Biological graphs from UniProt

Release:

6.1.2

Date:

Oct 28, 2026

Biological interaction graphs derived from the UniProt knowledgebase, where nodes are biological entities and edges are the relations between them (e.g. belongs_to, is_homologous_to); they support subgraph and path queries as in “Subgraph queries by context-free grammars”.

Graph	Num Nodes	Num Edges	Reachable pairs	Size (MB)	Download
unigraph_1	3082	11966	376578	0.972	unigraph_1.tar.gz 📥
unigraph_2	36468	168344	39888347	0.300	unigraph_2.tar.gz 📥
unigraph_3	41333	193866	52471840	0.344	unigraph_3.tar.gz 📥
unigraph_4	215481	1346130	808091802	2.25	unigraph_4.tar.gz 📥
unigraph_5	243839	1818404	2303590109	3.15	unigraph_5.tar.gz 📥
unigraph_6	286645	1708910	1722963921	2.94	unigraph_6.tar.gz 📥
unigraph_7	285577	2073268	2320964134	3.47	unigraph_7.tar.gz 📥
unigraph_8	449237	3385168	not available	5.72	unigraph_8.tar.gz 📥
unigraph_9	475479	3579034	not available	6.10	unigraph_9.tar.gz 📥
unigraph_10	2055882	17223588	not available	29.27	unigraph_10.tar.gz 📥

Canonical grammars

The grammar file is attached to the archive.

\[\begin{split}\begin{aligned} S &\to Seq \quad IsAssociated \quad IsSimilar \\ Seq &\to IsSimilar \quad (codes\_for \quad IsSimilar)? \\ IsSimilar &\to \varepsilon \\ &\mid has \quad IsSimilar \quad has_{r} \\ &\mid is\_homologous\_to \quad IsSimilar \quad is\_homologous\_to_{r} \quad IsSimilar \\ &\mid belongs\_to \quad IsSimilar \quad belongs\_to_{r} \\ &\mid participate\_in \quad IsSimilar \quad participate\_in_{r} \\ IsAssociated &\to refers\_to \quad refers\_to_{r} \end{aligned}\end{split}\]