Merge pull request #251 from FlyBase/release_2024-12-05

Release 2024-12-05

.github/workflows/qc.yml

@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5.2
+    container: obolibrary/odkfull:v1.5.4
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

fbcv.obo

@@ -1,6 +1,6 @@
 format-version: 1.2
-data-version: fbcv/releases/2024-10-17
-date: 17:10:2024 15:25
+data-version: fbcv/releases/2024-12-05
+date: 05:12:2024 13:42
 subsetdef: 1_STAR ""
 subsetdef: 2_STAR ""
 subsetdef: 3_STAR ""
@@ -47,15 +47,15 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
 idspace: terms http://purl.org/dc/terms/ 
 ontology: fbcv.obo
 property_value: attributionURL "http://dx.doi.org/10.1186/2041-1480-4-30" xsd:string
-property_value: dc:creator "http://orcid.org/0000-0002-1373-1705" xsd:string
-property_value: dc:creator "http://orcid.org/0000-0002-7073-9172" xsd:string
-property_value: dc:creator "https://orcid.org/0000-0001-5948-3092" xsd:string
-property_value: dc:creator "https://orcid.org/0000-0002-0027-0858" xsd:string
-property_value: dc:description "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO." xsd:string
-property_value: dc:title "FlyBase Controlled Vocabulary (FBcv)" xsd:string
 property_value: IAO:0000700 FBcv:0000000
-property_value: owl:versionInfo "2024-10-17" xsd:string
+property_value: owl:versionInfo "2024-12-05" xsd:string
+property_value: terms:creator "http://orcid.org/0000-0002-1373-1705" xsd:string
+property_value: terms:creator "http://orcid.org/0000-0002-7073-9172" xsd:string
+property_value: terms:creator "https://orcid.org/0000-0001-5948-3092" xsd:string
+property_value: terms:creator "https://orcid.org/0000-0002-0027-0858" xsd:string
+property_value: terms:description "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO." xsd:string
 property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string
+property_value: terms:title "FlyBase Controlled Vocabulary (FBcv)" xsd:string
 
 [Term]
 id: CHEBI:10432
@@ -2019,8 +2019,8 @@ def: "A uridine having a bromo substituent at the 5-position." []
 subset: 3_STAR
 synonym: "1-beta-ribofuranosyl-5-bromo-uracil" RELATED [ChemIDplus]
 synonym: "5-bromo-1-beta-D-ribofuranosylpyrimidine-2,4(1H,3H)-dione" RELATED [ChEBI]
-synonym: "5-bromouridine" EXACT [UniProt]
 synonym: "5-bromouridine" EXACT [ChEBI]
+synonym: "5-bromouridine" EXACT [UniProt]
 synonym: "BrU" RELATED [ChEBI]
 is_a: BFO:0000004
 is_a: CHEBI:27242 ! uridines
@@ -2411,7 +2411,7 @@ relationship: is_substituent_group_from CHEBI:17578 ! toluene
 id: CHEBI:228364
 name: NMR chemical shift reference compound
 namespace: chebi_ontology
-def: "Any compound that produces a peak used to reference an NMR spectrum during data pre-processing." []
+def: "Any compound that produces a peak used as reference frequency in the delta chemical shift scale." []
 subset: 3_STAR
 synonym: "NMR chemical shift reference compounds" RELATED [ChEBI]
 synonym: "NMR chemical shift standard" RELATED [ChEBI]
@@ -2716,7 +2716,7 @@ def: "An amino acid derivative resulting from reaction of cysteine at the amino
 subset: 3_STAR
 synonym: "cysteine derivative" EXACT [ChEBI]
 synonym: "cysteine derivatives" RELATED [ChEBI]
-is_a: CHEBI:83821 ! amino acid derivative
+is_a: CHEBI:83821 ! amino-acid derivative
 relationship: has_functional_parent CHEBI:15356 ! cysteine
 
