VertNet bettertaxonomy.py presentation

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1. Scientific names (genus, species)
2. Meaningless name Scientific names (genus, species) Meaningful name Semi-meaningless name
3. Meaningless name Scientific names (genus, species) Meaningful name Semi-meaningless name UNKNOWN Blank Incidental
4. Meaningless name Scientific names (genus, species) Meaningful name Semi-meaningless name UNKNOWN Blank Incidental FROG OR TOAD, UNIDENTIFIED Green bird with blunt bill. Unidentified. UNKNOWN ANTSHRIKE
5. Meaningless name Scientific names (genus, species) Meaningful name Outdated name Current name Semi-meaningless name UNKNOWN Blank Incidental FROG OR TOAD, UNIDENTIFIED Green bird with blunt bill. Unidentified. UNKNOWN ANTSHRIKE
6. Meaningless name Scientific names (genus, species) Meaningful name Outdated name Current name Semi-meaningless name UNKNOWN Blank Incidental FROG OR TOAD, UNIDENTIFIED Green bird with blunt bill. Unidentified. UNKNOWN ANTSHRIKE Oncifelis Acanthidositta Acanthocottus
7. Meaningless name Scientific names (genus, species) Meaningful name Outdated name Current name Semi-meaningless name UNKNOWN Blank Incidental FROG OR TOAD, UNIDENTIFIED Green bird with blunt bill. Unidentified. UNKNOWN ANTSHRIKE Oncifelis Acanthidositta Acanthocottus Leopardus Acanthisitta Myoxocephalus
8. Scientific names (genus, species) Python 3 script (bettertaxonomy.py)
9. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database
10. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists
11. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine
12. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine Local CSV
13. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine Local CSV Dropbox/GitHub
14. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine Local CSV Mammal Species of the World Dropbox/GitHub
15. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine Local CSV Mammal Species of the World ITIS Dropbox/GitHub
16. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine Local CSV Mammal Species of the World ITIS Dropbox/GitHub
17. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine Local CSV Mammal Species of the World ITIS Dropbox/GitHub
18. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine Local CSV Mammal Species of the World ITIS NCBI Taxonomy Dropbox/GitHub
19. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine Local CSV Mammal Species of the World ITIS NCBI Taxonomy Fishbase Dropbox/GitHub
20. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine Local CSV Mammal Species of the World ITIS NCBI Taxonomy Fishbase … Dropbox/GitHub
21. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine Local CSV Mammal Species of the World ITIS NCBI Taxonomy Fishbase … Dropbox/GitHub
22. Scientific names (genus, species) Python 3 script (bettertaxonomy.py) 1. Internal database 2. GBIF Checklists 3. TaxRefine Local CSV Mammal Species of the World ITIS NCBI Taxonomy Fishbase … Dropbox/GitHub Semi-meaningless names!
23. Usage • $ python3 better_taxonomy.py input.csv -i internal.csv > output.csv
24. Usage • $ python3 better_taxonomy.py input.csv -i internal.csv > output.csv • Program: https://github.com/gaurav/bettertaxonomy/tree/ develop
25. Usage • $ python3 better_taxonomy.py input.csv -i internal.csv > output.csv • Program: https://github.com/gaurav/bettertaxonomy/tree/ develop • From: https://docs.google.com/spreadsheets/d/16Dpuo- NqXjpjCLVrHHyQ0uvQxNQA35oIQOewPHrLLfg/edit? usp=sharing
26. Usage • $ python3 better_taxonomy.py input.csv -i internal.csv > output.csv • Program: https://github.com/gaurav/bettertaxonomy/tree/ develop • From: https://docs.google.com/spreadsheets/d/16Dpuo- NqXjpjCLVrHHyQ0uvQxNQA35oIQOewPHrLLfg/edit? usp=sharing • To: https://docs.google.com/spreadsheets/d/ 1Jpr6stWGR3qe0swQ4_215kogau2lqmWxaDivBbGVd60/ edit?usp=sharing
27. Next steps 1. Speed: caching, combine queries 2. Prioritise checklists: by class, in configuration file 3. Higher taxonomy: support semi-meaningful names