Using OAK for Environmental Ontologies
author: Chris Mungall
created: 2022-10-24
This tutorial walks through the neuro-relevant subset of the ENVO as well as SWEET.
to help understand the structure of ENVO
to show how to do advanced OAK queries and visualization (CLI and programmatic) on ENVO
demonstrate rudimentary text annotation
Running this notebook locally or on mybinder requires 0.1.41 or higher
Create an alias
For convenience we will set a bash alias within Jupyter.
The first time you run this, a copy of envo.db.gz is downloaded from S3, which may include a delay - for subsequent invocations, the cached copy will be used
[1]:
%alias envo runoak -i sqlite:obo:envo
Basic lookup
We will first lookup a term by name
[2]:
envo info biome
ENVO:00000428 ! biome
multiple terms can be entered, using either IDs or labels (later we will see how to include extensional terms that expand queries to sets of terms)
[15]:
envo info archipelago "hydrothermal vent" beach
ENVO:00000220 ! archipelago
ENVO:00000215 ! hydrothermal vent
ENVO:00000091 ! beach
hierarchical tree displays
The Oak Tree command will show a hierarchical tree for any set of terms.
Like any graph-oriented OAK command this is parameterized by --predicates (-p), so to show only is-a:
[4]:
envo tree biome -p i
* [] BFO:0000001 ! entity
* [i] BFO:0000002 ! continuant
* [i] BFO:0000004 ! independent continuant
* [i] BFO:0000040 ! material entity
* [i] RO:0002577 ! system
* [i] ENVO:01000254 ! environmental system
* [i] ENVO:01001110 ! ecosystem
* [i] **ENVO:00000428 ! biome**
note the default output is markdown-friendly, so this can be pasted into a GitHub issue (or a Jupyter cell) and it will render, like this:
[] BFO:0000001 ! entity
[i] BFO:0000002 ! continuant
[i] BFO:0000004 ! independent continuant
[i] BFO:0000040 ! material entity
[i] RO:0002577 ! system
[i] ENVO:01000254 ! environmental system
[i] ENVO:01001110 ! ecosystem
[i] ENVO:00000428 ! biome
We can also have the tree command show descendants (using --down).
The results can sometimes lead to “path explosions”, we can control this by setting a maximum number of hops using --max-hops:
[16]:
envo tree biome -p i --down --max-hops 2
* [] ENVO:01000254 ! environmental system
* [i] ENVO:01001110 ! ecosystem
* [i] **ENVO:00000428 ! biome**
* [i] ENVO:01001838 ! arid biome
* [i] ENVO:01001837 ! subalpine biome
* [i] ENVO:01001836 ! montane biome
* [i] ENVO:01000223 ! montane savanna biome
* [i] ENVO:01000216 ! montane shrubland biome
* [i] ENVO:01001835 ! alpine biome
* [i] ENVO:01001505 ! alpine tundra biome
* [i] ENVO:01001834 ! subpolar biome
* [i] ENVO:01001832 ! subtropical biome
* [i] ENVO:01001833 ! mediterranean biome
* [i] ENVO:01000229 ! mediterranean savanna biome
* [i] ENVO:01000217 ! mediterranean shrubland biome
* [i] ENVO:01000208 ! mediterranean woodland biome
* [i] ENVO:01000047 ! mediterranean sea biome
* [i] ENVO:01000857 ! temperate mediterranean sea biome
* [i] ENVO:01000128 ! dilution basin mediterranean sea biome
* [i] ENVO:01000004 ! concentration basin mediterranean sea biome
* [i] ENVO:01000222 ! subtropical woodland biome
* [i] ENVO:01000208 ! mediterranean woodland biome
* [i] ENVO:01000213 ! subtropical shrubland biome
