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XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and X. tropicalis.

Home Page: http://www.xenbase.org/

Dockerfile 0.05% Makefile 60.55% Shell 8.97% Batchfile 0.12% Python 22.95% Ruby 3.12% Scala 4.24%

xenopus-phenotype-ontology phenotype ontology xenopus xpo obofoundry

xenopus-phenotype-ontology's Introduction

Xenopus Phenotype Ontology

The Xenopus Phenotype Ontology represents and standardizes phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. It supports the annotation of phenotypes in Xenbase and is designed to integrate Xenopus data with genotype, phenotype, and disease data across species.

Browse and search XPO at the Ontology Lookup Service.

Versions

Stable release versions

The latest version of the ontology can always be found at: http://purl.obolibrary.org/obo/xpo.owl

Editors' version

Editors of this ontology should use the edit version: src/ontology/xpo-edit.owl

Contact

Please use this GitHub repository's issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.

Acknowledgements

This ontology repository was created using the Ontology Development Kit.

xenopus-phenotype-ontology's People

Contributors

Stargazers

Watchers

Forkers

standardgalactic erik-whiting dataxplora

xenopus-phenotype-ontology's Issues

Review current XPO with XenBase

@malcolmfisher103
@seger

we should set up a meeting soon to discuss next steps!

Obsolete 'bifurcated anterior-posterior axis' (XPO:0103469)

We would like the XPO term 'bifurcated anterior-posterior axis' (XPO:0103469) obsoleted as it is redundant with existing terms, such as 'abnormal(ly) open of neural tube (T)' (XPO:0115628) or 'duplicated anterior-posterior axis' (XPO:0115824).

Accidental duplicates

There are 4 duplicate cases that need to be purged from the id map;

id	iri
XAO:0001014-abnormallyDecreasedNumberOfAnatomicalEntity.tsv	http://purl.obolibrary.org/obo/XPO_0103597
XAO:0001014-abnormallyDecreasedNumberOfAnatomicalEntity.tsv	http://purl.obolibrary.org/obo/XPO_0103890
XAO:0003035-abnormallyDecreasedNumberOfAnatomicalEntity.tsv	http://purl.obolibrary.org/obo/XPO_0103589
XAO:0003035-abnormallyDecreasedNumberOfAnatomicalEntity.tsv	http://purl.obolibrary.org/obo/XPO_0103887
XAO:0003035-abnormallyIncreasedNumberOfAnatomicalEntity.tsv	http://purl.obolibrary.org/obo/XPO_0103627
XAO:0003035-abnormallyIncreasedNumberOfAnatomicalEntity.tsv	http://purl.obolibrary.org/obo/XPO_0103635
XAO:0003035-XAO:0004107-abnormallyIncreasedNumberOfAnatomicalEntityInLocation.tsv	http://purl.obolibrary.org/obo/XPO_0103413
XAO:0003035-XAO:0004107-abnormallyIncreasedNumberOfAnatomicalEntityInLocation.tsv	http://purl.obolibrary.org/obo/XPO_0103610

Steps to be taken:

pick one of the terms from each duplicate and obsolete it;
Remove the row corresponding to that obsoleted term from the id_map.tsv (in the src/patterns directory).
Make a pull request

Obsolete or remove 'malformed' terms.

We have decided that all malformed terms are essentially redundant with existing 'abnormal morphology' terms and should be obsoleted.

ID	name
XPO:0103678	'malformed Meckel's cartilage in left side'
XPO:0103677	'malformed cartilage element in head'
XPO:0103671	'malformed dorsal region'
XPO:0103658	'malformed left eye'
XPO:0103660	'malformed left inner ear'
XPO:0103662	'malformed left olfactory pit'
XPO:0103664	'malformed left optic vesicle'
XPO:0103669	'malformed left part of brain'
XPO:0103656	'malformed left part of branchial arch skeleton'
XPO:0103666	'malformed posterior region'
XPO:0103659	'malformed right eye'
XPO:0103661	'malformed right inner ear'
XPO:0103663	'malformed right olfactory pit'
XPO:0103665	'malformed right optic vesicle'
XPO:0103670	'malformed right part of brain'
XPO:0103657	'malformed right part of branchial arch skeleton'
XPO:0103679	'malformed tarsus in regenerating hindlimb'
XPO:0103668	'malformed ventral region'
XPO:0103667	'malformed ventral trunk'
XPO:0116035	'abnormal(ly) malformed of Meckel's cartilage in left (T)'
XPO:0116030	'abnormal(ly) malformed of brain in left (T)'
XPO:0116036	'abnormal(ly) malformed of branchial arch skeleton in left (T)'
XPO:0116027	'abnormal(ly) malformed of epithelium in foregut (T)'
XPO:0116031	'abnormal(ly) malformed of eye in left (T)'
XPO:0116026	'abnormal(ly) malformed of eye in lens (T)'
XPO:0116037	'abnormal(ly) malformed of eye in right (T)'
XPO:0116032	'abnormal(ly) malformed of inner ear in left (T)'
XPO:0116038	'abnormal(ly) malformed of inner ear in right (T)'
XPO:0116034	'abnormal(ly) malformed of olfactory pit in left (T)'
XPO:0116033	'abnormal(ly) malformed of optic vesicle in left (T)'
XPO:0116029	'abnormal(ly) malformed of ventral in trunk (T)'

