Annotation Conf. Call, February 14, 2012

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Agenda for Annotation Call

  • Update on communication mechanisms for changes to the GO taxon file. (Jane)
  • can we have a quick review of what is the preferred mechanism right now for feedback on PAINT annotations? (Kimberly)
  • new QC checks (Amelia) - see below
  • col 17 entry ID hierarchy - see below

Suggested QC Checks

Remove redundant GP info

The GP synonyms column must not contain information from other columns (GP symbol, GP name, DB object ID) as this info is redundant

e.g. incorrect:

1
DB 		2
DB object ID 		3
DB object symbol 		... 10
DB object name 		11
DB object synonym 		12
DB object type
PomBase SPCC1884.02 nic1 ... NiCoT heavy metal ion transporter Nic1 SPCC1884.02 | nic1 | SPCC757.01 gene


correct:

1
DB 		2
DB object ID 		3
DB object symbol 		... 10
DB object name 		11
DB object synonym 		12
DB object type
PomBase SPCC1884.02 nic1 ... NiCoT heavy metal ion transporter Nic1 SPCC757.01 gene


Col 17 ID format

Only one ID is allowed in col 17, and that ID should be formatted correctly and be from a database listed in GO.xrf_abbs.


Col 17 entities should always be related to the same col 2 entry

See the [docs on col 17 http://www.geneontology.org/GO.format.gaf-2_0.shtml#gene_product_form_id] for a refresher on col 17 contents

Where spliceforms exist, they must always have the same parent GP ID - unless you can think of any case in which this would not happen?

e.g. incorrect

1
DB 		2
DB object ID 		... 17
gene product form ID
MGI MGI:123456 ... UniProt:P0217K-3
MGI MGI:654321 ... UniProt:P0217K-3

Correct:

1
DB 		2
DB object ID 		... 17
gene product form ID
MGI MGI:123456 ... UniProt:P0217K-3
MGI MGI:123456 ... UniProt:P0217K-3


Possible exception:Some MODs assign protein identifiers based upon amino acid sequence. Thus, it's possible that, if column 2 contains a gene ID, then a given protein isoform ID in Column 17 could be associated with more than one gene ID. Groups could check their current annotations to see if this was the case for any existing annotations or if there are actually errors in their entries for either column 2 or column 17. If gene and protein identifiers from a database can easily be distinguished, then that might help determine when the QC check should be applied. --kimberly

Col 17 ID Hierarchy

Identifiers in column 17 come from a range of databases; propose creating a list of preferred databases from which the IDs are taken.

e.g. if the hierarchy were UniProtKB > VEGA > ENSEMBL 

If UniProtKB ID exists, use that
else if VEGA ID exists, use that
else if ENSEMBL ID exists, use that
else PANIC!

Different object types (protein, mRNA, etc.) may need to have different hierarchies.

DBs used so far:

Database GP form types # distinct IDs Assigned by
ENSEMBL protein 2464

BHF-UCL DFLAT GOC HGNC IntAct MGI RGD RefGenome UniProtKB

PR protein 3 MGI
protein_id protein 31 MGI
Protein_id [capitalization error] protein 1 MGI
RefSeq gene, protein 3215

BHF-UCL GOC IntAct MGI RGD RefGenome UniProtKB

TAIR RNA, gene_product, miRNA, protein, rRNA, snRNA, snoRNA, tRNA 45992

GOC IntAct RefGenome TAIR TIGR UniProtKB

UniProtKB protein 4601

BHF-UCL DFLAT GOC HGNC IntAct MGI PINC RGD RefGenome Roslin_Institute UniProtKB

UniPRotKB [capitalization error] protein 1 MGI
uniProtKB [capitalization error] protein 2 MGI
VEGA protein 13706

BHF-UCL DFLAT GOC HGNC IntAct MGI PINC RGD RefGenome Roslin_Institute UniProtKB

WB gene 4 WB
WP gene 6 WB
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