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Mapping habitats in SpireEcoConcepts #23

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GoogleCodeExporter opened this Issue Mar 28, 2015 · 9 comments

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GoogleCodeExporter commented Mar 28, 2015 

I am part of a project that is integrating species interaction data. We have a 
lot of data from SPIRE which uses the SpireEcoConcepts vocabulary. I have 
extracted the Habitat subset of SpireEcoConcepts below and would like each to 
map to an ENVO class (Unknown should point to the root).

I could easily do this using my string matching utils but this may be pointless 
if the habitat/biome part is to be refactored.

Ideally these would all point to the same sub-hierarchy (habitat in the current 
ENVO and biome in the next major release?) but this may not be practical.

http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Oceanic_vent
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Montane
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Abyssal
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Chaparral
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Tundra
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Desert_or_dune
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Rockpool
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Savannah_or_grassland
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Intertidal
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Polar
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Reef
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Carrion_substrate
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Taiga
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Temperate
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Treeholes
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Suburban
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Swamp
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Tropical
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Scrub_forest
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Mudflat
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Marine
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Riparian
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Estuarine
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Lake_or_pond
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Pelagic
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Rocky_shore
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Sublittoral
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Brackish_water
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Marsh
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Epipelagic_zone
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Freshwater
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Coastal
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Bog
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Ice_cap
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Forest
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Littoral
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Soil
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Galls
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Benthic
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Rainforest
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Temporary_pool
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Heath
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Mesopelagic_zone
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Un_known
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Dung
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Agricultural
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Plant_substrate
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Terrestrial
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#Urban
http://spire.umbc.edu/ontologies/SpireEcoConcepts.owl#River

Original issue reported on code.google.com by cmung...@gmail.com on 12 May 2013 at 5:04
@GoogleCodeExporter

GoogleCodeExporter commented Mar 28, 2015 

Preliminary
http://purl.obolibrary.org/obo/envo/mappings/spire-mapping.txt

Original comment by cmung...@gmail.com on 13 Sep 2013 at 11:05

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GoogleCodeExporter added the auto-migrated label Mar 28, 2015

@GoogleCodeExporter

GoogleCodeExporter commented Mar 28, 2015 


We can also see a breakdown by category:

http://purl.obolibrary.org/obo/envo/mappings/spire-mapping-by-type.txt

Original comment by cmung...@gmail.com on 13 Sep 2013 at 11:24

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@GoogleCodeExporter

GoogleCodeExporter commented Mar 28, 2015 

I have not mapped these - do we want to create new ENVO classes for these?

SPIRE:Montane ! Montane
SPIRE:Rockpool ! Rockpool
SPIRE:Carrion_substrate ! Carrion_substrate
SPIRE:Treeholes ! Treeholes
SPIRE:Suburban ! Suburban
SPIRE:Scrub_forest ! Scrub_forest
SPIRE:Riparian ! Riparian
SPIRE:Rocky_shore ! Rocky_shore
SPIRE:Sublittoral ! Sublittoral
SPIRE:Galls ! Galls
SPIRE:Temporary_pool ! Temporary_pool
SPIRE:Un_known ! Un_known
SPIRE:Plant_substrate ! Plant_substrate

Original comment by cmung...@gmail.com on 13 Sep 2013 at 11:25

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@GoogleCodeExporter

GoogleCodeExporter commented Mar 28, 2015 


Some mappings are one to many:

SPIRE:Lake_or_pond      ENVO:00000020 ! lake
SPIRE:Lake_or_pond      ENVO:00000033 ! pond
SPIRE:Savannah_or_grassland     ENVO:01000177 ! grassland biome
SPIRE:Savannah_or_grassland     ENVO:01000178 ! savanna biome

Original comment by cmung...@gmail.com on 13 Sep 2013 at 11:49

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@GoogleCodeExporter

GoogleCodeExporter commented Mar 28, 2015 

GloBI is now using ENVO for environment mapping through this SPIRE-ENVO 
mapping.  See https://github.com/jhpoelen/eol-globi-data/issues/19 for more 
info.

I noticed the SPIRE:Desert_or_dune mapping:

SPIRE:Desert_or_dune    Desert_or_dune  ENVO:01000179   desert biome

Could you please also add the ENVO dune mapping?  Otherwise SPIRE is telling us 
that seals live in the desert (do they? ; )).

Original comment by jhpoe...@gmail.com on 16 Sep 2013 at 5:49

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GoogleCodeExporter commented Mar 28, 2015 

Not reported so far, not that we've been looking for them there...  This is 
interesting- does that leave these SPIRE seals in the desert AND on the dunes? 
Are there lots of examples like this? If it's only a few, then crowd curation 
should take care of it.

Original comment by jen.hamm...@gmail.com on 16 Sep 2013 at 7:05

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@GoogleCodeExporter

GoogleCodeExporter commented Mar 28, 2015 

It's probably simplest to remove this mapping.

We could represent this in OWL as UnionOf(desert dune) - but this seems an odd 
class to name.

Original comment by cmung...@gmail.com on 16 Sep 2013 at 8:58

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@GoogleCodeExporter

GoogleCodeExporter commented Mar 28, 2015 

This is an example of where a class like "seal habitat" (which would specify 
dunes but not deserts) may come in handy.

Some thoughts on comment #3:

SPIRE:Un_known ! Un_known --> I don't think we can have such a class in ENVO.
SPIRE:Montane ! Montane   --> create montane zone?
SPIRE:Sublittoral ! Sublittoral --> neritic sub-littoral zone(ENVO:01000126)?
SPIRE:Suburban ! Suburban --> could map to dense settlement 
biome(ENVO:01000248), or create new subclass
SPIRE:Temporary_pool ! Temporary_pool --> consider intermittent 
pond(ENVO:00000504)? 
SPIRE:Rockpool ! Rockpool --> tidal pool(ENVO:00000317)
SPIRE:Rocky_shore ! Rocky_shore --> new subclass of shore(ENVO:00000304)?
SPIRE:Galls ! Galls --> gall as a new subclass of biotic mesoscopic physical 
object(ENVO:01000009)?
SPIRE:Plant_substrate ! Plant_substrate --> maybe a new material class, "plant 
matter"?

SPIRE:Scrub_forest ! Scrub_forest --> xeric shrubland biome(ENVO:01000218)? we 
could consider creating a corresponding feature class if "biome" is a problem.

SPIRE:Treeholes ! Treeholes --> perhaps a new class under biotic mesoscopic 
physical object? But then again, is a hole an object?

SPIRE:Riparian ! Riparian --> we have riparian area as a synonym of wetland, 
but I think creating riparian zone would be better.

SPIRE:Carrion_substrate ! Carrion_substrate --> we have carcass(ENVO:00002033), 
do we need carrion (probably as a subclass of env. material) or should this be 
a synonym? Carrion implies rotting, whereas a carcass could be 'fresh', 
supporting a new class.

Original comment by p.buttig...@gmail.com on 17 Sep 2013 at 9:26

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GoogleCodeExporter commented Mar 28, 2015 

PS: There could be a general issue with concepts which read like adjectives 
such as "polar" or "benthic". Some of these (e.g. polar) may be subclasses of 
"environmental condition" in ENVO and can be mapped to directly. Others (like 
benthic) will need to refer to a 'thing' like "benthic zone".

Original comment by p.buttig...@gmail.com on 17 Sep 2013 at 9:33

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pbuttigieg added to In Progress in blueMarble Mar 29, 2017

pbuttigieg added to In Progress in meteo Apr 4, 2017

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