EnvironmentOntology/envo: Protected planet

doi:10.5281/zenodo.1442753

Published October 2, 2018 | Version v2018-05-18

Software Open

EnvironmentOntology/envo: Protected planet

1. Lawrence Berkeley National Laboratory
2. Tokyo Institute of Technology

Eponyms for this release

IUCN protected landscape/seascape IUCN strict nature reserve IUCN protected area with sustainable use of natural resources

Description

This backdated release captures progress across several development threads. Major themes include:

The expression of IUCN protected area classification for use in SDGIO and other resources handling socio-ecological protection
Expression of more CMECs classes to enhance marine semantics
Addition of terms to support GFBio data brokerage to PANGAEA and ENA/EBI
Further development of environmental zone semantics, with waste disposal use cases
Further refinement of process hierarchies for generalisabilityF
Extension of atmospheric semantics across cloud and aerosol formation processes
Initialisation of dust patterns linked to natural and anthropogenic sources
Exploration of radiation semantics (processes, dispositions, material entities)
Import of FOODON classes required by the envoMEO subse now linked to the MEO vocabulary in MicrobeDB.jp

A large number of terms from other ontologies were imported to allow denser axiomatisation. However, many of these are likely to be pruned back in subsequent releases to improve stability. As shown in the commit log, we have also trimmed away imports which 1) are not heavily woven in to ENVO semantics and 2) are causing errors due to autophagic imports of stale ontologies.

New Terms

acidic soil acidic volcanic ash active ecosystem management process advective transport process aerosol formation event aerosol formation process agricultural process agronomic process algal material alluvial deposit alluvial sediment alluvium alpine tundra ecosystem aluminium dust anchor ice animal aquaculture process animal husbandry anthropised terrestrial environmental zone aquatic estuarine layer aquatic natural environment arable land arable or pasturable land arable area designated for human defecation area designated for waste storage area of developed space area of low atmospheric pressure area protected according to IUCN guidelines asphalt road atmospheric aerosol formation event atmospheric secondary aerosol formation process atmospheric wind direction atmospheric wind speed atmospheric zone barium dust Bondon cheese environment brackish water body brown sea ice brush fire bush area bush fire canopy cirrus cloud climate system cnidarian-associated environment coastal shrimp pond commercial building concrete road conservation-focused active ecosystem management process constructed pavement convective storm cosmic ray shielding disposition crater zone crop canopy cropland ecosystem crustacean farming process cyclone defence against flooding desert diurnal marine tidal flow process diurnal marine tidal flow zone driveway ecosystem decay ecosystem fragment ecosystem fragmentation process environment associated with an aquatic invertebrate environmental zone of processual equilibrium erosion estuarine coastal lower water column estuarine coastal pycnocline estuarine coastal surface layer estuarine coastal upper water column estuarine open water lower water column estuarine open water pycnocline estuarine open water surface layer estuarine open water upper water column estuarine tidal riverine coastal lower water column estuarine tidal riverine coastal pycnocline estuarine tidal riverine coastal surface layer estuarine tidal riverine coastal upper water column estuarine tidal riverine open water lower water column estuarine tidal riverine open water pycnocline estuarine tidal riverine open water surface layer estuarine tidal riverine open water upper water column extra-tropical cyclone finfish farming process floating ice mass forest canopy forest ecosystem fresh water body freshwater macrophyte farming process freshwater seep riverine anchor ice gamma-ray stellar radiation geodiversity glacial equlibrium line glacial ice accumulation zone grassland ecosystem habitat fragmentation process Hill sphere holothurian digestive tract contents holothurian digestive tract humic kerogen hydroclimate ice accumulation zone ice decumulation zone impermeable surface layer induced magnetosphere industrial fire infrared stellar radiation intrinsic magnetosphere ionising stellar radiation IUCN habitat/species management area IUCN natural monument or feature IUCN protected area with sustainable use of natural resources IUCN protected landscape/seascape IUCN strict nature reserve IUCN wilderness area kaolin dust kerogen labile kerogen Lagrangian point land fire liquid air-water interface layer liquid layer liquid surface layer lithification lumber production process magnetosphere marine environmental zone marine tidal flow process marine tidal flow zone marine tidal flow material accumulation zone material decumulation zone material isosurface microwave stellar radiation mollusc farming process newCloud newCloud nitrogen cycling office building office Paramo pasturable land pasture fire paved parking lot phosphorous cycling planktonic kerogen plant aquaculture process primary aerosol formation process radiation shielding disposition radio wave stellar radiation ranch recalcitrant kerogen residual kerogen rhizoplane riverine anchor ice rural stormwater sacred site saline shrimp pond water saline water body sapropelic kerogen seaweed farming process secondary aerosol formation process sediment surface semi-diurnal marine tidal flow process semi-diurnal marine tidal flow zone sidewalk silica dust slate dust solid layer solid surface layer stellar radiation stormwater sulfrous kerogen sulfur cycling swamp area talc dust tended pasturable land terrestrial environmental zone terrestrial natural environment thermal pollution of an aquatic system thermal pollution tidal flow process tidal mangrove shrubland transport of child feces to a designated site transport of household waste to a designated storage site transport of waste to a designated storage site tropical marginal sea biome tropical storm tundra ecosystem ultraviolet stellar radiation urban stormwater visible spectrum stellar radiation vog volcanic crater glacier volcanic crater zone volume of hydrological precipitation warm core cyclone waste disposal process water accumulation process water ice layer water surface water-based planetary surface wetland ecosystem woodland canopy woodland ecosystem x-ray stellar radiation

