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BiogeographicAreaOntology / bigaeon

repo for the Biogeographic Area Ontology
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Reference improved taxonomy #1

Open pbuttigieg opened 8 years ago

pbuttigieg commented 8 years ago

NCBI Taxonomy may not be sufficient for many working in this domain. @pyilmaz Pelin Yilmaz suggests examining the Integrated Taxonomic Information Service as a start. @rlwalls2008 - may be interesting for taxon-linked PCO classes (and thus ENVO habitats)

pbuttigieg commented 8 years ago

@cmungall - of interest in several projects.

@pyilmaz - bringing in SILVA would be desirable too: is there (or could one be made) a JSON, YAML, or TSV export of SILVA? It would be great if an OBO or OWL export could be made, but the other formats are workable too. With such an export, we can start linking more ontology classes to SILVA taxon IDs.

pyilmaz commented 8 years ago

@pbuttigieg - JSON or YAML export is not planned at this point, but we do have a TSV export: Please see: http://www.arb-silva.de/fileadmin/silva_databases/release_123/Exports/taxonomy/tax_slv_ssu_123.txt This is how the file is structured:

taxslv[ls]su_VERSION.txt

These files contain taxonomic rank designations for all taxonomic paths used in the SILVA taxonomies. Additionally, a unique numeric identifier is assigned to each taxon (path). These identifiers will be mostly stable in upcoming SILVA releases.

IDs used in the SSU and LSU files do not match.

Field description: path: The full taxonomic path including the name of the group itself. Segments are separated with ";" taxid: numerical identifier rank: The rank designation. remark: Can be empty ('') or a or w. a: Marks taxa of environmental origin. That is, taxa containing no sequence coming from a cultivated organism. w: Marks taxa scheduled for revision in the next release. release: The SILVA release version