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---------------Text extracted from ontology: DO NOT EDIT---------------
- OWL ID: GOREL_0000752
- label: has_direct_input
- synonyms [u'has_direct_target', u'directly_localizes', u'has_substrate']
Identifies an entity directly affected (transported, modified, consumed or destroyed) by the gene product's participation in a molecular function or biological process. It is expected that the gene product and entity will physically interact, this can be determined either by a direct binding assay or inferred from the activity of the gene product, for example, a gene product with catalytic activity is inferred to bind its substrate.
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 [GOC:ecd]
[valid_for_annotation_extension, AE_sequence_or_complex, AE_chemical, display_for_curators]
##local domain {u'BFO:0000015': u'process'}
{u'SO:0000839': u'polypeptide_region', u'CHEBI:24431': u'chemical entity', u'CHEBI:33697': u'ribonucleic acid', u'SO:0000673': u'transcript', u'GO:0032991': u'macromolecular complex', u'MI:0315': u'protein complex', u'PR:000000001': u'protein', u'SO:0000704': u'gene'}
---------------END AUTO GENERATED SECTION---------------
To use this relationship there must be evidence that the gene product in column 2 is known/predicted to bind the molecular target in column 16.
This can be a co-immunoprecipitation (for example) demonstrated in the paper being annotated, or from evidence available in another paper, or from evidence of protein interactions which have been demonstrated in another paper for orthologous molecules.
Without evidence of a relevant interaction use the relationship has_input
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 Atf-2 | GO:0001012 RNA polymerase II regulatory region DNA binding | PMID:21502138 | IDA | has_direct_input(WB:WBGene00000247)| has_direct_input(WB:WBGene00002980)| has_direct_input(WB:WBGene00003033) bec-1, lgg-1, 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 Vrk-1 | GO:0004672 protein kinase activity | PMID:17170708 | IDA | has_direct_input(WB:WBGene00000235)| has_direct_input(WB:WBGene00017895) baf-1, 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) |
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(SGD:B)| 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 A | GO:0004672 protein kinase activity | PMID:17170708 | IDA | has_direct_input(SGD:B)| has_direct_input(CHEBI:15422) ATP| has_output(SGD:B) | has_output(CHEBI:16761) ADP |
These are correct but this is pointless because the additional info is redundant with what we already know about kinase activity (this is actually made computable in MF x CHEBI)
Inclusion of the C16 information in the Molecular Function protein kinase and to the Biological Process phosphorylation can be useful, as these annotation extensions will not be created transitively. However, this information can be inferred computationally.
If protein SGD:A phosphorylates protein SGD:B and SGD:C 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)| has_direct_input(SGD:C) |
There is some redundancy with interaction databases here. Capturing this as GO annotation is more expressive as you can say "A phosphorylates B during pathway C". But if you want to capture this in interaction databases exclusively we have tools for generating GO annotations from these (just as we have tools for capturing GO annotations from pathway databases).
Using examples (from above) to demonstrate Folding_and_Unfolding using the relationship has_direct_input
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).
| Folded/unfolded | Gene Name (col 2) | GO ID (col 5) | Reference (col 6) | Evidence (col 7) | Annotation Extension (col 16) | Parent terms of new folded GO term |
|---|---|---|---|---|---|---|
| Unfolded | WBGene00000220 atf-2 | GO:0001012 RNA polymerase II regulatory region DNA binding | PMID:21502138 | IDA | has_direct_input(WB:WBGene00000247)| has_direct_input(WB:WBGene00002980)| has_direct_input(WB:WBGene00003033) bec-1, lgg-1, lin-48 | |
| Folded | WBGene00000220 atf-2 | GO:0001012 RNA polymerase II regulatory region DNA binding | PMID:21502138 | IDA | No new GO term created |
OWL class expression: is_a GO:0001012 RNA polymerase II regulatory region DNA binding AND has_direct_input SOME WBGene00000220 atf-2
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