Commit log

commit 2471a596b24fa8f3d1091dac530475dd055ca8eb Author: cmungall Date: Wed May 16 19:07:49 2018 -0700

regen

commit f60a8a487046229306904be9200dd76991180aa6 Author: cmungall Date: Wed May 16 19:03:38 2018 -0700

Removing CLO import and its one axiom, CLO has a very stale GO which causes issues, see #609

commit d05fdb54cf472e17e04eb829abe82b5acb62d25b Author: cmungall Date: Wed May 16 16:51:20 2018 -0700

Removing flopo import and 4 flopo-referencing axioms
Some alternate form of these axioms may be added back later
Fixes #612

commit cf03c3a57e7a2774559d6b2f45ac3060fbf7fac2 Author: cmungall Date: Wed May 16 16:48:48 2018 -0700

Regenerated imports
Success with foodon - needs a quite arcane series of owltools commands to
be able to remove the stale ENVO subset whilst retaining linkages

commit 2c684cd87c28f0231694a3943cc30c7ee273708b Author: cmungall Date: Wed May 16 14:19:36 2018 -0700

removing OMP import, #609

commit eef3063c8082d29013d435dd6000dba7e2db4c0e Author: cmungall Date: Wed May 16 10:58:28 2018 -0700

removing stray sdgio declaration, see #609

commit 922bcd98d9ab9e8d06a9f01ebfcc7323f9614db8 Author: cmungall Date: Wed May 16 10:56:30 2018 -0700

tweaking Makefile as stopgap measure to stop self-reference, see #610

commit 97680337615dc4c628bf492879ac49219f0fd48d Author: cmungall Date: Wed May 16 08:55:29 2018 -0700

regenerated SDGIO import without ENVO - we will still omit this from this next release, see #610

commit 2f76fb105033f5eef573e09ffa6c5f53df328909 Author: cmungall Date: Wed May 16 08:52:09 2018 -0700

temp removal of axiom connecting arable land to AGRO, fixes #611

commit 41ad6113b0ec87718aa95f7045a3b004367dfa9b Author: cmungall Date: Wed May 16 08:32:08 2018 -0700

Removed aerosol formation class with SDGIO, fixes #609

commit f0d48d99c7242f80852da062384ae705d01ab121 Author: cmungall Date: Wed May 16 08:31:43 2018 -0700

Removing imports to sdgio and agro, fixes #610. Removed leaking sdgio axiom, see #609

commit cdef8aea04f5c7d319f50ed66dafcd065a4d321e Author: cmungall Date: Sun May 13 09:03:47 2018 -0400

remove stale ENVO parts from foodon import

commit 057056193b1be9a00da77e1fa38cd5a095ede7f3 Author: cmungall Date: Sat May 12 15:10:58 2018 -0400