abnormalMorphologyOfAnatomicalEntity labels

The label for the auto generated 'abnormal morphology of {tissue}' classes should be changed to read 'abnormal {tissue} morphology' instead.

There are some classes with multiple labels. Investigate!

These are probably a few classes that are obsoleted but still being generated by some patterns..

ERROR	multiple_labels	XPO:0107424	rdfs:label	abnormal morphology of ventro-lateral region 	
ERROR	multiple_labels	XPO:0107424	rdfs:label	obsolete abnormal morphology of ventro-lateral region	
ERROR	multiple_labels	XPO:0107425	rdfs:label	abnormal morphology of dorso-lateral region 	
ERROR	multiple_labels	XPO:0107425	rdfs:label	obsolete abnormal morphology of dorso-lateral region	
ERROR	multiple_labels	XPO:0115343	rdfs:label	abnormal(ly) fused with of somite (T)	
ERROR	multiple_labels	XPO:0115343	rdfs:label	obsolete abnormal(ly) fused with of somite (T)	
ERROR	multiple_labels	XPO:0115577	rdfs:label	abnormal(ly) fused with of hindlimb digit (T)	
ERROR	multiple_labels	XPO:0115577	rdfs:label	obsolete abnormal(ly) fused with of hindlimb digit (T)	
ERROR	multiple_labels	XPO:0115701	rdfs:label	abnormal(ly) fused with of anterior branchial crest (T)	
ERROR	multiple_labels	XPO:0115701	rdfs:label	obsolete abnormal(ly) fused with of anterior branchial crest (T)	
ERROR	multiple_labels	XPO:0115739	rdfs:label	abnormal(ly) fused with of hindlimb digit 2 (T)	
ERROR	multiple_labels	XPO:0115739	rdfs:label	obsolete abnormal(ly) fused with of hindlimb digit 2 (T)

Add term for 'abnormal heart looping'

Add ‘abnormal heart looping’ term based on GO:0001947. This should be a child of ‘abnormal heart development’ (XPO:0116462).

Make sure correct XAO is references in Pattern Generation Pipeline

Currently, some probably stale version on old XP draft:
https://github.com/obophenotype/xenopus-phenotype-ontology/blob/master/src/patterns/Makefile

Create new edematous terms.

Create terms for ‘edematous [XAO]' (PATO:0001450) for the following XAO terms.

Name	Term ID
Ventral trunk	XAO:0005260
Hindlimb	XAO:0003031
Forelimb	XAO:0003030
Eye	XAO:0000179
Brain	XAO:0000010
Spinal cord	XAO:0000020
Limb bud	XAO:0003161
Tail	XAO:0003026
Circulatory system	XAO:0001010
Coelom	XAO:0004521
epidermis	XAO:0000028

Grouping class for biological process phenotypes

We should create a sublass of Xenopus Phenotype called 'abnormal biological process' that is a grouping class for some orphans that are currently themselves subclasses of Xenopus Phenotype:

http://purl.obolibrary.org/obo/XPO_0103447
http://purl.obolibrary.org/obo/XPO_0103443
http://purl.obolibrary.org/obo/XPO_0103444
http://purl.obolibrary.org/obo/XPO_0103445
http://purl.obolibrary.org/obo/XPO_0103446
http://purl.obolibrary.org/obo/XPO_0103772
http://purl.obolibrary.org/obo/XPO_0103884
http://purl.obolibrary.org/obo/XPO_0103642

The following are also orphan subclasses of Xenopus Phenotype but they are biological processes that are located in an anatomical location, e.g. 'absent axon regeneration in optic nerve'. Should these not be connected to the relevant part of the XPO, e.g. an abnormality of optic nerve?

