Duane-Stevenson-NOAA
commented
2 years ago This idea has come up a few times in the past, but Jay and I always resisted based on the thought that maintaining such an equivalency table could potentially be very time-consuming, particularly for invertebrates. We did (I really mean Jay, Nancy, and Heather did) produce a classification hierarchy table (RACEBASE.SPECIES_CLASSIFICATION) that includes classification of taxa from species to kingdom level. However, this table did not cross-reference ITIS or WoRMS codes, and is probably pretty outdated by now.
The production of a simple equivalency table (RACE species code = ITIS code) is probably not terribly difficult, and the maintenance of such a table might not be too bad (though not trivial). However, if the ambition is to establish heirarchical groupings and keep them parallel with ITIS, or some other external database, that will be a pit of despair for someone. Non-taxonomists are always shocked and dismayed by how often theories about higher level classification are revised and altered.
On Thu, Dec 1, 2022 at 1:20 PM Lewis-Barnett-NOAA @.***> wrote:
I wanted to put a placeholder here for considering how to streamline and augment our approach to coding taxonomy in RACEBASE.
As part of a NMFS/DFO working group @EmilyMarkowitz-NOAA https://github.com/EmilyMarkowitz-NOAA and I are participating in, it was identified that using data across NMFS and DFO regions (or those of other entities, such as ADFG) would require a common/unified system for classifying taxa (and updated names and taxonomies as they change over time). This would also be helpful for analyses that aim to aggregate data by a taxonomic level above that of the species.
While this would require a minor amount of manual checking once per year, it could reduce the amount of time we spend curating the taxonomic data by connecting our records to a widely-accepted taxonomic database. This would also be helpful for analyses that aim to aggregate data by a taxonomic level above that of the species. Most entities are gravitating toward ITIS https://www.itis.gov/ http://url for this purpose, and Emily has made great headway in matching our species definitions to those in ITIS (in addition to WoRMS). However, cases where matches aren't clear should probably be checked by those most familiar with the classification of the organisms we encounter...which would take some time up front but hopefully require little annual updating.
I defer to our taxonomists of course on if/how/when to approach this, but it would be great to have a conversation about it. @Duane-Stevenson-NOAA https://github.com/Duane-Stevenson-NOAA @SarahFriedman-NOAA https://github.com/SarahFriedman-NOAA @ThaddaeusBuser-NOAA https://github.com/ThaddaeusBuser-NOAA do you have any initial thoughts? Thanks!
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-- Duane Stevenson, Ph.D. Supervisory Fish Biologist Groundfish Assessment Program NMFS, Alaska Fisheries Science Center
EmilyMarkowitz-NOAA
Ned-Laman-NOAA
Lewis-Barnett-NOAA
NancyRoberson
SarahFriedman-NOAA
I wanted to put a placeholder here for considering how to streamline and augment our approach to coding taxonomy in RACEBASE.
As part of a NMFS/DFO working group @EmilyMarkowitz-NOAA and I are participating in, it was identified that using data across NMFS and DFO regions (or those of other entities, such as ADFG) would require a common/unified system for classifying taxa (and updated names and taxonomies as they change over time). This would also be helpful for analyses that aim to aggregate data by a taxonomic level above that of the species.
While this would require a minor amount of manual checking once per year, it could reduce the amount of time we spend curating the taxonomic data by connecting our records to a widely-accepted taxonomic database. This would also be helpful for analyses that aim to aggregate data by a taxonomic level above that of the species. Most entities are gravitating toward ITIS https://www.itis.gov/ for this purpose, and Emily has made great headway in matching our species definitions to those in ITIS (in addition to WoRMS). However, cases where matches aren't clear should probably be checked by those most familiar with the classification of the organisms we encounter...which would take some time up front but hopefully require little annual updating.
I defer to our taxonomists of course on if/how/when to approach this, but it would be great to have a conversation about it. @Duane-Stevenson-NOAA @SarahFriedman-NOAA @ThaddaeusBuser-NOAA do you have any initial thoughts? Thanks!