Occurs in: Difference between revisions

Revision as of 04:45, 21 September 2012

Definition

Identifies the cell, tissue, cellular component or anatomical entity in which the molecular function or biological process occurs.

Child terms

None.

Scope of use

Domain

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

Range

ENTITY_UNION:0000006 ! entity

Annotation Extension Usage Examples

Enhancing Molecular Function and Biological Process Annotations

Specifying the cell or tissue type in which a process happens

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

Sequestering of calcium ion at sarcoplasmic reticulum:

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).

Gene Name (col 2)	GO ID (col 5)	Reference (col 6)	Evidence (col 7)	Annotation Extension (col 16)
O14958 CASQ2	GO:0051208 sequestering of calcium ion	PMID:16908766	IMP	occurs_in(GO:0016529 sarcoplasmic reticulum), occurs_in(CL:0000746 cardiac muscle cell)

Back to Annotation usage examples for each annotation extension relation

@@ Line 28: / Line 28: @@
 ==== Specifying the subcellular location in which a process happens ====
-Biological process terms can be further specified by subcellular location. For example: ''plastid translational elongation''
+'''Sequestering of calcium ion at sarcoplasmic reticulum:'''
-At the time of writing this term is not declared in GO. We should use the occurs_in relation:
+Statement from paper:
-  Col 5: GO:0006414
+''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).''
-  Col 16: occurs_in(GO:0009536)
-Why, you might ask, can we not instead make two annotations to:
-* GO:0032544 ! plastid translation
+{| class="wikitable" border="1"
-* GO:0006414 ! translational elongation
+|-
+! 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>)
-The answer is that co-annotation carries less information. Computationally we have no way of knowing these two processes are linked.
+|}
-Note that the majority of the time, BP x CC cross-products should be pre-composed in the ontology. If the above scenario comes up, consider requesting a new term ''plastid translational elongation'' rather than using col 16.
-Also note that when using a GO ID in col 16, a redundant annotation should sometimes be added. See [[Annotation_Cross_Products#Guidelines]]
-=== Function-Process-Component threesomes ===
-  col5: GO Function ID
-  col16: part_of(GO PROCESS ID),occurs_in(GO CC ID)
-Also include 2 redundant annotation lines