View source for GAF Col17 GeneProducts

This page describes a proposal for a new [[GAF]] column, column 17. The proposal was ratified at the 2008 SLC GO meeting. However, it was not fully formulated at that time and was actually presented as a summary of problems with existing GAF practices. See  [[Annotation_of_Alternate_Spliceforms]] for this.

See http://www.geneontology.org/GO.format.gaf-2_0.shtml for the GAF 2.0 spec, which includes column 17.

== Summary of changes ==

# Addition of a NEW ''constraint'': the entity referenced by col 2 (DB_Object_ID) MUST be a '''canonical entity'''. In addition the GAF must be non-redundant with respect to canonical entities in a genome
# Addition of a NEW column: col 17, the '''spliceform''' column
# Change in meaning of an EXISTING column: col 12, the DB_Object_Type column now indicates the type of the entity in col 17. Previously it indicated the type of the entity in col 2.
# Addition of gaf-version header

Note that the first two changes are backwards compatible: software
built to the previous specification will not give erroneous
results. The first change essentially standardizes practice - many
groups already follow this constraint. The second change introduces a
new column, which can be ignored with only a loss of specificity. The
first change essentially standardizes practice - many groups already
follow this constraint.

However, the 3rd change introduces a change in meaning. As such, it is important ALL USERS ARE AWARE OF THIS CHANGE.

== Reason for changes ==

The full context is given in this document describing current practice in [[Annotation_of_Alternate_Spliceforms]].

To summarise, we needed to:

* standardize how groups were handling alternate splicing
* make it simpler to do gene-centric analyses
** remove the need for GAF consumers to map spliceform annotations to genes
** eliminate redundancy at the gene annotation level
* allow for the optional inclusion of annotation of alternate spliceforms

== Specification details ==

=== Col 2: Canonical entity ===

Previously, the DB_Object_ID, col2 (or rather cols1,2,3 as the GAF is a denormalized
table) could reference various kinds of entities: genes, proteins,
transcripts. GAFs could include separate entries for alternate
spliceforms - the only way to link these to the same gene would be to
use external ID mapping files.

Now, col 2 must always reference a '''canonical entity'''. In the
context of this specification, a canonical entity is either a gene OR
an abstract protein that has a 1-1 correspondence to a gene.

We anticipate that most MODs will (continue) to use gene identifiers
to reference canonical entities. UniProtKB will (continue) to provide
UniProtKB identifiers to reference canonical entities (TODO: add link
to UniProtKB docs stating how these abstract proteins are constructed).

This additional constraint essentially standardizes practice - many
groups already follow this constraint.

* ISSUE: there were some objections to the term ''canonical''. I am
not sure of a good alternative. "Normative Entity"? "Abstract Gene" (yuk)

=== Col 17: Spliceform ===

This is the meat of the proposal. A new column is introduced for
representing the specific spliceform of the gene product to which the
annotation in col 5 (GO ID) applies to.

This column is optional. Where no information is known about the
specific gene product spliceform, the column may be blank.

If this column is present, then the referenced spliceform must be a
gene product of the gene referenced in col 2 (if col 2 has a reference
to an abstract protein then the spliceform must be a gene product of
the gene that bears a 1-1 relation to the abstract protein)

The meaning of a line in a GAF now becomes:

* The entity in col 17 has either the function or localization indicated by the GO ID
* The gene referenced in col 2 encodes the gene product in col 17

This allows greater specificity in annotation. It is technically not a
change in semantics, as the gene in col 2 was always intended as a
proxy for referencing the gene product.

Thus col 17 can be ignored with only a loss of specificity, not correctness

The identifier used in col 17 must be a standard 2-part global identifier, see [[Identifiers]]

This identifier should be stable and dereferenceable in the usual
way. For example, if UniProtKB:QVCS5-1 is the spliceform ID then there
must be a stable UniProtKB record with this ID, with its own web page

Issues:

* Can this be blank? YES. If we don't know the isoform involved.
* Can the generic UniProtKB protein ID go in here? YES. If we don't know the specific isoform but we know the parent UniProtKB we can put this in here.
* Can non-UniProtKB IDs go in here?

=== 12: Type column : references spliceform ===

Previously, the type column referenced the type of the entity in col
2. Now it references the type of the spliceform entity in col 17.

* THIS IS A MAJOR CHANGE

IF col 17 is blank, col 12 MUST still be populated. The type will be the type of the entity believed to have the function/localization described (typically a protein)

* gene_product
** protein
** ncRNA
*** rRNA
*** tRNA
*** snRNA
*** snoRNA
*** ...or any subtype of ncRNA in SO

== Examples ==

=== UniProtKB example ===

OLD way:
   Column 1    2         3           4  5                Col 12
   UniProtKB   Q4VCS5    AMOT_HUMAN     GO:0031410  ...  protein  ...
   UniProtKB   Q4VCS5    AMOT_HUMAN     GO:0043532  ...  protein  ...
   UniProtKB   Q4VCS5-1  AMOT_HUMAN     GO:0043116  ...  protein  ...
   UniProtKB   Q4VCS5-2  AMOT_HUMAN     GO:0043532  ...  protein  ...
   UniProtKB   Q4VCS5-2  AMOT_HUMAN     GO:0043536  ...  protein  ...

NEW way:
   Column 1    2         3           4  5                Col 12        Col 17
   UniProtKB   Q4VCS5    AMOT_HUMAN     GO:0031410  ...  protein  ...
   UniProtKB   Q4VCS5    AMOT_HUMAN     GO:0043532  ...  protein  ...
   UniProtKB   Q4VCS5    AMOT_HUMAN     GO:0043116  ...  protein  ...  UniProtKB:QVCS5-1
   UniProtKB   Q4VCS5    AMOT_HUMAN     GO:0043532  ...  protein  ...  UniProtKB:QVCS5-2
   UniProtKB   Q4VCS5    AMOT_HUMAN     GO:0043536  ...  protein  ...  UniProtKB:QVCS5-2

== Issues ==

* col 17 - can it be left blank

== FAQ ==

=== What happened to column 16? ===

Column 16 has been reserved for [[Annotation_Cross_Products]] for some time now. It just so happens that col 17 will probably contain values prior to column 16, due to the complexity of the column 16 proposal

=== What goes in column 2? ===

Gene identifiers, except in the case of UniProtKB, who supply canonical protein IDs (these are essentially proxies for the gene)

=== How does this relate to the gp2protein file ===

the concatenation of col1 and col2 of the GAF (using ':') should have a match in col1 of the gp2protein file

=== What goes in col 12? ===

The type of the entity in col 17

=== What goes in col 12 if col 17 is blank? ===

* gene_product

=== What goes in col 17? ===

The DB:ID of the entity which has the function / participates in the process / localizes to the component.

[[Category:File Format‏‎]]