uberon ABA-Uberon bridge file updates

We have some expert-curated stuff for ABA-uberon bridge files that need to be updated CCF_to_UBERON.xlsx

Ignore verify for now
Remove mapping for nok - @shawntanzk to find out what the alternative is (can we replace with something more generic for now)
Change accordingly for gen

Apr 06 '22 15:04 shawntanzk

@shawntanzk, let me know if anything is unclear with the mappings or if you need anything at all.

Apr 06 '22 17:04 patrick-lloyd-ray

@patrick-lloyd-ray - just one thing, for the nok -> is there an alternative we can map to? something perhaps more generic or something? PS we assumed verify meant that it still needed to be verified

Apr 06 '22 18:04 shawntanzk

for the nok -> is there an alternative we can map to? something perhaps more generic or something?

If I could find a mapping that worked, I put it in column F. If F is empty, there should be 'add term' in G (meaning we would like to add a new term).

we assumed verify meant that it still needed to be verified

If column F is blank, then they are in need of verification. If there is a term in column F, that has been verified.

Apr 06 '22 19:04 patrick-lloyd-ray

Looks like many are fixed already - found some that aren't so will still go through the whole list and make the fixes. New terms don't seem to have been added, will slowly get through them - might take awhile as I will need to do research on each of them and all

Some terms are confusing - if its sensible to change the status, I will: eg http://purl.obolibrary.org/obo/DMBA_16339 (intercalate nucleus) - is nok and has add term but its mapped to exactly the same thing it uberon as http://purl.obolibrary.org/obo/HBA_9572 ( intercalate nucleus)

Apr 07 '22 08:04 shawntanzk

Terms to add (evolving list):

[x] periventricular hypothalamic nucleus, (+ anterior part, intermediate part)
[x] tuberal nucleus
[x] cerebral nuclei (currently as a related synonym for collection of basal ganglia)
[ ] anterior part of Int (Figure out this better)- DMBA
[x] fasciola cinerea (currently as a related synonym for fasciolar gyrus)
[x] ventrolateral preoptic nucleus (currently as a related synonym for pars postrema of ventral lateral nucleus)
[ ] inferior colliculus, dorsal nucleus (currently as a related synonym for pericentral nucleus of inferiror colliculus) - add and remove related synonym
[ ] mantle zone of cerebellar vermis
[x] A4 noradrenergic cell group
[ ] rhinal incisure
[ ] basolateral amygdaloid nucleus, (+ anterior part posterior part, ventral part)
[ ] pyramidal tract decussation
[ ] lateral olfactory tract
[x] visceral area (+ layer 4, layer 6b, layer 6a, layer 1)
[x] ventral auditory area, (+ layer 6a, layer 6b, layer 2/3, layer 1, layer 4)
[x] posterior auditory area (+ layer 1, layer 6a, layer 6b, layer 2/3, layer 4, layer 5)
[x] dorsal auditory area, layer 2/3
[x] anteromedial visual area, layer 6a
[x] lateral visual area, layer 2/3
[x] parapyramidal nucleus
[ ] somatomotor areas (+ Layer 1, Layer 2/3, Layer 5, Layer 6a, Layer 6b)
[ ] infralimbic area (+ layer 6b, layer 2/3, layer 1, layer 2, layer 5)
[ ] postpiriform transition area (has layer 1-3 in aba)
[x] superior olivary complex, periolivary region
[ ] gustatory areas, layer 4
[x] perihypoglossal nuclei
[x] anterior olfactory nucleus, (+ dorsal part, external part, medial part)
[x] parapyramidal nucleus, superficial part
[x] anterior olfactory nucleus, posteroventral part
[x] linear nucleus of the medulla
[x] rubroreticular tract
[ ] temporal association areas (+ layer 4, layer 5)
[x] dorsal auditory area, (+ layer 6b, layer 5)
[x] main olfactory bulb, outer plexiform layer
[x] striatum-like amygdalar nuclei
[x] anteromedial visual area, layer 1
[x] lateral tegmental nucleus
[ ] magnocellular nucleus
[x] magnocellular reticular nucleus
[ ] anterior area (+ layer 1, 2/3, 4, 5, 6a, 6b)
[ ] laterointermediate area (+ layer 1, 2/3, 4, 5, 6a, 6b)
[x] sublaterodorsal nucleus
[ ] gustatory areas, layer 1
[x] dorsal peduncular area, layer 2/3
[x] anteromedial visual area, (+ layer 4, layer 6b)
[x] medial corticohypothalmic tract
[x] infralimbic area
[x] bulbocerebellar tract
[x] bed nuclei of the stria terminalis, anterior division, (+ anteromedial area, fusiform nucleus, ventral nucleus, juxtacapsular nucleus, oval nucleus, rhomboid nucleus)
[x] bed nuclei of the stria terminalis, posterior division, (+ dorsal nucleus, principal nucleus, transverse nucleus, strial extension)
[x] postpiriform transition area (+ layers 1-3)
[x] supratrigeminal nucleus
[x] cochlear nucleus, subpedunclular granular region
[x] accessory facial motor nucleus
[x] efferent vestibular nucleus
[x] nucleus of the solitary tract, (+ central part, lateral part)
[x] interstitial nucleus of the vestibular nerve
[x] temporal association areas, layer 6b
[x] piriform-amygdalar area
[x] dorsal peduncular area
[ ] efferent cochlear group
[x] rhinocele
[x] interposed nucleus
[x] pontine gray
[x] corpus callosum, anterior forceps
[x] corpus callosum, posterior forceps
[ ] Pyramid

