EnvironmentOntology/envo: 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.: https://github.com/ESIPFed/sweet/issues/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 PURL label http://purl.obolibrary.org/obo/IAO_0000104 plan specification http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/IAO_0000100 data set http://purl.obolibrary.org/obo/IAO_0000584 time sampled measurement data set http://purl.obolibrary.org/obo/IAO_0000582 time stamped measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum http://purl.obolibrary.org/obo/IAO_0000136 is about http://purl.obolibrary.org/obo/IAO_0000221 is quality measurement of http://purl.obolibrary.org/obo/RO_0002404 causally downstream of http://purl.obolibrary.org/obo/RO_0002411 causally upstream of http://purl.obolibrary.org/obo/CHEBI_63248 oxidant http://purl.obolibrary.org/obo/PATO_0000318 blue http://purl.obolibrary.org/obo/PATO_0001855 horizontal http://purl.obolibrary.org/obo/PATO_0000411 circular http://purl.obolibrary.org/obo/PATO_0000964 transparent http://purl.obolibrary.org/obo/PATO_0001354 translucent http://purl.obolibrary.org/obo/PATO_0000963 opaque http://purl.obolibrary.org/obo/PATO_0001171 elastic http://purl.obolibrary.org/obo/PATO_0001172 inelastic http://purl.obolibrary.org/obo/PATO_0000689 continuous (of a process) http://purl.obolibrary.org/obo/PATO_0005011 continuous (of a material entity) http://purl.obolibrary.org/obo/PATO_0001688 increased elevation http://purl.obolibrary.org/obo/PATO_0001689 decreased elevation http://purl.obolibrary.org/obo/PATO_0000591 increased thickness http://purl.obolibrary.org/obo/PATO_0000592 decreased thickness http://purl.obolibrary.org/obo/PATO_0001781 irregular thickness Commit log

commit cb7178e00f41b15b9038b0d8a55ae2118d497426 Author: pbuttigieg Date: Sat Apr 15 11:06:00 2017 +0200

closes #466, added IAO imports

commit 886dfbc7e062caafcb4637225752b1992d398b6b 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 3dbcd1e0e189162f2fe8be62021c8fa147ac6260 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 b445dd57954a1d55741ee813181ff25bb12a146d Author: pbuttigieg Date: Wed Apr 12 18:55:24 2017 +0200

added IAO import and edited Makefile accordingly

commit fe2966e834151540bf9270a023b6047baf616ccb 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 3e8f57bb30d6db8c4de4e7d4a468099096b33624 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 dc8b426a52546b4fc9be70381be87d4733516880 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 1d9e25490eb8aa7eb91f17154389001b9bcdd2e0 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 bbba1845e1fdde1486b03bc11f29def6c2ca3a87 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 5359e45770941b41d65fc6e1e1d4e97ba856b7c5 Author: pbuttigieg Date: Mon Apr 10 20:57:59 2017 +0200

added causal relations to RO import

commit 1cdcf0fa99aaed10dfb9bca034cd913843966a7b 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 d81e45445e12742d6e245c75bfa86ef792013e9b 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 c85ef18e5a2160d4748cd1d7eb7a4abb7d5b03a7 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 fcbd366cd52e212a3fe95739e3769da585bb1f75 Merge: cf41b5a 73dccf6 Author: Kai Date: Fri Apr 7 10:42:17 2017 +0200

Merge remote-tracking branch 'upstream/master'

commit cf41b5a0d1c6de78207d3b1721b557cdc975f6fe 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 73dccf6dba1d8e48291f5e192359dd6e0ac25b58 Author: Pier Luigi Buttigieg Date: Thu Apr 6 18:17:01 2017 +0200

Resort and give ranges to new patterns in #492

commit 31ca0c713ec8f2dc2df70ce563a2141e5c4eb08d Author: pbuttigieg Date: Thu Apr 6 18:01:43 2017 +0200

added oxidant for #487

commit 9cdfcb158d1fb30fd5b22a9e69d365482819404c 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 9fa5ec862da9bc672ba62faa418a060d8357fa50 Author: pbuttigieg Date: Thu Apr 6 14:45:24 2017 +0200

imported PATO classes for #486 #487 #488

commit 43557c3a736eda95f7d8481e4689adb39bbfc091 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 47b20923876a11779c42d32f64f8f74135f5a379 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 e3e88c1d9c8b3833f697fa28882fcfcd91bb0429 Author: Kai Date: Thu Apr 6 08:13:04 2017 +0200

minor edits for #487

commit b0c253e40b37a5c203a8505b7663b01ab638ddc1 Author: Kai Date: Wed Apr 5 13:28:47 2017 +0200

modified sediment and arctic related classes as doccumented in #483 and #487

commit f144d1c1393ae3c8cdb2983a0a994bd02371ed06 Author: Kai Date: Fri Mar 31 19:29:51 2017 +0200

added more arctic classes see discussion in #483

commit b94e86b413f6e11d662356102d433aa8f15fb8a5 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 43150a7cd193fabc464e3ec86b5053946acf5c73 Author: Kai Date: Thu Mar 30 18:14:08 2017 +0200

final edits for #481

commit 17f65c62aad086330feeb5305a1802f1bdf5e78e Author: Kai Date: Thu Mar 30 18:01:54 2017 +0200

added additional axioms to #481

commit 8374d49ac47d3910e193b7be75fb3dc45f255516 Author: Kai Date: Thu Mar 30 17:09:22 2017 +0200

fixed axioms breaking build in #481

commit 855136b02cbb21c8f61a7a7233d7433ac6e47109 Author: Kai Date: Thu Mar 30 16:36:05 2017 +0200

added axioms for classes added in #481 and added powdery snow

commit cf835a3d6ed1444a8e9e55132bbfd83f986ac28e Author: Kai Date: Thu Mar 30 13:07:36 2017 +0200

fixed issues related to build failure for #481

commit 749ce2a4db8314f1af87dcf553fd89825148d5a5 Author: Kai Date: Wed Mar 29 18:22:55 2017 +0200

fixed issues for project cryophile 2nd pull request #481

commit b280935eab396e12a795c1c0b6072625080787e5 Author: Pier Luigi Buttigieg Date: Wed Mar 29 17:54:13 2017 +0200

Fixed subset wiki link

commit 55c5fff62194f303c5d923f09019d1ce98dcc56e Author: Kai Date: Tue Mar 28 20:15:19 2017 +0200

addressing #475 added: aeolian transport process, & soot

commit 14099a98718f847517065635df84affdbb94baf1 Author: Kai Date: Tue Mar 28 19:07:06 2017 +0200

addressing #474 & #475 added: blue ice, compaction process, material accumulation process, material transport process, ice gain, glacial transport process, updated alpine glacier, added: cirque glaciers, cirque basin, glacial erosion process, geographic basin, glacial ice loss, material decumulation process, glacial ice loss, and englacial stream.

commit 299650d5ff6521a67d4a646548997ebe5d5fea0e Author: Kai Date: Tue Mar 28 15:26:41 2017 +0200

revamped definition for glacier, added glacial ice as subclass of ice mass, erosionally enriched glacial ice, & glacial erosion process.

commit 135a712c1c793c860507e06c36aab52624645169 Author: Kai Date: Tue Mar 28 12:46:25 2017 +0200

added niviation

commit b8b6c594bcc96f01361c63191ae83c7f97b51d79 Author: Kai Date: Tue Mar 28 11:45:42 2017 +0200

updated definitions for neve and firn