Rework GECKO for OBO request

[beckyjackson]

GECKO for OBO is stored in a template here: https://docs.google.com/spreadsheets/d/1bYnbxvPPFO7D7zg9Tr2e32jb8l13kMZ81vP_iaSZCXg/edit#gid=0

I've reworked GECKO to be more in-line with OBO principles. This file is in src/ontology/gecko.owl, but is different than the IHCC browser needs. Because of this, I also generate an "IHCC view" at src/ontology/ihcc-gecko.owl which lines up with the categories and labels for the browser.

In this rework, I ended up removing some CINECA terms. These were terms that were not used in any of the mappings that I've done so far on various cohorts:

• venous or arterial (blood)
• microbial data (microbiology)
• biosample source/anatomical location (microbiology)
• available data format(s) (microbiology)
• sample size (genomics - replaced with biosample size)
• available data format(s) (genomics)
• availability (genomics)
• processing method (genomics)
• associated cell type/tissue type/biosample (genomics)
• associated phenotype (genomics)
• main diagnosis (genomics)
• associated disease (genomics)
• associated medication (genomics)
• diagnosis (diseases - this was merged up into "disease")
• non-pharmacological interventions (questionnaire/survey data - this was merged down into "surgical interventions")
• general research data documents
• posology (medication - merged into administration method)
• genealogy (socio-demographic and economic characteristics)

Many of the terms have also been renamed, but I've added an annotation property "IHCC browser label" with the old names. This is the label that is used in the IHCC view. The "IHCC category" is the parent that is used for the IHCC view.

The top-level IHCC categories do not appear as ontology terms in gecko.owl, but they do appear as grouping categories in ihcc-gecko.owl.

[jamesaoverton]

Sorry, I dropped the ball on this. I'll review it today.