Addresses #1582-NTR-epithelial_cells_DCT #1644

ghost · 2022-06-21T14:11:24Z

Addresses #1582-NTR-epithelial_cells_DCT

github-actions · 2022-06-21T14:16:18Z

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2022-06-23/cl-simple.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2022-06-23/cl-simple.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

CL_4030016 `http://purl.obolibrary.org/obo/CL_4030016`

Added

CL_4030016 definition "An epithelial cell located in the early distal convoluted tubule."
- database_cross_reference X
- database_cross_reference "PMID:24855283"
CL_4030016 label "epithelial cell of early distal convoluted tubule"
CL_4030016 date "2022-06-21T12:47:48Z"^^dateTime
CL_4030016 contributor 0000-0002-1773-2692
CL_4030016 has_broad_synonym "DCT1 cell"
- database_cross_reference "PMID:24855283"
Class: CL_4030016
CL_4030016 SubClassOf kidney distal convoluted tubule epithelial cell

CL_4030017 `http://purl.obolibrary.org/obo/CL_4030017`

Added

CL_4030017 label "epithelial cell of late distal convoluted tubule"
CL_4030017 comment "Although mineralocorticoid receptors are expressed throughout the entire [distal convoluted tubule], the DCT2 is sensitive to the actions of aldosterone, because it expresses an enzyme called 11-β hydroxysteroid dehydrogenase 2 (11-βHSD2)"
- database_cross_reference "PMID:24855283"
CL_4030017 definition "An epithelial cell located in the late distal convoluted tubule."
- database_cross_reference X
- database_cross_reference "PMID:24855283"
CL_4030017 has_broad_synonym "DCT2 cell"
- database_cross_reference "PMID:24855283"
CL_4030017 date "2022-06-21T13:51:46Z"^^dateTime
CL_4030017 contributor 0000-0002-1773-2692
Class: CL_4030017
CL_4030017 SubClassOf kidney distal convoluted tubule epithelial cell

serotonergic neuron `http://purl.obolibrary.org/obo/CL_0000850`

Added

serotonergic neuron database_cross_reference "FBbt:00005133"

github-actions · 2022-06-21T14:16:22Z

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
Version IRI: None
Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
Version IRI: None
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

CL_4030016 `http://purl.obolibrary.org/obo/CL_4030016`

Added

CL_4030016 definition "An epithelial cell located in the early distal convoluted tubule."^^string
- database_cross_reference "PMID:24855283"^^string
- database_cross_reference X
CL_4030016 label "epithelial cell of early distal convoluted tubule"
CL_4030016 date "2022-06-21T12:47:48Z"^^dateTime
CL_4030016 contributor 0000-0002-1773-2692
CL_4030016 has_broad_synonym "DCT1 cell"^^string
- database_cross_reference "PMID:24855283"^^string
Class: CL_4030016
CL_4030016 EquivalentTo epithelial cell and (part_of some early distal convoluted tubule)

CL_4030017 `http://purl.obolibrary.org/obo/CL_4030017`

Added

CL_4030017 label "epithelial cell of late distal convoluted tubule"
CL_4030017 comment "Although mineralocorticoid receptors are expressed throughout the entire [distal convoluted tubule], the DCT2 is sensitive to the actions of aldosterone, because it expresses an enzyme called 11-β hydroxysteroid dehydrogenase 2 (11-βHSD2)"^^string
- database_cross_reference "PMID:24855283"^^string
CL_4030017 definition "An epithelial cell located in the late distal convoluted tubule."^^string
- database_cross_reference "PMID:24855283"^^string
- database_cross_reference X
CL_4030017 has_broad_synonym "DCT2 cell"^^string
- database_cross_reference "PMID:24855283"^^string
CL_4030017 date "2022-06-21T13:51:46Z"^^dateTime
CL_4030017 contributor 0000-0002-1773-2692
Class: CL_4030017
CL_4030017 EquivalentTo epithelial cell and (part_of some late distal convoluted tubule)

