search

BgeeDB / anatomical-similarity-annotations

Project hosting resources used for annotating relations of similarity between anatomical structures
Creative Commons Zero v1.0 Universal
2 stars 2 forks source link

Release 2015-09-22 #12

Open fbastian opened 8 years ago

fbastian commented 8 years ago

@ANiknejad Following errors were produced when generating the release files: 

Problem detected, unknown or deprecated Uberon IDs: 
UBERON:0006269

Problem detected, Uberon IDs annotated with a taxon there are not supposed to exist in: 
UBERON:0001105 - 32440
UBERON:0000989 - 8459
UBERON:0000989 - 8492
UBERON:0000989 - 8509

Explanations of non-existence for UBERON:0001105 in taxon 32440 (Chondrostei):

For UBERON:0000989 in taxa 8459, 8492, 8509 (all Sauria):

fbastian commented 8 years ago

Generated warnings: 

Potentially missing annotation(s)! There exist negative annotation(s) with no associated positive annotations in same taxon or in sub-taxa. Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0006866] in taxon IDs: [33213] - There is no corresponding positive annotation for the same taxon, or for any sub-taxon.
Potentially missing annotation(s)! There exist negative annotation(s) with no associated positive annotations in same taxon or in sub-taxa. Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0001052] in taxon IDs: [33213] - There is no corresponding positive annotation for the same taxon, or for any sub-taxon.

Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0001046] in taxon IDs: [33213]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0000992] in taxon IDs: [33208]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0003078] in taxon IDs: [7711]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0006722] in taxon IDs: [32524]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0003063] in taxon IDs: [7711]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0002165] in taxon IDs: [7711]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0000991] in taxon IDs: [33208]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0001555] in taxon IDs: [33213]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0000996] in taxon IDs: [32524]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0001675] in taxon IDs: [7711]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0000473] in taxon IDs: [33208]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0001893] in taxon IDs: [7711]

An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0000014 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0000014, UBERON:0002097], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0002097 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0000014, UBERON:0002097], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0000931 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0000100, UBERON:0000931], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0003381 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0003381, UBERON:0006567], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0006567 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0003381, UBERON:0006567], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0002048 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0002048, UBERON:0006860], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0003382 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0003382, UBERON:0006566], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0006566 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0003382, UBERON:0006566], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0002049 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0002049, UBERON:0007798], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0007798 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0002049, UBERON:0007798], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
ANiknejad commented 8 years ago

CL:0000064 - 7742 Vertebrata ciliated cell def: "A cell that has a filiform extrusion of the cell surface." [GOC:tfm]

literature reports a conserved origin as early as in Vertebrates, so annotated on Vertebrates, even if with medium confidence...what is wrong???

Cilia establish the vertebrate left-right (LR) axis and are integral to the development and function of the kidney, liver, and brain. Left-right asymmetry is established in the ciliated ventral node cells of the mouse. The chiral structure of the cilium provides a reference asymmetry to impose handed LR asymmetric development on the bilaterally symmetric vertebrate embryo. A ciliary mechanism of LR development is evolutionarily conserved, as ciliated organs essential to LR axis formation, called LR organizers, are found in other vertebrates, including rabbit, fish, and Xenopus.

ANiknejad commented 8 years ago

CL:0000362 name: epidermal cell no reason to be rejected on 33208 Metazoa

CL:0000021 name: female germ cell no reason to be rejected on 33208 Metazoa

fbastian commented 8 years ago

Sorry, this was actually a bug :/ I'll keep you posted when I'll run the generation again.

The warnings are correct, though.

fbastian commented 8 years ago

@ANiknejad, I updated my first post with "correct" errors :p Only 2 Uberon terms involved.

edit: updated with explanations of taxon constraints.

fbastian commented 8 years ago

I re-run the pipeline with last Uberon version, results are: 

Problem detected, unknown or deprecated Uberon IDs:
UBERON:0006269

Problem detected, Uberon IDs annotated with a taxon there are not supposed to exist in:
UBERON:0001105 - 32440
UBERON:0007145 - 8459
UBERON:0007145 - 8493
UBERON:0002402 - 8457
UBERON:0001103 - 8459
UBERON:0001103 - 8493
UBERON:0000989 - 8459
UBERON:0000989 - 8492
UBERON:0000989 - 8509
UBERON:0009133 - 8457
ANiknejad commented 8 years ago

