Analysis of usage of BFO by ENVO

[cmungall]

Most OBO ontologies typically branch off of a handful of BFO tips - ENVO makes user of a number of different ones:

bfo	bfo label	direct children
BFO:0000006	spatial region	1
BFO:0000015	process	1
BFO:0000016	disposition	5
BFO:0000023	role	3
BFO:0000024	fiat object	4
BFO:0000027	object aggregate	7
BFO:0000029	site	5
BFO:0000030	object	5
BFO:0000034	function	2
BFO:0000038	one-dimensional temporal region	6
BFO:0000040	material entity	8
BFO:0000146	two-dimensional continuant fiat boundary	2

We can see the terms hanging off the tips here

• [] BFO:0000001 ! entity
  • [i] BFO:0000003 ! occurrent
    • [i] BFO:0000008 ! temporal region
      • [i] BFO:0000038 ! one-dimensional temporal region
        • [i] ENVO:01001641 ! glaciation
        • [i] ENVO:01001642 ! interglacial
        • [i] ENVO:01001643 ! ice age
        • [i] ENVO:01003005 ! day
        • [i] ENVO:03000096 ! season
        • [i] ENVO:09200037 ! hours of sunshine
    • [i] BFO:0000015 ! process
      • [i] ENVO:02500000 ! environmental system process
      • [i] GO:0008150 ! biological_process
      • [i] OBI:0000011 ! planned process
      • [i] PO:0009012 ! plant structure development stage
  • [i] BFO:0000002 ! continuant
    • [i] BFO:0000020 ! specifically dependent continuant
      • [i] BFO:0000017 ! realizable entity
        • [i] BFO:0000016 ! disposition
          • [i] BFO:0000034 ! function
            • [i] ENVO:00003076 ! glue
            • [i] ENVO:03510066 ! chemical colorant
            • [i] OBI:0000401 ! environment control function
          • [i] ENVO:01000452 ! environmental disposition
            • [i] ENVO:00000379 ! inundation disposition
            • [i] ENVO:01000455 ! material pooling disposition
            • [i] ENVO:01001082 ! climate
            • [i] ENVO:01001195 ! radiation shielding disposition
          • [i] ENVO:01003001 ! water-holding capacity
          • [i] ENVO:06105002 ! thermoplasticity
          • [i] ENVO:06105004 ! thermosetting disposition
          • [i] ENVO:2000015 ! energy
    • [i] BFO:0000004 ! independent continuant
      • [i] BFO:0000141 ! immaterial entity
        • [i] BFO:0000029 ! site
          • [i] ENVO:00000004 ! administrative region
          • [i] ENVO:00000102 ! cave entrance
          • [i] ENVO:00000564 ! archeological site
          • [i] ENVO:01000408 ! environmental zone
          • [i] ENVO:01001173 ! sacred site
        • [i] BFO:0000140 ! continuant fiat boundary
          • [i] BFO:0000146 ! two-dimensional continuant fiat boundary
            • [i] ENVO:00000486 ! shoreline
            • [i] ENVO:01001544 ! two-dimensional fiat ice surface
        • [i] BFO:0000006 ! spatial region
          • [i] ENVO:03501369 ! seam surface
      • [i] BFO:0000040 ! material entity
        • [i] BFO:0000024 ! fiat object part
          • [i] ENVO:00010483 ! environmental material
          • [i] ENVO:01000813 ! astronomical body part
        • [i] BFO:0000027 ! object aggregate
          • [i] ENVO:01001564 ! rain
          • [i] ENVO:03400009 ! falling sleet
          • [i] ENVO:03400013 ! falling snow
          • [i] ENVO:03501314 ! food production environmental monitoring zone 1
          • [i] ENVO:03501315 ! food production environmental monitoring zone 2
          • [i] ENVO:03501316 ! food production environmental monitoring zone 3
          • [i] ENVO:03501317 ! food production environmental monitoring zone 4
        • [i] BFO:0000030 ! object
          • [i] ENVO:00010358 ! fomite
          • [i] ENVO:01000498 ! pole
          • [i] ENVO:01000804 ! astronomical object
          • [i] ENVO:01001008 ! meteor
          • [i] ENVO:01001686 ! mass of environmental material
        • [i] CHEBI:24431 ! chemical entity
        • [i] CHEBI:36342 ! subatomic particle
        • [i] ENVO:00003074 ! manufactured product
        • [i] ENVO:01000281 ! layer
        • [i] ENVO:01001813 ! construction
        • [i] ENVO:03500005 ! anthropogenic litter
        • [i] NCBITaxon:1 ! root
        • [i] OBI:0000047 ! processed material
        • [i] OBI:0100026 ! organism
        • [i] PCO:0000031 ! organismal entity
        • [i] PO:0025131 ! plant anatomical entity
        • [i] RO:0002577 ! system
        • [i] UBERON:0000465 ! material anatomical entity

From a formal ontological perspective there is nothing inherently wrong here, but this has consequences for the usability of ENVO that need to be explored. We might expect this makes ENVO harder to use and contribute to by domain scientists, but this is something we can empirically investigate. If this turns out to be the case then we can explore some different approaches:

• adding more documentation to explain things to non-ontologists
• adding layers to ontology browsers like OLS that make it easier to navigate
• creating an application ontology layer, perhaps employing the Schulz conflation pattern that allows us to group things in more domain scientist friendly ways

[cmungall]

This analysis has been superseded by some welcome simplifications

https://github.com/EnvironmentOntology/envo/pull/1390

currently there are only a handful of immaterials: