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Update release to account for #1599
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Ran release again to account for NMDC changes by @turbomam
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matentzn committed Feb 5, 2025
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Showing 66 changed files with 15,432 additions and 7,822 deletions.
652 changes: 650 additions & 2 deletions src/envo/envo-simple.owl

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831 changes: 626 additions & 205 deletions src/envo/envo.json

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598 changes: 596 additions & 2 deletions src/envo/envo.obo

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653 changes: 650 additions & 3 deletions src/envo/envo.owl

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14 changes: 14 additions & 0 deletions src/envo/imports/seed.txt
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Expand Up @@ -4424,9 +4424,13 @@ http://purl.obolibrary.org/obo/ENVO_03605012
http://purl.obolibrary.org/obo/ENVO_03605013
http://purl.obolibrary.org/obo/ENVO_03605014
http://purl.obolibrary.org/obo/ENVO_03605015
http://purl.obolibrary.org/obo/ENVO_03605016
http://purl.obolibrary.org/obo/ENVO_03605017
http://purl.obolibrary.org/obo/ENVO_03605018
http://purl.obolibrary.org/obo/ENVO_03605019
http://purl.obolibrary.org/obo/ENVO_03605022
http://purl.obolibrary.org/obo/ENVO_03605023
http://purl.obolibrary.org/obo/ENVO_03605024
http://purl.obolibrary.org/obo/ENVO_03605201
http://purl.obolibrary.org/obo/ENVO_03605202
http://purl.obolibrary.org/obo/ENVO_03605203
Expand Down Expand Up @@ -5692,6 +5696,7 @@ https://extension.umn.edu/soil-management-and-health/soil-compaction
https://genomicsstandardsconsortium.github.io/mixs/0000012/
https://genomicsstandardsconsortium.github.io/mixs/0000013/
https://genomicsstandardsconsortium.github.io/mixs/0000014/
https://genomicsstandardsconsortium.github.io/mixs/0016010/
https://genomicsstandardsconsortium.github.io/mixs/0016012/
https://genomicsstandardsconsortium.github.io/mixs/0016014/
https://github.com/ESIPFed/sweet/issues/219
Expand All @@ -5711,6 +5716,15 @@ https://link.springer.com/chapter/10.1007/978-94-011-1226-0_1
https://mcgillcompost.com/mcgill-compost-products/biofiltration-bioremediation-compost
https://medical-dictionary.thefreedictionary.com/discharge+lounge
https://meshb.nlm.nih.gov/record/ui?ui=D010362
https://microbiomedata.github.io/submission-schema/EnvBroadScalePlantAssociatedEnum/
https://microbiomedata.github.io/submission-schema/EnvBroadScaleSoilEnum/
https://microbiomedata.github.io/submission-schema/EnvBroadScaleWaterEnum/
https://microbiomedata.github.io/submission-schema/EnvLocalScalePlantAssociatedEnum/
https://microbiomedata.github.io/submission-schema/EnvLocalScaleSoilEnum/
https://microbiomedata.github.io/submission-schema/EnvLocalScaleWaterEnum/
https://microbiomedata.github.io/submission-schema/EnvMediumPlantAssociatedEnum/
https://microbiomedata.github.io/submission-schema/EnvMediumSoilEnum/
https://microbiomedata.github.io/submission-schema/EnvMediumWaterEnum/
https://new.smm.org/learn/activities/build-an-alligator-nest
https://nsidc.org/cryosphere/glossary
https://orcid.org/0000-0001-5275-8866
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13 changes: 13 additions & 0 deletions src/envo/reports/envo-base-robot-report.tsv
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Expand Up @@ -261,9 +261,13 @@ WARN missing_definition NMDC Water value sets definition
WARN missing_definition NMDC Soil broad scale value set definition
WARN missing_definition NMDC Soil local scale value set definition
WARN missing_definition NMDC Soil environmental medium value set definition
WARN missing_definition NMDC PlantAssociated value sets definition
WARN missing_definition NMDC Water broad scale value set definition
WARN missing_definition NMDC Water local scale value set definition
WARN missing_definition NMDC Water environmental medium value set definition
WARN missing_definition NMDC PlantAssociated broad scale value set definition
WARN missing_definition NMDC PlantAssociated local scale value set definition
WARN missing_definition NMDC PlantAssociated environmental medium value set definition
WARN missing_definition sub-bitumous coal definition
WARN missing_definition generation of energy from coal definition
WARN missing_definition generation of energy from oil definition
Expand Down Expand Up @@ -315,6 +319,15 @@ WARN missing_definition has_related_synonym definition
WARN missing_definition has_synonym_type definition
WARN missing_definition in_subset definition
WARN missing_definition shorthand definition
WARN missing_subset_declaration NMDC Soil broad scale value set rdfs:subPropertyOf
WARN missing_subset_declaration NMDC Soil local scale value set rdfs:subPropertyOf
WARN missing_subset_declaration NMDC Soil environmental medium value set rdfs:subPropertyOf
WARN missing_subset_declaration NMDC Water broad scale value set rdfs:subPropertyOf
WARN missing_subset_declaration NMDC Water local scale value set rdfs:subPropertyOf
WARN missing_subset_declaration NMDC Water environmental medium value set rdfs:subPropertyOf
WARN missing_subset_declaration NMDC PlantAssociated broad scale value set rdfs:subPropertyOf
WARN missing_subset_declaration NMDC PlantAssociated local scale value set rdfs:subPropertyOf
WARN missing_subset_declaration NMDC PlantAssociated environmental medium value set rdfs:subPropertyOf
WARN missing_subset_declaration obo:envo#envoCloudAtlas rdfs:subPropertyOf
WARN missing_subset_declaration obo:envo#envoCryo rdfs:subPropertyOf
WARN missing_subset_declaration blank node rdfs:subPropertyOf
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12 changes: 6 additions & 6 deletions src/envo/reports/envo-basicReport.tsv
Original file line number Diff line number Diff line change
Expand Up @@ -1123,7 +1123,7 @@
"http://purl.obolibrary.org/obo/NCBITaxon_7003"
"http://purl.obolibrary.org/obo/ENVO_02000037" "A bodily fluid material which is composed primarily of sebum, an oily bodily fluid secreted from the sebaceous glads that is made of fat (lipids) and the debris of dead fat-producing cells. In the glands, sebum is produced within specialized cells and is released as these cells burst. Sebum acts to protect and waterproof hair and skin, and keep them from becoming dry, brittle and cracked. It can also inhibit the growth of microorganisms on skin."
"http://purl.obolibrary.org/obo/PATO_0001576" "A pressure which is relatively high."
"http://purl.obolibrary.org/obo/ENVO_00000038" "A sheet of saline water separated from the open sea by sand or shingle banks. The sheet of water between an offshore reef, especially of coral and mainland. The sheet of water within a ring or horseshoe shaped atoll." "EcoLexicon:lagoon FTT:221 Geonames:H.LGNS Geonames:H.LGN TGN:21125 FTT:899 SWEETRealm:Lagoon FTT:898 https://en.wikipedia.org/wiki/Lagoon"
"http://purl.obolibrary.org/obo/ENVO_00000038" "A sheet of saline water separated from the open sea by sand or shingle banks. The sheet of water between an offshore reef, especially of coral and mainland. The sheet of water within a ring or horseshoe shaped atoll." "EcoLexicon:lagoon FTT:221 Geonames:H.LGNS Geonames:H.LGN TGN:21125 SWEETRealm:Lagoon FTT:899 FTT:898 https://en.wikipedia.org/wiki/Lagoon"
"http://purl.obolibrary.org/obo/ENVO_01001841" "An andosol which derives its silica content from glass and tephra ejected during a volcanic eruption."
"http://purl.obolibrary.org/obo/PATO_0001545" "A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking."
"http://purl.obolibrary.org/obo/UBERON_0004766" "A bone that is part of a cranium."
