crawl nexus/newick tree

• fetch article info by pubmed.py with journal list

• fetch trees by fetch_tree.py which depends on dryad.py and figshare.py

• organize result and do statistics by organize_result.py, stats*.py

• output results by

  1. output_doi_info.py
  2. output_tree_info.py. This file will assign taxon to paper
  3. output_treefile.py. This program generate final json datasets get new taxon value.

• import to database

  • Use plant_tree_db's local_batch_submit.py. Cost hours since it mimics submit via web requests.

• integrated with treebase

  • export database
    • See crawl_out_for_draw.ipynb
  • fix treebase records
    • Treebase records may have invalid lineage assignment. Use output*.py to fix
    • Use old-new value table to update database
    • use count_taxon.ipynb to generate statistics output