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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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ABA-Uberon bridge file updates #2384

Closed shawntanzk closed 1 year ago

shawntanzk commented 2 years ago

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

patrick-lloyd-ray commented 2 years ago

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

shawntanzk commented 2 years ago

@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

patrick-lloyd-ray commented 2 years ago

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.

shawntanzk commented 2 years ago

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)

shawntanzk commented 2 years ago

Terms to add (evolving list):

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.):

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

shawntanzk commented 2 years ago

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.

shawntanzk commented 2 years ago

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.

shawntanzk commented 2 years ago

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

shawntanzk commented 2 years ago

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

shawntanzk commented 2 years ago

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):

shawntanzk commented 2 years ago

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

shawntanzk commented 2 years ago

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
patrick-lloyd-ray commented 2 years ago

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.

patrick-lloyd-ray commented 2 years ago

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].

patrick-lloyd-ray commented 2 years ago

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.

patrick-lloyd-ray commented 2 years ago

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.

patrick-lloyd-ray commented 2 years ago

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.

patrick-lloyd-ray commented 2 years ago

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.

uberon commented 2 years ago

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: @.***>

patrick-lloyd-ray commented 2 years ago

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

shawntanzk commented 2 years ago

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"

shawntanzk commented 2 years ago

@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#

shawntanzk commented 2 years ago

@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

shawntanzk commented 2 years ago

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

shawntanzk commented 2 years ago

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

patrick-lloyd-ray commented 2 years ago

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.

cmungall commented 2 years ago

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: @.***>

shawntanzk commented 2 years ago

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

shawntanzk commented 2 years ago

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.

shawntanzk commented 2 years ago

@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

patrick-lloyd-ray commented 2 years ago

Should I map MBA_911 as equivalent to UBERON_0002618 instead of UBERON_0001644?

Yes, MBA_911 should be mapped to UBERON_0002618 because the synonyms for UBERON_0002618 more closely align with MBA_911 than UBERON_0001644 (i.e., MBA_911 is closer to 'trochlear nerve tract' or 'trochlear nerve fibers' than the entire nerve -- just a difference in atlas/ontology terminology, I believe, not any fundamental disagreement in structure).

MBA_911 is marked 'IVn' in this diagram, if that helps: image

For DMBA_17746, it's the converse: UBERON_0002731 is "Either of the two roots that come of the vestibulocochlear nerve." but the atlas has it slightly differently, so it's better mapped to UBERON_0001648. (in this diagram DMBA_17746 is marked as '8n'): image

Also, DMBA is developmental, so the mappings are often not straightforward. If you look at the MBA, it's more closely aligned with UBERON for that structure, I believe.

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

Hmm, the only thing I can think of is that vomeronasal nerve is not present in adult humans but present in adult macrosmatic mammals (mouse), so I think that's why our anatomists found issue there. But, I see there is a note on UBERON_0009121 to that effect, so I'll leave it up to you.

shawntanzk commented 2 years ago

thanks! thats super helpful :) will map accordingly

cmungall commented 2 years ago

I think if we resolve this issue

then some of this becomes easier

shawntanzk commented 2 years ago

@patrick-lloyd-ray could you help me go through these to make sure I've made the right decision - if not im happy to change them the other way around. Thanks!

MBA_634 (nucleus of the posterior commissure) was given ok for both diencephalic nucleus UBERON_0006569 and nucleus of the posterior commissure UBERON_0002711. I've picked nucleus of the posterior commissure UBERON_0002711.

MBA_1019 corticospinal tract, crossed is mapped to both corticospinal tract UBERON_0002707 and lateral corticospinal tract UBERON_0002589 - I have chosen lateral corticospinal tract UBERON_0002589 as that was a original verified mapping rather than one chosen from a gen status

DMBA_17773 lateral olfactory tract is mapped to both olfactory tract UBERON_0002265 and lateral olfactory stria UBERON_0001888. I have chosen lateral olfactory stria UBERON_0001888 as hat was a original verified mapping rather than one chosen from a gen status.

MBA_665 lateral olfactory tract, body is mapped to both olfactory tract UBERON_0002265 and lateral olfactory stria UBERON_0001888. I have chosen lateral olfactory stria UBERON_0001888 as hat was a original verified mapping rather than one chosen from a gen status.

MBA_105 superior olivary complex, medial part is mapped to both UBERON_0002782 medial superior olivary nucleus and UBERON_0002128 superior olivary complex. I have chosen UBERON_0002782 medial superior olivary nucleus as that was a original verified mapping rather than one chosen from a gen status.

MBA_212 main olfactory bulb, glomerular layer is mapped to both UBERON_0005377 olfactory bulb glomerular layer and UBERON_0023934 olfactory bulb main glomerular layer. I have chosen UBERON_0005377 olfactory bulb glomerular layer as it is mapped twice that way (as opposed to once the other way)

MBA_554 bed nuclei of the stria terminalis, anterior division, oval nucleus is mapped to both UBERON_0011176 oval nucleus of stria terminalis and UBERON_0001880 bed nucleus of stria terminalis . I have chosen UBERON_0011176 oval nucleus of stria terminalis as that was a original verified mapping rather than one chosen from a gen status.