* [i] ENVO:01000217 ! mediterranean shrubland biome
* [i] ENVO:01000187 ! subtropical savanna biome
* [i] ENVO:01000229 ! mediterranean savanna biome
* [i] ENVO:01001831 ! temperate biome
* [i] ENVO:01000860 ! temperate marine upwelling biome
* [i] ENVO:01000856 ! temperate marginal sea biome
* [i] ENVO:01000221 ! temperate woodland biome
* [i] ENVO:01000215 ! temperate shrubland biome
* [i] ENVO:01000189 ! temperate savanna biome
* [i] ENVO:01001830 ! tropical biome
* [i] ENVO:01001230 ! tropical marginal sea biome
* [i] ENVO:01000859 ! tropical marine upwelling biome
* [i] ENVO:01000854 ! tropical marine coral reef biome
* [i] ENVO:01000220 ! tropical woodland biome
* [i] ENVO:01000214 ! tropical shrubland biome
* [i] ENVO:01000188 ! tropical savanna biome
* [i] ENVO:01000339 ! polar biome
* [i] ENVO:00002030 ! aquatic biome
* [i] ENVO:00000873 ! freshwater biome
* [i] ENVO:01000253 ! freshwater river biome
* [i] ENVO:00000890 ! small river biome
* [i] ENVO:00000889 ! large river delta biome
* [i] ENVO:00000888 ! large river headwater biome
* [i] ENVO:00000887 ! large river biome
* [i] ENVO:01000252 ! freshwater lake biome
* [i] ENVO:00000892 ! small freshwater lake biome
* [i] ENVO:00000891 ! large freshwater lake biome
* [i] ENVO:00000893 ! xeric basin biome
* [i] ENVO:00000447 ! marine biome
* [i] ENVO:01000858 ! marine upwelling biome
* [i] ENVO:01000860 ! temperate marine upwelling biome
* [i] ENVO:01000859 ! tropical marine upwelling biome
* [i] ENVO:01000048 ! ocean biome
* [i] ENVO:01000047 ! mediterranean sea biome
* [i] ENVO:01000857 ! temperate mediterranean sea biome
* [i] ENVO:01000128 ! dilution basin mediterranean sea biome
* [i] ENVO:01000004 ! concentration basin mediterranean sea biome
* [i] ENVO:01000046 ! marginal sea biome
* [i] ENVO:01001230 ! tropical marginal sea biome
* [i] ENVO:01000856 ! temperate marginal sea biome
* [i] ENVO:01000045 ! epeiric sea biome
* [i] ENVO:01000024 ! marine benthic biome
* [i] ENVO:01000127 ! marine cold seep biome
* [i] ENVO:01000030 ! marine hydrothermal vent biome
* [i] ENVO:01000054 ! marine basaltic hydrothermal vent biome
* [i] ENVO:01000053 ! marine ultramafic hydrothermal vent biome
* [i] ENVO:01000052 ! marine white smoker biome
* [i] ENVO:01000051 ! marine black smoker biome
* [i] ENVO:01000029 ! marine reef biome
* [i] ENVO:01000123 ! marine sponge reef biome
* [i] ENVO:01000050 ! marine subtidal rocky reef biome
* [i] ENVO:01000049 ! marine coral reef biome
* [i] ENVO:01000854 ! tropical marine coral reef biome
* [i] ENVO:01000028 ! marine hadal zone biome
* [i] ENVO:01000027 ! marine abyssal zone biome
* [i] ENVO:01000026 ! marine bathyal zone biome
* [i] ENVO:01000025 ! marine neritic benthic zone biome
* [i] ENVO:01000023 ! marine pelagic biome
* [i] ENVO:01000033 ! oceanic pelagic zone biome
* [i] ENVO:01000040 ! oceanic benthopelagic zone biome
* [i] ENVO:01000039 ! oceanic hadal pelagic zone biome
* [i] ENVO:01000038 ! oceanic abyssopelagic zone biome
* [i] ENVO:01000037 ! oceanic bathypelagic zone biome
* [i] ENVO:01000036 ! oceanic mesopelagic zone biome
* [i] ENVO:01000035 ! oceanic epipelagic zone biome
* [i] ENVO:01000034 ! oceanic sea surface microlayer biome
