duplicate human entries in the GO database

[kltm]

From @ValWood on June 29, 2018 11:29

We still have dupliciate entries in the GO database, which makes analyses difficult

These 15 identifiers were found to be ambiguous: ATP6AP2 CALM1 EIF3F GABARAP HIST1H2AI HOXD4 IDS KLK9 MED17 MUC21 NSG1 PI4K2B SUPT3H TMSB15B TRAPPC2L

ATP6AP2

and an unreviewed Trembl entry?
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:A0A1C7CYW4
and the annotated swiss prot entry
https://www.uniprot.org/uniprot/O75787

Calm1, the uniprot entry
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P0DP23
and an unannotated PR? entry
http://amigo.geneontology.org/amigo/term/PR:000004978

Can we get rid of the duplicates?
How do they get in?

Copied from original issue: geneontology/helpdesk#139

[kltm]

From @ValWood on June 29, 2018 11:30

FYI @Antonialock

[kltm]

I'm not quite sure what the question here is. For example, "GABARAP" is a symbol coming in from UniProt, MGI, and RGD. Symbols are quite often duplicates, which is why many services use namespaced identifiers or filtering mechanisms to isolate the actual entity they want.

[kltm]

From @ValWood on July 2, 2018 20:7

These are duplicate human entries.
We should only have one entry per GP in GO.

[kltm]

Human symbol "GABARAP":
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:O95166
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:H6UMI1

[kltm]

@ValWood You'd consider the above to be the same entity?
https://www.uniprot.org/uniprot/O95166
https://www.uniprot.org/uniprot/H6UMI1

[kltm]

From @ValWood on July 2, 2018 20:56

Yes,

https://www.uniprot.org/uniprot/O95166
https://www.uniprot.org/uniprot/H6UMI1
are the same entity.
Now I look more closely one is unreviewed, so it shouldn't get into GO?

Some might be exact duplicates at different loci (calmodulin histones and elongation factors), but these should be distinguished by having different names.

I think its a question for UniProt...

[kltm]

From @ValWood on July 2, 2018 20:58

So MED17, there is only one copy in the human genome, but we have

http://amigo.geneontology.org/amigo/gene_product/UniProtKB:A0A1W2PRB8
and
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:A0A1W2PRB8

http://amigo.geneontology.org/amigo/gene_product/UniProtKB:Q9NVC6
in GO

[kltm]

From @ValWood on July 2, 2018 21:2

I know it is only a small number (now), it is much improved, but we should find out what the problem is with the ingest that makes this possible. Presumably there is only one entry in reference proteomes. It's really really important to represent the human proteome uniquely and correctly for analysis.

[kltm]

From @cmungall on July 2, 2018 21:58

I think you meant this as the 2nd URL

http://amigo.geneontology.org/amigo/gene_product/UniProtKB:Q9NVC6

(which is the correct one)

This is how we get it from GOA:

curl -s -L ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/goa_human.gaf.gz | gzip -dc | grep MED17

e.g.

UniProtKB       A0A1W2PRB8      MED17           GO:0003712      GO_REF:0000002  IEA     InterPro:IPR019313      F       Mediator of RNA polymerase II transcription subunit 17  MED17|MED17     protein taxon:9606      20180616        InterPro
UniProtKB       A0A1W2PRB8      MED17           GO:0006351      GO_REF:0000038  IEA     UniProtKB-KW:KW-0804    P       Mediator of RNA polymerase II transcription subunit 17  MED17|MED17     protein taxon:9606      20180616        UniProt         
UniProtKB       A0A1W2PRB8      MED17           GO:0006357      GO_REF:0000002  IEA     InterPro:IPR019313      P       Mediator of RNA polymerase II transcription subunit 17  MED17|MED17     protein taxon:9606      20180616        InterPro                
UniProtKB       A0A1W2PRB8      MED17           GO:0016592      GO_REF:0000002  IEA     InterPro:IPR019313      C       Mediator of RNA polymerase II transcription subunit 17  MED17|MED17     protein taxon:9606      20180616        InterPro                
UniProtKB       Q9NVC6  MED17           GO:0003712      PMID:10198638   IDA             F       Mediator of RNA polymerase II transcription subunit 17  MED17|MED17|ARC77|CRSP6|DRIP77|DRIP80|TRAP80    protein taxon:9606      20030822        UniProt         
UniProtKB       Q9NVC6  MED17           GO:0003712      PMID:12218053   IDA             F       Mediator of RNA polymerase II transcription subunit 17  MED17|MED17|ARC77|CRSP6|DRIP77|DRIP80|TRAP80    protein taxon:9606      20030822        UniProt         
UniProtKB       Q9NVC6  MED17           GO:0003713      PMID:12037571   IDA             F       Mediator of RNA polymerase II transcription subunit 17  MED17|MED17|ARC77|CRSP6|DRIP77|DRIP80|TRAP80    protein taxon:9606      20101104        MGI             
[snip]

@tonysawfordebi and @alexsign can you take a look (I assigned you Alex, but Tony can reassign to himself if appropriate)

@dougli1sqrd and @pgaudet should we have a soft check / warning for >1 ID with the same symbol in a species? It would be useful to have this kind of reporting information up-front.

[kltm]

From @ValWood on July 2, 2018 22:4

should we have a soft check / warning for >1 ID with the same symbol in a species?

yes please, that would be a useful QC check

[kltm]

From @selewis on July 3, 2018 3:30

@chris Mungall [email protected]
Not sure if this is relevant, but I know in PANTHER there is a many2many
relationship between genes and proteins (though never both at once, just

1gene to 1 protein, or >1 protein to a gene)

-S

[kltm]

From @ValWood on July 3, 2018 6:5

found it
pantherdb/db-PAINT#1

[kltm]

From @tonysawfordebi on July 3, 2018 7:35

According to the data that we get from UniProt, both Q9NVC6 (Swiss-Prot) and A0A1W2PRB8 (TrEMBL) are canonical entries in the human GCRP, and they both have MED17 as the gene name, which doesn't seem right. I'll raise this with UniProt.

