Releases: EnvironmentOntology/envo
Technosphere, traps, and trucks -- oh my!
Release notes will be added in the next few days. Stay tuned!
Ecotone
This is a pre-release including a few terms and enhancements that were needed by our users. A full release with more informative notes will be posted soon.
Commit log
commit 05a3e3a
Author: pbuttigieg
Date: Wed May 10 17:29:15 2017 +0200
a pre-release for some urgent requests
commit 6f82b09
Author: pbuttigieg
Date: Wed May 10 16:57:55 2017 +0200
refinements on polar classes and some hierarchy organisation
commit e96e556
Author: pbuttigieg
Date: Wed May 10 16:44:43 2017 +0200
queued PCO:'microbial community' for import
commit 79fade1
Author: pbuttigieg
Date: Thu May 4 16:21:53 2017 +0200
added obsolete prefix to deprecated term labels
commit ba3c7dc
Author: pbuttigieg
Date: Thu May 4 15:47:00 2017 +0200
Fixing build: obsolete terms in axioms
commit 0e30ce4
Author: pbuttigieg
Date: Thu May 4 15:37:20 2017 +0200
addressing #507
commit 47dfa1f
Author: pbuttigieg
Date: Thu May 4 14:52:25 2017 +0200
fixed replaced_by reference for aerial habitat
commit a22bc5f
Author: pbuttigieg
Date: Sat Apr 29 12:43:09 2017 +0200
addressing #504, fixed def for desublimation of vapour to ice
commit 876be99
Author: pbuttigieg
Date: Sat Apr 29 12:13:53 2017 +0200
addressing #504
commit 35b8dd8
Author: Kai
Date: Thu Apr 27 18:03:21 2017 +0200
minor edits made to envo polar terms, typo corrections, added axiomatizations and added class errosion through nivation
commit e17a04a
Author: pbuttigieg
Date: Wed Apr 26 21:21:06 2017 +0200
addressing #500
commit 91b103a
Author: pbuttigieg
Date: Wed Apr 26 21:04:34 2017 +0200
Addresses #501
commit 0003422
Author: pbuttigieg
Date: Mon Apr 24 16:51:02 2017 +0200
adding new imports to release dirs
commit 7afcbbc
Author: pbuttigieg
Date: Mon Apr 24 16:42:36 2017 +0200
adding tsv for #494
commit be8a95d
Author: pbuttigieg
Date: Mon Apr 24 16:40:35 2017 +0200
adding CSV for classes in subset for issues such as #494
commit a38f57d
Author: pbuttigieg
Date: Mon Apr 24 15:56:53 2017 +0200
updated all reports
commit d438f3f
Author: pbuttigieg
Date: Sun Apr 23 23:34:39 2017 +0200
Addressing #502
commit d5fdb1d
Author: pbuttigieg
Date: Sun Apr 23 23:15:21 2017 +0200
Addressing #491
commit f1d6c0c
Author: pbuttigieg
Date: Sat Apr 15 21:16:22 2017 +0200
new release: Polar express
commit cb7178e
Author: pbuttigieg
Date: Sat Apr 15 11:06:00 2017 +0200
closes #466, added IAO imports
commit 886dfbc
Merge: b445dd5 3dbcd1e
Author: Pier Luigi Buttigieg
Date: Fri Apr 14 11:03:51 2017 +0200
Merge pull request #487 from kaiiam/master
This merge adds a healthy dose of classes and relations for project cryophile - covering environments and their processes in polar systems
commit 3dbcd1e
Merge: fe2966e b445dd5
Author: Kai
Date: Thu Apr 13 11:28:07 2017 +0200
Merge remote-tracking branch 'upstream/master'
Merged IAO imports and makefile changes from Pier.
commit b445dd5
Author: pbuttigieg
Date: Wed Apr 12 18:55:24 2017 +0200
added IAO import and edited Makefile accordingly
commit fe2966e
Author: Kai
Date: Tue Apr 11 17:23:52 2017 +0200
Added in_subset envoPolar for polar related classes, removed cirque basin as duplicate concept predating it cirque existed, and move the valley hierarchy under geographic depression. #487
commit 3e8f57b
Author: Kai
Date: Tue Apr 11 11:58:40 2017 +0200
Fixed bug in cryoconite hole axiomatization, changed causally downstream of some aeolian transport process to formed as result of some aeolian transport process.