* [i] ENVO:01000032 ! neritic pelagic zone biome
* [i] ENVO:01000043 ! neritic mesopelagic zone biome
* [i] ENVO:01000042 ! neritic epipelagic zone biome
* [i] ENVO:01000041 ! neritic sea surface microlayer biome
* [i] ENVO:01000022 ! marine salt marsh biome
* [i] ENVO:01000020 ! estuarine biome
* [i] ENVO:00000446 ! terrestrial biome
* [i] ENVO:01000219 ! anthropogenic terrestrial biome
* [i] ENVO:01000248 ! dense settlement biome
* [i] ENVO:01000249 ! urban biome
* [i] ENVO:01000247 ! rangeland biome
* [i] ENVO:01000246 ! village biome
* [i] ENVO:01000181 ! mangrove biome
* [i] ENVO:01000180 ! tundra biome
* [i] ENVO:01001505 ! alpine tundra biome
* [i] ENVO:01000176 ! shrubland biome
* [i] ENVO:01001369 ! tidal mangrove shrubland
* [i] ENVO:01000218 ! xeric shrubland biome
* [i] ENVO:01000216 ! montane shrubland biome
* [i] ENVO:01000215 ! temperate shrubland biome
* [i] ENVO:01000214 ! tropical shrubland biome
* [i] ENVO:01000213 ! subtropical shrubland biome
* [i] ENVO:01000217 ! mediterranean shrubland biome
* [i] ENVO:01000175 ! woodland biome
* [i] ENVO:01000222 ! subtropical woodland biome
* [i] ENVO:01000208 ! mediterranean woodland biome
* [i] ENVO:01000221 ! temperate woodland biome
* [i] ENVO:01000220 ! tropical woodland biome
* [i] ENVO:01000178 ! savanna biome
* [i] ENVO:01000223 ! montane savanna biome
* [i] ENVO:01000190 ! flooded savanna biome
* [i] ENVO:01000189 ! temperate savanna biome
* [i] ENVO:01000188 ! tropical savanna biome
* [i] ENVO:01000187 ! subtropical savanna biome
* [i] ENVO:01000229 ! mediterranean savanna biome
Search
In addition to specifying exact terms, you can specify query terms as inputs to most commands.
One form of query is a search query, which has structure:
PREDICATE-CODE SEARCH-SYMBOL SEARCH-TERM
For example, to search
for any matching label, (code
l)using a substring match (code
~)for the string “oak”
We can do:
[6]:
envo info l~oak
ENVO:01000239 ! oak woodland
[18]:
envo info t~deciduous
ENVO:00000109 ! woodland area
ENVO:00002989 ! obsolete Temperate broad-leaf forests or woodlands and subpolar deciduous thickets
ENVO:00002990 ! obsolete Tropical dry or deciduous forests (including Monsoon forests) or woodlands
ENVO:01000385 ! temperate deciduous broadleaf forest
ENVO:01000386 ! temperate deciduous needleleaf forest
ENVO:01000387 ! tropical deciduous broadleaf forest
ENVO:01000388 ! tropical semi-deciduous broadleaf forest
ENVO:01000816 ! area of deciduous forest
PATO:0001730 ! deciduous (generic)
PATO:0001731 ! deciduous (plant)
PATO:0001732 ! non-deciduous (any body part)
PATO:0001734 ! semi-deciduous(plant)
[20]:
envo info 'l/forest.*biome$'
ENVO:00000875 ! obsolete Temperate coniferous forest biome
ENVO:00000876 ! obsolete Temperate broadleaf and mixed forest biome
ENVO:00000878 ! obsolete Mediterranean forests, woodlands, and shrub biome
ENVO:00000879 ! obsolete Tropical and subtropical moist broadleaf forest biome
ENVO:00000880 ! obsolete Tropical and subtropical dry broadleaf forest biome
ENVO:00005806 ! obsolete Tropical and subtropical coniferous forest biome
ENVO:01000174 ! forest biome
ENVO:01000196 ! coniferous forest biome
ENVO:01000197 ! broadleaf forest biome