Adding target to make a debug file

commit 252cb69c14c785882f2a4659a1f9890c60ee3404 Author: cmungall Date: Sat May 12 14:53:48 2018 -0400

Fixes to pipeline in-progress

commit ea44ccc413c654c51dd0771e7edd43d761a46f36 Author: cmungall Date: Sat May 12 14:27:25 2018 -0400

fix foodon danglers

commit d1935da7efa2e2f53e179e6f79b62afa3e19fa6f Author: pbuttigieg Date: Sat May 12 19:17:09 2018 +0200

shortened Makefile and refreshed imports

commit 638823297d5a5852da49d86c8f61f0724ba4b940 Author: pbuttigieg Date: Fri May 11 03:17:10 2018 +0200

added terms.txt files for agro and sdgio imports

commit 4cc55fa042a3b41dad9a686dfd80dd2dfceb7f87 Author: pbuttigieg Date: Fri May 11 00:12:27 2018 +0200

multiple updates to zones, addressing #573 #580 and #603

commit 7c837d48570da3a94a372d44fc4b10baad13406a Author: pbuttigieg Date: Wed May 2 10:28:48 2018 +0200

Added mangrove linked CMECS semantics, xlink to PCO

commit c8828badc0e46b0ff35e0cf0d96300397f496621 Author: pbuttigieg Date: Mon Apr 30 20:06:07 2018 +0200

Addressing #602, adding aerosol formation hierarchy

commit bbc9c3222979ada4bc067aecb73327ea4ff8eb26 Author: pbuttigieg Date: Mon Apr 30 08:17:31 2018 +0200

Reimport foodon with fixes for build

commit 4e5163be979313ce10353e45af400f25bfed1858 Author: pbuttigieg Date: Fri Apr 27 19:13:50 2018 +0200

Polishing #583

commit 335004e841a3721892dadc293739fca2d97869fb Author: pbuttigieg Date: Fri Apr 27 19:01:41 2018 +0200

Addressing #593

commit 7ca32db48f03f2b75be6292f1293d95780582fb8 Author: pbuttigieg Date: Fri Apr 27 18:52:45 2018 +0200

Addressing #604

commit 10f2ef4ad68c9d0a3cc9f758d2c88174b6183ff3 Author: pbuttigieg Date: Fri Apr 27 15:26:47 2018 +0200

addressing #602

commit bb2afc0edd07d8bae8f6ec7ce698b6588bc75f6d Author: pbuttigieg Date: Fri Apr 27 10:58:18 2018 +0200

Foodon stripped of problematic axioms, attempting build check

commit 057cde4988d01b099074707a1ca91731d5f25098 Author: pbuttigieg Date: Wed Apr 25 19:21:30 2018 +0200

Addressing #557, #555, #556

commit 5a3a619fc8fef240d601292f5fae470597e8e89d Author: pbuttigieg Date: Wed Apr 25 18:50:37 2018 +0200

Addressing #585

commit 05babf84462322524483d56958ac65a5911d8129 Author: pbuttigieg Date: Wed Apr 25 18:19:19 2018 +0200

Addressing #604

commit e0e3fb5546251046a689075c4925b771238492a4 Merge: 42fcf16 c7e1fa5 Author: pbuttigieg Date: Wed Apr 25 17:21:30 2018 +0200

Merge branch 'master' of https://github.com/EnvironmentOntology/envo

commit 42fcf1648c6eed65fe784a4163bb2aed47545c78 Author: pbuttigieg Date: Wed Apr 25 17:21:18 2018 +0200

finished substituting has_condition

commit c7e1fa59346bd3e05a771c0e6a00eed60e8a3cde Author: Pier Luigi Buttigieg Date: Wed Apr 25 16:37:24 2018 +0200

Update README.md

commit d78cf89c00755e01c0ceb4afc4bd2405f11e1457 Author: pbuttigieg Date: Wed Apr 25 15:42:47 2018 +0200

