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Copying the Release files into the release directory #1607

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merged 4 commits into from
Feb 6, 2025
Merged

Copying the Release files into the release directory #1607

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f6c5113
Update release files 4th February 2025
matentzn Feb 4, 2025
d04fe52
Merge branch 'master' into release-2025-02-04
matentzn Feb 5, 2025
73f2089
Update release to account for #1599
matentzn Feb 5, 2025
93ab468
Update release files
matentzn Feb 5, 2025
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8,586 changes: 6,165 additions & 2,421 deletions envo-base.owl
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13,480 changes: 7,523 additions & 5,957 deletions envo.json
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5,574 changes: 3,090 additions & 2,484 deletions envo.obo
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13,540 changes: 7,153 additions & 6,387 deletions envo.owl
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544 changes: 4 additions & 540 deletions imports/chebi_import.obo
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960 changes: 8 additions & 952 deletions imports/chebi_import.owl
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2 changes: 1 addition & 1 deletion imports/fao_import.owl
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Expand Up @@ -298,5 +298,5 @@



<!-- Generated by the OWL API (version 4.5.24) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->

1,131 changes: 568 additions & 563 deletions imports/foodon_import.obo
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1,494 changes: 824 additions & 670 deletions imports/foodon_import.owl
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54 changes: 7 additions & 47 deletions imports/go_import.obo
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Expand Up @@ -9,11 +9,6 @@ is_a: GO:0032501 ! multicellular organismal process
[Term]
id: GO:0006091
name: generation of precursor metabolites and energy
is_a: GO:0044237 ! cellular metabolic process

[Term]
id: GO:0006807
name: nitrogen compound metabolic process
is_a: GO:0008152 ! metabolic process

[Term]
Expand All @@ -38,7 +33,7 @@ name: biological_process
[Term]
id: GO:0008152
name: metabolic process
is_a: GO:0008150 ! biological_process
is_a: GO:0009987 ! cellular process

[Term]
id: GO:0009058
Expand All @@ -63,7 +58,7 @@ is_a: GO:0008150 ! biological_process
[Term]
id: GO:0015947
name: methane metabolic process
is_a: GO:0043446 ! cellular alkane metabolic process
is_a: GO:0043446 ! alkane metabolic process

[Term]
id: GO:0015948
Expand All @@ -81,7 +76,7 @@ is_a: GO:0006091 ! generation of precursor metabolites and energy
[Term]
id: GO:0015979
name: photosynthesis
is_a: GO:0044237 ! cellular metabolic process
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0015980
Expand All @@ -91,7 +86,6 @@ is_a: GO:0006091 ! generation of precursor metabolites and energy
[Term]
id: GO:0019329
name: ammonia oxidation
is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0044281 ! small molecule metabolic process

[Term]
Expand All @@ -100,22 +94,19 @@ name: anaerobic respiration, using ammonium as electron donor
is_a: GO:0009061 ! anaerobic respiration
is_a: GO:0015975 ! energy derivation by oxidation of reduced inorganic compounds
is_a: GO:0019329 ! ammonia oxidation
is_a: GO:0034641 ! cellular nitrogen compound metabolic process

[Term]
id: GO:0019332
name: aerobic respiration, using nitrite as electron donor
is_a: GO:0009060 ! aerobic respiration
is_a: GO:0015975 ! energy derivation by oxidation of reduced inorganic compounds
is_a: GO:0034641 ! cellular nitrogen compound metabolic process

[Term]
id: GO:0019409
name: aerobic respiration, using ammonia as electron donor
is_a: GO:0009060 ! aerobic respiration
is_a: GO:0015975 ! energy derivation by oxidation of reduced inorganic compounds
is_a: GO:0019329 ! ammonia oxidation
is_a: GO:0034641 ! cellular nitrogen compound metabolic process

[Term]
id: GO:0019410
Expand Down Expand Up @@ -162,28 +153,20 @@ id: GO:0032501
name: multicellular organismal process
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0034641
name: cellular nitrogen compound metabolic process
is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0044237 ! cellular metabolic process

[Term]
id: GO:0042755
name: eating behavior
is_a: GO:0007631 ! feeding behavior

[Term]
id: GO:0043446
name: cellular alkane metabolic process
is_a: GO:0044237 ! cellular metabolic process
name: alkane metabolic process
is_a: GO:0120252 ! hydrocarbon metabolic process

[Term]
id: GO:0043447
name: alkane biosynthetic process
is_a: GO:0043446 ! cellular alkane metabolic process
is_a: GO:0044249 ! cellular biosynthetic process
is_a: GO:0043446 ! alkane metabolic process
is_a: GO:0120251 ! hydrocarbon biosynthetic process

[Term]
Expand All @@ -192,18 +175,6 @@ name: aerobic respiration, using arsenite as electron donor
is_a: GO:0009060 ! aerobic respiration
is_a: GO:0015975 ! energy derivation by oxidation of reduced inorganic compounds

[Term]
id: GO:0044237
name: cellular metabolic process
is_a: GO:0008152 ! metabolic process
is_a: GO:0009987 ! cellular process