commit dc8b426
Merge: 1d9e254 bbba184
Author: Kai
Date: Tue Apr 11 11:32:47 2017 +0200
Merge remote-tracking branch 'upstream/master'
Imported causal relations from RO.
commit 1d9e254
Author: Kai
Date: Tue Apr 11 11:31:35 2017 +0200
Began adding Pier’s orcid to the project cryophile classes created. Addressed the melt pond #489, and thaw hole hierarchies, creating the upper level class channel and moving tunnel under it. Also made issue requesting for a class such as PATO:microbial community #499.
commit bbba184
Merge: 5359e45 73dccf6
Author: pbuttigieg
Date: Mon Apr 10 20:58:20 2017 +0200
Merge branch 'master' of https://github.com/EnvironmentOntology/envo
syncing web-edited files with local push on imports
commit 5359e45
Author: pbuttigieg
Date: Mon Apr 10 20:57:59 2017 +0200
added causal relations to RO import
commit 1cdcf0f
Author: Kai
Date: Mon Apr 10 12:28:11 2017 +0200
Added final classes for project cryophile pull request 3 snowpack, perennial snow patch, move the precipitation process hierarchy to be subclass of material transport process, see https://github.com/EnvironmentOntology/envo/pull/487#issuecomment-292571243
commit d81e454
Author: Kai
Date: Sun Apr 9 01:21:30 2017 +0200
Added and modified more polar related terms, season generating process associated terms as well as snow melt and snow drift associated terms see latter half of https://github.com/EnvironmentOntology/envo/pull/487#issuecomment-292571243 starting with season generating process and ending with snow patch.
commit c85ef18
Author: Kai
Date: Fri Apr 7 19:20:53 2017 +0200
Modified and added classes polar and gas emission processes see https://github.com/EnvironmentOntology/envo/pull/487#issuecomment-292526931
commit fcbd366
Merge: cf41b5a 73dccf6
Author: Kai
Date: Fri Apr 7 10:42:17 2017 +0200
Merge remote-tracking branch 'upstream/master'
commit cf41b5a
Author: Kai
Date: Fri Apr 7 10:40:41 2017 +0200
Added ice formation process and ice type related classes see https://github.com/EnvironmentOntology/envo/pull/487#discussion_r110089957
commit 73dccf6
Author: Pier Luigi Buttigieg
Date: Thu Apr 6 18:17:01 2017 +0200
Resort and give ranges to new patterns in #492
commit 31ca0c7
Author: pbuttigieg
Date: Thu Apr 6 18:01:43 2017 +0200
added oxidant for #487
commit 9cdfcb1
Merge: 43557c3 9fa5ec8
Author: Kai
Date: Thu Apr 6 14:48:40 2017 +0200
Merge remote-tracking branch 'upstream/master'
importing pato terms from upstream
commit 9fa5ec8
Author: pbuttigieg
Date: Thu Apr 6 14:45:24 2017 +0200
imported PATO classes for #486 #487 #488
commit 43557c3
Author: Kai
Date: Thu Apr 6 10:43:37 2017 +0200
Added ice formation and ice flow related classes see https://github.com/EnvironmentOntology/envo/pull/487#discussion_r110089957
commit 47b2092
Author: Kai
Date: Thu Apr 6 08:45:18 2017 +0200
Added and updated meltpond related classes see https://github.com/EnvironmentOntology/envo/pull/487#discussion_r109682927 discussion which was somehow clipped of from #487
commit e3e88c1
Author: Kai
Date: Thu Apr 6 08:13:04 2017 +0200
minor edits for #487
commit b0c253e
Author: Kai
Date: Wed Apr 5 13:28:47 2017 +0200
modified sediment and arctic related classes as doccumented in #483 and #487
commit f144d1c
Author: Kai
Date: Fri Mar 31 19:29:51 2017 +0200
added more arctic classes see discussion in #483
commit b94e86b
Merge: b280935 43150a7
Author: Pier Luigi Buttigieg
Date: Thu Mar 30 18:33:42 2017 +0200
Merge pull request #481 from kaiiam/master
This PR has been reviewed and is ready for merging. There will still be edits that will follow, but in a new PR from @kaiiam.
