Anomalous entity entries in CSV output

[EmanuelFaria]

ISSUE: Using sciSpacy, to create CSV I noted a number of issues in the entities it found and the labels attached to them.

NOTE: I suspect at least some of the problem could be due to the output being comma-delimited, so I propose we try with tab-delimited output, and I'll re-run this test corpus and compare.

In the attached PDF and CSV you'll see I added two new columns — Anomaly and issue. (I did not identify the issue for most of these, but you'll get the gist)

In this case I was focusing on what entities were mis-labeled as DISEASE

The types of errors include the following being identified as DISEASE:

• email address
• author names (or parts thereof)
• apostrophe's (in many cases a lone apostrophe was labelled a DISEASE. Maybe before exporting we include a step to replace all smart quotes and apostrophes with dumb ones?)
• plant names and extracts
• organization names (or parts thereof)
• chemical compounds
• names of proteins
• measurements (or parts thereof)
• fatty acid is treated as a disease throughout
• microbes are treated as a disease throughout, but I suspect that is intentional
• factors such as TNF-alpha
• chemical terms such as dissolution/solubility
• Moroccan cultural heritage

Also, noticed some mis-labeled as CHEMICAL

• COVID-19
• random numbers

Also, many Abbreviations came up as entities, but were not expanded in the abbreviations_longform column