Integration of SAO terms into GO CC

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Aim: integrate terms from the SAO (Subcellular Anatomy Ontology for the nervous system) in GO as Cellular Component terms. A table of SAO terms has been generated by Fahim Imam and is attached (NIF-Subcell-GO-CC.xlsx). Currently working with Chris, Jane, David H, Fahim and Maryann Martone going through the list - some terms are already in GO, others are being discussed wrt placement in GO vs. UBERON, others may be out of scope of GO. Will post an update when the final list of terms for GO is ready. This task is also in Jira, but I'm adding it in SF as well as it supercedes two previous items, that are now closed:

https://sourceforge.net/tracker/?func=detail&aid=2891344&group\_id=36855&atid=440764 https://sourceforge.net/tracker/?func=detail&aid=2891355&group\_id=36855&atid=440764

Note to self: create new grouping term "neuron part"?

Reported by: paolaroncaglia

Original Ticket: geneontology/ontology-requests/9752

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Original comment by: paolaroncaglia

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First terms added:

GO:0097407 Bunina body GO:0097408 fibrillary inclusion GO:0097409 glial cytoplasmic inclusion

Original comment by: paolaroncaglia

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More terms added:

GO:0097412 hyaline inclusion GO:0097413 Lewy body GO:0097414 classical Lewy body GO:0097415 cortical Lewy body GO:0097416 Lewy body-like hyaline inclusion GO:0097417 nematosome GO:0097418 neurofibrillary tangle GO:0097419 Pick body GO:0097420 skein-like inclusion GO:0097422 tubular endosome GO:0097423 mitochondrion-associated adherens complex GO:0097424 nucleolus-associated heterochromatin GO:0097425 smooth endoplasmic reticulum part GO:0097426 glial filament GO:0097427 microtubule bundle GO:1901588 dendritic microtubule GO:1901589 axon microtubule bundle

Original comment by: paolaroncaglia

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More terms added: GO:0097433 dense body

GO:0097440 apical dendrite

GO:0097441 basilar dendrite

GO:0097442 CA3 pyramidal cell dendrite

GO:0097443 sorting endosome

GO:0097444 spine apparatus

GO:0097445 presynaptic active zone dense projection

GO:1990005 granular vesicle

GO:1990006 amorphous vesicle

GO:1990007 membrane stack

GO:1990008 neurosecretory vesicle

GO:1990011 laminated body

GO:1990012 complex laminated body

Original comment by: paolaroncaglia

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More terms added:

GO:1990013 presynaptic grid GO:1990014 orthogonal array GO:1990015 ensheathing process GO:1990016 neck portion of tanycyte GO:1990017 somatic portion of tanycyte GO:1990018 tail portion of tanycyte

GO:0097447 dendritic tree GO:0097448 spine mat GO:0097449 astrocyte projection GO:0097450 astrocyte end-foot GO:0097451 glial limiting end-foot GO:0097453 mesaxon GO:0097454 Schwann cell microvillus GO:0097455 spiny bracelet of Nageotte GO:0097456 terminal loop GO:0097457 hippocampal mossy fiber GO:0097458 neuron part GO:0097462 Lewy neurite GO:0097463 gemmule GO:0097464 thorny excrescence GO:0097465 somatic spine

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Other edits stemming from this project:

Added 'microvilli' as a related synonym of GO:0005902 microvillus

GO:0043209 myelin sheath: added narrow synonym 'astrocyte sheath'; changed synonym scope of 'Schwann Cell Myelin Sheath' to narrow (and edited lettercase)

Added/edited synonyms of GO:0043209 myelin sheath and GO:0043218 compact myelin

GO:0043219 lateral loop: Added 'Schwann cell paranodal termination', 'oligodendrocyte paranodal termination' and 'paranodal loop' as related synonyms

Made 'neuron projection' is_a 'neuron part'

Made the following terms is_a 'neuron part': dendritic tree Lewy body Lewy body-like hyaline inclusion nBAF complex neurofibrillary tangle neurofilament cytoskeleton neuronal cell body presynaptic active zone presynaptic membrane spine apparatus spine mat subplasmalemmal coating

Added the following link: spine apparatus part_of neuron spine

Deleted link subplasmalemmal coating part_of extrinsic to external side of plasma membrane, and made it part_of extrinsic to internal side of plasma membrane instead

Edited def. of GO:0043025 neuronal cell body

Added 'spine' as broad synonym of GO:0044309 neuron spine

Added the following as narrow synonym of GO:0043197 dendritic spine: branched dendritic spine mushroom dendritic spine sessile dendritic spine stubby dendritic spine thin dendritic spine

Original comment by: paolaroncaglia

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More new terms:

GO:1990024 C bouton GO:1990025 F bouton GO:1990026 hippocampal mossy fiber expansion GO:1990027 S bouton

Added 'motor endplate' as a related synonym of GO:0043679 axon terminus and GO:0031594 neuromuscular junction.

Original comment by: paolaroncaglia

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More done:

Added new terms: GO:1990030 pericellular basket GO:1990031 pinceau fiber GO:1990032 parallel fiber GO:1990033 dendritic branch point

Added 'terminal specialization' as related synonym of GO:0044292 dendrite terminus. Added 'trunk' as related synonym of GO:0043198 dendritic shaft.

Original comment by: paolaroncaglia

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Also

GO:1990037 Lewy body core GO:1990038 Lewy body corona

Original comment by: paolaroncaglia

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Added new terms: GO:1990039 hypolemmal cisterna GO:1990040 sub-surface cisterna

Added synonyms: Added 'cristae' as a broad synonym of GO:0030061 mitochondrial crista Added 'inner bounding mitochondrial membrane' as exact synonym of GO:0097002 mitochondrial inner boundary membrane Added 'pars fibrosa' as broad synonym of GO:0001651 dense fibrillar component Added 'pars granulosa' as broad synonym of GO:0001652 granular component

Original comment by: paolaroncaglia

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Added new terms: GO:0097470 ribbon synapse GO:0097471 mossy fiber rosette

Added 'dense material' as a narrow synonym of GO:0097444 spine apparatus

GO:0005911 cell-cell junction: Added NIF_Subcellular: sao1395777368 as a synonym xref

GO:0005921 gap junction: Added 'gap junction plaque' and 'gap junction macula' as exact synonyms

GO:0045202 synapse: Added 'electrotonic synapse' and 'mixed synapse' as narrow synonym

Original comment by: paolaroncaglia

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Changed synonym scope of 'electrotonic synapse' from narrow to related for GO:0045202 synapse. Added 'electrotonic synapse' and 'electrical synapse' as related synonyms of GO:0005921 gap junction.

Original comment by: paolaroncaglia

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• status: open --> closed-accepted

Original comment by: paolaroncaglia