Obsolete or rename 'microphthalmia' term (XPO:0107252).

Reason for obsoleting XPO:0107252 -

There is already an existing term 'decreased size of the eye' (XPO:0103336), which we intend to have 'microphthalmia' as a synonym for. The existing 'microphthalmia' (XPO:0107252) has an exact synonym 'abnormally small globe', so perhaps we merely need to rename XPO:0107252 to 'abnormally small globe' and ensure it no longer has 'microphthalmia' associated with it as a synonym.

Including GO Development terms

The XPO is currently missing a lot of GO based Development terms.

For instance, the GO term "hindgut development" [GO:0061525] could be the basis for "abnormal hindgut development", and connected to the hindgut portion of the XPO.

In regards to how these development terms are used, it would be helpful to follow the "develops from" relationships in the XAO. For instance, hindgut develops from hindgut primordium. This means that any morphological or developmental terms for hindgut primordium "is_a" abnormal hindgut development. However this "develops_from" graph path can only go so far. For instance, the central endoderm develops into the foregut endoderm, hindgut primordium, and midgut primordium. So, saying that there was an abnormal central endoderm morphology does not guarantee that there is an abnormal hindgut development, as the morphological abnormality in the central endoderm could be isolated to a region that isn't fated to be hindgut.

GO also has morphogenesis terms, however I do not believe we would use them much. I believe we would use the higher level morphology term.

Notes:

Abnormal morphology and abnormal development are disjoint from each other. For instance, an abnormal development could include developmental delay, but the morphology is correct.

Remove terms ending in 'in left'.

Temporary terms incorporating ‘In left’ should be obsoleted as duplicates of existing terms. These are the result of overspecific curation of unilaterally injected embryos.

Term ID	Name
XPO:0115948	abnormal(ly) absent of eye in left (T)'
XPO:0103678	malformed Meckel's cartilage in left side'
XPO:0116031	abnormal(ly) malformed of eye in left (T)'
XPO:0115851	abnormal(ly) quality of heart in left atrium (T)'
XPO:0116071	abnormal(ly) duplicated of eye in left (T)'
XPO:0116030	abnormal(ly) malformed of brain in left (T)'
XPO:0115949	abnormal(ly) absent of inner ear in left (T)'
XPO:0116070	abnormal(ly) duplicated of brain in left (T)'
XPO:0115997	abnormal(ly) increased size of eye in left (T)'
XPO:0116082	abnormal(ly) bifurcated of hindlimb in left (T)'
XPO:0116072	abnormal(ly) duplicated of forelimb in left (T)'
XPO:0116032	abnormal(ly) malformed of inner ear in left (T)'
XPO:0115950	abnormal(ly) absent of olfactory pit in left (T)'
XPO:0116034	abnormal(ly) malformed of olfactory pit in left (T)'
XPO:0116033	abnormal(ly) malformed of optic vesicle in left (T)'
XPO:0116162	abnormal(ly) oblique orientation of heart in left atrium (T)'
XPO:0116035	abnormal(ly) malformed of Meckel's cartilage in left (T)'
XPO:0116036	abnormal(ly) malformed of branchial arch skeleton in left (T)'
XPO:0116000	abnormal(ly) decreased size of branchial arch skeleton in left (T)'

Obsolete 'abnormal(ly) incomplete structure of cartilage element in head (T)'(XPO:0116167) and its children

Obsolete 'abnormal(ly) incomplete structure of cartilage element in head (T)'(XPO:0116167) and its children (XPO:0115724, XPO:0116166, XPO:0115708, XPO:0115729, XPO:0115608, XPO:0115731, XPO:0115734).

These terms seem redundant with existing terms for the specific head cartilage elements.

Obsolete paralysed muscle in limb terms.

Obsolete 'abnormal(ly) paralysed of forelimb in muscle (T)'(XPO:0116039) and 'abnormal(ly) paralysed of hindlimb in muscle (T)'(XPO:0116040). These terms are redundant with the new requested terms for paralysed hindlimb and forelimb.

Obsolete term 'increased width of hindbrain' (XPO:0103672).

Obsolete term 'increased width of hindbrain' (XPO:0103672). This is now considered redundant to the more generic 'increased size' term.

Exclude some XAO classes from auto-generation of 'abnormal' classes

The following classes in the XAO do not need to have corresponding 'abnormal' or 'abnormal morphology' classes in the XPO:

XAO:1000000 Xenopus developmental stage and all of its subclasses (i.e. all classes that has_obo_namespace xenopus_developmental_stage).

