• Correct minor typo contributing-to-obo-ontologies.md by @Silvia113-SM in #455
• Add 2023-Oct-17 OBO Academy recording by @sagehrke in #456
• Instructions for using ODK with Podman instead of Docker by @daniwelter in #457
• Update github-create-pull-request.md, add general guidance on what makes a good PR by @cmungall in #458
• Update schedule to cancel Nov 28, 2023 by @sagehrke in #460
• Add 17-Nov-2023 Recording and clean up Schedule by @sagehrke in #461
• correct link to chatgpt-ontology-curation by @nlharris in #463
• add content to stub page about OntoGPT by @nlharris in #464
• fix to glommed-together lines? by @nlharris in #465
• add pointer to relevant tutorial by @nlharris in #467
• Update OBO training schedule by @sagehrke in #468
• Add 2023-Dec-12 recording to OBO Academy page by @sagehrke in #469
• Updating OBO schedule by @sagehrke in #471
• Protege link was broken by @shawntanzk in #473
• Create licensing-data-and-software.md by @kltm in #475
• Update date annotation in Custom QC tutorial by @anitacaron in #476
• Add 2024-Jan-23 OBO Academy recording by @sagehrke in #474
• Add link to Metadata in OBO presentation by @anitacaron in #477
• Create vocabularies-for-bioinformatics.md by @nicolevasilevsky in #478
• Add draft specification for the base file approach by @matentzn in #387
• Add recording from 2024-Feb-20 by @sagehrke in #482
• Fix dead link in contributing-to-obo-ontologies by @shawntanzk in #484
• Add OBO Academy recording from 2024-March-05 by @sagehrke in #485
• Update tutorial title & presenters for April 2, 2024 by @sagehrke in #487
• Add links to slides or OBO page for OBO academy schedule by @sagehrke in #490
• Add youtube link for April 2, 2024 OBO Academy by @sagehrke in #491
• Grammar fix in docs/tutorial/sparql.md by @Daniel-Mietchen in #492
• Add Windows instruction link to setup-docker.md by @ehartley in #493
• Update Sabrina and Sarah's organization by @sagehrke in #494
• Update OBO Academy schedule by @sagehrke in #497
• Add OBO academy recording links by @sagehrke in #498
• Add Intro to Uberon youtube link by @sagehrke in #499
• Update monarch-obo-training.md by @sagehrke in #502
• Add agenda to ICBO 2024 tutorial by @nicolevasilevsky in #504
• Update icbo2024.md by @nicolevasilevsky in #507
• Update monarch-obo-training.md schedule by @sagehrke in #509
• Add a reference page for LLM resources to OBOOK by @matentzn in #510
• Update icbo2024.md by @sagehrke in #512
• Update idrange.md by @balhoff in #511
• Update schedule for OBO Academy by @sagehrke in #514
• Update schedule for Oct to Dec 2024 by @sagehrke in #516
• Add material for OntoGPT workshop by @caufieldjh in #519
• Update monarch-obo-training.md schedule by @sagehrke in #520
• Add section about using WSL on windows to howto/odk-setup.md by @StroemPhi in #517
• Add how to migrate to ODK .md and link to it by @StroemPhi in #521
• Fix markdown formatting errors in odk-migrate-to-odk.md by @StroemPhi in #522
• Update monarch-obo-training.md by @sagehrke in #523
• Fix typo in owl-building-blocks.md by @balhoff in #524
• Update monarch-obo-training.md by @sagehrke in #525
• Add documentation on subset to module extraction docs by @cmungall in #526
• Update monarch-obo-training.md by @sagehrke in #527
• add video explanations for PR review by @nicolevasilevsky in #528
• Fix broken link for types of taxon restrictions by @aleixpuigb in #531
• Update monarch-obo-training.md by @sagehrke in #532
• Update monarch-obo-training.md by @sagehrke in #533
• Update monarch-obo-training.md by @cmungall in #534
• Update setting-up-project-odk.md by @timalamenciak in #536
• Document ODK_GITNAME/ODK_GITEMAIL. by @gouttegd in #539
• Add mailing list link to monarch-obo-training.md by @matentzn in #540
• Update monarch-obo-training.md by @sagehrke in #541
• Update monarch-obo-training.md by @sagehrke in #543

New Contributors

• @matentzn made their first contribution in #1
• @nicolevasilevsky made their first contribution in #2
• @cmungall made their first contribution in #19
• @emquardokus made their first contribution in #26
• @shawntanzk made their first contribution in #30
• @beckyjackson made their first contribution in #42
• @caufieldjh made their first contribution in #46
• @rays22 made their first contribution in #54
• @joeflack4 made their first contribution in #73
• @kimrutherford made their first contribution in #74
• @sabrinatoro made their first contribution in #77
• @balhoff made their first contribution in #102
• @dosumis made their first contribution in #89
• @Daniel-Olson made their first contribution in #132
• @henrietteharmse made their first contribution in #142
• @chrisroederucdenver made their first contribution in #144
• @sagehrke made their first contribution in #166
• @katiermullen made their first contribution in #179
• @gouttegd made their first contribution in #178
• @ubyndr made their first contribution in #195
• @manulera made their first contribution in #205
• @turbomam made their first contribution in #276
• @LCCarmody made their first contribution in #309
• @ar-ibrahim made their first contribution in #314
• @laurenechan made their first contribution in #319
• @anitacaron made their first contribution in #316
• @yaseminbridges made their first contribution in #317
• @souzadevinicius made their first contribution in #334
• @StroemPhi made their first contribution in #351
• @slobentanzer made their first contribution in #359
• @clnsmth made their first contribution in #369
• @kevinschaper made their first contribution in #357
• @andrawaag made their first contribution in #394
• @iQuxLE made their first contribution in #396
• @nlharris made their first contribution in #422
• @JoyeuseMuj made their first contribution in #428
• @jamesaoverton made their first contribution in #443
• @lubianat made their first contribution in #453
• @Silvia113-SM made their first contribution in #455
• @daniwelter made their first contribution in #457
• @kltm made their first contribution in #475
• @Daniel-Mietchen made their first contribution in #492
• @ehartley made their first contribution in #493
• @aleixpuigb made their first contribution in #531
• @timalamenciak made their first contribution in #536

Full Changelog: https://github.com/OBOAcademy/obook/commits/v0.1