NCOL

NCOL (file extension .ncol) is a plain-text edge-list format for symbolic, optionally weighted graphs. It originates with LGL (Large Graph Layout), a network-visualization program written by Alex Adai around 2002-2003 in the laboratory of Edward Marcotte, and introduced in Adai et al., "LGL: Creating a Map of Protein Function...", Journal of Molecular Biology (2004). LGL was built to lay out very large biological networks, notably protein-homology and protein-interaction graphs, and .ncol is its principal input format.

The data model is deliberately minimal: the file is a text file with one edge per line, each edge given as two symbolic vertex names separated by whitespace, followed by an optional numeric weight. Vertex names are arbitrary strings that cannot themselves contain whitespace; weights may be negative or written in scientific notation. Vertices are not declared separately but are created implicitly the first time a name appears, so the vertex set is exactly the union of endpoints seen in the edge lines. There is no header, no attribute schema, and no separate node table. Consequently the format cannot represent an isolated (zero-degree) vertex, since a node exists only by virtue of appearing in an edge.

Notably, the file carries no information about directedness; whether the graph is read as directed or undirected is decided by the reader, not the file. LGL treats the graph as undirected and expects each edge only once, forbidding self-loops and reciprocal duplicates (both A-B and B-A). The related .lgl format captured by LGL uses a different, adjacency-style layout with pound-sign markers introducing each source vertex, so the two should not be conflated despite the shared toolchain.

In the format-conversion landscape NCOL occupies the same niche as other name-based edge lists such as SIF and generic Edge List or TSV data, trading expressiveness for simplicity and scalability to millions of edges. The library igraph is the most common gateway: its igraphreadgraphncol() and igraphwritegraphncol() (exposed in R and Python) import and export .ncol, letting users convert to richer formats like GraphML or GML. igraph does not enforce LGL's no-multi-edge, no-loop rule, so a file it writes may contain constructs that break the original LGL software. Its strengths are human readability, trivial parsing, and a compact single-file representation of weighted topology; its limitations are the absence of node/edge attributes beyond one weight, no isolated vertices, and no in-file declaration of direction or metadata.