commit 43150a7
Author: Kai
Date: Thu Mar 30 18:14:08 2017 +0200
final edits for #481
commit 17f65c6
Author: Kai
Date: Thu Mar 30 18:01:54 2017 +0200
added additional axioms to #481
commit 8374d49
Author: Kai
Date: Thu Mar 30 17:09:22 2017 +0200
fixed axioms breaking build in #481
commit 855136b
Author: Kai
Date: Thu Mar 30 16:36:05 2017 +0200
added axioms for classes added in #481 and added powdery snow
commit cf835a3
Author: Kai
Date: Thu Mar 30 13:07:36 2017 +0200
fixed issues related to build failure for #481
commit 749ce2a
Author: Kai
Date: Wed Mar 29 18:22:55 2017 +0200
...
Polar express
About this release
This release features a large collection of classes representing polar and cryosphere-related environments and environmental processes, primarily prepared by @kaiiam. These semantics are in aid of efforts such as the Alfred Wegener Institute's Frontiers in Arctic Marine Monitoring programme. Knowledge was harvested from numerous resources - such as the review by Boetius et al. (2015, Nat Rev Microbiol 13: 677–690) - which are cross referenced in each class. Efforts to align with existing resources have been initiated, e.g.: ESIPFed/sweet#7
Past and ongoing work related to this project is organised in project cryophile. This work has also motivated the general development of the environmental process hierarchy.
A number of other requests, such as that for fissures (see #466) are also bundled in this release.
As usual, the hyperlinks to the terms will be live once OntoBee runs its import cycle over the weekend; however, the PURLs are valid immediately.
To better axiomatise the new classes and enhance existing ones, we have also imported numerous classes from other OBO projects, detailed below.
New Terms
aeolian transport of snow
aeolian transport process
atmosphere and water column exposed melt pond
atmosphere-exposed melt pond
blue ice
brine channel formation process
brine channel
brine rejection from seawater
calving of ice from an iceberg
channel
cirque glacier
cold season
compaction process
continental subsurface zone
cryoconite hole
cryoconite
cryoform
depositional process
englacial stream
erosionally enriched glacial ice
erosionally enriched ice
explosion process
first year ice formation process
first year ice
fissure water
frazil ice formation
frazil ice
gas emission process
geographic basin
glacial erosion process
glacial ice calving process
glacial ice gain
glacial ice loss
glacial ice
glacial sintering
glacial transport process
grease ice layer
hydrocarbon gas emission process
ice ablation zone
ice floe
ice formation process
ice gain
iceberg calving process
ice-encased melt pond
intraglacial lake
marine sediment
material accumulation process
material decumulation process
material transformation process
material transport process
melt pond
methane gas emission process
methane-laden permafrost
methane-releasing thermokarst lake
methane-sourced permafrost crater
multiyear ice formation process
multiyear ice
new ice formation process
new ice
nilas formation process
nilas
nivation
pancake ice
perennial snow patch
permafrost methane explosion
permafrost thawing process
planetary subsurface zone
powdery snow avalanche
powdery snow
sea ice floe
sea ice formation process
sea ice formation process
season generating process
season
seasonal melting process
seasonal snow patch
second year ice formation
second year ice
sedimentation in a water body
shallow marine sediment
shuga formation process
shuga
slab avalanche
slab snow
slush formation process
slush ice layer
slush ice
snow drift formation
snow drift
snow mass
snow patch
snowpack
solid-phase sintering
soot
subglacial lake
supraglacial lake
thaw hole
thermokarst depression
thermokarst lake
thermokarst
warm season
water column exposed melt pond
wet snow avalanche
young ice formation process
young ice
New imported classes
Hot tub time machine
Hot tub time machine
Eponyms for this release:
hot tub
time crystal
In this release, we add several terms to address user requests for epidemiology, food science, Arctic research, and anthropogenic disasters. As usual, the hyperlinks to the terms will be live once OntoBee runs its import cycle over the weekend; however, the PURLs are valid immediately.