MBA_149 paraventricular nucleus of the thalamus is mapped to both UBERON_0002708 posterior periventricular nucleus and UBERON_0001920 paraventricular nucleus of thalamus. I've chosen UBERON_0001920 paraventricular nucleus of thalamus as it is more similar.

DMBA_15999 posterolateral cortical amygdaloid area is mapped to both UBERON_0034999 posterolateral cortical amygdaloid nucleus and UBERON_0035001 posteromedial cortical amygdaloid nucleus. I have chosen UBERON_0034999 posterolateral cortical amygdaloid nucleus as that was an original verified mapping rather than one chosen from a gen status

MBA_578 bed nuclei of the stria terminalis, posterior division, principal nucleus is mapped to both UBERON_0001880 bed nucleus of stria terminalis and UBERON_0011178 principal nucleus of stria terminalis. I have chosen UBERON_0011178 principal nucleus of stria terminalis as that was an original verified mapping rather than one chosen from a gen status.

MBA_594 bed nuclei of the stria terminalis, posterior division, transverse nucleus is mapped to both UBERON_0011179 transverse nucleus of stria terminalis and UBERON_0001880 bed nucleus of stria terminalis. I have chosen UBERON_0011179 transverse nucleus of stria terminalis as that was an original verified mapping rather than one chosen from a gen status.

MBA_1028 corticospinal tract, uncrossed is mapped to both UBERON_0002760 ventral corticospinal tract and UBERON_0002707 corticospinal tract. I have chosen UBERON_0002760 ventral corticospinal tract as that was an original verified mapping rather than one chosen from a gen status.

DMBA_16926 cerebellar white matter is mapped to both UBERON_0002317 white matter of cerebellum and UBERON_0024045 white matter of the cerebellar cortex. I have chosen UBERON_0002317 white matter of cerebellum as it is mapped that way 3/4 times

DMBA_17749 accessory nerve root is mapped to both UBERON_0014615 accessory nerve root and UBERON_0002019 accessory XI nerve. I have chosen UBERON_0014615 accessory nerve root as it is more similar.

MBA_30 periventricular hypothalamic nucleus, anterior part is mapped to both UBERON_0002622 preoptic periventricular nucleus and UBERON_0014667 periventricular nucleus of the hypothalamus. I have selected (subclass part of) UBERON_0014667 periventricular nucleus of the hypothalamus as it is more similar.

MBA_436 columns of the fornix is mapped to both UBERON_0004680 column of fornix and UBERON_0004680 body of fornix. I have selected UBERON_0004680 column of fornix as it is more similar.

MBA_908 anterior commissure, temporal limb is mapped to both anterior commissure anterior part UBERON_0003039 and UBERON_0003043 posterior part of anterior commissure. I've remapped it to subclass part of UBERON:0000935 anterior commissure for safety

patrick-lloyd-ray commented 2 years ago

MBA_634 (nucleus of the posterior commissure) was given ok for both diencephalic nucleus UBERON_0006569 and nucleus of the posterior commissure UBERON_0002711. I've picked nucleus of the posterior commissure UBERON_0002711.

Sounds good!

MBA_1019 corticospinal tract, crossed is mapped to both corticospinal tract UBERON_0002707 and lateral corticospinal tract UBERON_0002589 - I have chosen lateral corticospinal tract UBERON_0002589 as that was a original verified mapping rather than one chosen from a gen status

Yes, that works.

DMBA_17773 lateral olfactory tract is mapped to both olfactory tract UBERON_0002265 and lateral olfactory stria UBERON_0001888. I have chosen lateral olfactory stria UBERON_0001888 as hat was a original verified mapping rather than one chosen from a gen status.

MBA_665 lateral olfactory tract, body is mapped to both olfactory tract UBERON_0002265 and lateral olfactory stria UBERON_0001888. I have chosen lateral olfactory stria UBERON_0001888 as hat was a original verified mapping rather than one chosen from a gen status.

Yep, that's fine.

MBA_105 superior olivary complex, medial part is mapped to both UBERON_0002782 medial superior olivary nucleus and UBERON_0002128 superior olivary complex. I have chosen UBERON_0002782 medial superior olivary nucleus as that was a original verified mapping rather than one chosen from a gen status.

Yes, UBERON_0002782 is right for that one.

MBA_212 main olfactory bulb, glomerular layer is mapped to both UBERON_0005377 olfactory bulb glomerular layer and UBERON_0023934 olfactory bulb main glomerular layer. I have chosen UBERON_0005377 olfactory bulb glomerular layer as it is mapped twice that way (as opposed to once the other way)

Yes, that makes sense to me.