early distal convoluted tubule `http://purl.obolibrary.org/obo/UBERON_0005101`

Added

Class: early distal convoluted tubule

late distal convoluted tubule `http://purl.obolibrary.org/obo/UBERON_0005102`

Added

Class: late distal convoluted tubule

shawntanzk · 2022-06-21T14:53:02Z

Just to double - check early and late are segments and not time right? lol
I think if that is the case, it might be worth adding it in uberon and doing that part of accordingly given this cell type is defined by its locality. Also initially when looking at the definition and terms, I thought it was to do with time (eg early stage of life, late stage of life) (might also come from me coming from a developmental psychology lab, then a lab that did Alzheimers related stuff >.< ) Either way some clarity might be useful - an Uberon term with the appropriate definition would do the trick, but if you think its not useful to have in uberon, then perhaps some clarify in the defs

ghost · 2022-06-23T11:13:38Z

I think if that is the case, it might be worth adding it in uberon and doing that part of accordingly given this cell type is defined by its locality.

Thank you for the suggestion, @shawntanzk. I found that the UBERON terms already existed, but would need to be imported to CL.
This was my first attempt at an import, so I will especially appreciate you review. I see many files have changed in the process and I will have to resolve some conflicts.
FYI, @matentzn

…into 1582-NTR-epithelial-cells-of-distal-convoluted-tubule

shawntanzk · 2022-06-23T12:49:46Z

src/ontology/components/mappings.owl

@@ -142,6 +142,9 @@
  <Class rdf:about="http://purl.obolibrary.org/obo/CL_0000381">
    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005130</oboInOwl:hasDbXref>
  </Class>
+  <Class rdf:about="http://purl.obolibrary.org/obo/CL_0000850">
+    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005133</oboInOwl:hasDbXref>


@gouttegd - could you help make sure this is correct - I think it got updated with import updates

That’s correct, yes. It’s a change that I made recently in the FBbt-to-CL mappings. That it got picked up during an import update is the expected behaviour, I believe.

src/ontology/mappings/fbbt-mappings.sssom.tsv

shawntanzk · 2022-06-23T12:52:27Z

This was my first attempt at an import, so I will especially appreciate you review. I see many files have changed in the process and I will have to resolve some conflicts.

It all looks good - the file changes I'm not sure about but its not anything on you, I've asked @gouttegd to look at them to make sure they are right as its fly stuff. But basically you did everything right with imports :)

ghost · 2022-06-23T12:55:04Z

@shawntanzk, I resolved 9 conflicts in the merged_import.owl file, but most were arbitrary decisions. I would not know another way to approach it and do not know why so many conflicts appeared. If we there is a way to test that I did not make any breaking changes, pls advise.

FYI, @matentzn.

matentzn

All looks great - I am a bit puzzled but they fact that the components are refreshed although you just refresh the imports. What exact command did you run in the end?

shawntanzk · 2022-06-23T12:57:58Z

@bvarner-ebi - I think you can make equivalent classes and in fact I think you should follow exactly the the textual definition states and let the reasoner do the work (of course making sure the reasoner works, if not figuring out why). so:

epithelial cell of early distal convoluted tubule
def: Epithelial cell located in the early distal convoluted tubule.
Equivalent class: epithelial cell and ("part of" some "early distal convoluted tubule")

This should automatically place it under "kidney distal convoluted tubule epithelial cell" (if not we should look at where the modelling is wrong, or if your def needs to be edited, not sure if early distal convoluted tubule has kidney part, not sure of the biology)

PS - sorry for being annoying and not bringing this up earlier >.< just realised.

matentzn · 2022-06-23T12:59:22Z

@bvarner-ebi there should never be any conflicts on imports. The only way this can happen is if you opened a new branch, and someone else came to update the import before you, and then you didn't update your branch from master first. Generally:

Always update from master before running an import
Then run the import

I suggest you rerun: sh run.sh make no-mirror-refresh-merged just to be sure (after updating the branch from master)

ghost · 2022-06-23T13:05:33Z

All looks great - I am a bit puzzled but they fact that the components are refreshed although you just refresh the imports. What exact command did you run in the end?

sh run.sh make PAT=false imports/go_import.owl -B (I now know this was not correct)

sh run.sh make IMP=true MIR=true PAT=false imports/go_import.owl -B (I now know this was not correct)

sh run.sh make imports/merged_import.owl

matentzn · 2022-06-23T13:07:58Z

OK in the end it makes sense! All good. But I would still recommend rerunning the command i suggest above - never resolve conflicts on imports, always rerun!

gouttegd

All changes regarding the FBbt-CL mappings are normal and expected.

gouttegd · 2022-06-23T13:44:09Z

I am a bit puzzled but they fact that the components are refreshed although you just refresh the imports.

