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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, March 2018 (continue issue 25) #27

Open ANiknejad opened 6 years ago

ANiknejad commented 6 years ago

New list after closing issue #25

1.- 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.- 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.- 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.- 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.- 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.- 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.- 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.- 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]

9.- 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]

10.- 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]

11.- 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]

12.- 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]

13.- 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]

14.- 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]

15.- 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]

16.- 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]

17.- 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.- 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]

19.- 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]

20.- 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]

21.- 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]

22.- 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]

23.- 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]

24.- 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]

25.- 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]

26.- 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]

27.- 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]

28.- 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.- 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]

For a review of 'digit' homology UBERON:0002544, see these papers:

https://www.ncbi.nlm.nih.gov/pubmed/26605062

https://www.ncbi.nlm.nih.gov/pubmed/27994123

https://www.ncbi.nlm.nih.gov/pubmed/?term=12455618

https://www.biorxiv.org/content/early/2017/12/05/224147

and this discussion from 2014 (sic!) with Chris, here attached Re_ digits and homology - Anne Niknejad.pdf

linked to issue: https://github.com/obophenotype/uberon/issues/420

also see https://github.com/obophenotype/uberon/commit/3df47ebb3782f37d36a3765f3b2d47c9a6b44f72