Opened 2 years ago

Last modified 6 weeks ago

#832 _started task

emphasize group name conventions

Reported by: westram Owned by: westram
Priority: major Milestone:
Component: ARB_NTREE Version: SVN
Keywords: Cc:

Description (last modified by westram)

The following conventions for names of taxonomic groups are/shallBe used in arb databases.

Some characters are problematic

character problem implemented behavior

_

used for groups combining multiple taxonomic ranks
like in Ordername_Familyname

(V) warn-on-write since [19278]

~

used when a taxon is "spread" across the tree. In that case the taxonname may occur in an enumerated flavour like

  • TaxonXXX
  • TaxonXXX~1
  • TaxonXXX~2

(V) warn-on-write since [19278]

/

used by taxonomy() ACI-command.
Display in tree may be confusing when group names contain slashes.

(V) warn-on-write since [17110]

;

used in "tax…" entries to separate groups

(V) warn-on-write since [19278]

!

used as prefix for keeled groups
⇒ shall not occur at beginning of groupnames

(V) error-on-write since [17110]

Needed fixes:

  • extend ACI command taxonomy to accept a 3rd parameter to specify the separator to use, e.g. taxonomy(100,";")
  • predefined ACIs for generating tax entries shall
    • use new taxonomy parameter to directly create ';'-separated tax-entries
    • translate _;
    • remove enumerated suffixes
  • review parts of arb which auto-generate group names
    • make sure their defaults follow the above conventions:
    • do not notify about violation of group naming convention for each of e.g. 100 generated groups.
      Instead collect all and maybe show the first three warnings or so.
      (V) implemented with [19277].
  • implement #833 (generate taxonomic groups from tax…-entries)

Change History (11)

comment:1 Changed 2 years ago by westram

  • Description modified (diff)

comment:2 Changed 2 years ago by westram

  • Description modified (diff)

comment:3 Changed 2 years ago by westram

  • Description modified (diff)

comment:4 Changed 2 years ago by westram

  • Description modified (diff)

comment:5 Changed 6 weeks ago by westram

  • Owner changed from devel to westram
  • Priority changed from normal to major
  • Status changed from new to _started

comment:6 Changed 6 weeks ago by westram

  • Description modified (diff)

comment:7 Changed 6 weeks ago by westram

  • Description modified (diff)

comment:8 Changed 6 weeks ago by westram

  • Description modified (diff)

comment:9 Changed 6 weeks ago by westram

arb now complains about "unwanted" group names using the following messages:

  • will interfere with taxonomy when ; or / are used.
  • reserved for overlapping groups when _ is used.
  • reserved for splitted groups when ~NUM (e.g. ~13) is used at end of name.

comment:10 Changed 6 weeks ago by westram

  • Description modified (diff)

comment:11 Changed 6 weeks ago by westram

  • Description modified (diff)
Note: See TracTickets for help on using tickets.