evoweb

EvoWeb

EvoWeb - An Open Knowledge Graph of Co-evolving Genes (NIAID)

3.3M triples
1 classes
3 properties
18.3K subjects

EvoWeb is a weighted network of protein-protein functional relations, reconstructed from prior knowledge available from genomic sequences, allowing users to find hypothetical proteins involved in protein complexes or separate steps of a biochemical pathway, as well as 12 signals of coevolution to quantify the degree of shared evolution between genes.

This project is a continuation of work done in the EvoWeaver project (https://www.nature.com/articles/s41467-025-59175-6) going beyond individual protein pairs.

Get all organisms associated with protein groups (via UniProt) 
PREFIX uni: <http://purl.org/weso/uni/uni.html#>
PREFIX re: <http://www.w3.org/2000/10/swap/reason#>
PREFIX ref: <http://purl.org/vocab/relationship/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX uniprot: <http://purl.uniprot.org/uniprot/>
PREFIX uniprot-core: <http://purl.uniprot.org/core/>
PREFIX refs: <https://www.ncbi.nlm.nih.gov/protein/>
PREFIX ncbi: <http://purl.obolibrary.org/obo/NCBITaxon_>
PREFIX refs-uni: <http://purl.uniprot.org/refseq/>
PREFIX ncbi-uni: <http://purl.uniprot.org/taxonomy/>

select ?group ?groupLabel ?organism ?organismLabel {
  {
  ?group rdfs:label ?groupLabel ; skos:member ?member .
bind(iri(replace(str(?member),str(refs:),str(refs-uni:))) as ?member_uni)
  service <https://sparql.uniprot.org/sparql> {
    ?member_uni uniprot-core:organism ?organism_uni .
  }
}
  bind(iri(replace(str(?organism_uni),str(ncbi-uni:),str(ncbi:))) as ?organism)
  ?organism rdfs:label ?organismLabel
} limit 100

graph TD
Run in FRINK
SPARQL Endpoint https://frink.apps.renci.org/evoweb/sparql
Triple Pattern Fragments https://frink.apps.renci.org/ldf/evoweb
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