Add useful metadata to SBGN nodes/edges (glyphs, arcs, ports) either as nested xml elements ('bp:' or better define own schema if needed) inside <extensions/> and <notes/>, or simply using <![CDATA[...]]> and encoded JSON object in it.
Include, e.g.:
- HGNC, ChEBI, UniProt, PubMed IDs;
- BioPAX Class (name);
- synonyms (as
<label/> contains display name already);
- organism(s);
- data source(s);
- evidence ?
- generic or not (boolean)
One way to implement this feature in sbgn-converter, in a very flexible/extensible manner, would be using key:value entries from the Paxtools BioPAX object.annotations (bpe.getAnnotations()) map (and the annotations can be created in many different ways, e.g., within cPath2 or Sifgraph methods).
Add useful metadata to SBGN nodes/edges (glyphs, arcs, ports) either as nested xml elements ('bp:' or better define own schema if needed) inside
<extensions/>and<notes/>, or simply using<![CDATA[...]]>and encoded JSON object in it.Include, e.g.:
<label/>contains display name already);One way to implement this feature in sbgn-converter, in a very flexible/extensible manner, would be using key:value entries from the Paxtools BioPAX object.annotations (
bpe.getAnnotations()) map (and the annotations can be created in many different ways, e.g., within cPath2 or Sifgraph methods).