Occurs in: Difference between revisions

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Purpose of annotation extensions: See [[Annotation_Extension]]
The purpose of annotation extensions is described in the main [[Annotation_Extension]] documentation page.


==Usage guidelines==
==Usage guidelines==
===What to capture with the occurs_in relation===
===What to capture with the occurs_in relation===
* '''occurs_in''' is used to specify the cellular component, cell or anatomical structure in which a Molecular Function or a Biological Process take place.
* <code>occurs in</code> is used to specify the cellular component, cell or anatomical structure in which a Molecular Function or a Biological Process take place.
* Using occurs_in for a Biological Process is restricted to instances where all molecular functions that are part of the process occurs in the same cellular component/cell/anatomical structure. If different steps occur in different compartments/cells/anatomical structures, then one cannot assert that the Biological Process occurs in that compartments/cells/anatomical structure.
* More than one location may be captured for a single MF or BP using the <code>occurs in</code> relation.  This usage captures subcellular or anatomical structures for which the more granular structure is part of the less granular structure, e.g. ''occurs_in(mitochondrion),occurs_in(neuron),occurs_in(brain)''.  If a MF or a BP takes place at two different locations, this should be captured as independent annotations or independent annotation extensions for an annotation. (Note that in GO-CAM this is captured differently, i.e. structures that are part of other structures are linked to each other with the <code>part of</code> relation, while in annotation extensions, the GO term has a <code>occurs in</code> relation with each structure).


===What not to capture===
===What not to capture===
To be completed
* Localizations already present in the GO term label or definition; for example for ''GO:0050852 T cell receptor signaling pathway'', ''occurs in T-cell'' does not need to be added as an extension.
* Using <code>occurs in</code> for a Biological Process is restricted to instances where all molecular functions that are part of the process occurs in the same cellular component/cell/anatomical structure. If different steps occur in different compartments/cells/anatomical structures, then one cannot assert that the Biological Process occurs in that compartments/cells/anatomical structure.


==Scope of use==
==Scope of use==
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''Domain refers to the GO terms that can be further specified with the relation.
''Domain refers to the GO terms that can be further specified with the relation.
* [http://purl.obolibrary.org/obo/BFO_0000015 '''BFO:0000007 process'''], which corresponds to GO Biological Process and Molecular Function
* [http://amigo.geneontology.org/amigo/term/GO:0008150 GO:0008150 Biological Process] and [http://amigo.geneontology.org/amigo/term/GO:0003674 GO:0003674 Molecular Function]


'''Range'''
'''Range'''
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* [http://amigo.geneontology.org/amigo/term/GO:0110165 GO:0110165 cellular anatomical entity]
* [http://amigo.geneontology.org/amigo/term/GO:0110165 GO:0110165 cellular anatomical entity]
* [http://www.ontobee.org/ontology/CL Cell Ontology]
* [http://www.ontobee.org/ontology/CL Cell Ontology (CL)]
* [https://www.ebi.ac.uk/ols/ontologies/emapa EMAPA]
* [http://www.ontobee.org/ontology/UBERON Uberon]
* [http://www.ontobee.org/ontology/UBERON Uberon]
* [http://www.ontobee.org/ontology/WBbt C. elegans gross anatomy ontology]  
* [https://www.ebi.ac.uk/ols/ontologies/emapa Mouse Developmental Anatomy Ontology (EMAPA)]
* [http://www.ontobee.org/ontology/TO  Plant Trait Ontology]
* [https://www.ebi.ac.uk/ols/ontologies/fbbt Drosophila Anatomy Ontology (DAO)]
* [http://www.ontobee.org/ontology/WBbt C. elegans gross anatomy ontology (WBbt)]  
* [http://www.ontobee.org/ontology/TO  Plant Trait Ontology (TO)]
* [http://www.xenbase.org/anatomy/xao.do?method=display Xenopus anatomical entity]
* [http://www.xenbase.org/anatomy/xao.do?method=display Xenopus anatomical entity]
* [https://www.ebi.ac.uk/ols/ontologies/zfa Zebrafish anatomy and development ontology]
* [https://www.ebi.ac.uk/ols/ontologies/zfa Zebrafish anatomy and development ontology (ZFA)]
* and many others
* etc
----


==Usage examples for the occurs_in extension==
==Usage examples for the occurs_in extension==


===1. Specifying the cellular location in which a molecular function takes place ===
===1. Specifying the cellular location in which a molecular function takes place ===
Human [https://www.uniprot.org/uniprot/P49916 LIG3 Isoform 1] is targeted to mitochondria, where it functions as DNA ligase in mitochondrial base-excision DNA repair,  
Human [https://www.uniprot.org/uniprot/P49916 LIG3 Isoform 1] is targeted to mitochondria, where it functions as DNA ligase in mitochondrial base-excision DNA repair, [https://pubmed.ncbi.nlm.nih.gov/24674627/ PMID:24674627], [https://pubmed.ncbi.nlm.nih.gov/10207110/ PMID:10207110].
[https://pubmed.ncbi.nlm.nih.gov/24674627/ PMID:24674627], [https://pubmed.ncbi.nlm.nih.gov/10207110/ PMID:10207110].


