GloBI review of tick interaction database

[jhpoelen]

After fixing globi.json (trailing comma see 0063dac), I was able to generate a Elton review report - review report:

  / ____| |     |  _ \_   _| |  __ \          (_)               
 | |  __| | ___ | |_) || |   | |__) |_____   ___  _____      __ 
 | | |_ | |/ _ \|  _ < | |   |  _  // _ \ \ / / |/ _ \ \ /\ / / 
 | |__| | | (_) | |_) || |_  | | \ \  __/\ V /| |  __/\ V  V /  
  \_____|_|\___/|____/_____| |_|  \_\___| \_/ |_|\___| \_/\_/   
 | |           |  ____| | |                                     
 | |__  _   _  | |__  | | |_ ___  _ __                          
 | '_ \| | | | |  __| | | __/ _ \| '_ \                         
 | |_) | |_| | | |____| | || (_) | | | |                        
 |_.__/ \__, | |______|_|\__\___/|_| |_|                        
         __/ |                                                  
        |___/                                                   
Miller 5.3.0
s3cmd version 2.1.0
openjdk version "1.8.0_282"
OpenJDK Runtime Environment (build 1.8.0_282-8u282-b08-0ubuntu1~18.04-b08)
OpenJDK 64-Bit Server VM (build 25.282-b08, mixed mode)
using local elton found at [/usr/local/bin/elton]

Review of [ParasiteTracker/tick-interaction-database] using Elton version [0.10.7] started at [2021-03-08T21:06:10+01:00].
no update: using provided elton datasets dir [/var/cache/elton/datasets] instead.
creating review [ParasiteTracker/tick-interaction-database]... done.
listing interactions [ParasiteTracker/tick-interaction-database]... done.
listing nanopubs [ParasiteTracker/tick-interaction-database]... done.

Review of [ParasiteTracker/tick-interaction-database] included:
  - 511 interaction(s)
  - 24 note(s)
  - 512 info(s)

[ParasiteTracker/tick-interaction-database] has 24 reviewer note(s):
     24 target taxon name missing

See https://depot.globalbioticinteractions.org/reviews/ParasiteTracker/tick-interaction-database/README.txt for more information.

Note that the indexing of the tick database is a slightly delayed because of the minor syntax issue in globi.json - it should take a day or two for the tick interaction data to appear on https://globalbioticinteractions.org .

[jhpoelen]

@seltmann your tick database has been indexed by GloBI. See attached screenshot of https://www.globalbioticinteractions.org/?accordingTo=globi%3AParasiteTracker%2Ftick-interaction-database !

[jhpoelen]

@seltmann some questions about your data:

1. I noticed a taxon name notation [higher order] : [lower order], where the family name is often repeated in a separate column. E.g.,

targetTaxonName	targetFamilyName
Artiodactyla: Bovidae	Bovidae
Homo sapiens	Hominidae
Squamata: Scincidae	Scincidae
Squamata: Agamidae	Agamidae

Can you help me understand why you chose to use the ```[some name] : [some more specific name] notation?

2. to stick to naming conventions, suggest to rename targetFamilyName -> targetTaxonFamilyName. Similar for related source and common name column headers.

3. In lifestage column, I notice lists e.g.

sourceLifeStageName
All parasitic life stages
adults and nymphs
larvae and nymphs

Here, I would expect a new row for each life stage to help make explicit that specific life stages were observed to interact with specific hosts. Please let me know what your thoughts are on that.

Thanks again for sharing your data and I hope my comments were somewhat useful.