Fixes #1889 neuroendocrine cell

[aleixpuigb]

Fixes #1889 neuroendocrine cell

[aleixpuigb]

#gogoeditdiff

[github-actions]

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/2024-09-19/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/2024-09-19/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

adrenal cortex chromaffin cell http://purl.obolibrary.org/obo/CL_1000427

Removed

• adrenal cortex chromaffin cell SubClassOf adrenal gland glandular cell

adrenal medulla chromaffin cell http://purl.obolibrary.org/obo/CL_0000336

Added

• adrenal medulla chromaffin cell SubClassOf neurecto-epithelial cell

• adrenal medulla chromaffin cell SubClassOf glandular epithelial cell

  • is_inferred "true"

chromaffin cell http://purl.obolibrary.org/obo/CL_0000166

Removed

• chromaffin cell SubClassOf neural crest derived neuron

Added

• chromaffin cell SubClassOf develops from some migratory neural crest cell

chromaffin cell of adrenal gland http://purl.obolibrary.org/obo/CL_1000426

Removed

• chromaffin cell of adrenal gland SubClassOf glandular epithelial cell

chromaffin cell of ovary http://purl.obolibrary.org/obo/CL_1000465

Removed

• chromaffin cell of ovary SubClassOf ovarian surface epithelial cell

chromophil cell of anterior pituitary gland http://purl.obolibrary.org/obo/CL_0000637

Added

• chromophil cell of anterior pituitary gland SubClassOf neurecto-epithelial cell

lung neuroendocrine cell http://purl.obolibrary.org/obo/CL_1000223

Removed

• lung neuroendocrine cell SubClassOf neuronal receptor cell

Added

• lung neuroendocrine cell SubClassOf epithelial cell of lung

neuroendocrine cell http://purl.obolibrary.org/obo/CL_0000165

Removed

• neuroendocrine cell definition "A neuron that is capable of some hormone secretion in response to neuronal signals."

  • database_cross_reference "MESH:D055099"

• neuroendocrine cell comment "The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements.

The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron."

• database_cross_reference "PMID:5342440"

• database_cross_reference "https://www.clinicalkey.com/#!/content/book/3-s2.0-B9780323555968000073"

• neuroendocrine cell SubClassOf efferent neuron

• neuroendocrine cell SubClassOf neurecto-epithelial cell

Added

• neuroendocrine cell definition "An endocrine cell that is part of the neuroendocrine system. A neuroendocrine cell secretes hormones into the circulatory system in response to direct stimuli."

  • database_cross_reference "MESH:D055099"

  • database_cross_reference "PMID:2675281"

• neuroendocrine cell SubClassOf electrically responsive cell

neuroendocrine cell of epithelium of lobar bronchus http://purl.obolibrary.org/obo/CL_4033010

Removed

• neuroendocrine cell of epithelium of lobar bronchus SubClassOf epithelial cell of lung

parvocellular neurosecretory cell http://purl.obolibrary.org/obo/CL_1001505

Removed

• parvocellular neurosecretory cell SubClassOf neuroendocrine cell

Added

• parvocellular neurosecretory cell SubClassOf neuron

pinealocyte http://purl.obolibrary.org/obo/CL_0000652

Removed

• pinealocyte SubClassOf endocrine cell

Added

• pinealocyte SubClassOf neuroendocrine cell

type EC enteroendocrine cell http://purl.obolibrary.org/obo/CL_0000577

Added

• type EC enteroendocrine cell SubClassOf neurecto-epithelial cell

[github-actions]

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/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

chromaffin cell of adrenal gland http://purl.obolibrary.org/obo/CL_1000426

Removed

• chromaffin cell of adrenal gland SubClassOf glandular epithelial cell

lung neuroendocrine cell http://purl.obolibrary.org/obo/CL_1000223

Added

• lung neuroendocrine cell SubClassOf epithelial cell of lung

neuroendocrine cell http://purl.obolibrary.org/obo/CL_0000165

Removed

• neuroendocrine cell definition "A neuron that is capable of some hormone secretion in response to neuronal signals."

  • database_cross_reference "MESH:D055099"

• neuroendocrine cell comment "The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements.

The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron."

• database_cross_reference "PMID:5342440"

• database_cross_reference "https://www.clinicalkey.com/#!/content/book/3-s2.0-B9780323555968000073"

• neuroendocrine cell EquivalentTo neuron and (capable of some hormone secretion)

• neuroendocrine cell SubClassOf efferent neuron

• neuroendocrine cell SubClassOf neurecto-epithelial cell

Added

• neuroendocrine cell definition "An endocrine cell that is part of the neuroendocrine system. A neuroendocrine cell secretes hormones into the circulatory system in response to direct stimuli."

  • database_cross_reference "MESH:D055099"

  • database_cross_reference "PMID:2675281"

• neuroendocrine cell EquivalentTo endocrine cell and (part of some neuroendocrine system)

[aleixpuigb]

#gogoeditdiff

[github-actions]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so.

[aleixpuigb]

Hi @dosumis, I think all discussed edits have been implemented. Cheers!

[github-actions]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so.

[aleixpuigb]

#gogoeditdiff

[github-actions]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so.

[gouttegd]

@dosumis: Given that it has been a long time since the last discussion on #1889, is the fix proposed here (which is basically to define neuroendocrine cell as 'endocrine cell that is part_of some 'neuroendocrine system', as suggested in this comment) still your preferred approach? Or should we rethink about the entire issue?

[dosumis]

#gogoeditdiff

Note - we will ask for feedback on this issue from the Gut Cell Atlas team - who will be reviewing EC cells, a number of which are sometimes classified as neuro-endocrine.

[scheuerm]

This is also a cell type defined in the lung atlas and so we should make sure that the definition is consistent with this location as well.