10.09.2013 BiolDiv

Meeting notes: 10.09.2013 Afternoon

Participants: N.Bailly, E.Vanden Berghe, GP Coro, P.Pagano

Notes

Workflow for matching names and taxa

Elements and workflow:

1. Submitted file type: Unstructured text, Unstructured name list, Structured name list.
2. Dima’s Parser: If file type is Text or Unstructured name, apply Dima’s parser.
3. Reference files: CoL, WoRMS, CofF, FB, SLB. Possibility to select one or several or all.
4. Classification tree: Specify the taxon (taxa) in the reference files.
5. GSAy: Step by step approach: default selection of steps + possibility to remove/add some.
6. TaxaMatch fuzzy matching (Tony Rees): Removing or replacing letters. Selection of letters. Possibility to select genus and/or species.
7. Lexical distances (Fabio, Casey): Levinstein, other? Selection of distances. Selection of threshold. Possibility to select genus and/or species.
8. Soundex (Fabio, Casey): Java function. Selection of threshold. Possibility to select genus and/or species.
9. Taxonomic disambiguation: Check if the matched name corresponds to one or several taxa.
10. Taxonomic resolution (4D4Life classification comparison): Check if the family possibly provided by the user correspond to the family in the reference file. If not use the 4D4Life tool.
11. For final unmatched names, visual check of genera in the lower taxon provided (e.g., family is usual), list of species names by genus, list of species by family, list of species by other taxon if provided.

If the taxon was restricted (step 4), propose extension to other taxa for unmatched names, and restart the process.

From Step 5 to 9, and within them, each matching event gives a set of matched names, and non-matched. The matched names are porposed for display for visual control. The unmatched names are send to the next step.

Step description

File type

Users can submit: - unstructured texts where scientific names are cited inside the text (Unstructured type) - semi-structured name liss, one name per line, but not atomized in Classification/Genus/Species/Author/Year - structured list of names. Then it has to follow the proposed structure

Dima's Parser

In the case of unstructured or semi-structured, the files need to be parsed to get a structured file.

Classification tree

The user restricts the taxonomic framework in which he matches name, e.g., only fish names. It is done through a taxonomic tree. Several taxa may be selected (second priority option).

Nomenclatural and taxonomic authority files

The user selects