Further, terms have been edited, added, and imported in preparation for more anatomical environments, pest disasters, microbial biological processes, and food-linked environmental semantics.
New Terms
abattoir
ablation zone
animal cage
campground
closed animal house
day care building
dedicated campground
ecological corridor
firn
fish processing building
hot tub
ice ablation process
ice calving process
ice loss process
impromptu campground
knackery
migration path
mushroom environment
névé
nursing home
open animal house
petting zoo
plumbing drain
residential building
restaurant
rubbish landslide
time crystal
water ice sublimation process
Commit log
commit 2dc8f3b
Author: pbuttigieg
Date: Mon Mar 27 18:58:09 2017 +0200
addressing #460 and added time crystal
commit 717bcd6
Author: pbuttigieg
Date: Mon Mar 27 15:42:52 2017 +0200
addressing #470
commit 6f52486
Author: pbuttigieg
Date: Mon Mar 27 13:48:25 2017 +0200
linked methanogenesis to relevant bioreactor
commit 47b378d
Author: pbuttigieg
Date: Mon Mar 27 13:43:20 2017 +0200
added GO processes for microbial metabolism
commit 4ae859d
Author: pbuttigieg
Date: Fri Mar 24 14:48:18 2017 +0100
set up import for foodon terms (xref #464) and updated Makefile
commit 433b7d3
Author: Pier Luigi Buttigieg
Date: Thu Mar 23 23:10:35 2017 +0100
Update README.md
commit cee22bb
Author: pbuttigieg
Date: Thu Mar 23 22:59:03 2017 +0100
adding terms requested in #460
commit 0b9b64a
Author: pbuttigieg
Date: Thu Mar 23 22:24:45 2017 +0100
adding terms requested in #460
commit b5d2eb8
Author: Pier Luigi Buttigieg
Date: Thu Mar 23 16:27:07 2017 +0100
fixed headers
commit dfdf4e4
Merge: 2297c08 8c9a9db
Author: Pier Luigi Buttigieg
Date: Sat Mar 18 15:01:54 2017 +0100
Merge pull request #469 from kaiiam/master
First independent pull request
commit 8c9a9db
Author: Kai
Date: Thu Mar 16 16:22:27 2017 +0100
fixed neve and firn
commit 70faf2a
Merge: 6375e22 b7a1d6b
Author: Kai
Date: Thu Mar 16 14:10:17 2017 +0100
Merge branch 'master' of https://github.com/kaiiam/envo
commit 6375e22
Author: Kai
Date: Thu Mar 16 14:06:18 2017 +0100
added neve and firn
commit 2297c08
Merge: b06b420 b7a1d6b
Author: Pier Luigi Buttigieg
Date: Wed Mar 15 19:27:28 2017 +0100
Merge pull request #468 from kaiiam/master
Added ID space
commit b7a1d6b
Author: Pier Luigi Buttigieg
Date: Wed Mar 15 19:24:04 2017 +0100
Fixed idrange value
@kaiiam - your idrange conflicted with an existing editor
commit 0a1154e
Author: kaiiam
Date: Wed Mar 15 19:16:25 2017 +0100
fixed typo
commit 128008d
Author: Kai
Date: Wed Mar 15 19:12:39 2017 +0100
added ID space for Kai Blumberg
commit b06b420
Author: pbuttigieg
Date: Mon Mar 13 19:31:25 2017 +0100
Removed anaerobic axiom from marine anoxic zone, adding arctic classes, garbage landslide
commit 19d46ce
Author: pbuttigieg
Date: Mon Mar 13 16:09:37 2017 +0100
added some water defs, prepping for axioms
commit fc72a43
Author: pbuttigieg
Date: Mon Mar 13 15:27:22 2017 +0100
added text def for skin environment
commit b0ef775
Merge: 55b6f8b fff1128