 [Term]
@@ -2908,7 +2908,7 @@ name: glutamic acid derivative
 namespace: chebi_ontology
 def: "An amino acid derivative resulting from reaction of glutamic acid at the amino group or either of the carboxy groups, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing glutamic acid residues." []
 subset: 3_STAR
-is_a: CHEBI:83821 ! amino acid derivative
+is_a: CHEBI:83821 ! amino-acid derivative
 relationship: has_functional_parent CHEBI:18237 ! glutamic acid
 
 [Term]
@@ -3789,7 +3789,7 @@ name: phenylalanine derivative
 namespace: chebi_ontology
 def: "An amino acid derivative resulting from reaction of alanine at the amino group or the carboxy group, or from the replacement of any hydrogen of phenylalanine  by a heteroatom. The definition normally excludes peptides containing phenylalanine  residues." []
 subset: 3_STAR
-is_a: CHEBI:83821 ! amino acid derivative
+is_a: CHEBI:83821 ! amino-acid derivative
 relationship: has_functional_parent CHEBI:28044 ! phenylalanine
 
 [Term]
@@ -4721,7 +4721,7 @@ relationship: RO:0000087 CHEBI:25435 ! has role mutagen
 relationship: RO:0000087 CHEBI:35610 ! has role antineoplastic agent
 relationship: RO:0000087 CHEBI:47868 ! has role photosensitizing agent
 relationship: RO:0000087 CHEBI:50684 ! has role cross-linking reagent
-relationship: RO:0000087 CHEBI:61015 ! has role nephrotoxin
+relationship: RO:0000087 CHEBI:50909 ! has role nephrotoxic agent
 relationship: RO:0000087 CHEBI:68495 ! has role apoptosis inducer
 
 [Term]
@@ -5318,7 +5318,6 @@ is_a: CHEBI:18140 ! hydrogen halide
 is_a: CHEBI:37176 ! mononuclear parent hydride
 relationship: is_conjugate_acid_of CHEBI:17051 ! fluoride
 relationship: is_conjugate_base_of CHEBI:50314 ! fluoronium
-relationship: RO:0000087 CHEBI:228364 ! has role NMR chemical shift reference compound
 
 [Term]
 id: CHEBI:29234
@@ -6625,8 +6624,8 @@ name: alpha-amino-acid anion
 namespace: chebi_ontology
 def: "An amino-acid anion obtained by deprotonation of any alpha-amino acid." []
 subset: 3_STAR
+synonym: "alpha-amino acid anion" RELATED [ChEBI]
 synonym: "alpha-amino acid anions" RELATED [ChEBI]
-synonym: "alpha-amino-acid anion" EXACT [ChEBI]
 synonym: "alpha-amino-acid anions" RELATED [ChEBI]
 is_a: CHEBI:37022 ! amino-acid anion
 relationship: is_conjugate_base_of CHEBI:33704 ! alpha-amino acid
@@ -7028,7 +7027,7 @@ name: amino-acid cation
 namespace: chebi_ontology
 subset: 3_STAR
 synonym: "amino acid cation" RELATED [ChEBI]
-synonym: "amino-acid cation" EXACT [ChEBI]
+synonym: "amino acid cations" RELATED [ChEBI]
 synonym: "amino-acid cations" RELATED [ChEBI]
 is_a: CHEBI:25697 ! organic cation
 is_a: CHEBI:33702 ! polyatomic cation
@@ -7054,7 +7053,7 @@ xref: KEGG:C05167
 is_a: CHEBI:33709 ! amino acid
 relationship: is_conjugate_acid_of CHEBI:33558 ! alpha-amino-acid anion
 relationship: is_conjugate_base_of CHEBI:33719 ! alpha-amino-acid cation
-relationship: is_tautomer_of CHEBI:78608 ! alpha-amino acid zwitterion
+relationship: is_tautomer_of CHEBI:78608 ! alpha-amino-acid zwitterion
 