ENVO:01000198 ! mixed forest biome
ENVO:01000199 ! mediterranean forest biome
ENVO:01000200 ! tropical broadleaf forest biome
ENVO:01000201 ! subtropical broadleaf forest biome
ENVO:01000202 ! temperate broadleaf forest biome
ENVO:01000209 ! subtropical coniferous forest biome
ENVO:01000210 ! tropical coniferous forest biome
ENVO:01000211 ! temperate coniferous forest biome
ENVO:01000212 ! temperate mixed forest biome
ENVO:01000225 ! subtropical dry broadleaf forest biome
ENVO:01000226 ! subtropical moist broadleaf forest biome
ENVO:01000227 ! tropical dry broadleaf forest biome
ENVO:01000228 ! tropical moist broadleaf forest biome
ENVO:01000250 ! subpolar coniferous forest biome
ENVO:01001798 ! tropical mixed forest biome
[23]:
envo info .desc//p=i biome .and .desc//p=i,p ocean
ENVO:01000048 ! ocean biome
Visualization
The Oak Viz can be used to create flexible configurable visualizations centered around a set of input terms
[1]:
envo viz "oak woodland" -o output/oak-woodland.png
Cell In[1], line 1
envo viz "oak woodland" -o output/oak-woodland.png
^
SyntaxError: invalid syntax
Accessing SWEET
SWEET is also indexed in the SemSQL index, so we can download ready-made sqlite files
(the SWEET owl files can also be accessed directly using OAK, but we do not cover this in this tutorial)
First we will set up a Jupyter alias for convenience
[2]:
%alias sweet runoak -i sqlite:obo:sweetAll
[9]:
sweet search l~biome
sweet:realmBiolBiome/Biome ! biome
sweet:realmBiolBiome/TerrestrialBiome ! terrestrial biome
[24]:
sweet descendants sweet:realmBiolBiome/Biome
sweet:realmBiolBiome/Anthromes ! anthromes
sweet:realmBiolBiome/Barren ! barren
sweet:realmBiolBiome/Biome ! biome
sweet:realmBiolBiome/Biota ! biota
sweet:realmBiolBiome/Croplands ! croplands
sweet:realmBiolBiome/DenseSettlements ! dense settlements
sweet:realmBiolBiome/Forested ! forested
sweet:realmBiolBiome/Rangelands ! rangelands
sweet:realmBiolBiome/SparseTrees ! sparse trees
sweet:realmBiolBiome/Terrain ! terrain
sweet:realmBiolBiome/TerrestrialBiome ! terrestrial biome
sweet:realmBiolBiome/Villages ! villages
sweet:realmBiolBiome/Wildlands ! wildlands
[32]:
sweet tree .desc biome
* [] sweet:reprSciComponent/SystemComponent ! system component
* [i] sweet:reprSciComponent/Environment ! environment
* [i] **sweet:realmBiolBiome/Biome ! biome**
* [i] **sweet:realmBiolBiome/TerrestrialBiome ! terrestrial biome**
* [i] **sweet:realmBiolBiome/Rangelands ! rangelands**
* [i] **sweet:realmBiolBiome/Terrain ! terrain**
* [i] **sweet:realmBiolBiome/Wildlands ! wildlands**
* [i] **sweet:realmBiolBiome/SparseTrees ! sparse trees**
* [i] **sweet:realmBiolBiome/Barren ! barren**
* [i] **sweet:realmBiolBiome/DenseSettlements ! dense settlements**
* [i] **sweet:realmBiolBiome/Villages ! villages**
* [i] **sweet:realmBiolBiome/Biota ! biota**
* [i] **sweet:realmBiolBiome/Anthromes ! anthromes**
* [i] **sweet:realmBiolBiome/Forested ! forested**
* [i] **sweet:realmBiolBiome/Croplands ! croplands**
Accessing ENVO through Bioportal
[19]:
%alias bpenvo runoak -i bioportal:envo
[21]:
bpenvo annotate "Peatlands have acted as net CO2 sinks. Rock biome terrestrial biome"
match_type: PREF
object_id: ENVO:00001995
