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Merge pull request #446 from Planteome/release_may2019
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prepare release
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@cooperl09
cooperl09 authored May 21, 2019
2 parents 9d0b0ec + 4584433 commit 16c6e5e
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21 changes: 21 additions & 0 deletions catalog-v001.xml
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base="">
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/imports/chebi_import.owl" uri="imports/chebi_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/imports/envo_import.owl" uri="imports/envo_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/imports/go_import.owl" uri="imports/go_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/imports/ncbitaxon_import.owl" uri="imports/ncbitaxon_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/imports/pato_import.owl" uri="imports/pato_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/imports/peco_import.owl" uri="imports/peco_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/imports/po_import.owl" uri="imports/po_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/imports/ro_import.owl" uri="imports/ro_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/patterns/composition_pattern.owl" uri="patterns/composition/composition_pattern.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/patterns/eq_pattern.owl" uri="patterns/eq/eq_pattern.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/patterns/merge_patterns.owl" uri="patterns/merge_patterns.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/patterns/morphology_pattern.owl" uri="patterns/morphology/morphology_pattern.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/patterns/phenotype_pattern.owl" uri="patterns/phenotype/phenotype_pattern.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/patterns/ratio_pattern.owl" uri="patterns/ratio/ratio_pattern.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/patterns/responsivityNoEO_pattern.owl" uri="patterns/responsivityNoEO/responsivityNoEO_pattern.owl"/>
<uri id="Automatically generated entry, Timestamp=1558425202558" name="http://purl.obolibrary.org/obo/to/patterns/responsivity_pattern.owl" uri="patterns/responsivity/responsivity_pattern.owl"/>
</group>
</catalog>
260 changes: 218 additions & 42 deletions imports/chebi_import.obo
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1,159 changes: 926 additions & 233 deletions imports/chebi_import.owl
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224 changes: 53 additions & 171 deletions imports/envo_import.obo
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Expand Up @@ -8,14 +8,11 @@ name: entity
[Term]
id: BFO:0000002
name: continuant
def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." []
is_a: BFO:0000001 ! entity

[Term]
id: BFO:0000004
name: independent continuant
def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." []
def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant

Expand All @@ -27,9 +24,6 @@ is_a: BFO:0000020 ! specifically dependent continuant
[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." []
def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" []
def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
is_a: BFO:0000002 ! continuant

[Term]
Expand All @@ -46,19 +40,16 @@ is_a: BFO:0000040 ! material entity
[Term]
id: BFO:0000040
name: material entity
def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." []
is_a: BFO:0000004 ! independent continuant

[Term]
id: ENVO:00000000
name: geographic feature
synonym: "macroscopic spatial feature" EXACT []
is_a: ENVO:01000813 ! astronomical body part

[Term]
id: ENVO:00002297
name: environmental feature
def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088]
is_a: BFO:0000040 ! material entity
intersection_of: BFO:0000040 ! material entity
intersection_of: RO:0002508 ENVO:01000254 ! environmental system
Expand All @@ -67,266 +58,157 @@ relationship: RO:0002508 ENVO:01000254 ! environmental system
[Term]
id: ENVO:00010483
name: environmental material
def: "A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system." [DOI:10.1186/2041-1480-4-43, MA:ma, ORCID:0000-0002-4366-3088, URL:http\://ontology.buffalo.edu/smith/articles/niches.html]
def: "A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system." [DOI:10.1186/2041-1480-4-43, MA:ma, ORCID:0000-0002-4366-3088, URL:http\://ontology.buffalo.edu/smith/articles/niches.html]
synonym: "portion of environmental material" EXACT []
is_a: BFO:0000024 ! fiat object
is_a: BFO:0000040 ! material entity

[Term]
id: ENVO:01000254
name: environmental system
def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43]
synonym: "environment" EXACT []
is_a: RO:0002577 ! system

[Term]
id: ENVO:01000281
name: layer
def: "A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface." [Wiktionary:layer]
is_a: ENVO:00000000 ! geographic feature
relationship: RO:0000086 PATO:0002124 ! laminar

