OmniPath

OmniPath loading helpers from annnet.io.omnipath.

annnet.io.omnipath

Classes

Functions

from_omnipath

from_omnipath(
    df=None,
    *,
    dataset="omnipath",
    include=None,
    exclude=None,
    query=None,
    source_col=None,
    target_col=None,
    directed_col=None,
    weight_col=None,
    edge_id_col=None,
    slice_col=None,
    slice=None,
    default_directed=True,
    edge_attr_cols=None,
    dropna=True,
    annotations_backend=None,
    vertex_annotations_df=None,
    vertex_annotations_path=None,
    vertex_annotation_sources=None,
    load_vertex_annotations=True,
    **graph_kwargs
)

Build an AnnNet from OmniPath interaction data, with edge and vertex annotations.

Fetches a signaling interaction dataset from the OmniPath web service (or accepts a pre-loaded DataFrame), builds the graph structure via bulk operations, and optionally enriches vertices with annotations from the OmniPath annotation archive.

The annotation archive (~114MB) is downloaded once and cached at ~/.cache/annnet/omnipath_annotations.tsv.gz for fast subsequent loads.

Parameters:

Name	Type	Description	Default
`df`	`DataFrame - like`	If provided, skip the OmniPath network request and build from this table. Must contain at least source and target columns. Accepts Polars, pandas, or any Narwhals-compatible DataFrame.	`None`
`dataset`	`str`	OmniPath interaction dataset to fetch. One of: `"omnipath"` (default, curated core), `"all"`, `"posttranslational"`, `"pathwayextra"`, `"kinaseextra"`, `"ligrecextra"`, `"dorothea"`, `"tftarget"`, `"transcriptional"`, `"tfmirna"`, `"mirna"`, `"lncrnamrna"`, `"collectri"`.	`'omnipath'`
`include`	`optional`	Dataset include/exclude filters. Only used when `dataset="all"` (include/exclude) or `dataset="posttranslational"` (exclude only).	`None`
`exclude`	`optional`	Dataset include/exclude filters. Only used when `dataset="all"` (include/exclude) or `dataset="posttranslational"` (exclude only).	`None`
`query`	`dict`	Extra query parameters forwarded to the OmniPath web service. Example: `{"organism": "human", "genesymbols": True}`. Use `omnipath.interactions.<Dataset>.params()` to inspect available keys.	`None`
`source_col`	`str`	Column name for source node identifiers. Auto-detected from common OmniPath field names if omitted (`source`, `source_genesymbol`, etc.).	`None`
`target_col`	`str`	Column name for target node identifiers. Auto-detected if omitted.	`None`
`directed_col`	`str`	Column holding per-edge directedness flags (bool-like). If omitted, `default_directed` is used for all edges.	`None`
`weight_col`	`str`	Column holding edge weights. If omitted, weight defaults to 1.0.	`None`
`edge_id_col`	`str`	Column holding stable edge identifiers. If omitted, AnnNet assigns sequential IDs (`edge_0`, `edge_1`, ...).	`None`
`slice_col`	`str`	Column holding per-edge slice identifiers.	`None`
`slice`	`str`	Slice to place all edges into. Ignored if `slice_col` is provided.	`None`
`default_directed`	`bool`	Fallback directedness when `directed_col` is missing or null. Defaults to `True`.	`True`
`edge_attr_cols`	`list[str]`	Columns to store as edge attributes. If omitted, all non-structural columns are used. Pass `[]` to skip edge attribute loading entirely.	`None`
`dropna`	`bool`	If `True` (default), silently drop rows with null source or target. If `False`, raise `ValueError` on first null endpoint.	`True`
`annotations_backend`	`str`	Backend for AnnNet attribute tables. `None` uses AnnNet's configured dataframe backend default.	`None`
`vertex_annotations_df`	`DataFrame - like`	Pre-loaded annotation table in OmniPath long format `(genesymbol, source, label, value)`. Skips all file I/O. Fastest option when rebuilding the graph multiple times in one session — load the archive once and pass it here.	`None`
`vertex_annotations_path`	`str`	Path to a local OmniPath annotation file (`.tsv` or `.tsv.gz`). Skips the cache-check and download.	`None`
`vertex_annotation_sources`	`list[str]`	OmniPath annotation resource names to include as vertex attributes. If omitted, all resources in the annotation table are loaded (254 columns). Recommended subset for signaling graphs:: `[ 'HGNC', 'CancerGeneCensus', 'SignaLink_function', 'SignaLink_pathway', 'UniProt_location', 'HPA_subcellular', 'PROGENy', 'IntOGen', 'Phosphatome', 'kinase.com', ]`	`None`
`load_vertex_annotations`	`bool`	Whether to load vertex annotations at all. Set to `False` to skip annotation loading entirely and get a structure-only graph. Default `True`.	`True`
`**graph_kwargs`		Additional keyword arguments forwarded to the `AnnNet` constructor.	`{}`

Returns:

Type Description

AnnNet

Fully constructed graph with: - Vertices: one per unique gene symbol encountered as source or target. - Edges: one per interaction row, with incidence matrix weights encoding direction (+w source, −w target for directed; +w both for undirected). - edge_attributes: Polars DF with one row per edge and one column per entry in edge_attr_cols. - vertex_attributes: Polars DF with one row per vertex and one column per (source:label) annotation pair from the requested resources.

Notes

Edge and vertex attribute tables are populated via bulk operations — no per-row DataFrame allocations occur during loading.
History tracking is disabled during construction and re-enabled on return.
The annotation archive is ~114MB compressed. First call downloads and caches it; subsequent calls load from ~/.cache/annnet/omnipath_annotations.tsv.gz in ~2–3s.
source and target columns from the interaction table are redundant as edge attributes (the graph structure already encodes them). Exclude them via edge_attr_cols if not needed.