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BgeeDB / anatomical-similarity-annotations

Project hosting resources used for annotating relations of similarity between anatomical structures
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WARN org.bgee.pipeline.annotations.SimilarityAnnotation, January 2018 #25

Closed ANiknejad closed 6 years ago

ANiknejad commented 6 years ago

(to continue issue #12 in an updated way..)

ALL WARNINGS as given by Valentine 22KB Plain Text snippet created on January 16, 2018. This file is private.

1.- 18:53:14.389 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1682 checkAnnotations - Potentially missing annotation(s)! There exist negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0002544] in taxon IDs: [32524] - 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: [32523]

2.- 18:53:14.390 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1682 checkAnnotations - 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]

3.- 18:53:14.494 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1697 checkAnnotations - 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.

4.- 18:53:14.494 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1697 checkAnnotations - 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.

5.- 18:53:14.494 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1697 checkAnnotations - 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.

6.- 18:53:14.593 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

7.- 18:53:14.593 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

8.- 18:53:14.594 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

9.- 18:53:14.594 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

10.- 18:53:14.594 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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:0002544] in taxon IDs: [32524]

18:53:14.594 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

18:53:14.594 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

18:53:14.594 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

18:53:14.594 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

18:53:14.594 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

18:53:14.595 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

18:53:14.595 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

18:53:14.595 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

18:53:14.595 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

18:53:14.595 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

18:53:14.595 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

22.- 18:53:14.597 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

23.- 18:53:14.597 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

24.- 18:53:14.597 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

25.- 18:53:14.597 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

26.- 18:53:14.598 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

27.- 18:53:14.598 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

28.- 18:53:14.598 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

29.- 18:53:14.598 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

30.- 18:53:14.599 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

31.- 18:53:14.599 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

32.- 18:53:14.599 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

33.- 18:53:14.599 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0011288 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0002328, UBERON:0011288], 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]

34.- 18:53:14.600 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

35.- 18:53:14.600 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

36.- 18:53:14.600 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

37.- 18:53:14.600 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

38.- 18:53:14.600 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0011288 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0002328, UBERON:0011288, UBERON:0035147], 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]

39.- 18:53:14.600 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

40.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

41.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

42.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

43.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

44.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

45.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

46.- 18:53:14.602 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

47.- 18:53:14.602 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

48.- 18:53:14.602 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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 6 years ago

1.- 18:53:14.389 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1682 checkAnnotations - Potentially missing annotation(s)! There exist negative annotation(s) for HOM ID - Uberon ID: HOM:0000007 - [UBERON:0002544] in taxon IDs: [32524] - 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: [32523]

UBERON:0002544 digit negative annotation on 32524 | Amniota also positive annotations in parent Tetrapoda Negative annotations potentially missing in taxa: [32523] Tetrapoda

-> 'negative annotation on 32524 | Amniota' is a recent (2017) evidence (low confidence) challenging digit homology among Amniota, which is so far supposed (as far as I understand) to be accepted because digit homology on Tetrapoda is accepted (see evidence on Tetrapoda). I now added positive annotation on Amniota (medium confidence), instead of adding a fake negative annotation on Tetrapoda.

ANiknejad commented 6 years ago

2.- 18:53:14.390 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1682 checkAnnotations - 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 negative annotation on Passeriformes 9126 Negative annotations potentially missing in taxa: [8825] Neognathae

-> negative annotation on Passeriformes is low confidence, and there is also positive annotation (also low confidence) on Passeriformes, but positive annotation on Neognathae is medium confidence, so no reason to force a negative annotation on Neognathae

ANiknejad commented 6 years ago

3.- 18:53:14.494 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1697 checkAnnotations - 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:0002227, UBERON:0013731 UBERON:0013731, UBERON:0002227 basilar papilla, spiral organ of cochlea Negative annotation on Amphibia 8292

TETRAPODA | 32524 Amniota YES | 8292 Amphibia NOT

-> sounds to miss positive annotation on sub-taxons of Amphibia: Batrachia and Gymnophiona. But so far there is no annotation on Tetrapoda, and for me sounds here logical to also detect a potentially missing negative annotation on tetrapoda, while detecting potentially missing positive annotations on sub-taxons of Amphibia @vrechdelaval thoughts?

-> so far, no change done, and just considered as a warning (no literature information to support or discard 'UBERON:0013731, UBERON:0002227 basilar papilla, spiral organ of cochlea' homology in Batrachia and in Gymnophiona)

And also this book

https://link.springer.com/book/10.1007%2F978-1-4419-8957-4

"It is apparent that, while the amniote descendants of the stem reptiles all inherited a rather simple hearing papilla largely supported by the basilar papilla, the ancestors of modern amphibians developed to separate epithelia. As Smotherman and Narins describe in Chapter 6, it is possible, perhaps even probable, that strictly speaking, neither of these epithelia is homologous with the basilar papilla of amniotes (in spite of one of them bearing the same name). Nonetheless, as the authors also point out, all of these epithelia originate during ontogeny from one common epithelium with the vestibular sensory patch. The long history of the amphibians since the development of a tympanic middle ear was obviously accompanied by the evolution of different papillar specializations in different amphibian groups. In the anuran amphibians, these papillae are well enough developed, though small, to support sophisticated acoustic communication behaviors."

