What is a KGML file?

The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format. KGML enables automatic drawing of KEGG pathways and provides facilities for computational analysis and modeling of gene/protein networks and chemical networks.

How do I import a KEGG pathway into cytoscape?

To search and import a KEGG pathway to Cytoscape simply go to Apps > CytoKegg > Search Pathways. Once there, select the target organism, type a pathway title and the click search. After that, select the target pathway and click open.

How do you use a KEGG API?

The Search&Color procedure can be accomplished s follows:

Create a dataset containing KEGG identifiers and color specifications.
Upload the dataset.
Use the idmap operation for the search.
Process the idmap result to create the list.
Use the map/ operation for coloring.

What is KO annotation?

KO assignment Genome annotation in KEGG is to assign KO identifiers (or K numbers) to individual genes in the genome, rather than giving text description of functions.

What is KEGG Orthology?

The KEGG ORTHOLOGY (KO) database is a collection of manually defined ortholog groups, called KOs, that correspond to the nodes (boxes) of the KEGG pathway maps or the nodes (bottom leaves) of the BRITE functional hierarchies.

What does KEGG pathway do?

It is a collection of pathway maps integrating many entities including genes, proteins, RNAs, chemical compounds, glycans, and chemical reactions, as well as disease genes and drug targets, which are stored as individual entries in the other databases of KEGG. Human diseases. Drug development.

What is ClueGO?

ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes.

How do you cite Cytoscape?

Please cite the original Cytoscape paper when you use Cytoscape. This is critical to sustaining our federal funding. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.

What is Brite KEGG?

KEGG BRITE is a collection of hierarchical classification systems capturing functional hierarchies of various biological objects, especially those represented as KEGG objects.

What are KEGG Orthologies?

The KO (KEGG Orthology) database is a database of molecular functions represented in terms of functional orthologs. The addendum category of the GENES database allows functionally characterized individual protein sequences to be included in KEGG.

What are KEGG identifiers?

KEGG objects are biological entities from molecular to higher levels that are represented as database entries in KEGG, such as genes and protein, small molecules, reactions, pathways, diseases and drugs.

What program opens KML files?

Google Earth is the most common program to open KMZ files since it also supports KML and ETA formats. If you are unfamiliar with Google Earth, it is a global mapping program you can download to obtain views of different locations.

What is KML format?

Keyhole Markup Language (KML) is an XML-based format for storing geographic data and associated content and is an official Open Geospatial Consortium (OGC) standard.

How does a KML file work?

KML files use XML format to store geographic modeling information. These files contain lines, points, images and polygons. They are used to label locations and create overlay textures and camera angles for the maps that are created by the mapping applications.

https://www.youtube.com/watch?v=gEj5SkoE6lM