Author: pbuttigieg
Date: Mon Mar 13 12:29:56 2017 +0100
Merge branch 'master' of https://github.com/EnvironmentOntology/envo
commit 55b6f8b
Author: pbuttigieg
Date: Mon Mar 13 12:25:33 2017 +0100
cleaned up makefile and go_terms.txt, switched NCBI import to ROBOT, added locusts and corals
commit fff1128
Author: pbuttigieg
Date: Mon Mar 13 12:25:33 2017 +0100
cleaned up makefile and go_terms.txt, switched NCBI import to ROBOT
2017-03-13
NOTE: PURLs to the new classes will be resolvable through OntoBee when it performs its import cycle on Saturday. Until then, please see the released ontology files to view the new classes: https://github.com/EnvironmentOntology/envo#stable-release-versions
New terms
aquaculture process
automated teller machine
biocrust
cloud condensation nucleus
feasting pit site
geothermally heated river
nucleation of cloud condensation
shrimp pond
soil biocrust
New terms via design patterns
| New term ID | Quality ID | Quality label | Env. material ID | Env. material label |
|---|---|---|---|---|
| ENVO:09200012 | PATO:0000146 | temperature | ENVO:00001998 | soil |
| ENVO:09200013 | PATO:0001822 | wetness | ENVO:00001998 | soil |
Commit log
commit 1dbd26c
Author: pbuttigieg
Date: Mon Mar 13 06:48:55 2017 +0100
Closes #450
commit cd7953b
Author: pbuttigieg
Date: Mon Mar 13 06:21:34 2017 +0100
Refined lava def and axioms
commit 4476718
Author: pbuttigieg
Date: Mon Mar 13 06:16:28 2017 +0100
Closes #444
commit 06a4ada
Author: pbuttigieg
Date: Mon Mar 13 06:05:39 2017 +0100
Addressing #438
commit d59882e
Author: pbuttigieg
Date: Mon Mar 13 04:22:48 2017 +0100
Closes #446
commit f7e6c41
Author: pbuttigieg
Date: Mon Mar 13 04:04:33 2017 +0100
Closes #448
commit 1cc3f57
Author: pbuttigieg
Date: Mon Mar 13 03:20:46 2017 +0100
Closes #462
commit 3d7c7f0
Author: pbuttigieg
Date: Mon Mar 13 03:15:13 2017 +0100
Closes #461
commit 5c25e48
Author: pbuttigieg
Date: Mon Mar 13 03:12:44 2017 +0100
updating for entity-attribute patterns and addressing #461
commit 4dacdff
Author: pbuttigieg
Date: Mon Mar 13 03:05:22 2017 +0100
Added aquaculture process for #467
commit 264f97a
Author: pbuttigieg
Date: Mon Mar 13 02:50:33 2017 +0100
Updated storm definition to reflect increased rates
commit b8005a7
Author: pbuttigieg
Date: Mon Mar 13 02:37:53 2017 +0100
Closed #467
commit b790b48
Author: pbuttigieg
Date: Mon Feb 27 19:31:20 2017 +0100
refined lightning semantics and minor edits
commit cb1c376
Author: pbuttigieg
Date: Mon Feb 27 18:48:12 2017 +0100
added comment stating algal bloom process isn't ready for use
commit 4b5037d
Author: pbuttigieg
Date: Mon Feb 27 18:36:22 2017 +0100
fixed def error for area of dwarf scrub, cf #458
commit 9940b9b
Author: Pier Luigi Buttigieg
Date: Sun Feb 26 18:31:27 2017 +0100
Update README.md
2017-02-26 release
Release notes
Main issues addressed:
#465 housekeeping
#458 NLCD classification, new subset
#442 Extension of storm semantics and environmental hazard subset
New axioms, improved defintions and some clean-up of existing axioms performed.