Unless I’m missing something, I believe this is normal.

Components are listed in OTHER_SRC:

OTHER_SRC = $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/mappings.owl

OTHER_SRC is a prerequisite for SRC_MERGED, which itself is a prerequisite for PRESEED and ultimately for the $(IMPORTDIR)/merged_terms_combined.txt, which is updated when imports are refreshed.

ghost · 2022-06-23T13:47:25Z

OK in the end it makes sense! All good. But I would still recommend rerunning the command i suggest above - never resolve conflicts on imports, always rerun!

Steps I'm now doing:

git checkout 1582-NTR-epithelial-cells-of-distal-convoluted-tubule
git merge master
"Already up to date."

sh run.sh make no-mirror-refresh-merged
sh run.sh make imports/merged_import.owl

ghost · 2022-06-23T13:48:00Z

@bvarner-ebi - I think you can make equivalent classes and in fact I think you should follow exactly the the textual definition states and let the reasoner do the work (of course making sure the reasoner works, if not figuring out why). so:

epithelial cell of early distal convoluted tubule def: Epithelial cell located in the early distal convoluted tubule. Equivalent class: epithelial cell and ("part of" some "early distal convoluted tubule")

This should automatically place it under "kidney distal convoluted tubule epithelial cell" (if not we should look at where the modelling is wrong, or if your def needs to be edited, not sure if early distal convoluted tubule has kidney part, not sure of the biology)

PS - sorry for being annoying and not bringing this up earlier >.< just realised.

Great suggestion. I updated that in the latest commit.

shawntanzk

see inline (just last bit of tidying up :))

src/ontology/cl-edit.owl

matentzn · 2022-06-23T14:32:41Z

sh run.sh make no-mirror-refresh-merged
sh run.sh make imports/merged_import.owl

No need: sh run.sh make no-mirror-refresh-merged is all you needed to do!

ghost · 2022-06-23T14:52:29Z

sh run.sh make no-mirror-refresh-merged
sh run.sh make imports/merged_import.owl

No need: sh run.sh make no-mirror-refresh-merged is all you needed to do!

OK. I was following the advice from Slack: "CL uses merged import so you want to run sh run.sh make imports/merged_import.owl"

https://oboacademy.github.io/obook/howto/update-import/#Refresh-imports

matentzn · 2022-06-23T14:57:32Z

@bvarner-ebi I think in the general case, the instructions on obook are fine for the general case - sh run.sh make imports/merged_import.owl just downloads all the mirrors which seems wasteful (the no-mirror command skips downloading ontologies).

ghost · 2022-06-23T15:05:54Z

@bvarner-ebi I think in the general case, the instructions on obook are fine for the general case - sh run.sh make imports/merged_import.owl just downloads all the mirrors which seems wasteful (the no-mirror command skips downloading ontologies).

Thanks for explaining.
If there is a page explaining what mirrors are and how to check if they are updated, that would be helpful to link to the instructions.
I read "if your mirrors are updated... ", but did not know how to check if they were.

matentzn · 2022-06-23T15:23:52Z

Can you make an obook issue about this I will deal with it asap

Addresses #1582-NTR-epithelial_cells_DCT

60bb841

ghost self-assigned this Jun 21, 2022

ghost added new term request HuBMAP kidney labels Jun 21, 2022

ghost requested review from emquardokus and shawntanzk June 21, 2022 14:25

ghost linked an issue Jun 21, 2022 that may be closed by this pull request

[NTR] [ASCT+B table] epithelial cell of distal convoluted tubule (2 terms for early and late segments) #1582