Layer stuff (note, dont think they need be added, but can instead be like 'has soma location' some 'primary somatosensory area' and 'has soma location' some 'cortical layer 1' etc.):

[x] paraflocculus, granular layer
[x] paraflocculus, Purkinje layer
[x] paraflocculus, molecular layer
[x] flocculus, granular layer
[x] flocculus, Purkinje layer
[x] flocculus, molecular layer
[x] uvula (IX), granular layer
[x] uvula (IX), Purkinje layer
[x] uvula (IX), molecular layer
[x] nodulus (X), granular layer
[x] nodulus (X), Purkinje layer
[x] nodulus (X), molecular layer
[x] lingula (I), granular layer
[x] lingula (I), Purkinje layer
[x] lingula (I), molecular layer
[x] lobule II, granular layer
[x] lobule II, Purkinje layer
[x] lobule II, molecular layer
[x] lobule III, granular layer
[x] lobule III, Purkinje layer
[x] lobule III, molecular layer
[x] lobule IV, granular layer
[x] lobule IV, Purkinje layer
[x] lobule IV, molecular layer
[x] lobule V, granular layer
[x] lobule V, Purkinje layer
[x] lobule V, molecular layer
[ ] lobules IV-V, granular layer
[ ] lobules IV-V, Purkinje layer
[ ] lobules IV-V, molecular layer
[x] simple lobule, granular layer
[x] simple lobule, Purkinje layer
[x] simple lobule, molecular layer
[x] crus 1, granular layer
[x] crus 1, Purkinje layer
[x] crus 1, molecular layer
[x] crus 2, granular layer
[x] crus 2, Purkinje layer
[x] crus 2, molecular layer
[x] paramedian lobule, granular layer
[x] paramedian lobule, Purkinje layer
[x] paramedian lobule, molecular layer
[x] declive (VI), granular layer
[x] declive (VI), Purkinje layer
[x] declive (VI), molecular layer
[x] folium-tuber vermis (VII), granular layer
[x] folium-tuber vermis (VII), Purkinje layer
[x] folium-tuber vermis (VII), molecular layer
[x] pyramus (VIII), granular layer
[x] pyramus (VIII), Purkinje layer
[x] pyramus (VIII), molecular layer
[x] primary somatosensory area, barrel field, layer 1
[x] primary somatosensory area, barrel field, layer 2/3
[x] primary somatosensory area, barrel field, layer 4
[x] primary somatosensory area, barrel field, layer 5
[x] primary somatosensory area, barrel field, layer 6a
[x] primary somatosensory area, barrel field, layer 6b
[x] primary visual area, layer 2/3
[x] primary visual area, layer 4
[x] primary visual area, layer 5
[x] primary visual area, layer 6a
[x] copula pyramidis, granular layer
[x] copula pyramidis, Purkinje layer
[x] copula pyramidis, molecular layer

Doesn't have "Add Term" in excel sheet but mapping seems wrong and needs term adding:

[x] uvula (IX)
[x] nodulus (X)
[ ] lobules IV-V

Apr 07 '22 08:04 shawntanzk

To verify @patrick-lloyd-ray MBA_820 (inferior colliculus, dorsal nucleus) is mapped to the same as MBA_811 (inferior colliculus, central nucleus) - UBERON_0002563 (central nucleus of inferior colliculus) Bridge file currently maps MBA_820 to UBERON_0002577 (pericentral nucleus of inferior colliculus) which seems more correct - I hence didnt want to change it.

