• Table of contents
• 2013-06-13 conference call
  • To do for Brad
    • determine higher_plant_group node names in Tropicos/APGIII backbone
    • ask Naim to include TNRS version columns in CSV download
    • e-mail out which meeting dates not available this summer
  • To do for Aaron
    • include GCC when running TNRS
    • fix higher_plant_group_nodes mapping
    • plant/non-plant genus/family homonyms
    • observation filtering
    • switch from NCBI backbone to Tropicos
    • analytical_stem_view: add disambiguating prefix for TNRS accepted name terms
    • analytical_stem_view: add combination of TNRS accepted and matched name
    • add species_binomial
    • FIA filtering
    • document TNRS terms in VegCore data dictionary
    • include TNRS version and settings in TNRS cache
    • include our TNRS client's version in TNRS cache
    • future GBIF exports
  • Availability

2013-06-13 conference call¶

To do for Brad¶

determine higher_plant_group node names in Tropicos/APGIII backbone¶

see higher_plant_group node names in Tropicos APGIII

• is the list in the BIEN2 analytical DB overview (p. 12 bottom > higherPlantGroup) complete?
  "bryophytes", "ferns and allies", "flowering plants", "gymnosperms (conifers)", "gymnosperms (non-conifer)"
  • e.g. there is an entry for "seed plants and ferns" under polyphyletic clades (p. 13 bottom > last ¶), but it is not in the list above
• on Monday?

ask Naim to include TNRS version columns in CSV download¶

Naim has been e-mailed and a feature request submitted at *TNRS-185* .

In order to know when to refresh our TNRS cache, it would be useful to have the following CSV columns indicating when the TNRS source code or database has changed:

• Start_time (e.g. Thu Jun 13 11:42:01 MST 2013)
• TNRS_app_version (e.g. 3.2)
• TNRS_db_version
• Github_revision_number (e.g. e18a25f79bfc1a3cd6c2a4f0803c84e49f8d19aa)

• the TNRS source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/

e-mail out which meeting dates not available this summer¶

To do for Aaron¶

include GCC when running TNRS¶

• it provides more synonyms than Tropicos for Asteraceae, and the accepted names still match the Tropicos backbone
• positioned before Tropicos in the sources list, so that GCC will be used instead when it provides a result
• we had originally removed this along with USDA because "GCC is for only one family (Asteraceae)" (r5691)

fix higher_plant_group_nodes mapping¶

• contrary to the list in the BIEN2 analytical DB overview (p. 13 bottom > last ¶), "ferns and allies" should not include all the nodes in bryophytes
  "ferns and allies": bryophytes (see above) + "Moniliformopses"

plant/non-plant genus/family homonyms¶

• genus and family homonyms are now both available in a delimited format
• can't use species homonyms to whitelist binomials because the list is not exhaustive

observation filtering¶

• observation_is_plant
• range_model_include
• counts of names, observations that are/are not plants

switch from NCBI backbone to Tropicos¶

see higher_plant_group node names in Tropicos APGIII

• this will avoid family+genus mismatch problems due to NCBI using a different family classification (needed when determining higher_plant_group)
• NCBI is also missing a number of genera from Tropicos
• use Tropicos name and classification tables, joined together
• using the TNRS copy of Tropicos at ssh://arjuna.iplantcollaborative.org:1657 :
  

  ssh -p 1657 aaronmk@arjuna.iplantcollaborative.org
  

• TNRS batch-downloads the names from the Tropicos web service once a year (script runs overnight)

analytical_stem_view: add disambiguating prefix for TNRS accepted name terms¶

analytical_stem_view: add combination of TNRS accepted and matched name¶

• TNRS "no opinion" names don't have a taxon concept (accepted name), just a matched name

add species_binomial¶

• species_binomial: (from Brad)
  

  IF(Accepted_species IS NOT NULL, Accepted_species,
  IF(Specific_epithet_matched IS NOT NULL,CONCAT(Genus_matched,' ',Specific_epithet_matched),
  NULL)
  )
  

FIA filtering¶

document TNRS terms in VegCore data dictionary¶

include TNRS version and settings in TNRS cache¶

• this helps determine when the TNRS cache needs to be reloaded (and which names to reload)
• retrieve this from the TNRS web app's download settings file (using Download settings button displayed once results returned)

• the following attributes should be included as cache table columns:
  • TNRS URL
  • Job type
  • Contains Id
  • Start time
  • TNRS version
  • github revision (from https://github.com/iPlantCollaborativeOpenSource/TNRS)
  • TNRS DB version (not yet included)
  • Sources selected
  • Match threshold
  • Classification
  • Allow partial matches?
  • Constrain by higher taxonomy
• the following attributes are not needed:
  • E-mail (always set to tnrs@lka5jjs.orv when using the web app download)
  • Id (the session key)
  • Finish time (unused, always null)

include our TNRS client's version in TNRS cache¶

• in addition to the TNRS web service's version, the client version is needed to track changes to the format we encode data in

• the following columns are needed:
  • global svn revision
  • /lib/tnrs.py revision (currently r9525)
  • /bin/tnrs_db revision (currently r9530)

• for existing rows, this information can be reconstructed from the Time_submitted

future GBIF exports¶

• change runscripts to not hardcode date in export filename

Availability¶

• Brad won't be available for some meetings this summer
  (he's full-time iPlant until end of June, then traveling in Canada and doing consulting)
  • Brad will send meeting dates he won't be available
• Bob not here (getting ready for trip)