Unlink Bondon environment from the now information-based FOODON class: https://github.com/FoodOntology/foodon/issues/42

commit 4358853e6a2e0b2773f742db35f39661afef7edc Author: pbuttigieg Date: Wed Apr 25 14:57:09 2018 +0200

consolidating edits and prepping for release

commit 9e52c7d57b7390b083dc73805c4f658c96b88ff7 Author: pbuttigieg Date: Mon Apr 9 08:25:44 2018 +0200

further CMECs edits, attempt to fix build with FOODON refresh

commit 32a78c82d590f1bdd0f49fc88b2a42c934b90768 Author: pbuttigieg Date: Fri Apr 6 17:47:07 2018 +0200

Expanded imports and added CMECS semantics for estuarine layers and tidal flows

commit 3dbf42b556abbe432b1c59b056ce189ea4029d87 Author: pbuttigieg Date: Wed Mar 21 16:58:28 2018 +0100

refreshing and extending IAO import, FOODON import

commit da0a18603540a29efdaaa8388d9fe0aecf37d7b4 Author: pbuttigieg Date: Wed Mar 21 16:43:42 2018 +0100

extended quality repertoire from PATO, initialised cyclone semantics

commit bd75915cec59526b87c32f70685a17b5689bb289 Author: pbuttigieg Date: Wed Mar 21 15:39:10 2018 +0100

logic fix for combustion processes

commit fa7abfec6396676effcd6293e1d9fb3fd64eb916 Author: pbuttigieg Date: Wed Mar 21 15:36:33 2018 +0100

Adding more classes for #247

commit a04bb7d30cf354a03289d065eecd165da82f012f Author: pbuttigieg Date: Wed Mar 21 14:23:08 2018 +0100

Added SDGIO import routines for ecosystem services, natural capital, and UN sustainable development semantics, etc.

commit 46688a459c27e0aee5fa287283d2c33d2de7c519 Author: pbuttigieg Date: Wed Mar 21 00:02:38 2018 +0100

added mysteriously missing classes to the new chebi_terms.txt file

commit 821754a0003e326d2551dd89d92b749e326286bc Author: pbuttigieg Date: Tue Mar 20 23:45:11 2018 +0100

Further addressing #583, with more CHEBI content and updated Makefile

commit 26781122537b0ddffcfe2c388b604b03953ee346 Author: pbuttigieg Date: Tue Mar 20 22:52:16 2018 +0100

Addressing #583

commit a1d889e1f82b46af876850d487216db8d9c71424 Author: pbuttigieg Date: Tue Mar 20 22:24:26 2018 +0100

improved layer semantics, added pavements

commit c65c05533ab65e29a11c4b6518d92b250ebcfedc Author: pbuttigieg Date: Tue Mar 20 17:50:40 2018 +0100

axiom fix to preserve build

commit 6f67b6a8c374a9684553e0d06f8924b1c348ee08 Author: pbuttigieg Date: Tue Mar 20 17:47:45 2018 +0100

Addressing #598

commit 1e92a6bfd3d48d6226d8271073872bece70b306b Author: pbuttigieg Date: Mon Mar 19 13:32:42 2018 +0100

aquaculturing semantics enhanced to address GFBio request DSUB-110

commit 604206d4c8dc7becf6c605ec31f2b87ea954a392 Author: pbuttigieg Date: Wed Mar 7 15:12:49 2018 +0100

addressing #593 with associated refinements to vegetated areas and their parts

commit 7578b661d6ebb390be3b260b186823bbb61de5cf Author: Pier Luigi Buttigieg Date: Fri Mar 2 17:44:40 2018 +0100

Update README.md

commit fa57f3b5cc7774f5cb6cbf056b5a6bbd52786866 Author: pbuttigieg Date: Tue Feb 27 05:52:55 2018 +0100

added basic kerogen types, relevant to #433, #11, #527

commit 7fa9012e313c415ec4945127cc42706817bd6873 Author: pbuttigieg Date: Mon Feb 26 02:19:29 2018 +0100

Addressing #580

commit 6c4add07c7b8fb6d52ab900a2bd446955e22a56c Author: pbuttigieg Date: Sun Feb 25 21:39:44 2018 +0100

