Has output: Difference between revisions

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Back to [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation  Annotation usage examples for each annotation extension relation]
==Definition==
==Definition==


Identifies an entity that is changed or created after participation in a molecular function or biological process.
Identifies an entity that is changed or created after participation in a molecular function or biological process.
==Comment==
[http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_participant#Comment '''More details on the limited use of has_output with biological process annotations''']


==Child terms==
==Child terms==
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===Domain===
===Domain===


BFO:0000007 ! process (Biological Process or Molecular Function)  
GO:0008150 ! process (Biological Process)


===Range===
===Range===
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==Annotation Extension Usage Examples==
==Annotation Extension Usage Examples==


'''1. Product of catalytic activity'''
'''1. FGF production in response to stimulation of protein A'''  
 
Statement from paper: 
 
''Hypoxia significantly induced PGIS expression in highly vascularized tissues, including lung, brain, and kidney (Fig. 9A). Additionally, plasma levels of 6-oxo-PGF1α were significantly increased (about 2-fold) in mice exposed to hypoxia (Fig. 9B). These findings demonstrate that hypoxia stimulates the release of PGI2 in vivo and support the contribution of vascular PGIS to this effect.''




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! Annotation Extension (col 16)
! Annotation Extension (col 16)
|-
|-
| Q16647 <span style="color:green">Prostacyclin synthase</span>
| Pxxxx
|GO:0008116 <span style="color:green">prostaglandin-I synthase activity</span>
|Protein A
| PMID:21296955
|GO:0090269 <span style="color:green">fibroblast growth factor production</span>
| IDA
|PMID:xxx
|
|has_output (UniProt:Q9GZV9 <span style="color:green">FGF23</span>)
has_output(CHEBI:15552 <span style="color:green">prostaglandin I2</span>)
|
 
|}
 
'''2. Abnormal G-CSF and chemokine production in G6PT-deficient mice'''
 
Statement from paper: 
 
''The neutropenia and stimulation of myelopoiesis in G6PT−/− mice suggest that G-CSF (20,21) levels might be elevated. During the first 2–3 weeks, when neutropenia is most severe and the elevation in CFU-G is highest, the plasma G-CSF level in G6PT−/− mice is elevated to 17 263±4917 pg/ml, compared with 10±7 pg/ml in the G6PT+/+ or G6PT+/− mice (Fig. 5A). After weaning, with the improvement in neutropenia and decline in overproduction of CFU-G, the plasma G-CSF level in G6PT-deficient mice drops significantly. However, even at 22 weeks of age, the plasma G-CSF in the G6PT−/− mice remains 12-fold higher than age-matched controls (Fig. 5A), suggesting an underlying problem with neutrophil production. '' 
 
 
{| class="wikitable" border="1"
|-
! Gene Name (col 2)
! GO ID (col 5)
! Reference (col 6)
! Evidence (col 7)
! Annotation Extension (col 16)
|-
| MGI:1316650 <span style="color:green">Putative glycogen storage disease type 1b protein</span>
| GO:0001816 <span style="color:green">cytokine production</span>
| PMID:12925567
| IMP
| has_output(MGI:1339751 <span style="color:green">Granulocyte colony-stimulating factor</span>)


|}
|}


== Using examples to demonstrate [[Folding_and_Unfolding]] using the relationship activated_by ==
== Using examples to demonstrate [[Folding_and_Unfolding]] using the relationship has_output ==


1. zinc activated ligand-gated ion channel (ZACN) is activated by Zn2+, PMID:12381728
'''1. FGF production in response to stimulation of protein A'''


{| class="wikitable" border="1"
{| class="wikitable" border="1"
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|-
|-
| Unfolded
| Unfolded
|Q401N2
| Pxxxx
|ZACN
|Protein A
|GO:0048471 <span style="color:green">ligand-gated ion channel activity</span>
|GO:0090269 <span style="color:green">fibroblast growth factor production</span>
|PMID:12381728
|PMID:xxx
|activated_by (ChEBI:29105, <span style="color:green">zinc ions</span>)
|has_output (UniProt:Q9GZV9 <span style="color:green">FGF23</span>)
|
|
|-
|-
| Folded
| Folded
|Q401N2
| Pxxxx
|ZACN
|Protein A
|New GO term <span style="color:green">zinc-gated ion channel activity</span>  
|New GO term <span style="color:green">FGF23 fibroblast growth factor cytokine production</span>
|PMID:12381728
|PMID:xxx
|
|
|is_a GO:0048471 <span style="color:red">ligand-gated ion channel activity</span>
|is_a GO:0090269 <span style="color:red">fibroblast growth factor production</span>
|-
|-
|}
|}


'''OWL class expression:''' GO:0090269 <span style="color:red">fibroblast growth factor production</span> AND has_output SOME UniProt:Q9GZV9 <span style="color:red">FGF23</span>
----
----
----
----
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[[Category:relations]]
[[Category:relations]]
[[Category:annotation extension]]
[[Category:annotation extension]]
[[Category: GO-CAM Relations]]

Revision as of 11:53, 13 April 2019

Back to Annotation usage examples for each annotation extension relation

Definition

Identifies an entity that is changed or created after participation in a molecular function or biological process.

Comment

More details on the limited use of has_output with biological process annotations

Child terms

  • None

Scope of use

Domain

GO:0008150 ! process (Biological Process)

Range

ENTITY_UNION:0000005 ! chemical, gene product, or complex

Annotation Extension Usage Examples

1. FGF production in response to stimulation of protein A


Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
Pxxxx Protein A GO:0090269 fibroblast growth factor production PMID:xxx has_output (UniProt:Q9GZV9 FGF23)

Using examples to demonstrate Folding_and_Unfolding using the relationship has_output

1. FGF production in response to stimulation of protein A

Folded/unfolded DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Extension (Col 16) Parent terms for new folded GO term
Unfolded Pxxxx Protein A GO:0090269 fibroblast growth factor production PMID:xxx has_output (UniProt:Q9GZV9 FGF23)
Folded Pxxxx Protein A New GO term FGF23 fibroblast growth factor cytokine production PMID:xxx is_a GO:0090269 fibroblast growth factor production

OWL class expression: GO:0090269 fibroblast growth factor production AND has_output SOME UniProt:Q9GZV9 FGF23




Back to Annotation usage examples for each annotation extension relation