Apr 07 '22 08:04 shawntanzk

There are some marked "cerebellum" which dont seem to be in the bridge file. The MBA stuff seem to require specific layers to be added to UBERON anyway. My suggestion is that I add them to uberon and add them to bridge file after.

Apr 07 '22 09:04 shawntanzk

Whole bunch not in bridge file - not sure how it is being mapped? Not sure what to do with them Screenshot 2022-04-07 at 10 27 53

Apr 07 '22 09:04 shawntanzk

MBA_985 (primary motor area) is mapped to primary motor cortex in uberon which is right from what I see in the brain atlas - it is marked ok but also has "add term" to it - will ignore it for now, but in case it means something, please do let me know

Apr 07 '22 10:04 shawntanzk

DMBA Long list of terms to add (kept this separate as its really long and clustered together (some are 'HAS PARALLEL', not sure what this means, but best to check for mappings before adding anything anyway):

[ ] blood vessels of spinal cord
[ ] ventricular zone of SpA
[ ] mantle zone of SpA
[ ] ventricular zone of SpB
[ ] mantle zone of SpB
[ ] ventricular zone of SpF
[ ] mantle zone of SpF
[ ] periventricular stratum of SpF
[ ] intermediate stratum of SpF
[ ] superficial stratum of SpF
[ ] ventricles, spinal cord
[ ] ventricles, SpC roof plate
[ ] ventricles, SpC alar plate
[ ] ventricles, SpC basal plate (anterior horn)
[ ] ventricles, SpC floor plate
[ ] SpC roof plate
[ ] SpC alar plate
[ ] medial (cornucommissural) part of the spinal alar plate
[ ] ventricular zone of the SpAM
[ ] mantle zone of the SpAM
[ ] periventricular stratum of the SpAM
[ ] alar medial part of Rexed's layer 10
[ ] intermediate stratum of the SpAM
[ ] cornucommissural part of Rexed's layer 4
[ ] internal basilar (cervical) nucleus
[ ] dorsal (thoracic) nucleus of Clarke
[ ] lumbar dorsal commissural nucleus
[ ] sacral dorsal commissural nucleus
[ ] superficial stratum of the SpAM
[ ] lateral (dorsal horn) part of the spinal alar plate
[ ] ventricular zone of the SpAL
[ ] alar lateral part of Rexed's layer 10
[ ] mantle zone of the SpAL
[ ] periventricular stratum of the SpAL
[ ] intermediate stratum of the SpAL
[ ] Rexed's layer 3
[ ] Rexed's layer 4 (main or lateral part)
[ ] superficial stratum of the SpAL
[ ] Rexed's layer 1 (marginal layer)
[ ] Rexed's layer 2 (gelatinous substance)
[ ] ventral (liminal) part of the spinal alar plate
[ ] ventricular zone of the SpAV
[ ] mantle zone of the SpAV
[ ] periventricular stratum of the SpAV
[ ] alar ventral part of Rexed's layer 10
[ ] intermediate stratum of the SpAV
[ ] Rexed's layer 5 (neck of dorsal horn)
[ ] medial (deep) part of 5Sp
[ ] lateral (superficial) part of 5Sp
[ ] Rexed's layer 6 (basis of dorsal horn)
[ ] medial (deep) part of 6Sp
[ ] lateral (superficial) part of 6Sp
[ ] superficial stratum of the SpAV
[ ] SpC basal plate (anterior horn)
[ ] lateral part of SpB
[ ] ventricular zone of SpBL
[ ] mantle zone of SpBL
[ ] periventricular stratum of SpBL
[ ] basal lateral part of Rexed's layer 10
[ ] intermediate stratum of SpBL
[ ] Rexed's layer 7 (intermediate zone)
[ ] lumbar precerebellar nucleus
[ ] sacral precerebellar nucleus
[ ] central cervical nucleus
[ ] ventral horn lateral interneurons
[ ] intermediomedial nucleus
[ ] intermediolateral nucleus (lateral horn)
[ ] laterodorsal commissural nucleus
[ ] sacral parasympathetic preganglionic neurons
[ ] superficial stratum of SpBL
[ ] intermediate part of SpB
[ ] ventricular zone of SpBI
[ ] mantle zone of SpBI
[ ] periventricular stratum of SpBI
[ ] basal intermediate part of Rexed's layer 10
[ ] intermediate stratum of SpBI
[ ] Rexed's layer 9
[ ] motoneuron columns
[ ] medial motoneuron columns
[ ] lateral motoneuron columns
[ ] central motoneuron columns
[ ] Onuf's nucleus
[ ] medial (anal) part of Onuf's nucleus
[ ] lateral (urethral) part of Onuf's nucleus
[ ] superficial stratum of SpBI
[ ] medial part of SpB
[ ] ventricular zone of SpBM
[ ] mantle zone of SpBM
[ ] periventricular stratum of SpBM
[ ] basal medial part of Rexed's layer 10
[ ] intermediate stratum of SpBM
[ ] Rexed's layer 8
[ ] ventral horn medial interneurons
[ ] superficial stratum of SpBM
[ ] SpC floor plate