{| class="wikitable"  border="1"
{| class="wikitable"  border="1"
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----
----
===2. Specifying the cell type in which a molecular function takes place ===
===2. Specifying both the cellular location and the cell type in which a molecular function takes place ===
Type 4 phosphodiesterase [https://www.uniprot.org/uniprot/P27815 PDE4A] is a critical regulator in TCR signaling by attenuating the negative constraint of cAMP, [https://pubmed.ncbi.nlm.nih.gov/17404263/ PMID:17404263].
Human [https://www.uniprot.org/uniprot/O14958 CASQ2] sequesters calcium ions in the sarcoplasmic reticulum of cardiac muscle cells, [https://pubmed.ncbi.nlm.nih.gov/16908766/ PMID:16908766]


{| class="wikitable"  border="1"
{| class="wikitable"  border="1"
| colspan="2" align="center"| '''MF Annotation for PDE4A'''
| colspan="2" align="center"| '''Annotation for CASQ2'''
|-
|-
| style="width: 20%"| '''Gene product'''
| style="width: 20%"| '''Gene product'''
| style="width: 80%"| UniProtKB:P27815 ''PDE4A''
| style="width: 80%"| UniProtKB:O14958 ''CASQ2''
|-
|-
| '''GP2term relation'''
| '''GP2term relation'''
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|-
|-
| '''GO term'''
| '''GO term'''
| GO:0004115 ''3',5'-cyclic-AMP phosphodiesterase activity'', '''occurs in'''(CL:0000084 ''T-cell'')
| GO:0140314 ''calcium ion sequestering activity'', '''occurs_in'''(''GO:0016529 sarcoplasmic reticulum''), '''occurs_in'''(CL:0000746 ''cardiac muscle cell'')
|-
|-
| '''Evidence'''  
| '''Evidence'''  
| IDA
| IMP
|-
|-
| '''Reference'''  
| '''Reference'''  
| PMID:17404263
| PMID:16908766
|-
|-
|}
|}
Note the use of the comma to create a compound annotation extension. The interpretation of this annotation is CASQ2 enables sequestering calcium ions in the sarcoplasmic reticulum of cardiac muscle cell.
----
===3. Specifying the cellular component in which a biological process takes place ===
Human [https://www.uniprot.org/uniprot/Q9NQ11 ATP13A2] mediates autophagosome organization in cerebral cortex neurons, [https://pubmed.ncbi.nlm.nih.gov/22186024/ PMID:22186024]


{| class="wikitable"  border="1"
{| class="wikitable"  border="1"
| colspan="2" align="center"| '''BP Annotation for PDE4A'''
| colspan="2" align="center"| '''Annotation for ATP13A2'''
|-
|-
| style="width: 20%"| '''Gene product'''
| style="width: 20%"| '''Gene product'''
| style="width: 80%"| UniProtKB:P27815 ''PDE4A''
| style="width: 80%"| UniProtKB:Q9NQ11 ''ATP13A2''
|-
|-
| '''GP2term relation'''
| '''GP2term relation'''
| involved in
| enables
|-
|-
| '''GO term'''
| '''GO term'''
| GO:0043951 ''negative regulation of cAMP-mediated signaling'', '''occurs in'''(CL:0000084 ''T-cell'')
| GO:1905037 ''autophagosome organization'' '', '''occurs in'''(CL_0002609 ''neuron of cerebral cortex'')
|-
|-
| '''Evidence'''  
| '''Evidence'''  
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|-
|-
| '''Reference'''  
| '''Reference'''  
| PMID:17404263
| PMID:22186024
|-
|-
|}
|}