[Term]
id: ENVO:01000355
name: vegetation layer
def: "A layer which is determined by a form of vegetation." []
synonym: "forest layer" RELATED []
synonym: "forest stratum" RELATED []
synonym: "woodland layer" RELATED []
synonym: "woodland stratum" RELATED []
is_a: ENVO:01000281 ! layer
intersection_of: ENVO:01000281 ! layer
intersection_of: RO:0002473 NCBITaxon:33090 ! Viridiplantae
relationship: RO:0002473 NCBITaxon:33090 ! Viridiplantae

[Term]
id: ENVO:01000637
name: outer space
def: "Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies." [https://en.wikipedia.org/wiki/Outer_space]
synonym: "space" BROAD []
is_a: ENVO:00002297 ! environmental feature
is_a: ENVO:00010483 ! environmental material

[Term]
id: ENVO:01000799
name: astronomical body
def: "An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space." [https://en.wikipedia.org/wiki/Astronomical_object]
synonym: "celestial body" RELATED []
is_a: ENVO:01000804 ! astronomical object

[Term]
id: ENVO:01000804
name: astronomical object
def: "An object which is composed of one or more gravitationally bound structures that are associated with a position in space." [https://en.wikipedia.org/wiki/Astronomical_object]
synonym: "celestial object" RELATED []
is_a: BFO:0000030 ! object
is_a: ENVO:00002297 ! environmental feature
relationship: BFO:0000051 ENVO:01000799 {minCardinality="1"} ! astronomical body
relationship: BFO:0000051 ENVO:01000799 ! astronomical body
relationship: RO:0000086 ENVO:01001164 ! geodiversity
relationship: RO:0002219 ENVO:01000637 ! outer space

[Term]
id: ENVO:01000813
name: astronomical body part
def: "A material part of an astronomical body." []
is_a: BFO:0000024 ! fiat object
is_a: ENVO:00002297 ! environmental feature
relationship: BFO:0000050 ENVO:01000799 ! astronomical body
relationship: RO:0000086 ENVO:01001164 ! geodiversity

[Term]
id: ENVO:01000998
name: environmental system determined by a material
def: "An environmental system within which an environmental material strongly influences the system's composition and properties." []
is_a: ENVO:01000254 ! environmental system
intersection_of: ENVO:01000254 ! environmental system
intersection_of: RO:0002507 ENVO:00010483 ! environmental material
relationship: RO:0002507 ENVO:00010483 ! environmental material

[Term]
id: ENVO:01001110
name: ecosystem
def: "An environmental system which includes both living and non-living components." [https://en.wikipedia.org/wiki/Ecosystem]
is_a: ENVO:01000254 ! environmental system

[Term]
id: ENVO:01001164
name: geodiversity
def: "A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms." [https://en.wikipedia.org/wiki/Geodiversity]
is_a: PATO:0001241 ! physical object quality

[Term]
id: ENVO:01001241
name: crop canopy
def: "A canopy which is composed of the aboveground portion, or crowns, of a community of crop plants." []
is_a: ENVO:01001242 ! canopy
relationship: BFO:0000050 ENVO:01001244 ! cropland ecosystem

[Term]
id: ENVO:01001242
name: canopy
def: "A vegetation layer which is formed by a collection of individual plant crowns, themselves constituting part of the aboveground portion of a plant community." [https://en.wikipedia.org/wiki/Canopy_%28biology%29]
is_a: ENVO:01000355 ! vegetation layer

[Term]
id: ENVO:01001244
name: cropland ecosystem
def: "An ecosystem which is determined by communities of annual crops, perennial woody crops, or by actively tilled land." []
is_a: ENVO:01001110 ! ecosystem

[Term]
id: NCBITaxon:1
name: root
is_a: BFO:0000040 ! material entity

[Term]
id: NCBITaxon:10239
name: Viruses
is_a: NCBITaxon:1 ! root
is_a: OBI:0100026 ! organism

[Term]
id: NCBITaxon:131567
name: cellular organisms
is_a: NCBITaxon:1 ! root

[Term]
id: NCBITaxon:2
name: Bacteria
is_a: NCBITaxon:131567 ! cellular organisms
is_a: OBI:0100026 ! organism

[Term]
id: NCBITaxon:2157
name: Archaea
is_a: NCBITaxon:131567 ! cellular organisms
is_a: OBI:0100026 ! organism