Expand Down Expand Up @@ -1350,7 +1350,7 @@
"http://purl.obolibrary.org/obo/ENVO_03600021" "A human construction which is used as a storage area for mining tailings."
"http://purl.obolibrary.org/obo/NCBITaxon_1163"
"http://purl.obolibrary.org/obo/ENVO_00002057"
"http://purl.obolibrary.org/obo/ENVO_00000463" "A landform which provides shelter from atmospheric weather and marine currents, waves, and other dynamics." "https://en.wikipedia.org/wiki/Harbor SWEETRealm:Harbor"
"http://purl.obolibrary.org/obo/ENVO_00000463" "A landform which provides shelter from atmospheric weather and marine currents, waves, and other dynamics." "SWEETRealm:Harbor https://en.wikipedia.org/wiki/Harbor"
"http://purl.obolibrary.org/obo/PATO_0001429" "An medium acidity quality inhering in a solution by virtue of the bearer's a high concentration of H+ ions."
"http://purl.obolibrary.org/obo/ENVO_01001733" "An upslope wind driven by heating at the slope surface under fair-weather conditions."
"http://purl.obolibrary.org/obo/ENVO_00005785" "https://en.wikipedia.org/wiki/Volcanic_soil"
Expand Down Expand Up @@ -1699,7 +1699,7 @@
"http://purl.obolibrary.org/obo/ENVO_01000409" "A freshwater littoral zone is a littoral zone which extends offshore from the shore of a freshwater body of water to the limit of occupancy of rooted plants."
"http://purl.obolibrary.org/obo/ENVO_00003090" "A portion of kynurenate enriched soil is a portion of soil with elevated levels of kynurenate."
"http://purl.obolibrary.org/obo/ENVO_00002186" "EcoLexicon:water_pollution https://en.wikipedia.org/wiki/Contaminated_water"
"http://purl.obolibrary.org/obo/ENVO_00002006" "An environmental material primarily composed of dihydrogen oxide in its liquid form." "https://en.wikipedia.org/wiki/Water LTER:617 EcoLexicon:water"
"http://purl.obolibrary.org/obo/ENVO_00002006" "An environmental material primarily composed of dihydrogen oxide in its liquid form." "EcoLexicon:water https://en.wikipedia.org/wiki/Water LTER:617"
"http://purl.obolibrary.org/obo/ENVO_03501186" "A medical clinic which is used to provide family medicine services."
"http://purl.obolibrary.org/obo/ENVO_01000734" "A sheet intrusion (or concordant pluton) that has been injected between two layers of sedimentary rock. The pressure of the magma is high enough that the overlying strata are forced upward, giving the laccolith a dome or mushroom-like form with a generally planar base."
"http://purl.obolibrary.org/obo/PO_0025337" "A maximal whole plant development stage." "PO_GIT:230"
Expand Down Expand Up @@ -1741,7 +1741,7 @@
"http://purl.obolibrary.org/obo/ENVO_01000253" "A freshwater river ecosystem which is in its climactic successional state."
"http://purl.obolibrary.org/obo/CHEBI_33704"
"http://purl.obolibrary.org/obo/OBI_0000401" "An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature."
"http://purl.obolibrary.org/obo/ENVO_00000023" "A watercourse which is linear and flows across the solid portion of a planetary surface." "TGN:21107 FTT:1221 TGN:21109 FTT:721 FTT:303 Geonames:H.STMS LTER:562 FTT:1261 FTT:1225 Geonames:H.STM FTT:371 FTT:593 EcoLexicon:stream https://en.wikipedia.org/wiki/Stream SWEETRealm:Stream TGN:21106 FTT:105 TGN:21108"
"http://purl.obolibrary.org/obo/ENVO_00000023" "A watercourse which is linear and flows across the solid portion of a planetary surface." "TGN:21108 FTT:303 Geonames:H.STM SWEETRealm:Stream LTER:562 Geonames:H.STMS FTT:721 TGN:21109 EcoLexicon:stream FTT:1225 FTT:1221 TGN:21106 FTT:1261 https://en.wikipedia.org/wiki/Stream FTT:593 FTT:371 FTT:105 TGN:21107"
"http://purl.obolibrary.org/obo/ENVO_01001531" "An ice field which is primarily composoed of sea ice floes greater than 10 kilometers across." "http://sweetontology.net/realmCryo/IceField"
"http://purl.obolibrary.org/obo/FOODON_03420164" "Material that derives from some animal." "http://www.langual.org/langual_thesaurus.asp?termid=C0164"
"http://purl.obolibrary.org/obo/ENVO_0010032"
Expand Down Expand Up @@ -2670,7 +2670,7 @@
"http://purl.obolibrary.org/obo/ENVO_02000170" "A modular structure created by bees (Anthophila) from beeswax, consisting of a mass of hexagonal prismatic cells used to store honey, pollen, and house brood (eggs, larvae, and pupae)."