Addressing #592

commit 9ffbeee459102b2151a5735e0ad74c0e0fb53b9c Author: pbuttigieg Date: Tue Feb 6 01:20:50 2018 +0100

major updates aligning to BFO and deconvoluting sites and systems, several issues addressed en passant

commit 1e5494d59cfa44e5bbc94694dc5a5b74e477cb49 Author: pbuttigieg Date: Sat Nov 4 22:02:31 2017 +0100

numerous updates, in the process of refactoring env feature, reasoner errors abound for now

commit ebfed79d0ecc765aada60d095a494613a9bf16f4 Author: pbuttigieg Date: Mon Oct 9 18:44:35 2017 +0200

fixing build, reinstate surface water

commit fd8ae573c4375a9d7319712e88c5339c6afeee56 Author: pbuttigieg Date: Mon Oct 9 18:22:17 2017 +0200

Addressing #566, #565, #564, #563,  #499, adding more semantics for ecosystem fragmentation. Cleaned up ENVO classes derived from UBERON bodily fluid branch. Extended PATO, UBERON, and NCBITaxon imports.

commit eb9b60cf16a782f4fae46fb975efeeac978a65b4 Author: pbuttigieg Date: Thu Sep 14 07:43:11 2017 +0100

continuing MEO alignment, added AGRO import, updated UBERON import to ROBOT

commit 4d2467ee7c3ad296a3221ad4c452165173b110c3 Author: pbuttigieg Date: Wed Sep 13 05:55:00 2017 +0100

addressing #562

commit 964eee7be182fa782a05365c5cfa2a846a5cb78e Author: pbuttigieg Date: Tue Sep 12 15:26:55 2017 +0100

Regenerated FOODON import following #574

commit 369cb3d38c127ea2df1a942bef9d9c5a5045d8d1 Merge: a1586f6 a9cd6ac Author: Pier Luigi Buttigieg Date: Tue Sep 12 15:17:52 2017 +0100

Merge pull request #575 from TaskeHAMANO/patch-1

Add microbial environment to export class collection from FoodOn

commit a1586f66b52a96f7a771f535dab063f4158cb924 Author: pbuttigieg Date: Tue Sep 12 14:56:05 2017 +0100

Fixing build, strange axiom emerged for aerosol formation processes

commit a9cd6ac547b21aae488ea8ec8d7863a1f2df748a Merge: 16fd7e7 be4927f Author: Shinya SUZUKI Date: Tue Sep 12 22:38:21 2017 +0900

Merge branch 'patch-1' of github.com:TaskeHAMANO/envo into patch-1

commit 16fd7e75c4b22df2ff9aa9105645ee57fba0e932 Author: Shinya SUZUKI Date: Tue Sep 12 14:56:27 2017 +0900

Added FOODON terms for ENVO-MEO-FOODON mapping

Note:
* Jelly is mapped to fruits jelly, because it is used to express "goosberry jelly" in MEO and MicrobeDB.jp.
* kojac is mapped to kojac plant, because it is used to express "kojac biome planted on the plowlands soil" in MEO and MicrobeDB.jp.

commit be4927f1b9c48976cd7b0026e01e25003bbcfeb8 Author: Shinya SUZUKI Date: Tue Sep 12 14:56:27 2017 +0900

Added FOODON terms for ENVO-MEO-FOODON mapping

commit 24fd76912eb4c2ec489b39678c327468d8272911 Author: pbuttigieg Date: Tue Sep 12 06:41:48 2017 +0200

MEO/ENVO alignment, foodon imports, and various cleanup, PCO import fix

commit 28d30cd65d3e3241a1432d0f2a24172524cb980a Author: Pier Luigi Buttigieg Date: Mon Sep 11 10:09:28 2017 +0100

Update README.Md

commit 5a59a79f2ed94e2c034846e2702ccc16c80f769a Author: Pier Luigi Buttigieg Date: Mon Sep 11 10:08:53 2017 +0100

Update README.Md

commit bd40b791ebaf9f771f00c3d8968007069d1509fd Author: pbuttigieg Date: Tue Sep 5 18:09:43 2017 +0200

Addressing conservation semantics #571 #568 #567 #570 #572

commit 097f0357671422d3d6f120a08183ea808dcc2101 Author: pbuttigieg Date: Mon Sep 4 12:39:05 2017 +0200

initial work for #526

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EnvironmentOntology/envo: Protected planet

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