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GNOme Ontology Traversal

Valid Monosaccharides

The following monosaccharides are indexed by GNOme:

  1. Hex
  2. HexNAc
  3. dHex
  4. NeuAc
  5. NeuGc
  6. Pen
  7. Fuc

The following "free" substituents are also included:

  1. S - sulfate
  2. P - phosphate

In order to map a glycan composition to an entry in GNOme, it must be composed of only these components. Glycans containing other monosaccharides may be included, but they will be encoded as "Xxx".

Resolution Algorithm

Step 1. Build Subsumption Graph

  1. Construct a directed graph where all terms are nodes.
  2. For each term p, find all terms C which have an is_a relationship with them and create an edge from p to c for each c in C.

Step 2. Construct Mass Index

  1. For each child term of GNO:00000001 c, if the name of c matches the pattern /molecular weight (\d+(\.\d+)?) Da/, then add c to a list of (term, mass) pairs I.
  2. Sort I by mass.

Step 3. Index Traversal

  1. For query glycan G, compute the neutral monoisotopic mass of G. Search the index I from Step 2 for the mass of G, finding the nearest available term within 0.1 Da.