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datanodes.Rmd
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datanodes.Rmd
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```{r, include=FALSE}
#Load necessary libraries
library(knitr)
```
# Data Nodes
A Data Node denotes a biological entity that forms a node in a pathway. We have two categories of Data Node Types: Molecular DataNodes and Concept DataNodes.
```{r fig.align="center", echo=FALSE, out.width="70%", fig.cap = "Object Panel options for Data Nodes"}
knitr::include_graphics("images/screenshots/datanodes.png")
```
## Molecular DataNodes
### GeneProduct {width=300}
An entity representing any product of a given gene, including DNA, RNA and Protein. This is the most generic representation of a gene-based biomolecule and is useful when more than one representation might be useful in the given context
### Metabolite {width=300}
An entity representing a metabolite, including chemical compounds that participate in or are produced by metabolic reactions, but also other chemical compounds that participate in a pathway otherwise.
### Protein {width=300}
A biomolecular polymer of amino acids, translated from mRNA.
### DNA {width=300}
An entity representing a DNA polymer.
### RNA {width=300}
An entity representing a RNA peptide, including mRNA, miRNA, etc. This is commonly used to explicitly represent mRNA transcripts (excluding DNA or protein forms) or other RNA species, like miRNA, exRNA, lncRNA, etc
### Complex (deprecated)
The Complex Data Node Type is deprecated. Its use was similar to that of [Alias](#alias).
## Concept DataNodes
### Pathway {width=300}
A biological process representing a set of interactions and relationships among genes, proteins, metabolites, and other factors in the context of cellular compartments, tissues and organisms.
### Disease {width=300}
### Phenotype {width=300}
### Alias {width=300}
An Alias is a special type of Data Node which can represent a Group pathway element (or other entity). Please see [Aliases](#aliases) for more information!
### Event {width=300}
### CellNode {width=300}
### Organ {width=300}
### Undefined {width=300}
An unspecified biological entity or factor. Should only be used if the type is truly unknown or is different from the ones covered by other data node types.