object_label: rock
object_source: https://data.bioontology.org/ontologies/ENVO
subject_end: 43
subject_label: ROCK
subject_start: 40
---
match_type: PREF
object_id: ENVO:00000428
object_label: biome
object_source: https://data.bioontology.org/ontologies/ENVO
subject_end: 49
subject_label: BIOME
subject_start: 45
---
match_type: PREF
object_id: ENVO:00000428
object_label: biome
object_source: https://data.bioontology.org/ontologies/ENVO
subject_end: 67
subject_label: BIOME
subject_start: 63
---
match_type: PREF
object_id: ENVO:00000446
object_label: terrestrial biome
object_source: https://data.bioontology.org/ontologies/ENVO
subject_end: 67
subject_label: TERRESTRIAL BIOME
subject_start: 51
---
[27]:
%alias agroportal runoak -i agroportal:
[33]:
agroportal annotate "Peatlands have acted as CO2 sinks"
match_type: SYN
object_id: http://www.yso.fi/onto/afo/p122
object_label: bogs
object_source: http://data.agroportal.lirmm.fr/ontologies/AFO
subject_end: 9
subject_label: PEATLANDS
subject_start: 1
---
match_type: PREF
object_id: http://id.agrisemantics.org/gacs/C10734
object_label: peatlands
object_source: http://data.agroportal.lirmm.fr/ontologies/GACS
subject_end: 9
subject_label: PEATLANDS
subject_start: 1
---
match_type: PREF
object_id: http://aims.fao.org/aos/agrovoc/c_13929
object_label: peatlands
object_source: http://data.agroportal.lirmm.fr/ontologies/AGROVOC
subject_end: 9
subject_label: PEATLANDS
subject_start: 1
---
match_type: PREF
object_id: http://www.yso.fi/onto/afo/p902
object_label: peatlands
object_source: http://data.agroportal.lirmm.fr/ontologies/AFO
subject_end: 9
subject_label: PEATLANDS
subject_start: 1
---
match_type: SYN
object_id: https://www.tno.nl/agrifood/ontology/common-greenhouse-ontology#CO2
object_label: Carbon Dioxide
object_source: http://data.agroportal.lirmm.fr/ontologies/CGO
subject_end: 27
subject_label: CO2
subject_start: 25
---
match_type: PREF
object_id: http://opendata.inra.fr/resources/hSC9z#co2
object_label: CO2
object_source: http://data.agroportal.lirmm.fr/ontologies/TRANSMAT
subject_end: 27
subject_label: CO2
subject_start: 25
---
match_type: SYN
object_id: http://aims.fao.org/aos/agrovoc/c_1302
object_label: carbon dioxide
object_source: http://data.agroportal.lirmm.fr/ontologies/AGROVOC
subject_end: 27
subject_label: CO2
subject_start: 25
---
match_type: PREF
object_id: http://www.yso.fi/onto/afo/p4770
object_label: CO2
object_source: http://data.agroportal.lirmm.fr/ontologies/AFO
subject_end: 27
subject_label: CO2
subject_start: 25
---
match_type: SYN
object_id: CHEBI:16526
object_label: carbon dioxide
object_source: http://data.agroportal.lirmm.fr/ontologies/PECO
subject_end: 27
subject_label: CO2
subject_start: 25
---
match_type: SYN
object_id: http://id.agrisemantics.org/gacs/C381
object_label: carbon dioxide
object_source: http://data.agroportal.lirmm.fr/ontologies/GACS
subject_end: 27
subject_label: CO2
subject_start: 25
---
match_type: SYN
object_id: http://opendata.inra.fr/anaeeThes/c2_2680
object_label: carbon dioxide
object_source: http://data.agroportal.lirmm.fr/ontologies/ANAEETHES
subject_end: 27
subject_label: CO2
subject_start: 25
---
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