XAO:0003185 anatomical direction and all of its subclasses.

XAO:0003003 unspecified

Several standard PATO terms to apply to most XAO terms.

We would like to have terms for

‘absent’(PATO:0000462),
‘mislocalized’(PATO:0000628),
‘decreased size’ (PATO:0000587)
‘increased size’ (PATO:0000586)

for all XAO terms that aren’t

‘anatomical directions’ (XAO:0003185) or its children,
‘anatomical entity in vitro’ (XAO:0003007) or its children,
‘anatomical axis’ (XAO:0005200) or its children, excepting 'anterior-posterior axis' (XAO:0005202),
‘anatomical side’ (XAO:0005205) or its children,
‘unspecified’ (XAO:0003003).
Add 'necrotic [XAO]' (PATO:0000647) terms for the same set above but including 'anterior-posterior axis' (XAO:0005202) in the terms to be excluded and excluding 'anatomical space' (XAO:0003190) and its children.

Get XPO ready for curation

Ids should be assigned automatically if left blank

Adjust and test this:
https://github.com/obophenotype/xenopus-phenotype-ontology/blob/master/src/scripts/assign_unique_ids.py

So that identifiers to not have to be assigned during manual curation.

Obsolete select 'region' terms.

There are several region based terms that are redundant in the XPO as they describe a discrete anatomical feature. They are useful to have in the XAO for gene expression but not in the XPO. Please find attached a tab separated txt file suggesting terms for obsoletion, appropriate replacement terms where applicable and indicating which terms would need new terms to provide a suitable replacement. Most of the terms that have no suggested replacement are for abstract anatomical regions that apply to almost any anatomical entity rather than being specific anatomical entities themselves.

Region_term_review.txt

New Cilium term requests

cilia XPO term requests.xlsx

Attached is a table with sets of XAO terms to be combined to create new XPO terms related to cilium.

(e.g.,(increased size) of (cilium) in the (left-right organizer))

There is a total of 14 combined new cilium terms that we request have the following PAT0 terms applied:

increased number (PATO_0000470 )
decreased number (PATO_0001997)
Absent (PATO_0000462)
mislocalised (PATO_0000628)
increased size (PATO_0000586)
decreased size (PATO_0000587)
abnormal (PATO_0000460) morphology (PATO_0000051)

The terms that have 'yes' marked in the 'has motile cilia' column should also have the following terms applied:

increased mobility (PATO_0000051)
decreased mobility (PATO_0002283)
immobile (PATO_0000300)

These should all have the parent term 'abnormal cilium'

Synonyms

increased mobility (increased motility)
decreased mobility (decreased motility)
immobile (immotile)

Obsolete all 'abnormal(ly) disorganized of [XAO] (T)' terms

Obsolete the following 'disorganized' terms. These terms seem redundant with other 'abnormal morphology' terms.

ID	name
XPO:0115438	abnormal(ly) disorganized of dermatome (T)'
XPO:0115443	abnormal(ly) disorganized of foregut (T)'
XPO:0115398	abnormal(ly) disorganized of intestine (T)'
XPO:0115375	abnormal(ly) disorganized of midgut (T)'
XPO:0115703	abnormal(ly) disorganized of motor neuron (T)'
XPO:0116045	abnormal(ly) disorganized of muscle fiber development in skeletal muscle (T)'
XPO:0116044	abnormal(ly) disorganized of myofibril assembly in heart (T)'
XPO:0115471	abnormal(ly) disorganized of myotome (T)'
XPO:0116046	abnormal(ly) disorganized of regenerating tail in neuron (T)'
XPO:0115344	abnormal(ly) disorganized of somite (T)'

Implement multi-anatomy sync pipeline

The idea is to have a way to create automatically phenotype classes from anatomy terms against patterns, but having the flexibility to blacklist by pattern. I was thinking of having a JSON file like this:

global
- blacklist_branch:
  - XAO:001
- blacklist_term:
  - XAO:003
pattern
- abnormalMorphologyOfAnatomicalEntity
  - blacklist_branch:
    - XAO:0010
  - blacklist_term:
    - XAO:0030

Which allows us to regulate what is coming in for each pattern. Global options are applied universally; local options (by pattern) are applied on top of the global options.

Obsolete 'blistered' terms

Obsolete the following blistered terms. Blistered terms are essentially synonymous with edematous terms.