[Term]
id: NCBITaxon:2759
name: Eukaryota
is_a: NCBITaxon:131567 ! cellular organisms
is_a: OBI:0100026 ! organism

[Term]
id: NCBITaxon:33090
name: Viridiplantae
is_a: NCBITaxon:2759 ! Eukaryota

[Term]
id: OBI:0100026
name: organism
is_a: BFO:0000040 ! material entity
union_of: NCBITaxon:10239 ! Viruses
union_of: NCBITaxon:2 ! Bacteria
union_of: NCBITaxon:2157 ! Archaea
union_of: NCBITaxon:2759 ! Eukaryota

[Term]
id: PATO:0000001
name: quality
def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG]
synonym: "trait" EXACT []
is_a: BFO:0000020 ! specifically dependent continuant

[Term]
id: PATO:0000051
name: morphology
def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." []
is_a: BFO:0000019 ! quality
is_a: PATO:0001241 ! physical object quality

[Term]
id: PATO:0000141
name: structure
def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." []
synonym: "conformation" BROAD []
synonym: "relational structural quality" EXACT []
is_a: PATO:0000051 ! morphology

[Term]
id: PATO:0001241
name: physical object quality
def: "A quality which inheres in a continuant." [PATOC:GVG]
synonym: "monadic quality of a continuant" EXACT []
synonym: "monadic quality of an object" NARROW []
synonym: "monadic quality of continuant" NARROW []
synonym: "multiply inhering quality of a physical entity" EXACT []
synonym: "quality of a continuant" EXACT []
synonym: "quality of a single physical entity" EXACT []
synonym: "quality of an object" EXACT []
synonym: "quality of continuant" EXACT []
is_a: PATO:0000001 ! quality

[Term]
id: PATO:0002124
name: laminar
def: "A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer." []
is_a: PATO:0000141 ! structure

[Term]
id: RO:0002577
name: system
def: "A material entity consisting of multiple components that are causally integrated." []
is_a: BFO:0000040 ! material entity

[Typedef]
id: BFO:0000050
is_transitive: true
is_a: RO:0002131
inverse_of: BFO:0000051

[Typedef]
id: BFO:0000051
is_transitive: true
is_a: RO:0002131

[Typedef]
id: FOODON:00002420
holds_over_chain: BFO:0000051 RO:0001000

[Typedef]
id: RO:0000052
is_a: RO:0002314
inverse_of: RO:0000053

[Typedef]
id: RO:0000053
range: BFO:0000020 ! specifically dependent continuant

[Typedef]
id: RO:0000080
is_a: RO:0000052
inverse_of: RO:0000086

[Typedef]
id: RO:0000086
range: BFO:0000019 ! quality
is_a: RO:0000053

[Typedef]
id: RO:0001000
is_reflexive: true
inverse_of: RO:0001001

[Typedef]
id: RO:0002131
holds_over_chain: BFO:0000050 BFO:0000050
holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
holds_over_chain: BFO:0000051 RO:0002131
is_a: RO:0002323

[Typedef]
id: RO:0002163
is_a: RO:0002323

[Typedef]
id: RO:0002219
is_a: RO:0002220
inverse_of: RO:0002221

[Typedef]
id: RO:0002220
domain: BFO:0000004 ! independent continuant
range: BFO:0000004 ! independent continuant
is_a: RO:0002163

[Typedef]
id: RO:0002221
is_a: RO:0002220

[Typedef]
id: RO:0002314
holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: RO:0002502
transitive_over: BFO:0000050

[Typedef]
id: RO:0002410
is_a: RO:0002609

[Typedef]
id: RO:0002506
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002410

[Typedef]
id: RO:0002507
domain: RO:0002577 ! system
range: BFO:0000040 ! material entity
is_a: BFO:0000050
is_a: RO:0002509
is_a: RO:0002559
inverse_of: RO:0002508

[Typedef]
id: RO:0002508
is_a: RO:0002566

[Typedef]
id: RO:0002509
domain: RO:0002577 ! system
range: BFO:0000040 ! material entity
holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: RO:0002131
is_a: RO:0002506

[Typedef]
id: RO:0002559
is_a: RO:0002506
inverse_of: RO:0002566

[Typedef]
id: RO:0002566
is_a: RO:0002506

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