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VertNet bettertaxonomy.py presentation

Gaurav Vaidya
May 28, 2014
Science
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54

VertNet bettertaxonomy.py presentation

Gaurav Vaidya

May 28, 2014
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Transcript

  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 Meaningless name Scientific names (genus, species) Meaningful name Outdated name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 Meaningless name Scientific names (genus, species) Meaningful name Outdated name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 Meaningless name Scientific names (genus, species) Meaningful name Outdated name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