Add COSMOS PKN vignette; link metabo service in landing page

New vignette docs/vignettes/cosmos.md covering: 6 PKN categories,
get_pkn() with organism/category/resource filtering, multi-organism,
AnnNet conversion, convenience functions, REST API endpoints.

Updated index.md: added COSMOS PKN to Learn more + metabo.omnipathdb.org
to Services table.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: deeenes

docs/index.md

@@ -72,6 +72,8 @@ op.values('exports/interactions', 'entity_types')    # allowed values
   taxonomy, orthology, reference lists
 - **[OmniPath Database vignette](vignettes/database.md)** -- interactions,
   annotations, complexes
+- **[COSMOS PKN vignette](vignettes/cosmos.md)** -- multi-layer
+  prior-knowledge network for multi-omics causal reasoning
 - **[API Reference](reference/index.md)** -- full function documentation
 - **[Installation](installation.md)** -- setup instructions
 
@@ -81,3 +83,4 @@ op.values('exports/interactions', 'entity_types')    # allowed values
 |---------|-----|-----------------|
 | OmniPath Database | [dev.omnipathdb.org](https://dev.omnipathdb.org) | Interactions, annotations, complexes, ontology |
 | OmniPath Utils | [utils.omnipathdb.org](https://utils.omnipathdb.org) | ID translation, taxonomy, orthology, reference lists |
+| OmniPath Metabo | [metabo.omnipathdb.org](https://metabo.omnipathdb.org) | COSMOS PKN, metabolite-protein interactions |

docs/vignettes/cosmos.md

@@ -0,0 +1,130 @@
+# COSMOS Prior-Knowledge Network
+
+This vignette shows how to use omnipath-client to access the COSMOS
+prior-knowledge network (PKN) -- a multi-layer network designed for
+multi-omics causal reasoning with
+[cosmosR](https://github.com/saezlab/cosmosR).
+
+The COSMOS PKN integrates metabolite-protein interactions, protein-protein
+signaling, and gene regulation from curated databases into a single
+directed signed network. It is served by the
+[metabo.omnipathdb.org](https://metabo.omnipathdb.org) web service and
+built by the [omnipath-metabo](https://github.com/saezlab/omnipath-metabo)
+package.
+
+## Setup
+
+```python
+pip install omnipath-client
+```
+
+```python
+import omnipath_client as oc
+```
+
+## Network categories
+
+The PKN is organized into six categories covering different layers of
+molecular interaction:
+
+| Category | Description |
+|----------|-------------|
+| `transporters` | Metabolite transport across membranes (TCDB, SLC, GEMs, MRCLinksDB) |
+| `receptors` | Metabolite-receptor binding at the cell surface (STITCH, MRCLinksDB) |
+| `allosteric` | Allosteric regulation of enzymes by metabolites (BRENDA, STITCH) |
+| `enzyme_metabolite` | Enzyme-metabolite stoichiometric reactions from GEMs |
+| `ppi` | Protein-protein signaling from OmniPath |
+| `grn` | Gene regulatory network from CollecTRI / DoRothEA |
+
+## Fetch the full PKN
+
+```python
+# Full human PKN (all 6 categories)
+df = oc.cosmos.get_pkn('human')
+```
+
+The result is a DataFrame with columns `source`, `target`, and `sign`
+(mode of regulation: 1 = stimulation, -1 = inhibition).
+
+## Filter by category
+
+```python
+# Only transporters and receptors
+df = oc.cosmos.get_pkn('human', categories=['transporters', 'receptors'])
+
+# PPI layer only
+df = oc.cosmos.get_pkn('human', categories='ppi')
+```
+
+## Filter by resource
+
+```python
+# Only STITCH receptor edges
+df = oc.cosmos.get_pkn(
+    'human',
+    categories='receptors',
+    resources='STITCH',
+)
+```
+
+## Multi-organism support
+
+The PKN is available for human, mouse, and rat. The `organism` parameter
+accepts NCBI taxonomy IDs, common names, Latin names, or short codes.
+
+```python
+# Mouse PKN
+df_mouse = oc.cosmos.get_pkn('mouse')
+
+# Rat PKN
+df_rat = oc.cosmos.get_pkn('rat')
+
+# Using NCBI taxonomy ID
+df = oc.cosmos.get_pkn(10090)
+```
+
+## AnnNet graph conversion
+
+Convert the PKN to an [AnnNet](https://github.com/saezlab/annnet)
+graph object for network analysis:
+
+```python
+# Directly as an AnnNet graph
+g = oc.cosmos.get_pkn('mouse', format='annnet')
+
+# Or convert an existing DataFrame
+df = oc.cosmos.get_pkn('human')
+g = oc.cosmos.to_annnet(df)
+```
+
+## Convenience functions
+
+Explore what is available on the server:
+
+```python
+# Available categories
+oc.cosmos.categories()
+# ['transporters', 'receptors', 'allosteric', 'enzyme_metabolite', 'ppi', 'grn']
+
+# Supported organisms
+oc.cosmos.organisms()
+# [9606, 10090, 10116]
+
+# Resources per category
+oc.cosmos.resources()
+# {'transporters': ['TCDB', 'SLC', 'GEM:Human-GEM', ...], ...}
+```
+
+## Web service
+
+The COSMOS PKN is served at
+[metabo.omnipathdb.org](https://metabo.omnipathdb.org). You can also
+query the REST API directly:
+
+```
+GET https://metabo.omnipathdb.org/cosmos/pkn?organism=9606&categories=all
+GET https://metabo.omnipathdb.org/cosmos/pkn?organism=10090&categories=transporters,ppi
+GET https://metabo.omnipathdb.org/cosmos/categories
+GET https://metabo.omnipathdb.org/cosmos/organisms
+GET https://metabo.omnipathdb.org/cosmos/resources
+```

docs/vignettes/index.md

@@ -6,3 +6,5 @@ In-depth tutorials and worked examples.
   and reference lists via the utils web service
 - [**OmniPath Database**](database.md) — Querying the OmniPath molecular
   biology database for interactions, annotations, and complexes
+- [**COSMOS PKN**](cosmos.md) — Multi-layer prior-knowledge network for
+  multi-omics causal reasoning with cosmosR

mkdocs.yml

@@ -39,6 +39,7 @@ nav:
     -   Overview: vignettes/index.md
     -   OmniPath Utils: vignettes/utils.md
     -   OmniPath Database: vignettes/database.md
+    -   COSMOS PKN: vignettes/cosmos.md
 -   API Reference: reference/index.md
 -   About: about.md