"http://purl.obolibrary.org/obo/UBERON_0034878" "The area of axial mesoderm that develops into the prechordal plate."
"http://purl.obolibrary.org/obo/ENVO_0010056"
"http://purl.obolibrary.org/obo/ENVO_00000213" "The zone of an ocean immediately below the photic zone down to a depth where the water temperature is 10degC (the thermocline)." "https://en.wikipedia.org/wiki/Mesopelagic_zone SWEETRealm:MesopelagicZone SPIRE:Mesopelagic_zone EcoLexicon:mesopelagic_zone"
"http://purl.obolibrary.org/obo/ENVO_00000213" "The zone of an ocean immediately below the photic zone down to a depth where the water temperature is 10degC (the thermocline)." "SPIRE:Mesopelagic_zone https://en.wikipedia.org/wiki/Mesopelagic_zone EcoLexicon:mesopelagic_zone SWEETRealm:MesopelagicZone"
"http://purl.obolibrary.org/obo/ENVO_00000386" "The end of a stream where it enters a standing water body such as a lake, sea or ocean." "https://en.wikipedia.org/wiki/River_mouth TGN:21156"
"http://purl.obolibrary.org/obo/ENVO_00002926"
"http://purl.obolibrary.org/obo/ENVO_01001660" "A material transport process during which alternate freezing and thawing of moisture in soil, rock and other materials results modifications of those materials and in the formation of structures on, or in, the ground."
Expand Down Expand Up @@ -3305,7 +3305,7 @@
"http://purl.obolibrary.org/obo/ENVO_00000219" "An inland sea which is not connected with an ocean by a lentic or lotic water body." "FTT:871 FTT:221"
"http://purl.obolibrary.org/obo/ENVO_01000202" "A broadleaf forest which is subject to temperate climate patterns."
"http://purl.obolibrary.org/obo/ENVO_01001223" "A process during which wood is processed into beams or planks."
"http://purl.obolibrary.org/obo/ENVO_00000258" "A relatively flat and gently sloping landform found at the base of a range of hills or mountains, formed by the deposition of alluvial soil over a long period of time by one or more streams coming from the mountains." "https://en.wikipedia.org/wiki/Alluvial_plain SWEETRealm:AlluvialPlain EcoLexicon:alluvial_plain"
"http://purl.obolibrary.org/obo/ENVO_00000258" "A relatively flat and gently sloping landform found at the base of a range of hills or mountains, formed by the deposition of alluvial soil over a long period of time by one or more streams coming from the mountains." "https://en.wikipedia.org/wiki/Alluvial_plain EcoLexicon:alluvial_plain SWEETRealm:AlluvialPlain"
"http://purl.obolibrary.org/obo/ENVO_01000405" "A portion of respirable suspended particulate matter is a form of particulate matter composed primarily of solid particles each with a diameter of 10 micrometers or less."
"http://purl.obolibrary.org/obo/NCBITaxon_3028117"
"http://purl.obolibrary.org/obo/ENVO_00003885" "A brewery is a building in which alcoholic beverages are produced by brewing, that is, steeping a starch source (commonly cereal grains) in water and fermenting the resulting sweet liquid with yeast. At times, the products are also sold from the brewery."
Expand Down
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