Category:Virtual biology ontologies - Revision history

Fkolpakov@gmail.com: SBO, KiSAO, TEDDY

2015-01-08T07:25:23Z

SBO, KiSAO, TEDDY

Fkolpakov@gmail.com: GO, FMA, OPB

2015-01-08T06:35:40Z

GO, FMA, OPB

Fkolpakov@gmail.com: start, under constuction

2015-01-07T20:13:47Z

start, under constuction

New page

Ontologies are hierarchically structured vocabularies of terms and relationships that are clearly defined and designed to represent and communicate information about a particular scientific domain.

Virtual biology uses several biomedical ontologies for unambiguous, systematic descriptions of physiological, biological, chemical and physics-based entities and processes
as well as their interrelations <cite>Courtot2011</cite>.

Key elements in annotating models with ontology terms include <cite>Beard2013, Courtot2011</cite>:
* associating codewords in the model with appropriate unambiguous ontology identifiers;
* specifying components and subcomponents in the model utilizing the hierarchical structure within an ontology;
* linking the model and its components and subcomponents to supporting measured experimental data.

The use of multiple ontologies for defining components and subcomponents of models could allow them to be compared and integrated to form composite models in an automated manner <cite>Beard2013</cite>.

Standardizing biological information with organized vocabularies and ontologies already has proven to be valuable in formally defining components of models and representations of complex systems<cite>Beard2013, Courtot2011</cite>. For example, describing multiscale processes in mouse development mathematical models using a combination of GO and Cell Type Ontology terms has been shown to be effective to provide clear definitions of function and to allow comparison of function under different conditions <cite>Bard2007</cite>.

The table below contains brief description of these ontologies.

{| class="wikitable"
!Ontology, URL, references!!Brief description!!Used in projects
|-
|
<br><cite>Beard2013</cite>
|

|-
|
|
|}

Gene Ontology (GO) describes gene function through properties of proteins and includes hierarchical information in the three domains of cellular location, molecular functions, and biological processes.1,19

FMA http://sig.biostr.washington.edu/projects/fm/
OPB http://sbp.bhi.washington.edu/projects/the-ontology-of-physics-for-biology-opb

==References==

<biblio>
#Beard2013 pmid=22805979

#Courtot2011 pmid=22027554

#Bard2007 pmid=17566825

</biblio>

[[Category:Virtual_biology]]

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 ==References==
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 #Harris2004 pmid=14681407
 #Rosse2003 pmid=14759820
 #Cook2011 pmid=22216106

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 {| class="wikitable"
-!Ontology, URL, references!!Brief description!!Used in projects
+!Ontology, references!!Brief description, URL!!Used in projects
 |-
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-−
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 |-
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 |}
 ==References==
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 #Bard2007 pmid=17566825
 </biblio>
+#Rosse2003 pmid=14759820
 [[Category:Virtual_biology]]