incatools/ontobot-change-agent

A GitHub bot for modifying ontology resources.

Update ontologies using change language.

Getting Started

Read the docs

Ontology resources that are powered by ontobot-change-agent:

• EnvironmentOntology/envo
• geneontology/go-ontology
• monarch-initiative/mondo
• obophenotype/cell-ontology
• obophenotype/uberon
• pato-ontology/pato

License

The code in this package is licensed under the MIT License.

ontobot-change-agent's Issues

CL:kgcl-java commands

Hey ontobot, apply:

• create class CL:00000099999999 'ABCD'
• add definition 'new definition ABCD' to CL:00000099999999
• create synonym 'ABCD1' for CL:00000099999999
• create exact synonym 'ABCD2' for CL:00000099999999
• create broad synonym 'ABCD3' for CL:00000099999999
• create narrow synonym 'ABCD4' for CL:00000099999999
• create related synonym 'ABCD5' for CL:00000099999999
• obsolete CL:0000001
• obsolete CL:0000002 with replacement CL:000000X
• obsolete CL:0000002 with alternative CL:000000X, CL:000000Y
• rename CL:0000010 from 'cultured cell' to 'cultured cell ABCD'
• remove synonym 'neuronal receptor cell (sensu Animalia)' for CL:0000006
• change synonym from 'cell in vivo' to 'cell in vivo ABCD' for CL:0000003
• create edge CL:00000099999999 rdfs:subClassOf CL:0000001

Fbbt:Obsolete term

Hey ontobot! apply:

• obsolete FBbt:00004752 with replacement FBbt:00004754

---

FbBT: Add definition

Hey ontobot, apply:

• add definition 'This is a dummy description.' to FBbt:00000017

PR issue title and main issue title should be easier to distinguish

I often get confused by the issue and PR having the same title

issue titles should be requests, PR title requests should be actions

Even just prepending the PR title with "Applying changes for: ..." would help

Ontobot does not detect the `ontobot apply` pattern if it is not on the first line of the issue’s body

The Ontobot is enabled on the Uberon repository, but if failed to create a PR on the following issue: obophenotype/uberon#3158

The workflow was successfully triggered but Ontobot wrongly concluded that the issue “doesn’t need ontobot’s attention”.

I believe this is because of this regex matching attempt here:

elif re.match(r"(.*)ontobot(.*)apply(.*):(.*)", issue[BODY]):

By default the . character does not match newline characters, so the regex can only detect the pattern if ontobot, apply, and : all appears on the first line of the body. The DOTALL flag should be used to allow . to match newline characters:

elif re.match(r"(.*)ontobot(.*)apply(.*):(.*)", issue[BODY], re.DOTALL):

ontobot-change-agent should allow using the plugin version of KGCL-Java

The ontobot-change-agent can optionally work by delegating the task of actually modifying the ontology to KGCL-Java (if a Jar archive is specified using the --jar-path option).

Currently, it requires that the Jar archive be a customised full version of ROBOT in which the apply command is “built-in”. Such a version of ROBOT can be found in the KGCL-Java releases. It used to be the only way to use the apply command, when ROBOT had no support for plugins.

Now, since version 1.9.5, ROBOT does support plugins, so it would be nice if ontobot-change-agent could exploit that. After all, the ODK already provides ROBOT, so it’s a bit of a shame that one must download another version of ROBOT (nearly ~90 MB) just to be able to use the apply command.

What I would suggest is for ontobot-change-agent to support being used in two different ways:

1. The first way is the current one: the user provides the path to the ROBOT archive to be used, and ontobot-change-agent simply uses that archive as it is.

2. In the second way, the user provides the name under which the KGCL plugin is available, and ontobot-change-agent then simply invokes ROBOT and instructs it to use that plugin. That is, if the user indicates (e.g. through a new command line option) that the KGCL plugin is available on his system under the name kgcl, then ontobot-change-agent executes the following command:

robot kgcl:apply -i <input_file> -k <KGCL_command> convert -f ofn -o <output_file>

instead of

java -jar <jar_path> apply -i <input_file> ...