----
----
  TO REVIEW
=== Enhancing Molecular Function and Biological Process Annotations ===
==== Specifying the cell or tissue type in which a process happens ====
More examples of this usage of occurs_in can be found on the documentation page for [[Column_16:_Cell_Type]]
==== Specifying the subcellular location in which a process happens ====
1. '''Protein interaction in a particular location in the cell:'''
Statement from paper:
''Canine cardiac junctional SR vesicles were solubilized with 2% Triton X-100 and loaded on the affinity column equilibrated in EGTA-containing buffer (Fig.1). Calsequestrin-binding proteins were then eluted in buffer containing 20 mm CaCl2, a calcium concentration sufficient to disrupt all calsequestrin protein-binding interactions. Immunoblotting of the eluted fractions with triadin antibody revealed that triadin bound completely to the column and was eluted as a discrete peak in Ca2+-containing buffer (Fig. 1 A, upper)''
{| class="wikitable" border="1"
|-
! Gene Name (col 2)
! GO ID (col 5)
! Reference (col 6)
! Evidence (col 7)
! With (col 8)
! Annotation Extension (col 16)
|-
| P12637 <span style="color:green">CASQ2</span>
| GO:0005515 <span style="color:green">protein binding</span>
| PMID:9287354
| IPI
| P82179 <span style="color:green">TRDN</span>
| occurs_in(GO:0016529 <span style="color:green">sarcoplasmic reticulum</span>)
|}
2. '''Sequestering of calcium ion at a particular location in the cell:'''
Statement from paper: 
''To characterize the effects of the new CASQ2 mutations on SR Ca2+ handling in vivo, we performed experiments in adult rat ventricular myocytes infected with adenoviral constructs. Caffeine (10 mmol/L) was applied to myocytes expressing either WT or mutant CASQ2 to evaluate the SR Ca2+-storing capacity by measurement of fluo-3 fluorescence and of Na+/Ca2+ exchange current (INCX; Figure 4A; Table 1).21 Expression of WT increased the SR Ca2+ content by 50%, whereas CASQ2 G112+5X reduced the SR content, not only as compared with WT expression but also as compared with native cells (Ad-control).'' 
{| class="wikitable" border="1"
|-
! Gene Name (col 2)
! GO ID (col 5)
! Reference (col 6)
! Evidence (col 7)
! Annotation Extension (col 16)
|-
| O14958 <span style="color:green">CASQ2</span>
| GO:0051208 <span style="color:green">sequestering of calcium ion</span>
| PMID:16908766
| IMP
| occurs_in(GO:0016529 <span style="color:green">sarcoplasmic reticulum</span>), occurs_in(CL:0000746 <span style="color:green">cardiac muscle cell</span>)
|}
Note the use of the comma to create a compound annotation extension. The interpretation of this annotation is CASQ2 is involved in sequestering calcium ions in the sarcoplasmic reticulum of cardiac muscle cell.


==Cross-reference to Relations Ontology (RO) term==
==Cross-reference to Relations Ontology (RO) term==
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== Review Status ==
== Review Status ==


Last reviewed: 2021-09-29
Last reviewed: 2021-10-07


Back to [[Annotation_Extension]]
Back to [[Annotation_Extension]]

Revision as of 11:55, 7 October 2021

The purpose of annotation extensions is described in the main Annotation_Extension documentation page.

Usage guidelines

What to capture with the occurs_in relation

  • occurs in is used to specify the cellular component, cell or anatomical structure in which a Molecular Function or a Biological Process take place.
  • More than one location may be captured for a single MF or BP using the occurs in relation. This usage captures subcellular or anatomical structures for which the more granular structure is part of the less granular structure, e.g. occurs_in(mitochondrion),occurs_in(neuron),occurs_in(brain). If a MF or a BP takes place at two different locations, this should be captured as independent annotations or independent annotation extensions for an annotation. (Note that in GO-CAM this is captured differently, i.e. structures that are part of other structures are linked to each other with the part of relation, while in annotation extensions, the GO term has a occurs in relation with each structure).

What not to capture

  • Localizations already present in the GO term label or definition; for example for GO:0050852 T cell receptor signaling pathway, occurs in T-cell does not need to be added as an extension.
  • Using occurs in for a Biological Process is restricted to instances where all molecular functions that are part of the process occurs in the same cellular component/cell/anatomical structure. If different steps occur in different compartments/cells/anatomical structures, then one cannot assert that the Biological Process occurs in that compartments/cells/anatomical structure.

Scope of use

Domain

Domain refers to the GO terms that can be further specified with the relation.

Range

Range describes the types of entities that can be used with the relation.

Usage examples for the occurs_in extension

1. Specifying the cellular location in which a molecular function takes place

Human LIG3 Isoform 1 is targeted to mitochondria, where it functions as DNA ligase in mitochondrial base-excision DNA repair, PMID:24674627, PMID:10207110.

Annotation for LIG3
Gene product UniProtKB:P23743 LIG3
GP2term relation enables
GO term GO:0003909 DNA ligase activity, occurs in(GO:0005739 mitochondrion)
Evidence IDA
Reference PMID:24674627

2. Specifying both the cellular location and the cell type in which a molecular function takes place

Human CASQ2 sequesters calcium ions in the sarcoplasmic reticulum of cardiac muscle cells, PMID:16908766

Annotation for CASQ2
Gene product UniProtKB:O14958 CASQ2
GP2term relation enables
GO term GO:0140314 calcium ion sequestering activity, occurs_in(GO:0016529 sarcoplasmic reticulum), occurs_in(CL:0000746 cardiac muscle cell)
Evidence IMP
Reference PMID:16908766

Note the use of the comma to create a compound annotation extension. The interpretation of this annotation is CASQ2 enables sequestering calcium ions in the sarcoplasmic reticulum of cardiac muscle cell.


3. Specifying the cellular component in which a biological process takes place

Human ATP13A2 mediates autophagosome organization in cerebral cortex neurons, PMID:22186024

Annotation for ATP13A2
Gene product UniProtKB:Q9NQ11 ATP13A2
GP2term relation enables
GO term GO:1905037 autophagosome organization , occurs in(CL_0002609 neuron of cerebral cortex)
Evidence IDA
Reference PMID:22186024



Cross-reference to Relations Ontology (RO) term

BFO:0000066 occurs in

Review Status

Last reviewed: 2021-10-07

Back to Annotation_Extension