ANiknejad commented 6 years ago

4.- 18:53:14.494 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1697 checkAnnotations - 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.

UBERON:0006866 terminal part of digestive tract Negative annotation on 33213 Bilateria

-> so far there is no taxon constraint in UBERON:0006866 terminal part of digestive tract, but this information: property_value: curator_notes "this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future." xsd:string

So no way to put positive annotation on Cnidaria and Ctenophora (same taxon). Maybe to put positive annotation on Deuterostomia and Protosotmia (sub-taxon)

Note: there is currently a consensus to have 'mouth' opening homologous in Bilaterian, with 'anus' having independent evolution. See also https://github.com/obophenotype/uberon/wiki/The-digestive-tract

ANiknejad commented 6 years ago

5.- 18:53:14.494 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1697 checkAnnotations - 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.

UBERON:0001052 rectum

-> see 'UBERON:0006866 terminal part of digestive tract' at point 4.- above, closely related classes

ANiknejad commented 6 years ago

6.- 18:53:14.593 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

UBERON:0000992 ovary Negative annotation on 33208 Metazoa Positive annotations on 33213 Bilateria (the ONE sub-taxon) and on 7742 Vertebrata

-> not possible to add positive annotation on Cnidaria (another sub-taxon of Metazoa) because: "cnidarians cannot be said to have true ovaries and testes because they lack organs." https://www.britannica.com/animal/cnidarian -> possible to put annotation on Ctenophora...

(paper to check https://www.geneseo.edu/~bosch/Ctenophores_Older.pdf)

ANiknejad commented 6 years ago

7.- 18:53:14.593 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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 Negative annotation on 32524 Amniota Positive annotations on 40674 Mammalia (the ONE sub-taxon)

-> other potential sub-taxon of Amniota is Saurospida -> not possible to add annotation on Sauropsida (the other sub-taxon of Amniota) because 'diaphragm' is not a Sauropsida structure.

"Crocodylians, mammals and turtles have all evolved accessory respiratory muscles that reduce or eliminate their reliance on costal aspiration. These are all sometimes called diaphragm muscles, presumably by analogy with the mammalian diaphragm muscle, but they are not homologous structures."

Crocodylians and Turtles = Archelosauria (parent= Sauropsida) 'diaphragm' is not a crocodylia structure, we have requested and get a specific class (diaphragmaticus muscle), see annotation on UBERON:0036071

ANiknejad commented 6 years ago

8.- 18:53:14.594 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1711 checkAnnotations - 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]

UBERON:0003078 epibranchial placode Negative annotation on 7711 Chordata Positive annotations on 7742 Vertebrata

-> other potential sub-taxons are

-> 'Epibranchial placode homologues have also not been identified outside the vertebrates.' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552413/

-> Negative annotation on 7711 Chordata was to report the fact that epibranchianl placode is a vertebrate structure, it would be difficult to have a specific reference for Cephalochordata and/or Tunicata, but if needed for pipeline purpose, I could add it, however here this could be an example of generation of error by 'artificial' annotation, if Uberon would consider 'epibranchial placode' with a taxon constraint on Vertebrate

I understand that here I do not use NOT correctly..I do not have to put NOT on Chordata, just to conserve the positive annotation on Vertebrates, see issue #26

-> I now commented the line with NOT on Chordata

ANiknejad commented 6 years ago

Items 9.- up to 21.-, correspond to warning type 3 in issue #24:

3.- There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several).

-> this warning is the more easy to skip, depending on the number of sub-taxon

, I skip them now and go to warning type 4: (22.- up to 48.-.....very time consuming, brief review here)

22.-/23.- 18:53:14.597 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0000014 zone of skin UBERON:0002097 skin of body

this double annotation is just to 'link' both terms, because both terms may be/were used in expression data annotation (potential inconsistency of the annotation, to check!) but maybe not necessary? @fbastian

ANiknejad commented 6 years ago

24.- 18:53:14.597 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0000100, UBERON:0000931 | blastopore, proctodeum

-> added annotation on UBERON:0000931 for 50557 | Insecta (just copy/paste the evidence for the double annotation)

ANiknejad commented 6 years ago

25.- 18:53:14.597 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0002038, UBERON:2000633 | substantia nigra, caudal tuberculum

-> added annotation on UBERON:2000633 | caudal tuberculum for 32443 | Teleostei (just copy/paste the evidence for the double annotation)

