diff --git a/datanodes.Rmd b/datanodes.Rmd index af43522..4a5abd2 100644 --- a/datanodes.Rmd +++ b/datanodes.Rmd @@ -14,19 +14,19 @@ knitr::include_graphics("images/screenshots/datanodes.png") ## Molecular DataNodes -### GeneProduct ![](images/figures/datanodes/geneproduct.PNG){width=300} +### GeneProduct ![](images/figures/datanodes/geneproduct.png){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 ![](images/figures/datanodes/metabolite.PNG){width=300} +### Metabolite ![](images/figures/datanodes/metabolite.png){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 ![](images/figures/datanodes/protein.PNG){width=300} +### Protein ![](images/figures/datanodes/protein.png){width=300} A biomolecular polymer of amino acids, translated from mRNA. -### DNA ![](images/figures/datanodes/dna.PNG){width=300} +### DNA ![](images/figures/datanodes/dna.png){width=300} An entity representing a DNA polymer. -### RNA ![](images/figures/datanodes/rna.PNG){width=300} +### RNA ![](images/figures/datanodes/rna.png){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) @@ -36,22 +36,22 @@ The Complex Data Node Type is deprecated. Its use was similar to that of [Alias] ## Concept DataNodes -### Pathway ![](images/figures/datanodes/pathway.PNG){width=300} +### Pathway ![](images/figures/datanodes/pathway.png){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 ![](images/figures/datanodes/disease.PNG){width=300} +### Disease ![](images/figures/datanodes/disease.png){width=300} -### Phenotype ![](images/figures/datanodes/phenotype.PNG){width=300} +### Phenotype ![](images/figures/datanodes/phenotype.png){width=300} -### Alias ![](images/figures/datanodes/alias.PNG){width=300} +### Alias ![](images/figures/datanodes/alias.png){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 ![](images/figures/datanodes/event.PNG){width=300} +### Event ![](images/figures/datanodes/event.png){width=300} -### CellNode ![](images/figures/datanodes/cellnode.PNG){width=300} +### CellNode ![](images/figures/datanodes/cellnode.png){width=300} -### Organ ![](images/figures/datanodes/organ.PNG){width=300} +### Organ ![](images/figures/datanodes/organ.png){width=300} -### Undefined ![](images/figures/datanodes/undefined.PNG){width=300} +### Undefined ![](images/figures/datanodes/undefined.png){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.