Documentation

[lnilya]

Hello!

I would be keen to use this package, but I can't get it to run.

The documentation is unclear to me.

1. What is a a source ID
2. Why do I need to provide column names? (They are in the CSV file already!?)
3. Is it possible to just use it as part of my python application and have some form of function pytaxon.getSynonyms(listOfSpciesnames...)?

It would be great if you had more explanation and example data to understand better how to use it.

Thank you!

[lnilya]

After tinkering and debugging a while I found out what the source ID is, but regardless of what I do, the result is always the same, the resulting xlsx file has Rank "Data Incomplete" and has all the entries in my original CSV file.

I uploaded my file SpeciesInfo.csv

The Species inside this file are all somewhat New Zealand specific and ~50-100 of them will not be found by this name elsewhere. I need to somehow found synonyms that would work in the TRY database for example.

Any chance you could help?

[marcos-sem-s]

Hello mr. Shabanov!

Sorry for the delay and thanks for opening the issue! I've just found out i've been using my secondary email for Github and not my professional one ;p, just fixed it though.

As for your questions, let's go each by each:

1. Pytaxon is a tool that connects to biodiversity databases using the Global Names Verifier API and corrects your research spreadsheet accordingly with which you choose, as the database is selected by the "source ID". The entire list of source ID may be viewed here: https://verifier.globalnames.org/data_sources. As for your database, the "TRY" one, would it be this one? https://www.try-db.org/TryWeb/Home.php? If so, I don't think it is present in the curated list of GNV, although I've found some others New Zealand biodiversity oriented databases inside GNV. They are: 139 - New Zealand Animalia & 209 - New Zealand Organizm Register. Unfortunattely both are yet not curated inside Pytaxon, as GNV API has some instabilities and inconsitencies in its API and we have to treat the data once again. But we will be adding the 139 and 209 as soon as possible! (as well as the other ones :D ).

2. It is necessary to provide the column names so Pytaxon can identify which columns are going to be identified and suggested corrections! For the database you attached in the issue, you'd use the "Species" and "Family" columns, it'd go something like this: pytaxon -r 'x, x, x, x, Family, x, Species, Species' -os 'SpeciesInfo.csv' -ss 'SpeciesInfoSuggestion.csv' -si 139.

3. Unfortunattely it is not yet possible, it is only avaiable by CLI and GUI, but soon we shall make avaiable by functions and our own API!

So that is it by now :D, if I can help with something else, you can reach out to me by here with the issue and by e-mail! For some further help, perharps reading our paper would clarify some things: https://doi.org/10.3897/BDJ.13.e138257. Once again, thank you the issue!

[lnilya]

Hi Marcos,

Thanks for the reply. Unfortunately I still can't get it to work. using "-si 139" creates an error. I think it is due to these being the only options:

    id_links = {
                1: ('COL ID Source', f'=HYPERLINK("https://www.catalogueoflife.org/data/taxon/{id_number}", "{id_number}")'),
                4: ('NCBI ID Source', f'=HYPERLINK("https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={id_number}", "{id_number}")'), 
                11: ('GBIF ID Source', f'=HYPERLINK("https://www.gbif.org/species/{id_number}", "{id_number}")'),
                180: ('INAT ID Source', f'=HYPERLINK("https://www.inaturalist.org/taxa/{id_number}, {id_number}")')
            }

But either of these numbers produces the same empty table (using the command line prompt you sent)

Any idea what to do?