#10209 "arabinose polymer" vs arabinan

[Chris Mungall]

In GO we use "arabinose polymer"

[Term]
id: GO:0042899
name: arabinose polymer transport
def: "The directed movement of an arabinose polymer, a repeating chain of arabinose monomers, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl]
subset: gosubset_prok  ! Prokaryotic GO subset
is_a: GO:0015751  ! arabinose transport

as well as "arabinan"

[Term]
id: GO:0031221
name: arabinan metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving arabinan, a branched homopolymer of L-arabinose." [GOC:mlg, ISBN:0198506732]
synonym: "arabinan metabolism" EXACT []
intersection_of: GO:0008152 ! metabolic process
intersection_of: has_participant CHEBI:22590 ! arabinan
is_a: GO:0005976  ! polysaccharide metabolic process
is_a: GO:0044723  ! single-organism carbohydrate metabolic process

The definitions are similar but not the same.

In this CHEBI request, Marcus suggests that the existing "arabinan" CHEBI term be defined as "A polysaccharide composed of arabinose residues."

https://sourceforge.net/p/chebi/curator-requests/2142/

Suggesting they are the same. If so we should relabel and add the appropriate logical def (and request a syn from CHEBI).

If not then we should answer in the CHEBI tracker.

We should use the CHEBI def in our embedded def in either case.

Note we also have:

[Term]
id: GO:0010402
name: pectic arabinan metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving **arabinan**, a polymer with an alpha-(1->5)-linked L-arabinofuranose (Araf) backbone that can be substituted with Araf-alpha-(1->2)-, Araf-alpha-(1->3)-, and/or Araf-alpha-(1->3)-Araf-alpha-(1->3)-side chains. **Arabinan** can be found as a side chain of the pectin rhamnogalacturonan I." [GOC:tair_curators]
synonym: "pectic arabinan metabolism" EXACT []
intersection_of: GO:0008152 ! metabolic process
intersection_of: has_participant CHEBI:61264 ! pectic arabinan
is_a: GO:0010400  ! rhamnogalacturonan I side chain metabolic process

The text def talks about generic "arabinan". To avoid confusion, it should say "pectic arabinan". Ideally the CHEBI text def should be used:

[Term]
id: CHEBI:61264
name: pectic arabinan
namespace: chebi_ontology
def: "Arabinofuranosyl groups which are arabinan side chains of pectin composed of alpha-(1->5)-linked Araf residues, and which can be further branched by alpha-L-Araf units at O-2 and/or O-3." []
xref: SUBMITTER:17383990
is_a: CHEBI:59595  ! arabinofuranosyl group

[Jane Lomax]

Changed 'arabinose polymer' to 'arabinan' and went with Marcus's suggested definition for all. Also fixed xps.