Add all UBERONParcellations from UBERON Minimal Nervous System subset

[UlrikeS91]

We did not add all relevant UBERONParcellations. Since there have been a few requests for adding more parcellations and these are very straight forward to add, I decided to pull the entire subset and create the openMINDS instances.

A short summary:

• the subset contains both cell ontology (CL) terms and UBERON terms
  • I have created CellType instances for the CL terms but I will not make a PR for those (yet), we need to resolve Need for naming convention of cell type terms - urgent #94 before I want to make any major updates
  • I have created UBERONParcellation instances for the UBERON terms and will make several PRs since this is a list of over 2800 terms
• the UBERONParcellation instances are structured to following way:
  • at_id and at_type: as usual, name part of the at_id in lowerCamelCase with exception for terms that have a proper name (e.g., Ammon's horn remains capitalized "AmmonsHorn")
  • definition:
  • auto-generated from ontology properties "is_a" and "relationship" (which is always "is part of") in two sentences, but not all terms have both
  • reference:
    • only "is_a": [auto-generated from 'is_a' property of the [UBERON ontology term](http://purl.obolibrary.org/obo/UBERON_<<ID>>)]
    • only "relationship": [auto-generated from 'relationship' property of the [UBERON ontology term](http://purl.obolibrary.org/obo/UBERON_<<ID>>)]
    • both: [auto-generated from properties of the [UBERON ontology term](http://purl.obolibrary.org/obo/UBERON_<<ID>>) ('is_a' and 'relationship')]
  • description:
    • minimally cleaned-up text from ontology property "def" (definition)
      • capitalized first letter if it was lower case
      • added period at the end if ti was missing
      • removed some random symbols (e.g., a single [ at the end of the string)
      • added spaces after a period and capitalized first letter of the next sentence
      • I removed the citation/reference within the definition because it wasn't very useful for our instances (e.g., sometimes had abbreviation of another ontology as reference which wouldn't make sense to keep like this in openMINDS instances)
      • reference: I added [definition of the [UBERON ontology term](http://purl.obolibrary.org/obo/UBERON_<<ID>>)] instead, so that users can go there and see the original reference in its original context where it makes more sense
  • interlexIdentifier: I had a list from quite a few years back which had some terms mapped; I only added those, I don't think all UBERON terms are mapped in InterLex (@tgbugs?) anyway, but if they are it should be easy to supplement them with this later
  • knowledgeSpaceLink: with very few exceptions, all terms received this link; I tested very single one and all lead to the correct term, the exceptions are the ones where I could not find the correct UBERON ID in KS
  • name == UBERON term name
  • preferredOntoloyIdentifier: always UBERON ID (as IRI: http://purl.obolibrary.org/obo/UBERON_<<ID>>)
  • synonym:
    • I only kept "EXACT" synonyms and excluded any "BROAD", "NARROW" or "RELATED" synonyms
    • additionally I excluded "EXACT DEPRECATED" (seemed very old nd/or outdated), "EXACT DUBIOUS" (seemed to be mainly exact synonyms but with typos) and "EXACT PLURAL" (we don't collect the plural as synonyms)
    • the remaining types that were kept are:
      • EXACT
      • EXACT ABBREVIATION
      • EXACT BRAIN_NAME_ABV
      • EXACT HUMAN_PREFERRED
      • EXACT LATIN
      • EXACT NON_AMNIOTE
      • EXACT SENSU

Please note that it is up for discussion which of the over 2800 terms should be added as an UBERONParcellation! I don't think we should add all from this subset, but I want those discussions to happen in the repo (or offline with a conclusion in the corresponding PR).

