ITADN

[Feature Request] Fuzzy name search to taxonomy identifier

#15Closedjolespin 创建于 2023-11-01
J
jolespincommented
Similar to https://github.com/etetoolkit/ete/blob/1582ea2aa0d28065f4757b8b5af74367f6abe19f/ete4/ncbi_taxonomy/ncbiquery.py#L112C30-L112C30 ``` def get_fuzzy_name_translation(self, name, sim=0.9): """Return taxid, species name and match score from the NCBI database. The results are for the best match for name in the NCBI database of taxa names, with a word similarity >= `sim`. :param name: Species name (does not need to be exact). :param 0.9 sim: Min word similarity to report a match (from 0 to 1). """ ``` For example, EukZoo has an annotation from a source organism id `AddRef0031` labeled as species `Paramecium tetraurelia` and strain `Stock d4-2`. A manual search for this shows https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=412030 but the keyword "stock" is missing even though they are certainly the same. Would it be possible to include this type of searching?
关闭于 2024-08-03 7 条评论