Go:create class

Hey ontobot, apply:

• create GO:9999999999 'ABCD'

Fbbt:Deepen request

Hey ontobot, apply:

• deepen FBbt:00004895 from FBbt:00048491 to FBbt:00048550

Test issue

Test comment

Fbbt:Create node issue

Hey ontobot, apply:

• create node FBbt:99999999 'foo'

Fbbt:Create synonym

Hey ontobot, apply:

• create broad synonym 'ABCD3' for FBbt:00004751
• create exact synonym 'ABCD2' for http://purl.obolibrary.org/obo/FBbt_00004751

New Request

I request the following changes to ontology ABCD:

• obsolete ABCD:1234
• create synonym "abcd not defghhs" for ABCD:234
• Yeah

GO:Create synonym

• create broad synonym 'ABCD3' for GO:0000011
• create exact synonym 'ABCD2' for http://purl.obolibrary.org/obo/GO_0000011

Abcd

Request dfjkdsbvudfhdjbhdf

Go:create node

Hey ontobot, apply:

• create node http://purl.obolibrary.org/obo/GO_99999999 'foo'

Go:Rename terms

• rename http://purl.obolibrary.org/obo/GO_0000011 from 'vacuole inheritance' to 'vacuole inheritance ABCD'

KGCL methods that have no cases

• delete
• shallow
• unobsolete
• create_class
• move
• change_annotation
• remove_from_subset
• add_to_subset

Uberon: create synonym

• create broad synonym 'ABCD3' for UBERON:0000009

New body format test

Lorem ipsum dolor sit amet. Sit quis alias et mollitia itaque ab eaque perspiciatis ut exercitationem natus est molestias quia ea velit ipsum qui dolores ratione. Aut nobis totam aut nemo esse et asperiores ipsam in maxime internos sed tempore earum ut voluptatem omnis.

Hey ontobot! apply the following:

• rename FBbt:00004750 from 'wing septum 2' to 'wing septum 2 ABCD'
• rename FBbt:00004751 from 'wing vein' to 'wing vein ABCD'

---

Cum consequatur earum qui illum possimus a debitis officia ex ipsam enim nobis dolores 33 consectetur aliquam. Et dolorum esse aut culpa blanditiis in sint amet ad quis veniam nam officiis cumque eum odio provident.

Make ontobot easier to debug

I frequently forget to RTD and get the invocation syntax wrong. I don't see a PR and don't know how to debug.

We should make the regex more inclusive. If in the rare situation someone does an accidental "hey siri" type situation the worst that will happen is that OCA will not know how to interpret the full message.

I feel there are other situations where I make mistakes and OCA is silent, I don't recall precisely, sorry, but in general if it could be more chatty

Fbbt:Delete edge issue

Hey ontobot, apply:

• delete edge FBbt:00004751 BFO:000050 FBbt:00006051

FbBT:Delete node

Hey ontobot, apply:

• delete FBbt:00048550

Add workflow for making a PR based on user filing issues

We can copy what Charlie did here:

https://github.com/biopragmatics/bioregistry/blob/main/.github/workflows/new_prefix_pr.yml

This triggers:

https://github.com/biopragmatics/bioregistry/blob/main/src/bioregistry/gh/new_prefix.py

• user submits an issue using KCDL DSL
• gh action periodically runs ocrawl (analogous to new_prefix_pr.yml)
• ocrawl executes changes and modifies the src ontology file (analogous to new_prefix.py)
• make a PR (covered in the workflow above)

FbBt: remove synonym

Hey ontobot!, apply:

• remove synonym 'whole organism' for FBbt:00000001

Go: Obsolete term

• obsolete GO:0000011

Request

I request the following changes to ontology ABCD:

• obsolete ABCD:1234
• create synonym "abcd not defghhs" for ABCD:234
• Yeah

Fbbt:Create Edge issue

Hey ontobot!, apply:

• create edge FBbt:00004751 BFO:000050 FBbt:00006051

Automate `ochange` based on Issue template

For now let's start with the label New term request whose template looks like this.

New body format test without ending `---`

Hey ontobot! apply the following:

• rename FBbt:00004750 from 'wing septum 2' to 'wing septum 2 ABCD'
• rename FBbt:00004751 from 'wing vein' to 'wing vein ABCD'

test comment

Fbbt:Change relationship

Hey ontobot, apply:

• change relationship between http://purl.obolibrary.org/obo/FBbt_00004751 and FBbt:00006015 from part_of to http://purl.obolibrary.org/obo/BFO_0000050

FbBT: Remove definition

Hey ontobot, apply:

• remove definition for FBbt:00000001

`\n` creates issues in reading instructions

e.g.:

## Hey ontobot! apply:\n\n* create broad synonym 'bad hip' for MONDO:0025086\n\n---\n\nComment: Test comment

Fbbt:Rename terms

• rename http://purl.obolibrary.org/obo/FBbt_00004750 from 'wing septum 2' to 'wing septum 2 ABCD'

FbBT: Update definition

Hey ontobot, apply:

• change definition of FBbt:00000001 to 'member of species Drosophila melanogaster.'

Add new flag `--normalize`

This flag basically runs robot normalize on the resource before creating the PR.

More on this: INCATools/ontology-development-kit#832