Apr 08 '22 07:04 shawntanzk

spot checked on row 4670-5051 -> they don't seem to be in bridge file at all

Apr 08 '22 08:04 shawntanzk

These mappings seem a bit odd - its MBA but mapped to Broadann area which can't be right yeah?

superclass_iri	subclass_name	subclass_iri	Analysis	Recommended Mapping	Type of mapping issue
http://purl.obolibrary.org/obo/UBERON_0010314	prelimbic area, layer 6b	http://purl.obolibrary.org/obo/MBA_132	Verify	Brodmann (1909) area 32 (http://purl.obolibrary.org/obo/UBERON_0013560)	OR ADD LAYER
http://purl.obolibrary.org/obo/UBERON_0010314	prelimbic area, layer 1	http://purl.obolibrary.org/obo/MBA_171	Verify	Brodmann (1909) area 32 (http://purl.obolibrary.org/obo/UBERON_0013560)	OR ADD LAYER
http://purl.obolibrary.org/obo/UBERON_0010314	anterior cingulate area, layer 6a	http://purl.obolibrary.org/obo/MBA_179	Verify	Brodmann (1909) area 24 (http://purl.obolibrary.org/obo/UBERON_0006101)	OR ADD LAYER

Apr 11 '22 10:04 shawntanzk

Some terms are confusing - if its sensible to change the status, I will: eg http://purl.obolibrary.org/obo/DMBA_16339 (intercalate nucleus) - is nok and has add term but its mapped to exactly the same thing it uberon as http://purl.obolibrary.org/obo/HBA_9572 ( intercalate nucleus)

Yeah, that might be a problem that has since been fixed, the mapping file I received is a few years old, so it's possible some of these have gotten patched up since.

Apr 11 '22 18:04 patrick-lloyd-ray

These mappings seem a bit odd - its MBA but mapped to Broadann area which can't be right yeah?

Yeah, that's a mistake -- they are supposed to be: prelimbic area, layer [X].

Apr 11 '22 18:04 patrick-lloyd-ray

Doesn't have "Add Term" in excel sheet but mapping seems wrong and needs term adding:

Yeah, there are going to be some of these too -- it's a lot of lines/structures to check, so I've surely made some mistakes trying to get these done sort-of quickly. I appreciate the verifications.

Apr 11 '22 18:04 patrick-lloyd-ray

Layer stuff (note, dont think they need be added, but can instead be like 'has soma location' some 'primary somatosensory area' and 'has soma location' some 'cortical layer 1' etc.):

For these (and ones like them), the atlases are pretty fine-grained but this sounds like a fine solution for annotating cell location.

Apr 11 '22 18:04 patrick-lloyd-ray

MBA_985 (primary motor area) is mapped to primary motor cortex in uberon which is right from what I see in the brain atlas - it is marked ok but also has "add term" to it - will ignore it for now, but in case it means something, please do let me know

Yes, that is a typo.

Apr 11 '22 19:04 patrick-lloyd-ray

DMBA Long list of terms to add (kept this separate as its really long and clustered together (some are 'HAS PARALLEL', not sure what this means, but best to check for mappings before adding anything anyway):

HAS PARALLEL means (as I was using it) that the structure is parallel to some other structure that already exists in UBERON. e.g., central glial substance is parallel to or surrounds the central canal.

Apr 11 '22 19:04 patrick-lloyd-ray

Can we go through some of these on a call?