ANiknejad commented 6 years ago

26.- 18:53:14.598 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:2001427 anterior naris on 7776 | Gnathostomata (as the common ancestor of all fishes) (just copy/paste the evidence for the double annotation)

-> added annotation UBERON:2001427 anterior naris

ANiknejad commented 6 years ago

27.- 18:53:14.598 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:4000172 lepidotrichium

-> added annotation of lepidotrichium on Actinopterygii with new reference PMID:20574421, but maybe needs further work here. see also https://onlinelibrary.wiley.com/doi/pdf/10.1080/00241160510013141 and 'Clock-face’ model of Thorogood (1991)

ANiknejad commented 6 years ago

28.- 18:53:14.598 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0015202 lymph heart

-> added annotation on Vertebrate (copy/paste)

ANiknejad commented 6 years ago

29.- and 30.- 18:53:14.598 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0006567, UBERON:0003381 | right ventricle myocardium, cardiac muscle of right ventricle

and

45.- and 46.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0006566, UBERON:0003382 | left ventricle myocardium, cardiac muscle of left ventricle

->I skip here, because multiple annotation was done to map expression annotation on both terms, because they should be identical actually, see https://github.com/BgeeDB/anatomical-similarity-annotations/issues/9 and comment from Chris:

ugh. I need to review notes & tickets for myocardium vs cardiac muscle tissue, there are some oddities here.

ANiknejad commented 6 years ago

31.- 18:53:14.599 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

CTENO:0000033 anal pore

-> added annotation on 10197 | Ctenophora

ANiknejad commented 6 years ago

32.- 18:53:14.599 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0013731 basilar papilla

-> added annotation on 8457 | Sauropsida (copy/paste)

ANiknejad commented 6 years ago

33.- and 38.- 18:53:14.599 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - An annotation uses multiple entity IDs, but there is no annotation for the individual entity: UBERON:0011288 - annotation: RawAnnotationBean [homId=HOM:0000007, homLabel=null, entityIds=[UBERON:0002328, UBERON:0011288], 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]

UBERON:0011288 stomochord

-> added annotation on 10219 | Hemichordata

ANiknejad commented 6 years ago

34.- 18:53:14.600 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0013477 blowhole

-> annotation added on 9722 | Odontoceti (single blowhole) and on9761 | Mysticeti (paired blowhole)

and an issue created for Chris

https://github.com/obophenotype/uberon/issues/1417

ANiknejad commented 6 years ago

35.- 18:53:14.600 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0002436 primary visual cortex

-> annotation done on 314146 | Euarchontoglires with new reference https://www.ncbi.nlm.nih.gov/pubmed/?term=25071460

ANiknejad commented 6 years ago

36.- 18:53:14.600 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0014756 Wulst

-> annotation done on 'birds' = Aves 8782 (copy/paste)

ANiknejad commented 6 years ago

37.- 18:53:14.600 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0002376 cranial muscle

-> annotation done on 7776 | Gnathostomata (new reference)

ANiknejad commented 6 years ago

39.- 18:53:14.600 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0000024 forelimb wing

-> added annotation on 32524 | Amniota (copy/paste)

ANiknejad commented 6 years ago

40.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0035602 collar nerve cord

-> annotation done on 10220 | Enteropneusta (copy/paste)

ANiknejad commented 6 years ago

41.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0005305 thyroid follicle

-> annotation done on 7742 | Vertebrata (identical ref but other evidence tag)

ANiknejad commented 6 years ago

42.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

CL:0000092 osteoclast

-> annotation done on 7742 | Vertebrata (identical ref but other evidence tag)

ANiknejad commented 6 years ago

43.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

CL:0000453 Langerhans cell

-> annotation done on 117571 | Euteleostomi (new reference)

ANiknejad commented 6 years ago

44.- 18:53:14.601 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0002048 lung

-> currently there is a commented annotation on 7776 | Gnathostomata, which sounds ok but it is commented because there is an issue, see #701 about taxon constraint, MAYBE TO REMOVE THE COMMENT HERE ?

ANiknejad commented 6 years ago

47.- and 48.- 18:53:14.602 [main] WARN org.bgee.pipeline.annotations.SimilarityAnnotation 1733 checkAnnotations - 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]

UBERON:0002049 vasculature relationship: part_of UBERON:0007798 ! vascular system

->this double annotation is just to 'link' both terms, because both terms may be/were used in expression data annotation (potential inconsistency of the annotation, to check!) but maybe not necessary? @fbastian

-> see also issue https://gitlab.isb-sib.ch/Bgee/expression-annotations/issues/17

ANiknejad commented 6 years ago

I close this issue, the status of the 'bgee_trans_similarity_annotations_edit.tsv' file as processed by Valentine on March 28 is the one for the current Bgee release. Next updates will be in issue #27