This directory holds regression tests that can be used to check either the taxonomy or the synthetic tree.
The files with names of the form monophyly*.csv have rows like the following:
Diptera,661378,"http://www.jstor.org/stable/2666712"
meaning:
"Raise an alert if the taxon Diptera (as it is defined by OTT by ottid 661378) does not show up as monophyletic. Evidence for this monophyly claim may be found in the article with DOI http://dx.doi.org/10.1006/mpev.2001.1055 ."
Similarly, the files inclusions*.csv have rows like the following:
Taxon1,Taxon2,"remarks"
E.g.
Odontomachus rixosus,Hymenoptera,788940,"http://dx.doi.org/10.1242/jeb.015263"
meaning:
"Raise an alert if the taxon Odontomachus rixosus (with ottid 788940) does not show up as included in the taxon Hymenoptera. Evidence for this inclusion claim may be found in the article with DOI http://dx.doi.org/10.1242/jeb.015263 ."
Or:
Aeropyrum camini,Archaea,"http://www.ncbi.nlm.nih.gov/taxonomy accessed 2014-07-24"
"Aeropyrum camini is in Archaea, according to http://www.ncbi.nlm.nih.gov/taxonomy as it was when accessed on 2014-07-24."
"Inclusion" can be indirect, i.e. it doesn't refer to taxon parent/child relationships but rather logical inclusion, as if the taxa were sets of individual organisms or samples.
Remarks are free text. Please make them as verbose as necessary in order to help persuade a skeptic who doubts the claim at some unknown future point in time.
Where there is any question, taxon names are as defined by OTT. OTT ids can be given in lieu of names, for truly difficult homonym situations. (For this to really work well the meaning of OTT ids has to be anchored and stable. This is work in progress.)
The python script 'generate_test_scripts.py' will read the csv files "monophyly_tests.sh" and "inclusion_tests.sh" and generate shell scripts containing curl calls that will collect the desired data.