Subsets released
- ncld2011 subset
- environmental_hazards (update)
- wwfBiome
For details see this wiki page
New classes in this release
The NLCD subset
- area of barren land
- area of cropland
- area of deciduous forest
- area of developed open space
- area of developed space with high usage intensity
- area of developed space with low usage intensity
- area of developed space with medium usage intensity
- area of dwarf scrub
- area of emergent herbaceous wetland
- area of evergreen forest
- area of gramanoid or herbaceous vegetation
- area of lichen-dominated vegetation
- area of mixed forest
- area of moss-dominated vegetation
- area of open water
- area of pastureland or hayfields
- area of perennial ice or snow
- area of perennial snow
- area of perennial water ice
- area of scrub
- area of sedge- and forb-dominated herbaceious vegetation
- area of woody wetland
NLCD-related terms for axioms
Storm semantics
2017-01-07 release
This release contains an important bug fix, see #455 for details.
New terms in this release:
+[Term]
+id: ENVO:01000870
+name: ground deformation process
+def: "A process in which a solid planetary surface is deformed." []
+comment: This is a class to be filled by inference.
+is_a: ENVO:02500000 ! environmental system process
+relationship: has_input ENVO:01000635 ! land
+
+[Term]
+id: ENVO:01000871
+name: puddle of water
+def: "A puddle is a small accumulation of water, on a surface. It can form either by pooling in a depression on the surface, or by surface tension upon a fla
+comment: This class refers only to puddles of water, see https://github.com/EnvironmentOntology/envo/issues/337
+is_a: ENVO:00000549 ! intermittent water body
+
+[Term]
+id: ENVO:01000872
+name: balast water
+def: "Ballast water is water contained in the ballast tanks of sea-going vessels." [http://www.nature.com/news/four-routes-to-better-maritime-governance-1.21
+is_a: ENVO:00002006 ! water
+
+[Term]
+id: ENVO:01000873
+name: ballast tank
+def: "A ballast tank is a compartment within a boat, ship or other floating structure that holds water, which is used as ballast to provide stability for a v
+comment: Consider using http://purl.obolibrary.org/obo/OBI_0000967 as a super-class
+is_a: ENVO:00003074 ! manufactured product
2016-11-20 release
New classes:
- coal dust
- ore
- uranium mine
- iron mine
- coal
- platinum ore
- gold ore
- iron ore
- uranium ore
- oil shale
- paraffin wax
- welding fume
- fume
- copper ore
- open-pit mine
- natural wax
- aluminum welding fume
- vanadium fume
- paraffin wax fume
- zinc chloride fume
- lead paint
- paint
- peat drainage
- peat extraction
- transportation
- dust from plant parts
- cotton dust
- grain dust
- fibrous glass dust
- fibrous dust
- mineral dust
- asbestos dust
- clay dust
- cement dust
- metallic dust
- smog
- pyrolysis
- fog
- thermolysis
- flower-rich field margin strip
- water ice crystal
- crystal
- flower strip
- hair ice
- combustion process
- smoke
- mouth of liquid discharge conduit
- overflow structure
- temperate marine upwelling biome
- turbulent aquatic surface layer
- marl
- coral bleaching process
- tropical marine coral reef biome
- methane clathrate
- clathrate material
- temperate mediterranean sea biome
- temperate marginal sea biome
- tropical marine upwelling biome
- marine upwelling biome
- environmental system process quality
- atmospheric wind intensity
- porosity of soil
- mass density of soil
- concentration of of ammonium in soil
- concentration of of nitrate in soil
- composition of soil
- structure of soil
- acidity of soil
- ionosphere
- boundary layer
- glaze ice layer
- exosphere
- atmospheric layer
- ozone layer
- mass of biological material
- eutrophic lake
2016-05-17
In this release, multiple user requests for terms in our process, feature, and environmental system hierarchies have been addressed. Notably, astronomical objects and bodies have been added to help clarify planetary scale processes. This is likely to impact EnvO's hierarchies quite strongly in the near future, offering realist alternatives to problematic classes such as "geographic feature".
2016-02-18
In this release, several classes supporting the SDGIO have been added as well as a number of classes responding to user requests. Some routine curation has also been performed.