UBERON:0005745 name: optic canal namespace: uberon alt_id: UBERON:0006269

I tried to correct in "similarity.tsv" (anatomical-similarity-annotations\release) respecting the defined format (cf https://github.com/BgeeDB/expression-annotations/wiki/TSV-file) but sounds like all the file would change just modifying this id, @fred could you try yourself? (I discarded the change I tried to do)

---> I will do it soon, no more problem to edit the file ANN

ANiknejad commented 8 years ago

Chondrostei Taxonomy ID: 32440 Inherited blast name: bony fishes AND UBERON:0001105 clavicle bone

how do you exclude this taxon? evidence is: DOI:10.1080/02724634.1984.10012024 Olsen PE, The skull and pectoral girdle of the parasemionotid fish Watsonulus eugnathoides from the Early Triassic Sakamena Group of Madagascar, with comments on the relationships of the holostean fishes. Watsonulus eugnathoides occupies a critical position within the Neopterygii of Patterson (1 973) because it shares two primitive characters with chondrosteans that are derived in other neopterygians. These are 1) unreduced clavicles, and 2) a preoperculum with a broad dorsal limb. Journal of Vertebrate Paleontology (1984)"

ANiknejad commented 8 years ago

@fbastian could you explain the taxon exclusion cited above? Thank you.

The clavicle first appears as part of the skeleton in primitive bony fish (WP)

(just to avoid spending time here if there is still some bug ;-) )

fbastian commented 8 years ago

UBERON:0001105 "clavicle bone" is_a UBERON_0003461 "shoulder bone" UBERON_0003461 "shoulder bone" has_part part_of UBERON_0016884 "shoulder joint" UBERON_0016884 "shoulder joint" part of UBERON:0001467 "shoulder" UBERON:0001467 "shoulder" only_in_taxon NCBITaxon:32523 "Tetrapoda"

ANiknejad commented 8 years ago

@fbastian are you sure this relation is correctly generated?

UBERON_0003461 "shoulder bone" has_part part_of UBERON_0016884 "shoulder joint"

I mean, UBERON:0003461 and UBERON:0016884 have no link in composite-metazoan.obo and ext.obo

I am wondering, because 'clavicle' was already reviewed by Uberon:

https://github.com/obophenotype/uberon/issues/103

fbastian commented 8 years ago

Opened a ticket: https://github.com/obophenotype/uberon/issues/1227

ANiknejad commented 8 years ago

UBERON:0007145 - 8459 UBERON:0007145 dome of diaphragm Taxonomy ID: 8459 Testudines

AND

UBERON:0001103 - 8459 UBERON:0001103 diaphragm

Error from the annotation: correction done by commenting lines 332 and 1947 (turtles - diaphragm AND dome of diaphragm) and creating new lines 336 and 1951 with information:

NOT 1329799 Archelosauria

(There are still automatic annotations related to 'diaphragm' not corrected so far)

ANiknejad commented 8 years ago

UBERON:0007145 - 8493 UBERON:0007145 dome of diaphragm Taxonomy ID: 8493 Crocodylidae

AND

UBERON:0001103 - 8493 UBERON:0001103 diaphragm

the above correction (previous post) consider that 'diaphragm' also appeared independently in crocodiles. Hovewer maybe we need a new class: 'diaphragmaticus'

see https://github.com/obophenotype/uberon/issues/1229

'crocodilians lack a muscular structure homologous or analogous to the mammalian diaphragm and a combination of three other muscular mechanisms power ventilation; namely, the intercostal, abdominal and diaphragmaticus muscles...The diaphragmaticus muscle of crocodilians is not homologous to the mammalian diaphragm (Gans, 1971; Klein and Owerkowicz, 2006) and its main function may have been non-respiratory (Uriona and Farmer, 2008) as crocodilian ancestors became secondarily adapted to life in water (Seymour et al., 2004). '