Term ID	Name
XPO_0103788	abnormally blistered ventral trunk
XPO_0103782	abnormally blistered epidermis in trunk
XPO_0103787	abnormally blistered anterior dorsal fin

Grouping class for behavior phenotypes

We should create a sublass of Xenopus Phenotype called 'abnormal behavior' that is a grouping class for a couple of orphans that are currently themselves subclasses of Xenopus Phenotype:

http://purl.obolibrary.org/obo/XPO_0103783 - absent hatching behavior
http://purl.obolibrary.org/obo/XPO_0103784 - absent swimming

There will be more behavior classes added to the XPO in the future.

Obsoletion method: pattern

If term in manual pipeline: Remove term that should be obsoleted and add to patterns/data/manual/obsoleteTerm.tsv
if term in anatomy pipeline: Add term that should be obsoleted to anatomy blacklist (src/pattern/blacklist.txt) and add to patterns/data/manual/obsoleteTerm.tsv
(create obsolete.yaml with standard obsoletion fields)

Rename and merge patterns

decreasedNumberOfAnatomicalEntity.tsv
decreasedNumberOfAnatomicalEntityInLocation.tsv
increasedNumberOfAnatomicalEntity.tsv
increasedNumberOfAnatomicalEntityInLocation.tsv

@seger can you change those to abnormallyDecreasedNumberOfAnatomicalEntity.tsv etc (both ins spreadsheet and filenames)

Terms for dorsalization, ventralization, anterioralization and posterioralization.

We would like terms made for each of the following PATO qualities for the XAO term 'embryo' (XAO:0000113). We also want to create 'tadpole' terms but this will need to wait on the creation of a non stage 'tadpole' term in the XAO.

Term ID	Name
PATO:0000620	wholly dorsalized
PATO:0030005	partially dorsalized
PATO:0000636	wholly ventralized
PATO:0030007	partially ventralized
PATO:0000615	wholly anterioralized
PATO:0030004	partially anterioralized
PATO:0000630	wholly posterioralized
PATO:0030006	partially posterioralized

OBO release versions are not legal obo due to lack of declarations

OBO format files should declare subsets and synonym types.

Merging imports into the OBO release file has led to OBO files that lack some of these declarations.

e.g. xpo.obo

has

[Term]
id: CHEBI:24431
name: chemical entity
namespace: chebi_ontology
def: "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances." []
subset: 3_STAR
synonym: "chemical entity" EXACT [UniProt]

but the subset is not declared in the header

This prevents consumption by a number of legacy tools. I suspect this is a general ODK release issue, possibly stemming from ROBOT filtering. It may prevent adoption of complete ODK release pipeline by some resources using legacy OBO loaders.

CC @matentzn

Obsolete some edematous terms.

Obsolete 'abnormal(ly) edematous of ventral in trunk (T)'(XPO:0116050) and 'abnormal(ly) edematous of embryo in ventral (T)' (XPO:0116049). These will be redundant to other terms we wish to introduce.

Implement abnormalMorphologyOfPartOfAnatomicalEntity pattern

Probably uPheno.

Add term for 'abnormally paralyzed tail'.

Preferred term label

paralyzed tail

PATO:0000763^XAO:0003026

Suggested parent term

'abnormal tail' (XPO:0100726)

Obsolete several 'whole organism terms' for dorsalization/ventralization etc..

Obsolete existing ‘whole organism’ (XAO:0003004) terms for dorsalized, ventralized, posterioralized and anterioralized.

ID	Name
XPO:0115502	'abnormal(ly) wholly dorsalized of whole organism (T)'
XPO:0115504	'abnormal(ly) wholly ventralized of whole organism (T)'
XPO:0115501	'abnormal(ly) wholly anterioralized of whole organism (T)'
XPO:0115503	'abnormal(ly) wholly posterioralized of whole organism (T)'

These terms should be obsoleted as they are too general, a separate ticket will be raised to create replacement and additional terms for embryo and tadpole stages.

Tail curvature terms for obsoletion.

Please obsolete the following XPO terms, these are redundant to the more general terms 'abnormal morphology of tail’ and ‘abnormal bending of tail’ terms.

Term ID	Name
XPO_0115536	‘abnormal(ly) curved of tail (T)'
XPO_0115551	'abnormal(ly) kinked of tail (T)'
XPO_0115538	'abnormal(ly) delayed of tail (T)'
XPO_0115550	'abnormal(ly) deformed of tail (T)'
XPO_0115549	'abnormal(ly) immature of tail (T)'
XPO_0115545	'abnormal(ly) undulate of tail (T)'
XPO_0115365	'abnormal(ly) undulate of tail region (T)'
XPO_0115544	'abnormal(ly) truncated of tail (T)'
XPO_0115380	'abnormal(ly) truncated of tail bud (T)'
XPO_0103703	'abnormal bending of dorsal tail'
XPO_0115548	'abnormal(ly) duplicated of tail (T)'

Decide which terms should be obsoleted before first official release

Manually add synonyms

@matentzn Do we have a process or patterns for manually adding synonyms?

