Metabolites2Network - Discovery

• ScalaJs functional implementation based of the ontology based matching describe in the "Improving lipid mapping in Genome Scale Metabolic Networks using ontologies." [1] using the Chemical Entities of Biological Interest (ChEBI)

API

• ontology_based_matching : build path possibility between an URI and a list of URIs
• build_graph : get a sequence of chebiid using results from ontology_based_matching
• graph_html : get html item list using the sequence of chebiid resulting from build_graph
• get_has_role : get role defining by the RO_0000087 relation about a chebidid
• get_description : get information about a chebidid

ontology_based_matching Javascript Examples

• input :

  • chebid a reference ChEBI id : String
  • listChebIds a list of CheBid : Array[String]
  • score (optional) max score to reach : Double (default : 4.5)

• output : list of object {uri: <string>, property: <string> , score: <double>}

  • uri uri from the input list
  • property possible value : "is_conjugate_acid_of", "is_conjugate_base_of", "has_functional_parent","is_tautomer_of","chas_parent_hydride","is_substituent_group_from", "is_enantiomer_of"
  • score distance between uri and chebid . distance is positive (1.0) when chebid matches a more generic class in the list. The distance is slightly increased (by 0.1) when a relation different tha is_a of the lipid is present in the listChebIds

cdn

<script type="text/javascript" src="https://cdn.jsdelivr.net/gh/emetabohub/chebi-discovery@latest/dist/chebi-discovery-web.js">

<script type="text/javascript" src="https://cdn.jsdelivr.net/gh/emetabohub/chebi-discovery@latest/dist/chebi-discovery-web.js"> </script>
<script>
  let config = `{
             "sources" : [{
               "id"  : " - Forum Semantic Metabolomics - ",
			         "url" : "https://forum.semantic-metabolomics.fr/sparql"
             }]
        }`;
        
        
        let chebIdRef="http://purl.obolibrary.org/obo/CHEBI_15756";
        let lIdChebis = ["http://purl.obolibrary.org/obo/CHEBI_7896"];
        let maxDeep = 3.0 ;
        
        ChebiDiscovery(config)
           .ontology_based_matching(chebIdRef,lIdChebis,maxDeep)
               .then ( (lTupleObject) => {
                   let div = document.createElement("div") ;
                   div.innerHTML = "<h3>ontology based matching of</h3> <pre>"+JSON.stringify(lTupleObject)+"</code>" ;
                   document.body.appendChild(div);
               })
               .catch( msg => { console.error(msg) ; } ) ;
                
</script>
<body/>

see jsfiddle example

Scala Example

see example : test

Dev/Test environment (sparql endpoint with ChEBI.owl)

docker-compose up -d

check if the chebi ontology is loaded with docker-compose logs

open ./test.html in the web browser.

Lib generation

## devel ->  <script type="text/javascript" src="<root>/chebi-discovery/target/scala-2.13/scalajs-bundler/main/chebi-discovery-fastopt-bundle.js"> </script> 
sbt fastOptJS::webpack
## cdn
./update_cdn_libjs.sh

References

[1] Poupin, N., Vinson, F., Moreau, A. et al. Improving lipid mapping in Genome Scale Metabolic Networks using ontologies. Metabolomics 16, 44 (2020). https://doi.org/10.1007/s11306-020-01663-5