http://www.ncbi.nlm.nih.gov/pubmed/?term=22323207

ANiknejad commented 8 years ago

UBERON:0002402 - 8457 UBERON:0002402 pleural cavity Taxonomy ID: 8457 Sauropsida

AND

UBERON:0009133 - 8457 UBERON:0009133 pleuroperitoneal membrane Taxonomy ID: 8457 Sauropsida 'In most living diapsids (some lizards, snakes, crocodiles, and birds) as well as all mammals, additional folds of coelomic epithelium separate de paired pleural recesses from the rest of the pleuroperitoneal cavity. The coelom of these animals thus consists of four compartments: the pericardial cavity, two pleural cavities, and the peritoneal cavity. [...] In reptiles and birds, the folds separating the pleural cavities from the peritoneal cavity form the oblique septum. In mammals, the separation between the two pleural cavities and the peritoneal cavity develops by the pleuroperitoneal membranes, which push in from the dorsolateral body wall, and by other folds that extend laterally from the mesenteries and medially from the body wall to meet the pleuroperitoneal membranes.' ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.162-163

These annotations sound OK for me, sorry I am not able to find the problem

ANiknejad commented 8 years ago

UBERON:0000989 - 8459 UBERON:0000989 - 8492 UBERON:0000989 - 8509

UBERON:0000989 penis

your previous explanation (see earlier in the issue):

I guess, this relation should be discarded:

'All amniotes studied to date initiate external genital development with the formation of paired genital swellings. In mammals, archosaurs, and turtles, these swellings merge to form a single genital tubercle, the precursor of the penis and clitoris'

http://www.ncbi.nlm.nih.gov/pubmed/24960313

fbastian commented 8 years ago

UBERON:0002402 pleural cavity Taxonomy ID: 8457 Sauropsida

UBERON:0002402 "pleural cavity" luminal space of UBERON:0009778 "pleural sac"
UBERON:0009778 "pleural sac" has part UBERON:0000977 "pleura"
UBERON:0000977 "pleura" only_in_taxon NCBITaxon:40674 "Mammalia"

UBERON:0009133 pleuroperitoneal membrane Taxonomy ID: 8457 Sauropsida => No explanation, it's weird, let's wait for the other corrections to see what happens.

ANiknejad commented 7 years ago

@fbastian

I re-run the pipeline with last Uberon version, results are: Problem detected, unknown or deprecated Uberon IDs: UBERON:0006269 Problem detected, Uberon IDs annotated with a taxon there are not supposed to exist in: UBERON:0001105 - 32440 UBERON:0007145 - 8459 UBERON:0007145 - 8493 UBERON:0002402 - 8457 UBERON:0001103 - 8459 UBERON:0001103 - 8493 UBERON:0000989 - 8459 UBERON:0000989 - 8492 UBERON:0000989 - 8509 UBERON:0009133 - 8457

All these issues are commented in previous posts above. I consider I finished the review of these issues, please let me know if there is something else to do from my part. Chris had relaxed TC for the issues I reported to him, please see

https://github.com/obophenotype/uberon/issues/1230 https://github.com/obophenotype/uberon/issues/1231

vrechdelaval commented 6 years ago

I re-run the pipeline with last Uberon version, results are:

Problem detected, unknown or deprecated Uberon IDs: UBERON:0005641

Problem detected, Uberon IDs annotated with a taxon there are not supposed to exist in: UBERON:0007145 - 1329799 UBERON:0007145 - 8493 UBERON:0001103 - 1329799 UBERON:0001103 - 8493

ANiknejad commented 6 years ago

UBERON:0005641 obsolete otocyst epithelium consider: UBERON:0003051 ear vesicle

annotation on UBERON:0005641 was a Curator inference, so -> DISCARDED (annotation on UBERON:0003051 ear vesicle is already done in the annotation file)

Problem detected, Uberon IDs annotated with a taxon there are not supposed to exist in: UBERON:0007145 - 1329799 UBERON:0007145 - 8493 UBERON:0001103 - 1329799 UBERON:0001103 - 8493

reannotation done an new class:

UBERON:0036071 name: diaphragmaticus muscle

for crocodylian 'diaphragm' (analog to the mammalian UBERON:0001103 diaphragm) cut currently commited because UBERON:0036071 sounds not to be in the database, Valentine says

vrechdelaval commented 6 years ago

I re-run the pipeline with last Uberon version, results are: Problem detected, Uberon IDs annotated with a taxon there are not supposed to exist in: UBERON:0006435 - 8459 UBERON:0006435 - 8492 UBERON:0006435 - 8509 UBERON:0002200 - 88770 UBERON:4440011 - 32523 UBERON:4000173 - 32523 UBERON:4000175 - 32523

ANiknejad commented 6 years ago

UBERON:0006435 - 8459 Testudines UBERON:0006435 - 8492 Archosauria UBERON:0006435 - 8509 Squamata

UBERON:0006435 name: os penis intersection_of: part_of UBERON:0000989 ! penis relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia

there is no manual similarity annotation on this UBERON class, but instead on

UBERON:0000989 penis

---> inferred annotation

NOT | CIO:0000003 | High confidence assertion | 32524 | Amniota   | CIO:0000003 | High confidence assertion | 40674 | Mammalia   | CIO:0000003 | High confidence assertion | 8459 | Testudines   | CIO:0000003 | High confidence assertion | 8509 | Squamata   | CIO:0000003 | High confidence assertion | 8492 | Archosauria   | CIO:0000005 | low confidence from single evidence | 32524 | Amniota

and these annotation do not generate error, as 'penis' does not have UBERON taxon constraint

see similar problem with develops_from inference UBERON:0000989 "penis" develops_from UBERON:0005876 "undifferentiated genital tubercle"

https://github.com/obophenotype/uberon/issues/1230

UBERON:0002200 - 88770 Panarthropoda

UBERON:0002200 name: vasculature of head

----> inferred annotation

?????????

UBERON:4440011 - 32523 Tetrapoda

UBERON:4440011 paired fin lepidotrichium

---> inferred annotation

UBERON:4000173 - 32523 Tetrapoda

UBERON:4000173 pelvic fin lepidotrichium

---> inferred annotation

UBERON:4000175 - 32523 Tetrapoda

UBERON:4000175 pectoral fin lepidotrichium

---> inferred annotation

ANiknejad commented 6 years ago

Problem detected, Uberon IDs annotated with a taxon there are not supposed to exist in: UBERON:0006435 - 8459 UBERON:0006435 - 8492 UBERON:0006435 - 8509 UBERON:0002200 - 88770 UBERON:4440011 - 32523 UBERON:4000173 - 32523 UBERON:4000175 - 32523

1) UBERON:0006435 os penis is actually NOT allowed in taxons UBERON:0006435 - 8459 Testudines UBERON:0006435 - 8492 Archosauria UBERON:0006435 - 8509 Squamata cause it is a mammal organ (if any), so please follow Uberon taxon constraint defined in UBERON:0006435

relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia

2) UBERON:0002200 vasculature of head

as defined in Uberon, this class is tagged 'subset: vertebrate_core' and then NOT allowed to be reported on 88770 Panarthropoda (and any others sub-taxons such as 'Tardigrada')

3) UBERON:4440011 paired fin lepidotrichium UBERON:4000173 pelvic fin lepidotrichium UBERON:4000175 pectoral fin lepidotrichium

NOT present in 32523 Tetrapoda

----> So I agree with the reasoner 'Uberon IDs annotated with a taxon there are not supposed to exist in:'

vrechdelaval commented 6 years ago

@ANiknejad I re-run the pipeline with the Uberon version used in Bgee v14 (2016-07-14). Problem detected, Uberon IDs annotated with a taxon there are not supposed to exist in: UBERON:0004880 - 6340 UBERON:0002328 - 6340 UBERON:0011649 - 118072 UBERON:4000160 - 118072