[Term]
id: GO:0044249
name: cellular biosynthetic process
is_a: GO:0009058 ! biosynthetic process
is_a: GO:0044237 ! cellular metabolic process

[Term]
id: GO:0044281
name: small molecule metabolic process
Expand All @@ -214,25 +185,14 @@ id: GO:0045333
name: cellular respiration
is_a: GO:0015980 ! energy derivation by oxidation of organic compounds

[Term]
id: GO:0071704
name: organic substance metabolic process
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0120251
name: hydrocarbon biosynthetic process
is_a: GO:0009058 ! biosynthetic process
is_a: GO:0120252 ! hydrocarbon metabolic process
is_a: GO:1901576 ! organic substance biosynthetic process

[Term]
id: GO:0120252
name: hydrocarbon metabolic process
is_a: GO:0071704 ! organic substance metabolic process

[Term]
id: GO:1901576
name: organic substance biosynthetic process
is_a: GO:0009058 ! biosynthetic process
is_a: GO:0071704 ! organic substance metabolic process
is_a: GO:0008152 ! metabolic process

78 changes: 7 additions & 71 deletions imports/go_import.owl
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Expand Up @@ -82,17 +82,8 @@
<!-- http://purl.obolibrary.org/obo/GO_0006091 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0006091">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0044237"/>
<rdfs:label>generation of precursor metabolites and energy</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GO_0006807 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0006807">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008152"/>
<rdfs:label>nitrogen compound metabolic process</rdfs:label>
<rdfs:label>generation of precursor metabolites and energy</rdfs:label>
</owl:Class>


Expand Down Expand Up @@ -135,7 +126,7 @@
<!-- http://purl.obolibrary.org/obo/GO_0008152 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0008152">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0009987"/>
<rdfs:label>metabolic process</rdfs:label>
</owl:Class>

Expand Down Expand Up @@ -210,7 +201,7 @@
<!-- http://purl.obolibrary.org/obo/GO_0015979 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0015979">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0044237"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008152"/>
<rdfs:label>photosynthesis</rdfs:label>
</owl:Class>

Expand All @@ -228,7 +219,6 @@
<!-- http://purl.obolibrary.org/obo/GO_0019329 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0019329">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0006807"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0044281"/>
<rdfs:label>ammonia oxidation</rdfs:label>
</owl:Class>
Expand All @@ -241,7 +231,6 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0009061"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0015975"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0019329"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0034641"/>
<rdfs:label>anaerobic respiration, using ammonium as electron donor</rdfs:label>
</owl:Class>

Expand All @@ -252,7 +241,6 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0019332">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0009060"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0015975"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0034641"/>
<rdfs:label>aerobic respiration, using nitrite as electron donor</rdfs:label>
</owl:Class>

Expand All @@ -264,7 +252,6 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0009060"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0015975"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0019329"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0034641"/>
<rdfs:label>aerobic respiration, using ammonia as electron donor</rdfs:label>
</owl:Class>

Expand Down Expand Up @@ -347,16 +334,6 @@



<!-- http://purl.obolibrary.org/obo/GO_0034641 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0034641">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0006807"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0044237"/>
<rdfs:label>cellular nitrogen compound metabolic process</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GO_0042755 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0042755">
Expand All @@ -369,9 +346,8 @@
<!-- http://purl.obolibrary.org/obo/GO_0043446 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0043446">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0044237"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0120252"/>
<rdfs:label>cellular alkane metabolic process</rdfs:label>
<rdfs:label>alkane metabolic process</rdfs:label>
</owl:Class>


Expand All @@ -380,7 +356,6 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0043447">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0043446"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0044249"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0120251"/>
<rdfs:label>alkane biosynthetic process</rdfs:label>
</owl:Class>
Expand All @@ -397,26 +372,6 @@



<!-- http://purl.obolibrary.org/obo/GO_0044237 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0044237">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008152"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0009987"/>
<rdfs:label>cellular metabolic process</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GO_0044249 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0044249">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0009058"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0044237"/>
<rdfs:label>cellular biosynthetic process</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GO_0044281 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0044281">
Expand All @@ -435,20 +390,11 @@



<!-- http://purl.obolibrary.org/obo/GO_0071704 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0071704">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008152"/>
<rdfs:label>organic substance metabolic process</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GO_0120251 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0120251">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0009058"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0120252"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_1901576"/>
<rdfs:label>hydrocarbon biosynthetic process</rdfs:label>
</owl:Class>

Expand All @@ -457,22 +403,12 @@
<!-- http://purl.obolibrary.org/obo/GO_0120252 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0120252">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0071704"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008152"/>
<rdfs:label>hydrocarbon metabolic process</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GO_1901576 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_1901576">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0009058"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0071704"/>
<rdfs:label>organic substance biosynthetic process</rdfs:label>
</owl:Class>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.24) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->

2 changes: 1 addition & 1 deletion imports/iao_import.owl
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Expand Up @@ -489,5 +489,5 @@



<!-- Generated by the OWL API (version 4.5.24) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->

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