Design and implement scala model for ncbiTaxonomy

[alberskib]

Implement scala model for ncbiTaxonomy (similar like model for GO)

[alberskib]

That's all relationships and properties that we would like to store for ncbiTaxonomy?

  val schema = GraphSchema("ncbiTaxonomy", 
    properties = 
      id :~:
      name :~:
      comment :~:
      scientificName :~:
      ∅, 
    vertexTypes = 
      NcbiTaxon :~: 
      Rank :~:
      ∅,
    edgeTypes = 
      Parent :~: 
      AssignedRank :~:
      Subrank :~:
      ∅
  )

from https://github.com/bio4j/scala-model/blob/master/src/main/scala/bio4j/model/module/ncbiTaxonomy.scala

[alberskib]

@bio4j/dynamograph Bump

[laughedelic]

I think, that's all. @pablopareja maybe you know it better?

[pablopareja]

So far we were not modelling Rank as a vertex but rather as a simple property for NCBITaxon.
I actually don't know if it's worth it to include it and/or whether it's reliable...? 😕
Maybe @rtobes and @marina-manrique can help us out with this?

[rtobes]

Rank is very important because there are many analysis based on rank. Biologically is more expressive than the level in the taxonomy tree.
One important thing is to add to each rank a number indicating the order of taxonomical specificity. It allows ordering by specificity many things as for example the assignments in metagenomics analysis. I don't know how to model the order number but perhaps as a property?

[eparejatobes]

@rtobes yes a property for the level is a nice addition. And there should be a vertex type for rank (there is onesuch in what @alberskib wrote).

[rtobes]

To clarify. This is the rank order number that I am talking about:
Order number Rank
0 no rank
1 superkingdom
2 kingdom
3 superphylum
4 phylum
5 subphylum
6 class
7 subclass
8 order
9 suborder
10 family
11 subfamily
12 tribe
13 subtribe
14 genus
15 subgenus
16 species group
17 species subgroup
18 species
19 subspecies

After reading the @alberskib comment I see that the edgeType subrank will allow to infer the order number but to have this number as a property perhaps would do easier to organize some query results.