On Tue, Apr 12, 2022 at 3:52 AM Shawn Tan @.***> wrote:

I've changed the mapping for MBA_436 (columns of the fornix) to UBERON_0004680 (body of fornix - has exact synonym "columns of fornix") - it was previously mapped to body of fornix (UBERON_0004680) with "add term"

— Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/2384#issuecomment-1096566690, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGZRCDWLDA7HCLOB33TNITVEVIWZANCNFSM5SWNXLPA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Apr 12 '22 14:04 uberon

I think @lydiang would like to be in the loop here.

Apr 12 '22 17:04 patrick-lloyd-ray

For layers: general class with part relations to both

eg primary somatosensory area, barrel field, layer 1 Regional part of cerebral layer and part of "Primary somatosensory area, barrel field" and part of "layer 1"

Apr 13 '22 16:04 shawntanzk

@cmungall @patrick-lloyd-ray @lydiang @dosumis Would have been nice if we could use a BDS ontology call to discuss this, but the next 2 are holidays in the UK. Perhaps we could use part of the UBERON call on 25/04/22 to discuss this? For those who don't have the invite to it and would like to attend, please see agenda here for details: https://docs.google.com/document/d/1XvMbNvr0FEsdqGhg79BYCYEHSqUxRHMcvhbGizEAht8/edit#

Apr 14 '22 07:04 shawntanzk

@patrick-lloyd-ray - looking to start adding stuff to bridge file and want to provide provenance to the source of mapping. I'm guessing it isn't just you who looked at it and there isn't a easy way to separate who did what - Could we put source as allen institute using https://ror.org/03cpe7c52

Apr 14 '22 09:04 shawntanzk

Note to self: Not all that are "OK" in the mapping file are correctly mapped in bridge file Probably a better idea to robot template a whole new bridge file based on the spreadsheet

Example: MBA_594 is ok in sheet and rightly mapped to UBERON_0011179, but wrongly mapped to UBERON_0001880 in bridge

Apr 14 '22 11:04 shawntanzk

@tgbugs - this is the ticket. See this comment for meeting https://github.com/obophenotype/uberon/issues/2384#issuecomment-1098796442

Apr 14 '22 15:04 shawntanzk

Perhaps we could use part of the UBERON call on 25/04/22 to discuss this?

I can make the call on the 25th. If we need a separate call, then that would be fine as well.

Could we put source as allen institute using https://ror.org/03cpe7c52

Absolutely.

Apr 14 '22 15:04 patrick-lloyd-ray

I'll be there!

On Thu, Apr 14, 2022 at 8:20 AM Patrick Lloyd Ray @.***> wrote:

Perhaps we could use part of the UBERON call on 25/04/22 to discuss this?

I can make the call on the 25th. If we need a separate call, then that would be fine as well.

Could we put source as allen institute using https://ror.org/03cpe7c52

Absolutely.

— Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/2384#issuecomment-1099295360, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOI4CSIPFWA346ZOEWLVFAZVBANCNFSM5SWNXLPA . You are receiving this because you were mentioned.Message ID: @.***>

Apr 15 '22 02:04 cmungall

Bridge files generated from using xrefs through https://github.com/obophenotype/uberon/blob/master/src/scripts/make-bridge-ontologies-from-xrefs.pl

Apr 25 '22 13:04 shawntanzk

Differentiate provenance from those that came originally from the bridge file to those that come from the ABA experts. Original bridge - credit to Chris Mungall; Approved by experts using Allen Brain Institute ROR - using another annotation. @shawntanzk to pick whatever AP for now, and we can change this when we discuss further.

Apr 25 '22 17:04 shawntanzk

@patrick-lloyd-ray - just wondering what mapping changed like that mean? Should I map MBA_911 as equivalent to UBERON_0002618 instead of UBERON_0001644? Seems odd to map that way by name but I do understand that name and atlas is different.

superclass_name_linked	superclass_iri	subclass_name	subclass_iri	Analysis	Recommended Mapping
trochlear nerve	http://purl.obolibrary.org/obo/UBERON_0001644	trochlear nerve	http://purl.obolibrary.org/obo/MBA_911	gen	root of trochlear nerve	http://purl.obolibrary.org/obo/UBERON_0002618
vestibulocochlear nerve root	http://purl.obolibrary.org/obo/UBERON_0002731	vestibulocochlear nerve root	http://purl.obolibrary.org/obo/DMBA_17746	Verify	vestibulocochlear nerve	http://purl.obolibrary.org/obo/UBERON_0001648

Thanks

Also: vomeronasal nerve (MBA_949) is mapped to vomeronasal nerve (UBERON_0009121) - but it writes Add Term

Apr 27 '22 16:04 shawntanzk