Closed

ghost added this to In progress in ASCT+B_validation_review via automation Jun 21, 2022

ghost mentioned this pull request Jun 22, 2022

import early and late distal convoluted tubule Uberon terms to CL #1645

Closed

bvarner-ebi added 2 commits June 22, 2022 14:24

Update cl-edit.owl

5f0d304

refreshed import for UBERON terms

532f9c7

Merge branch 'master' of https://github.com/obophenotype/cell-ontology …

4dea1dc

…into 1582-NTR-epithelial-cells-of-distal-convoluted-tubule

shawntanzk reviewed Jun 23, 2022

View reviewed changes

src/ontology/mappings/fbbt-mappings.sssom.tsv Show resolved Hide resolved

shawntanzk requested a review from gouttegd June 23, 2022 12:52

matentzn approved these changes Jun 23, 2022

View reviewed changes

gouttegd approved these changes Jun 23, 2022

View reviewed changes

Updated import, added EAs

8b67e67

shawntanzk requested changes Jun 23, 2022

View reviewed changes

src/ontology/cl-edit.owl Show resolved Hide resolved

src/ontology/cl-edit.owl Show resolved Hide resolved

Update cl-edit.owl

1a6447d

ghost requested a review from shawntanzk June 23, 2022 14:53

shawntanzk approved these changes Jun 24, 2022

View reviewed changes

ghost mentioned this pull request Jun 24, 2022

Please add details on "mirrors" as they relate to refreshing imports OBOAcademy/obook#191

Open

ghost merged commit c107f7f into master Jun 24, 2022

ASCT+B_validation_review automation moved this from In progress to Done Jun 24, 2022

ghost deleted the 1582-NTR-epithelial-cells-of-distal-convoluted-tubule branch June 24, 2022 10:40

This pull request was closed.

Addresses #1582-NTR-epithelial_cells_DCT #1644

Addresses #1582-NTR-epithelial_cells_DCT #1644

Conversation

ghost commented Jun 21, 2022

github-actions bot commented Jun 21, 2022 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

CL_4030016 http://purl.obolibrary.org/obo/CL_4030016

Added

CL_4030017 http://purl.obolibrary.org/obo/CL_4030017

Added

serotonergic neuron http://purl.obolibrary.org/obo/CL_0000850

Added

github-actions bot commented Jun 21, 2022 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

CL_4030016 http://purl.obolibrary.org/obo/CL_4030016

Added

CL_4030017 http://purl.obolibrary.org/obo/CL_4030017

Added

early distal convoluted tubule http://purl.obolibrary.org/obo/UBERON_0005101

Added

late distal convoluted tubule http://purl.obolibrary.org/obo/UBERON_0005102

Added

shawntanzk commented Jun 21, 2022

ghost commented Jun 23, 2022

shawntanzk Jun 23, 2022

Choose a reason for hiding this comment

gouttegd Jun 23, 2022

Choose a reason for hiding this comment

shawntanzk commented Jun 23, 2022

ghost commented Jun 23, 2022

matentzn left a comment

Choose a reason for hiding this comment

shawntanzk commented Jun 23, 2022 • edited Loading

matentzn commented Jun 23, 2022

ghost commented Jun 23, 2022

matentzn commented Jun 23, 2022

gouttegd left a comment

Choose a reason for hiding this comment

gouttegd commented Jun 23, 2022

ghost commented Jun 23, 2022

ghost commented Jun 23, 2022

shawntanzk left a comment

Choose a reason for hiding this comment

matentzn commented Jun 23, 2022

ghost commented Jun 23, 2022 • edited by ghost Loading

matentzn commented Jun 23, 2022

ghost commented Jun 23, 2022

matentzn commented Jun 23, 2022

github-actions bot commented Jun 21, 2022 •

edited

Loading

CL_4030016 `http://purl.obolibrary.org/obo/CL_4030016`

CL_4030017 `http://purl.obolibrary.org/obo/CL_4030017`

serotonergic neuron `http://purl.obolibrary.org/obo/CL_0000850`

github-actions bot commented Jun 21, 2022 •

edited

Loading

CL_4030016 `http://purl.obolibrary.org/obo/CL_4030016`

CL_4030017 `http://purl.obolibrary.org/obo/CL_4030017`

early distal convoluted tubule `http://purl.obolibrary.org/obo/UBERON_0005101`

late distal convoluted tubule `http://purl.obolibrary.org/obo/UBERON_0005102`

shawntanzk commented Jun 23, 2022 •

edited

Loading

ghost commented Jun 23, 2022 •

edited by ghost

Loading