[kltm]

From @ValWood on July 3, 2018 7:41

Proteins nearly good, RNA's, same issues looming
geneontology/amigo#511
I filed this on the AmiGO tracker, because that's where I saw the problem. But it's clearly the wrong place.
Who would be the correct person for this part of the pipeline?
geneontology/amigo#511

[kltm]

From @tonysawfordebi on July 3, 2018 7:57

I just checked the list of genes from the top of this thread, and this is what I found:

Gene Name	Entry	Type
ATP6AP2	O75787	Swiss-Prot
ATP6AP2	A0A1C7CYW4	TrEMBL
CALM1	P0DP23	Swiss-Prot
EIF3F	O00303	Swiss-Prot
GABARAP	O95166	Swiss-Prot
GABARAP	H6UMI1	TrEMBL
HOXD4	P09016	Swiss-Prot
HOXD4	A0A087WSZ3	TrEMBL
IDS	P22304	Swiss-Prot
IDS	B3KWA1	TrEMBL
KLK9	Q9UKQ9	Swiss-Prot
KLK9	Q2XQG4	TrEMBL
MED17	Q9NVC6	Swiss-Prot
MED17	A0A1W2PRB8	TrEMBL
MUC21	Q5SSG8	Swiss-Prot
MUC21	A0A0G2JKD1	TrEMBL
MUC21	A0A140T8X8	TrEMBL
NSG1	P42857	Swiss-Prot
PI4K2B	Q8TCG2	Swiss-Prot
PI4K2B	G5E9Z4	TrEMBL
SUPT3H	O75486	Swiss-Prot
TMSB15B	P0CG35	Swiss-Prot
TMSB15B	A0A087X1C1	TrEMBL
TRAPPC2L	Q9UL33	Swiss-Prot
TRAPPC2L	H3BP13	TrEMBL

So, it appears that there's no ambiguity as far as CALM1, EIF3F, NSG1, and SUPT3H are concerned (there's only one canonical entry in the GCRP), but for the others there definitely appears to be something amiss (particularly MUC21).

[kltm]

From @ValWood on July 3, 2018 8:1

For CALM1 in AmiGO I see

http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P0DP23
and
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P62158

[kltm]

From @ValWood on July 3, 2018 8:3

For NSG1
I see
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:A0A0A6YYJ2
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P42857

[kltm]

From @tonysawfordebi on July 3, 2018 8:7

This is what we have (taken from UniProt):

Gene	Entry	Type	Proteome	Canonical Entry
CALM1	P0DP23	Swiss-Prot	Canonical
CALM1	B4DJ51	TrEMBL	none
CALM1	G3V479	TrEMBL	Isoform	P0DP23
CALM1	E7ETZ0	TrEMBL	Isoform	P0DP23
CALM1	Q96HY3	TrEMBL	Isoform	P0DP23
CALM1	M0QZ52	TrEMBL	Isoform	P0DP23
CALM1	G3V226	TrEMBL	Isoform	P0DP23
CALM1	G3V361	TrEMBL	Isoform	P0DP23
EIF3F	O00303	Swiss-Prot	Canonical
EIF3F	A0A1W2PP79	TrEMBL	Isoform	O00303
EIF3F	E9PQV8	TrEMBL	Isoform	O00303
EIF3F	B3KSH1	TrEMBL	none
EIF3F	B4DMT5	TrEMBL	none
EIF3F	H0YDT6	TrEMBL	Isoform	O00303
NSG1	P42857	Swiss-Prot	Canonical
NSG1	A0A0A6YYJ2	TrEMBL	Isoform	P42857
SUPT3H	O75486	Swiss-Prot	Canonical
SUPT3H	Q5VWT9	TrEMBL	Isoform	O75486
SUPT3H	B4E1H0	TrEMBL	Isoform	O75486
SUPT3H	Q5U608	TrEMBL	none
SUPT3H	A0A024RD67	TrEMBL	none

[kltm]

From @ValWood on July 3, 2018 8:8

actually these are different proteins, with the same name. How does that happen?
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:A0A0A6YYJ2
Neuron-specific protein family member 1

http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P42857
Neuronal vesicle trafficking-associated protein 1

[kltm]

From @ValWood on July 3, 2018 8:15

CALM1 https://www.uniprot.org/uniprot/P62158 is obsolete

[kltm]

From @cmungall on July 3, 2018 16:27

I filed this on the AmiGO tracker, because that's where I saw the problem. But it's clearly the wrong place. Who would be the correct person for this part of the pipeline?

In this case it's inputs to the pipeline rather than the pipeline itself, and Tony is already on it. In general I would say the go-annotations tracker is good for coordinating with any contributing group about their annotations. helpdesk always fine for triaging, and I suggest keeping this discussion here to avoid breaking history.

[kltm]

From @dougli1sqrd on July 3, 2018 18:18

@cmungall Yeah we could do something like that. So, the check would have to find different gene product ids that have the same label? Do we have labels in the RDF for gene products? I can take a look.

[kltm]

@cmungall As whole tickets are ported, including comments, there would be no break in history.

@dougli1sqrd symbols are not globally unique; in fact, occasionally not locally either--it may be worth asking whether there should be a mechanism per-species.

[kltm]

Looks like I won't be moving it: google/github-issue-mover#128 (comment)

[cmungall]

Looks like discussion has continued in original ticket, so closing this rather than forking discussion

[pgaudet]

I think this is fixed?