This concerns recent annotations that I will comment on in the branch bgee_v14

entity entity name taxon ID taxon name date
UBERON:0004880, UBERON:0035148 chordamesoderm, presumptive axochord 6340 Annelida 2017-11-21
UBERON:0004880, UBERON:0035148 chordamesoderm, presumptive axochord 6340 Annelida 2017-11-21
UBERON:0004880, UBERON:0035148 chordamesoderm, presumptive axochord 6340 Annelida 2017-11-21
UBERON:0002328, UBERON:0035147 notochord, axochord 6340 Annelida 2017-11-21
UBERON:0002328, UBERON:0035147 notochord, axochord 6340 Annelida 2017-11-21
UBERON:0002328, UBERON:0035147 notochord, axochord 6340 Annelida 2017-11-21
UBERON:0002328, UBERON:0011288 notochord, stomochord 33511 Deuterostomia 2016-08-29
entity entity name taxon ID taxon name date
UBERON:0011649 levator operculi 118072 Coelacanthimorpha 2017-11-20
entity entity name taxon ID taxon name date
UBERON:4000160 anocleithrum 118072 Coelacanthimorpha 2017-05-23

Now, I have only warnings: the same as before (https://github.com/BgeeDB/anatomical-similarity-annotations/issues/12#issuecomment-143759906) and the following ones:

Potentially missing annotation(s)! There exist negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0009078] in taxon IDs: [9126] - There are also positive annotations in parent taxa for same HOM ID - Uberon ID, but some miss a corresponding negative annotation. Negative annotations potentially missing in taxa: [8825]
Potentially missing annotation(s)! There exist negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0001075] in taxon IDs: [117571] - There are also positive annotations in parent taxa for same HOM ID - Uberon ID, but some miss a corresponding negative annotation. Negative annotations potentially missing in taxa: [7776]

Potentially missing annotation(s)! There exist negative annotation(s) with no associated positive annotations in same taxon or in sub-taxa. Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0002227, UBERON:0013731] in taxon IDs: [8292] - There is no corresponding positive annotation for the same taxon, or for any sub-taxon.

Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0001103] in taxon IDs: [32524]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0007145] in taxon IDs: [32524]
Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:4000160] in taxon IDs: [1338369, 8287]

An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:2000633 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0002038, UBERON:2000633], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:2001427 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0005928, UBERON:2001427], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:4000172 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0002544, UBERON:4000172], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0015202 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0011765, UBERON:0015202], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: CTENO:0000033 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[CTENO:0000033, UBERON:0001245], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0013731 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0002227, UBERON:0013731], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0013477 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0005928, UBERON:0013477], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0002436 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0002436, UBERON:0014756], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0014756 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0002436, UBERON:0014756], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0002376 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0000948, UBERON:0002376], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0000024 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0000024, UBERON:0002102], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0035602 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0001049, UBERON:0035602], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0005305 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0005305, UBERON:0006870], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: CL:0000092 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[CL:0000092, CL:0000453], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
An annotation uses multiple entity IDs, but there is no annotation for the individual entity: CL:0000453 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[CL:0000092, CL:0000453], entityNames=null, ncbiTaxonId=0, taxonName=null, negated=false, cioId=null, cioLabel=null, supportingText=null, refId=null, refTitle=null, ecoId=null, ecoLabel=null, assignedBy=null, curator=null, curationDate=null]
ANiknejad commented 6 years ago

see issue https://github.com/obophenotype/uberon/issues/1392 where I ask for taxon release for both UBERON:0004880 chordamesoderm and UBERON:0002328 notochord

and issue https://github.com/obophenotype/uberon/issues/1393 where I complain about more general problem, how to deal with Uberon taxon constraints and new hypothesis of homology?

ANiknejad commented 6 years ago

Potentially missing annotation(s)! There exist negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0009078] in taxon IDs: [9126] - There are also positive annotations in parent taxa for same HOM ID - Uberon ID, but some miss a corresponding negative annotation. Negative annotations potentially missing in taxa: [8825] --> UBERON:0009078 pessulus

8825 Neognathae YES (medium confidence) 9126 Passeriformes NOT (low confidence) ... (lot of classes sister of Passeriformes) ... 137529 Philepittidae YES (high confidence) *** 81928 Eurylaimidae YES (high confidence)

To solve this warning (?), I added positive annotation (but still confidence is low...) on 9126 Passeriformes. Negative annotation on 8825 Neognathae is more difficult to do! To annotate all the sister branches of Passeriformes????

