Annotation Extension Relation:has direct input

Definition

Identifies an entity directly affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in a Molecular Function or Biological Process.

Comment

If the entity is indirectly bound/acted upon by the gene product that is the subject of an annotation, then the relation: has_indirect_input should be considered.

Synonyms

directly_localizes (NARROW)

has_direct_target (EXACT)

has_substrate (NARROW)

Child terms

• None

Scope of use

Domain

BFO:0000007 ! process (Biological Process or Molecular Function)

Range

ENTITY_UNION:0000005 ! chemical, gene product, or complex

Annotation Extension Usage Examples

Transcription factor binding to potential target sequences in vitro:

Statement from paper:

By performing gel electrophoretic mobility shift assays, we could detect efficient binding of ATF-2 to the elements found in the bec-1 and lgg-1 promoters (Fig. 5C).

(Note that binding to lin-48 is also reported as a positive control).

Gene Name (col 2)	GO ID (col 5)	Reference (col 6)	Evidence (col 7)	Annotation Extension (col 16)
WBGene00000220	GO:0001012 RNA polymerase II regulatory region DNA binding	PMID:21502138	IDA	has_direct_input(WB:WBGene00000247 bec-1)|has_direct_input(WB:WBGene00002980 lgg-1)|has_direct_input(WB:WBGene00003033 lin-48)

Targets of protein kinase activity:

Example 1 Statement from paper:

A final line of evidence that BAF-1 is a substrate for VRK-1 was obtained with purified recombinant proteins, which demonstrated that BAF-1 was phosphorylated by VRK-1 in vitro (Figure 4H, lower panel). In addition, VRK-1 was autophosphorylated (Figure 4H, upper panel).

Gene Name (col 2)	GO ID (col 5)	Reference (col 6)	Evidence (col 7)	Annotation Extension (col 16)
WBGene00017895	GO:0004672 protein kinase activity	PMID:17170708	IDA	has_direct_input(WB:WBGene00000235 baf-1)|has_direct_input(WB:WBGene00017895 vrk-1)

Example 2:

If protein SGD:A phosphorylates protein SGD:B then annotate A to:

Gene Name (col 2)	GO ID (col 5)	Reference (col 6)	Evidence (col 7)	Annotation Extension (col 16)
SGD:A	GO:0004672 protein kinase activity	PMID:17170708	IDA	has_direct_input(SGD:B B)

NOTE we would not include a separate annotation line for B, because we only have annotation lines for active participants

Strictly speaking, the input is SGD:B in the unphosphorylated state and the output is SGD:B in the phosphorylated state. However, currently we do not have IDs for these separate protein forms. Really B is both an input and an output. We standardize on has_input here.

Note there is no need to say:

Gene Name (col 2)	GO ID (col 5)	Reference (col 6)	Evidence (col 7)	Annotation Extension (col 16)
SGD:A	GO:0004672 protein kinase activity	PMID:17170708	IDA	has_direct_input(CHEBI:15422 ATP)

Or even:

Gene Name (col 2)	GO ID (col 5)	Reference (col 6)	Evidence (col 7)	Annotation Extension (col 16)
SGD:A	GO:0004672 protein kinase activity	PMID:17170708	IDA	has_direct_input(CHEBI:15422 ATP)|has_output(SGD:B B)|has_output(CHEBI:16761 ADP)

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