diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 00000000..e69de29b diff --git a/404.html b/404.html new file mode 100644 index 00000000..7a1a6ed1 --- /dev/null +++ b/404.html @@ -0,0 +1,420 @@ + + + +
+ + + + + + + + + + + + + + +Please refer to https://oboacademy.github.io/obook/howto/create-new-term/
+ + + + + + + + + + + + + +Please refer to https://oboacademy.github.io/obook/tutorial/setting-up-project-odk/
+ + + + + + + + + + + + + +See https://oboacademy.github.io/obook/tutorial/managing-ontology-project/.
+ + + + + + + + + + + + + +Please refer to https://oboacademy.github.io/obook/howto/deal-with-large-ontologies/
+ + + + + + + + + + + + + +Please refer to https://oboacademy.github.io/obook/explanation/deleting-asserted-sub-classes/
+ + + + + + + + + + + + + +sh run.sh make update_repo
+
sh run.sh make update_docs
+
sh run.sh make prepare_release
+
sh run.sh make refresh-%
+
Example:
+sh run.sh make refresh-chebi
+
sh run.sh make refresh-imports
+
sh run.sh make refresh-imports-excluding-large
+
sh run.sh make test
+
sh run.sh make odkversion
+
(of a specific file)
+sh run.sh make validate_profile_%
+
sh run.sh make validate_profile_hp-edit.owl
+
See https://oboacademy.github.io/obook/pathways/ontology-curator-go-style/
+ + + + + + + + + + + + + +Refer to https://oboacademy.github.io/obook/reference/formatting-license/.
+ + + + + + + + + + + + + +Please refer to https://oboacademy.github.io/obook/howto/merge-terms/
+ + + + + + + + + + + + + +Please refer to https://oboacademy.github.io/obook/howto/add-new-slim/
+ + + + + + + + + + + + + +Please refer to https://oboacademy.github.io/obook/howto/add-new-slim/
+ + + + + + + + + + + + + +ODK is constantly being updated, but we release new versions only once every 3-4 months. +For people with a nack to beta-testing and experimental features, or those which need to use the latest versions of the bundled tools, +we provide a "development" snapshot of the ODK which is updated roughly once per week:
+Look for dev
tag in https://hub.docker.com/r/obolibrary/odkfull/tags
You can install the development snapshot like this:
+docker pull obolibrary/odkfull:dev
+
Important:
+dev
snapshot of ODK is unstable, and therefore will have bugs. You use it at your own risk!If you want to use the development snapshot with your run.sh
docker wrapper, you will have to make sure that have enabled it correctly.
docker pull obolibrary/odkfull:dev
As mentioned above, this command installs the development snapshotdocker pull obolibrary/odkfull
IMAGE=odkfull:dev sh run.sh make update_repo
, else ODK_TAG=dev sh run.sh make update_repo
ODK_TAG=dev sh run.sh make update_repo
(again, if you ran it above)You have now set your repo up to run via the development snapshot. At the top of the file, in the comments, your automatically-generated src/ontology/Makefile should now reference the development snapshot you have installed rather than the stable production release.
+Finally:
+run.sh
docker wrapper. Just make sure you use the appropriate prefix depending on your version of the ODK:IMAGE=obolibrary/odkfull:dev sh run.sh make update_repo
(or whatever other command you wanted to run).dev
image), run: ODK_TAG=dev sh run.sh make update_repo
(or whatever other command you wanted to run).Please refer to https://oboacademy.github.io/obook/howto/obsolete-term/
+ + + + + + + + + + + + + +Please refer to https://oboacademy.github.io/obook/reference/release-artefacts/
+ + + + + + + + + + + + + +Please refer to https://oboacademy.github.io/obook/reference/synonyms-obo/
+ + + + + + + + + + + + + +Please refer to https://oboacademy.github.io/obook/howto/add-taxon-restrictions/
+ + + + + + + + + + + + + +Please refer to https://oboacademy.github.io/obook/explanation/term-comments/
+ + + + + + + + + + + + + +Since version 1.9.5, the ROBOT tool allows to use plugins that provide supplementary commands that are not part of the default command set.
+Before you can use plugins in a custom workflow, the ODK must be aware of those plugins. There are several ways to do that.
+Add a new robot_plugins
section to your ODK configuration file (src/ontology/ONT-odk.yaml
). That section should contain a single plugins
key, which itself should contain the list of the plugins you want to use. Each entry in the list must contain at least a name
key, which is the name under which the plugin will be available, and optionally a mirror_from
key, pointing to an online location from which the plugin can be downloaded.
For example, to use the Uberon plugin:
+robot_plugins:
+ plugins:
+ - name: uberon
+ mirror_from: https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.2.0/uberon.jar
+
If you do not specify a download location with the mirror_from
key, a dummy rule ${ROBOT_PLUGINS_DIRECTORY}/uberon.jar
will be generated in the standard Makefile. You will need to override that rule in your ontology-specific Makefile:
${ROBOT_PLUGINS_DIRECTORY}/uberon.jar:
+ curl -L -o $@ https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.2.0/uberon.jar
+
If for whatever reason you do not want to modify your ODK configuration, you can still set up a plugin by adding a rule such as the one above in the custom Makefile, and listing the plugin in the custom_robot_plugins
variable. For example, again with the KGCL lplugin:
${ROBOT_PLUGINS_DIRECTORY}/uberon.jar:
+ curl -L -o $@ https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.2.0/uberon.jar
+
+custom_robot_plugins: $(ROBOT_PLUGINS_DIRECTORY)/uberon.jar
+
plugins
directory¶Any Jar file found in the repository’s top-level plugins
directory (if such a directory exists) will automatically be found by the ODK, without requiring any change to the ODK configuration or the custom Makefile.
Some plugins are already bundled with the ODK and don’t need to be declared or downloaded from somewhere else. For now, there are only two such plugins:
+More default plugins may be added in future ODK versions.
+Any Make rule that involves the use of a ROBOT plugin MUST depend on the all_robot_plugins
target. This will ensure that all plugins have been properly set up in the runtime ROBOT plugins directory.
{"use strict";/*!
+ * escape-html
+ * Copyright(c) 2012-2013 TJ Holowaychuk
+ * Copyright(c) 2015 Andreas Lubbe
+ * Copyright(c) 2015 Tiancheng "Timothy" Gu
+ * MIT Licensed
+ */var Va=/["'&<>]/;qn.exports=za;function za(e){var t=""+e,r=Va.exec(t);if(!r)return t;var o,n="",i=0,a=0;for(i=r.index;i