Potentially missing annotation(s)! There exist negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0001075] in taxon IDs: [117571] - There are also positive annotations in parent taxa for same HOM ID - Uberon ID, but some miss a corresponding negative annotation. Negative annotations potentially missing in taxa: [7776] --> UBERON:0001075 bony vertebral centrum

7776 Gnathostomata YES low confidence 7777 Chondrichthyes 7778 Elasmobranchii YES high confidence 117570 Teleostomi (117571 Euteleostomi) NOT medium confidence ** 7898 Actinopterygii YES high confidence 8287 Sarcopterygii YES high confidence

To solve this warning (?), I added an annotation NOT on 7776 Gnathostomata low confidence And missing annotation on Chondrichthyes ? TO DO

Potentially missing annotation(s)! There exist negative annotation(s) with no associated positive annotations in same taxon or in sub-taxa. Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0002227, UBERON:0013731] in taxon IDs: [8292] - There is no corresponding positive annotation for the same taxon, or for any sub-taxon. --> UBERON:0013731, UBERON:0002227 basilar papilla, spiral organ of cochlea

*32523 Tetrapoda 32524 Amniota YES 8292 Amphibia NOT 41666 Batrachia 8445 Gymnophiona

Missing annotations on Batrachia and Gymnophiona TO DO

ANiknejad commented 6 years ago

Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0001103] in taxon IDs: [32524] --> UBERON:0001103 diaphragm *32524 Amniota NOT 40674 Mammalia YES 1329799 Archelosauria NOT (but commented) * Archosauria 8493 Crocodylia YES (but commented) Dinosauria * 8459 Testudines YES (but commented)

(5 taxons annotated)

--> Does removing comment on 1329799 Archelosauria NOT solve the warning? So that all the sub-taxons of Amniota are annotated. And we should relax the comments on Crocodylia and Testudines too, I do not understand why we have to comment these lines @vrechdelaval So far I remove all the comments here. And missing annotation on Archosauria TO DO

Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0007145] in taxon IDs: [32524] --> UBERON:0007145 dome of diaphragm *32524 Amniota NOT 40674 Mammalia YES 1329799 Archelosauria NOT (but commented) * Archosauria 8493 Crocodylia YES (but commented) Dinosauria * 8459 Testudines YES (but commented)

(5 taxons annotated)

Issue identical to the one above, so I also de-comment the annotations. And missing annotation on Archosauria TO DO

Potentially missing annotation(s)! There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several). Negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:4000160] in taxon IDs: [1338369, 8287] --> UBERON:4000160 anocleithrum *8287 Sarcopterygii NOT 7894 Coelacanthiformes YES 1338369 Dipnotetrapodamorpha NOT 7878 Dipnoi YES Tetrapoda

Missing annotation on Tetrapoda TO DO

ANiknejad commented 6 years ago

Missing individual annotations for:

UBERON:2000633 caudal tuberculum UBERON:2001427 anterior naris UBERON:4000172 lepidotrichium UBERON:0015202 lymph heart CTENO:0000033 anal pore UBERON:0013731 basilar papilla UBERON:0013477 blowhole UBERON:0002436 primary visual cortex UBERON:0014756 Wulst UBERON:0002376 cranial muscle UBERON:0000024 forelimb wing UBERON:0035602 collar nerve cord UBERON:0005305 thyroid follicle CL:0000092 osteoclast CL:0000453 Langerhans cell

ANiknejad commented 6 years ago

https://github.com/obophenotype/uberon/issues/1229

https://books.google.ch/books?isbn=0444634959 'Turtles and crocodilians have a diaphragmaticus muscle. However, neither the diaphragmaticus muscle of turtles, nor the diaphragmaticus muscle of crocodiles, nor the mammalian diaphragm are homologous structures.

I re-open this issue for Chris, because 'diaphragmaticus' has currently a definition restricted to Crocodylians, while Turtles have a 'diaphragmaticus', even if not homologous to the one of Crocodylians, but Uberon is not supposed to create classes based on homology relationships, but on anatomical structure, right @fbastian ?

fbastian commented 6 years ago

Well, it depends, Uberon often tries to be consistent evolution-wise, unless it really complicates the ontology too much I guess. Report your information and we will see what they decide to do.