What is a "most wanted name"?
It is a species-rank name that does not match to the GBIF backbone. A names in this context is any "reasonable looking" string of characters. Since un-interpreted free text from data publishers can vary significantly, it is necessary filter these verbatim names to get back something worth pursuing.
A "reasonable looking" binomial name has the following properties according to the most wanted names script:
- Has two words of at least 4 characters each separated by a space.
- Is not a OTU (Operational taxonomic unit)
- Is not a fossil (it might be reasonable to not match below Family for a fossil).
- Matches above Genus level
- Is labeled as rank SPECIES by the publisher
- Passes through the GBIF name parser as either
type: "SCIENTIFIC" or "INFORMAL" - Has more than 10 occurrence records tied to the name
- Is flagged as TAXON_MATCH_HIGHERRANK
Importantly this script might miss wanted names that do not fill in the v_taxonrank field. This is probably pretty common.
matchable_names.scala generates a table of most wanted names and exports them to custom downloads.
The most wanted names according to the most recent run.
| kingdom | v_scientificname | publisher_rank | taxonrank | occ_count | n_dataset | n_publisher |
|---|---|---|---|---|---|---|
| Plantae | Rhynchelytrium nepeng | SPECIES | FAMILY | 4562 | 2 | 1 |
| Plantae | Aliaria petiolata (M.Bieb.) Cavara & Grande | SPECIES | FAMILY | 1579 | 3 | 1 |
| Plantae | Iris xiphium (L.) Dryand. ex Ait. | SPECIES | FAMILY | 1202 | 2 | 1 |
| Fungi | Candolleomyces candolleanus | SPECIES | FAMILY | 1150 | 1 | 1 |
| Animalia | Expapillata firmatoi (Barretto, Martins & Pellegrino, 1956) | SPECIES | FAMILY | 1024 | 1 | 1 |
| Plantae | Callophycus laxus | SPECIES | FAMILY | 828 | 5 | 5 |
| Animalia | Tropicagama temporalis | SPECIES | FAMILY | 686 | 3 | 3 |
| Fungi | Sterile sorediate crust | SPECIES | FAMILY | 604 | 1 | 1 |
| Animalia | Ganglionus catenatus | SPECIES | FAMILY | 482 | 2 | 2 |
| Animalia | Deanemyia samueli (Deane, 1955) | SPECIES | FAMILY | 460 | 1 | 1 |
find the full dataset here.
Names like "Sterile sorediate crust" might need to be added to the blacklist.
This is simply a scala-spark script. It could be developed further into something that runs periodically or after each backbone build to compare wanted names.
Setup copy taxon_rank_mappings.tsv to hdfs.
FILE_NAME="taxon_rank_mappings.tsv"
COPY_DIR="/cygdrive/c/Users/ftw712/Desktop/gbif_most_wanted_names/data/"
scp -r $COPY_DIR$FILE_NAME jwaller@c5gateway-vh.gbif.org:/home/jwaller/
ssh jwaller@c5gateway-vh.gbif.org
hdfs dfs -put taxon_rank_mappings.tsvRun the scala script matchable_names.scala.
spark2-shell