Release 2015-09-22 #12
Comments
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Generated warnings: |
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CL:0000064 - 7742 Vertebrata 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. |
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CL:0000362 CL:0000021 |
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Sorry, this was actually a bug :/ I'll keep you posted when I'll run the generation again. The warnings are correct, though. |
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@ANiknejad, I updated my first post with "correct" errors :p Only 2 Uberon terms involved. edit: updated with explanations of taxon constraints. |
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I re-run the pipeline with last Uberon version, results are: |
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UBERON:0005745 I tried to correct in "similarity.tsv" (anatomical-similarity-annotations\release) ---> I will do it soon, no more problem to edit the file ANN |
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Chondrostei how do you exclude this taxon? |
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@fbastian 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 ;-) ) |
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UBERON:0001105 "clavicle bone" is_a UBERON_0003461 "shoulder bone" |
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@fbastian 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: |
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Opened a ticket: obophenotype/uberon#1227 |
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UBERON:0007145 - 8459 AND UBERON:0001103 - 8459 Error from the annotation: NOT 1329799 Archelosauria (There are still automatic annotations related to 'diaphragm' not corrected so far) |
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UBERON:0007145 - 8493 AND UBERON:0001103 - 8493 the above correction (previous post) consider that 'diaphragm' also appeared independently in crocodiles. '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). ' |
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UBERON:0002402 - 8457 AND UBERON:0009133 - 8457 These annotations sound OK for me, sorry I am not able to find the problem |
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UBERON:0000989 - 8459 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' |
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UBERON:0002402 pleural cavity UBERON:0009133 pleuroperitoneal membrane |
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. |
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I re-run the pipeline with last Uberon version, results are: Problem detected, unknown or deprecated Uberon IDs: Problem detected, Uberon IDs annotated with a taxon there are not supposed to exist in: |
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UBERON:0005641 obsolete otocyst epithelium annotation on UBERON:0005641 was a Curator inference, so -> DISCARDED
reannotation done an new class: UBERON:0036071 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 |
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I re-run the pipeline with last Uberon version, results are: |
UBERON:0006435 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 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"
UBERON:0002200 ----> inferred annotation ?????????
UBERON:4440011 paired fin lepidotrichium ---> inferred annotation
UBERON:4000173 pelvic fin lepidotrichium ---> inferred annotation
UBERON:4000175 pectoral fin lepidotrichium ---> inferred annotation |
relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia
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') UBERON:4440011 paired 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:' |
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@ANiknejad I re-run the pipeline with the Uberon version used in Bgee v14 (2016-07-14). This concerns recent annotations that I will comment on in the branch
Now, I have only warnings: the same as before (#12 (comment)) and the following ones: |
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see issue and issue |
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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] *8825 Neognathae YES (medium 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! 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] *7776 Gnathostomata YES low confidence To solve this warning (?), I added an annotation NOT on 7776 Gnathostomata low confidence 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. *32523 Tetrapoda Missing annotations on Batrachia and Gymnophiona TO DO |
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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] (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 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] (5 taxons annotated) Issue identical to the one above, so I also de-comment the annotations. 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] Missing annotation on Tetrapoda TO DO |
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Missing individual annotations for: UBERON:2000633 caudal tuberculum |
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https://books.google.ch/books?isbn=0444634959 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 ? |
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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. |
@ANiknejad Following errors were produced when generating the release files:
Explanations of non-existence for UBERON:0001105 in taxon 32440 (Chondrostei):
For UBERON:0000989 in taxa 8459, 8492, 8509 (all Sauria):
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