Obsolete XPO:0115644.

Obsolete or remove 'abnormal(ly) surrounding of retinal pigmented epithelium (T)' (XPO:0115644). This term seems to have been one of the EQE terms from our phenote legacy annotations that has not translated properly into the XPO.

Share table of annotations and map to XPO

@malcolmfisher103 will share the table of all annotations of the past year, and nico will import them and map them to XPO.

@seger The advantage is that @malcolmfisher103 and Christina can start curating against XPO, even if the hierarchy is not yet very uPheno conformant.

Was great meeting you guys!

Linking abnormal morphologies through developmental time

Because Xenopus uses a lot of early embryonic tissues, it is appropriate to have XPO terms such as abnormal optic field morphology. While this phenotype does not 100% guarantee an abnormal eye morphology (the final developmental tissue of the optic field), it "most likely causes" abnormal eye morphology. It would be helpful to have these terms linked somehow so that graph paths, and searches based on these graph paths will return these terms appropriately.

Additional neural crest cell migration terms.

Add terms for ‘decreased cell migration of branchial crest’, ‘decreased cell migration of hyoid crest’ and ‘decreased cell migration of mandibular crest’. ‘decreased cell migration of branchial crest’ should have children ‘decreased cell migration of anterior branchial crest’ and ‘decreased cell migration of posterior branchial crest’.

Term ID	Name
XAO:0000026	branchial crest
XAO:0000025	hyoid crest
XAO:0000024	mandibular crest
XAO:0000026	branchial crest
XAO:0004187	anterior branchial crest
XAO:0004188	posterior branchial crest

Additional Behavioral terms

Erik asked previously for some other behavioral terms that should be included in the behavior class (#30) besides swimming and hatching. From a review of the literature we identified several types of behavior associated with Xenopus phenotypes. Of these 8 have precise GO terms ...

ID	Name
GO:0071625	vocalization behavior
GO:0007619	courtship behavior
GO:0048266	behavioral response to pain
GO:0042048	olfactory behavior
GO:0007638	mechanosensory behavior
GO:0007632	visual behavior
GO:0007634	optokinetic behavior
GO:0035176	social behavior

We also identified 3 types of behavioral phenotypes that lack a clear GO term equivalent ...

Name
collision avoidance behavior/ visual avoidance behavior
schooling behavior
escape behavior

Can these non GO terms be added as is or is the correct procedure to request additional terms be added to GO and then use those new GO terms as the basis for XPO terms?

All of these that can be added should probably have 'abnormal behavior' and 'abnormal absence of behavior' terms. Sorry I didn't have these ready in time for the last release.

Create higher level gut looping term.

Create term for ‘abnormal coiling[PATO:0001794] of small intestine[XAO:0000130]’, should have synonym for ‘abnormal coiling of gut’. This should be a child of 'abnormal morphology of small intestine'(XPO:0101993).

Make ‘abnormally uncoiled small intestine’ (XPO:0115399) a child of ‘abnormal coiling of small intestine’. Should other existing terms such as 'abnormal(ly) uncoiled of external coil of the small intestine (T)' (XPO:0115765) and 'abnormal(ly) uncoiled of internal coil of the small intestine (T)' (XPO:0115767) be children of ‘abnormal coiling of small intestine’.

Obsolete truncation terms

We would like the following terms to be obsoleted as they are now redundant with existing decreased size terms.

Term ID	Name
XPO_0116042	'abnormal(ly) truncated of anterior in embryo (T)'
XPO_0115519	'abnormal(ly) truncated of head (T)'
XPO_0116043	'abnormal(ly) truncated of posterior in tail (T)'
XPO_0115544	'abnormal(ly) truncated of tail (T)'
XPO_0115380	'abnormal(ly) truncated of tail bud (T)'
XPO_0115530	'abnormal(ly) truncated of trunk (T)'

XPO:0115852 definition is broken

('inheres in' some 
(hindlimb and ('part of' some metacarpus)

According to XAO metacarpus is part of the hand, which makes it a forelimb. Cannot be both! Probably best to deprecate.