Using the Freebase and the Bioportal Widgets to create a semantic object.
The following HTML code uses:
- a Widget from the NCBO Bioportal for the Protein-protein interaction Ontology
- And two Widgets from Freebase, linking to the proteins, the genes and the diseases.
After completion, it generates a JSON object describing a semantic object:
{
"subject":"http://www.freebase.com/view/en/nsp3",
"predicate":"http://purl.org/obo/owl/MI#MI_0407",
"value":"http://www.freebase.com/view/en/roxan",
"pmid":15047801
} 
Source
You can download the source and test it:
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| <html> | |
| <head> | |
| <link type="text/css" rel="stylesheet" href="http://freebaselibs.com/static/suggest/1.3/suggest.min.css" /> | |
| <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"></script> | |
| <script type="text/javascript" src="http://freebaselibs.com/static/suggest/1.3/suggest.min.js"></script> | |
| <script type="text/javascript" src="http://bioportal.bioontology.org/javascripts/widgets/form_complete.js"></script> | |
| <script type="text/javascript"> | |
| var freebase_topics= { | |
| type:[ '/biology/protein','/biology/gene','/medicine/disease'] | |
| }; | |
| function update_json_field() | |
| { | |
| var o={subject:null,predicate:null,value:null,pmid:null}; | |
| var p=document.getElementById("prot1").value; | |
| if(p.indexOf("http://")==0) o["subject"]=p; | |
| p=document.getElementById("prot2").value; | |
| if(p.indexOf("http://")==0) o["value"]=p; | |
| p=document.getElementById("predicate").value; | |
| if(p.indexOf("http://")==0) o["predicate"]=p; | |
| p=document.getElementById("pmid").value; | |
| if(p.length!=0 && p.match(/[1-9][0-9]*/)) o["pmid"]= parseInt(p); | |
| var root=document.getElementById("json"); | |
| root.value=JSON.stringify(o); | |
| } | |
| $(function() { | |
| $("#prot1").suggest(freebase_topics).bind("fb-select",function(e, data) | |
| { | |
| var root=document.getElementById("prot1"); | |
| root.value="http://www.freebase.com/view"+data.id; | |
| update_json_field(); | |
| }); | |
| }); | |
| $(function() { | |
| $("#prot2").suggest(freebase_topics).bind("fb-select",function(e, data) | |
| { | |
| var root=document.getElementById("prot2"); | |
| root.value="http://www.freebase.com/view"+data.id; | |
| update_json_field(); | |
| }); | |
| }); | |
| </script> | |
| </head> | |
| <body> | |
| <fieldset class="search"> | |
| <legend>Create a new Fact</legend> | |
| <table> | |
| <tr> | |
| <th><label for="prot1">Protein 1:</label></th> | |
| <td><input type="text" placeholder="Protein 1..." id="prot1" size="50"/></td> | |
| </tr> | |
| <tr> | |
| <th><label for="predicate">Predicate:</label></th> | |
| <td><input type="text" placeholder="Predicate..." id="predicate" class="bp_form_complete-1040-uri" size="50"/></td> | |
| </tr> | |
| <tr> | |
| <th><label for="prot2">Protein 2:</label></th> | |
| <td><input type="text" placeholder="Protein 2..." id="prot2" size="50" onchange="update_json_field();"/></td> | |
| </tr> | |
| <tr> | |
| <th><label for="pmid">PMID:</label></th> | |
| <td><input type="number" min="1" placeholder="PMID..." id="pmid" size="50" onchange="update_json_field();"/></td> | |
| </tr> | |
| <tr> | |
| <th><label for="json">JSON</label></th> | |
| <td><textarea type="text" cols="50" rows="5" readonly="true" placeholder="{}" id="json" size="50"></textarea></td> | |
| </tr> | |
| </table> | |
| </fieldset> | |
| </body> | |
| </html> |
That's it,
Pierre
1 comment:
Nice! This is exactly the kind of use case people should be thinking about.
I doesn't validate the input right now, does it? That is, make sure the selected protein is a protein? At least, I noted that also things other than proteins where shown upon the autocomplete. Also, the predicate should of course allow linking two proteins... I haven't looked at the ontology yet, but perhaps the range and domains are not defined in that ontoloty anyway...
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