MBA_554 bed nuclei of the stria terminalis, anterior division, oval nucleus is mapped to both UBERON_0011176 oval nucleus of stria terminalis and UBERON_0001880 bed nucleus of stria terminalis . I have chosen UBERON_0011176 oval nucleus of stria terminalis as that was a original verified mapping rather than one chosen from a gen status.

Yes, it should be UBERON_0011176.

MBA_149 paraventricular nucleus of the thalamus is mapped to both UBERON_0002708 posterior periventricular nucleus and UBERON_0001920 paraventricular nucleus of thalamus. I've chosen UBERON_0001920 paraventricular nucleus of thalamus as it is more similar.

Yes, should be UBERON_0001920.

DMBA_15999 posterolateral cortical amygdaloid area is mapped to both UBERON_0034999 posterolateral cortical amygdaloid nucleus and UBERON_0035001 posteromedial cortical amygdaloid nucleus. I have chosen UBERON_0034999 posterolateral cortical amygdaloid nucleus as that was an original verified mapping rather than one chosen from a gen status

Yes, that makes sense to me.

MBA_578 bed nuclei of the stria terminalis, posterior division, principal nucleus is mapped to both UBERON_0001880 bed nucleus of stria terminalis and UBERON_0011178 principal nucleus of stria terminalis. I have chosen UBERON_0011178 principal nucleus of stria terminalis as that was an original verified mapping rather than one chosen from a gen status.

Yes, that works.

MBA_594 bed nuclei of the stria terminalis, posterior division, transverse nucleus is mapped to both UBERON_0011179 transverse nucleus of stria terminalis and UBERON_0001880 bed nucleus of stria terminalis. I have chosen UBERON_0011179 transverse nucleus of stria terminalis as that was an original verified mapping rather than one chosen from a gen status.

Yes, that works too.

MBA_1028 corticospinal tract, uncrossed is mapped to both UBERON_0002760 ventral corticospinal tract and UBERON_0002707 corticospinal tract. I have chosen UBERON_0002760 ventral corticospinal tract as that was an original verified mapping rather than one chosen from a gen status.

Okay, that works.

DMBA_16926 cerebellar white matter is mapped to both UBERON_0002317 white matter of cerebellum and UBERON_0024045 white matter of the cerebellar cortex. I have chosen UBERON_0002317 white matter of cerebellum as it is mapped that way 3/4 times

Yes, UBERON_0002317 works best.

DMBA_17749 accessory nerve root is mapped to both UBERON_0014615 accessory nerve root and UBERON_0002019 accessory XI nerve. I have chosen UBERON_0014615 accessory nerve root as it is more similar.

Yes, UBERON_0014615 makes sense for this mapping. #298 might affect this but I'll defer to your design decisions.

MBA_30 periventricular hypothalamic nucleus, anterior part is mapped to both UBERON_0002622 preoptic periventricular nucleus and UBERON_0014667 periventricular nucleus of the hypothalamus. I have selected (subclass part of) UBERON_0014667 periventricular nucleus of the hypothalamus as it is more similar.

Yes, that makes sense to me.

MBA_436 columns of the fornix is mapped to both UBERON_0004680 column of fornix and UBERON_0004680 body of fornix. I have selected UBERON_0004680 column of fornix as it is more similar.

Okay, that's fine.

MBA_908 anterior commissure, temporal limb is mapped to both anterior commissure anterior part UBERON_0003039 and UBERON_0003043 posterior part of anterior commissure. I've remapped it to subclass part of UBERON:0000935 anterior commissure for safety

Okay, that's a good idea. Thanks, @shawntanzk!

shawntanzk commented 2 years ago

@patrick-lloyd-ray is sublaterodorsal nucleus (SLD) the same as sublaterodorsal tegmental nucleus? (from literature that's all I seem to be able to find and the acronym is the same)

patrick-lloyd-ray commented 2 years ago

Yes, they should be the same.

shawntanzk commented 2 years ago

Note to self: rhinocele is problematic as uberon obsoleted rhinencephalon (UBERON_0008981) with the reason: "Obsoleted because The term rhinencephalon has been used to describe different structures at different points in time.[ISBN 0-8493-8631-4]. May refer to: a specific structure in aves; a part of the brain involved with olfaction;" I'd imagine that the rhinocele will have the same issue. Consider mapping it as subclass of part of telencephalic ventricle (UBERON:0002285) instead

shawntanzk commented 2 years ago

@patrick-lloyd-ray - could you help me with the questions found in: https://docs.google.com/document/d/1DYiaGNa8KLZZRU7pxd9XL6YJwvXsap-JTs3g3tM4Meo/edit Feel free to answer directly on the google docs, thanks :)

patrick-lloyd-ray commented 2 years ago

Will do -- might take me a bit to get to them, but just ping me if anything needs immediate attention and I'll prioritize it.

github-actions[bot] commented 1 year ago

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

patrick-lloyd-ray commented 1 year ago

I'm fairly certain this can be closed.