EDIT (17.01.2025):

The checklist represents the PRs related to this issue. When there is just a name and no link, the PR still needs to be made. When a link is added, the PR exists. Number in brackets is the number of terms included in each PR. Once ticked off, the PR is merged (and conclusion for what has been added or not is in the thread of the PR).
The terms were sorted in the same order of the checklist. This is important to know since some terms contain multiple keywords that I sorted by. For example, 'blood brain barrier' was sorted into 'blood related terms' because this was done before sorting by 'border related terms'. Over 2000 terms were sorted following a specific logic/logical grouping (details will be described in each PR), and each PR has different number of terms included. The remaining 600 terms are sorted alphabetically and each PR contains 50 terms (A01 - A12).

• with specific reference to a publication in name (94) UBERON terms with specific references in their names #187
• invertebrate related terms (30) Invertebrate related UBERON terms #189
• with 'receptor' in name (19) UBERON terms with 'receptor' in their name #190
• blood related terms (45) Blood related UBERON terms #134 & Blood related UBERON terms (addition) #188
• with 'nerve' in name (284) UBERON terms with 'nerve' in their name #191
• with 'future' in name (12) UBERON terms with 'future' in their name #192
• with 'taste bud' in name (12) UBERON terms with 'taste bud' in their name #193
• unspecific classes (13) UBERON terms representing rather unspecific classes #194
• with 'system' in name (36)
• eye related terms (22)
• with 'mater' in name (27)
• with 'organ' in name (14)
• nuclei related terms (477)
• with 'ganglion' in name (118)
• hippocampus related terms (113)
• brain fold related terms (178)
• border related terms (24)
• with 'layer' in name (128)
• with 'spinal cord' in name (141)
• cortex/area related terms (122)
• cerebellum related terms (73)
• with 'olfactory' in name (16)
• with 'cell group' in name (13)
• with 'lobe' in name (34)
• with 'ventricle' in name (36)
• with 'white matter' or 'grey matter' in name (21)
• with 'tract' in name (55)
• with 'cephalon' in name (33)
• with 'lobule' in name (22)
• with 'rhombomere' in name (30)
• commissure related terms (21)
• A01 (50; accessoryMedullaryLaminaOfGlobusPallidus - capsuleOfMedialGeniculateBody)
• A02 (50; caudaEquina - cuneateFasciculus)
• A03 (50; cuneateFasciculusOfMedulla - epitheliumOfUtricle)
• A04 (50; externalMedullaryLaminaOfThalamus - hyperpalliumApicale)
• A05 (50; hypothalamus - lateralZoneOfHypothalamus)
• A06 (50; leftCerebralHemisphere - medullaryRapheNuclearComplex)
• A07 (50; medullaryReticularFormation - ophthalmicPlexus)
• A08 (50; opticChiasma - posteriorColumnOfFornix)
• A09 (50; posteriorCoronaRadiata - ramusSupraotic)
• A10 (50; ramusVentral - striosome)
• A11 (50; subarachnoidCistern - thalamicComplex)
• A12 (50; thalamicEminence - zonaLimitansIntrathalamica)

[UlrikeS91]

related issues with UBERON requests:
#131
#104

[UlrikeS91]

This will also be an update of existing terms since the convention for the definition (and description) has change e.g., definitions don't start with the repetition of the name of the term anymore.

[lzehl]

@UlrikeS91 what is the status if this is reopened?

[UlrikeS91]

I envisioned this issue to be used to collect all PRs related to this. @Raphael-Gazzotti closed it after we merged the first PR related to this issue, but the idea was to make multiple smaller PRs for all the UBERON parcellations and link them to this issue. And then, once we integrated all relevant terms into openMINDS, close this issue. We can organize this differently if you'd like. I'm open to suggestions 🙂

[lzehl]

@UlrikeS91 generally comment: we should aim for issues that we can close within one PR. If this is not feasible (because sometimes issues are just bigger) we need to have at least a concrete list of PRs todo so that someone not overseeing the outreach of the issue can follow up what the status is.

For this issue, maybe provide a checklist of TODOs and mark those who were already accomplished in an PR. You can connect the PR IDs to each checklist point when you (or someone else) started the PR for that point. Is this feasible for this issue? (I know that this covers a lot of changes)