 [Term]
 id: CHEBI:33708
@@ -7063,6 +7062,7 @@ namespace: chebi_ontology
 def: "When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue." []
 subset: 3_STAR
 synonym: "amino acid residue" RELATED [ChEBI]
+synonym: "amino acid residues" RELATED [ChEBI]
 synonym: "amino-acid residues" RELATED [JCBN]
 is_a: CHEBI:33247 ! organic group
 relationship: is_conjugate_acid_of CHEBI:64898 ! anionic amino-acid residue
@@ -7092,8 +7092,8 @@ id: CHEBI:33719
 name: alpha-amino-acid cation
 namespace: chebi_ontology
 subset: 3_STAR
+synonym: "alpha-amino acid cation" RELATED [ChEBI]
 synonym: "alpha-amino acid cations" RELATED [ChEBI]
-synonym: "alpha-amino-acid cation" EXACT [ChEBI]
 synonym: "alpha-amino-acid cations" RELATED [ChEBI]
 is_a: CHEBI:33703 ! amino-acid cation
 relationship: is_conjugate_acid_of CHEBI:33704 ! alpha-amino acid
@@ -7501,18 +7501,20 @@ subset: 3_STAR
 synonym: "(+)H3N-CH(CH2SH)-COO(-)" RELATED [ChEBI]
 synonym: "2-ammonio-3-mercaptopropanoate" RELATED [ChEBI]
 synonym: "cysteine zwitterion" EXACT [IUPAC]
-is_a: CHEBI:35238 ! amino acid zwitterion
+is_a: CHEBI:35238 ! amino-acid zwitterion
 relationship: is_conjugate_acid_of CHEBI:32456 ! cysteinate(1-)
 relationship: is_conjugate_base_of CHEBI:32458 ! cysteinium
 relationship: is_tautomer_of CHEBI:15356 ! cysteine
 
 [Term]
 id: CHEBI:35238
-name: amino acid zwitterion
+name: amino-acid zwitterion
 namespace: chebi_ontology
 def: "The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group." []
 subset: 3_STAR
-synonym: "amino acid zwitterion" EXACT [ChEBI]
+synonym: "amino acid zwitterion" RELATED [ChEBI]
+synonym: "amino acid zwitterions" RELATED [ChEBI]
+synonym: "amino-acid zwitterions" RELATED [ChEBI]
 is_a: CHEBI:27369 ! zwitterion
 
 [Term]
@@ -8607,8 +8609,8 @@ id: CHEBI:37022
 name: amino-acid anion
 namespace: chebi_ontology
 subset: 3_STAR
+synonym: "amino acid anion" RELATED [ChEBI]
 synonym: "amino acid anions" RELATED [ChEBI]
-synonym: "amino-acid anion" EXACT [ChEBI]
 synonym: "amino-acid anions" RELATED [ChEBI]
 is_a: CHEBI:29067 ! carboxylic acid anion
 is_a: CHEBI:35352 ! organonitrogen compound
@@ -9500,6 +9502,7 @@ synonym: "CH3-CH3" RELATED [IUPAC]
 synonym: "dimethyl" RELATED [NIST_Chemistry_WebBook]
 synonym: "Ethan" RELATED [ChEBI]
 synonym: "ETHANE" EXACT [PDBeChem]
+synonym: "ethane" EXACT [UniProt]
 synonym: "ethyl hydride" RELATED [NIST_Chemistry_WebBook]
 synonym: "methylmethane" RELATED [NIST_Chemistry_WebBook]
 synonym: "R-170" RELATED [ChEBI]
@@ -10420,7 +10423,7 @@ subset: 3_STAR
 id: CHEBI:50908
 name: hepatotoxic agent
 namespace: chebi_ontology
-def: "A role played by a chemical compound exihibiting itself through the ability to induce damage to the liver in animals." []
+def: "A role played by a chemical compound exhibiting itself through the ability to induce damage to the liver in animals." []
 subset: 3_STAR
 synonym: "agente hepatotoxico" RELATED [ChEBI]
 synonym: "hepatotoxic agents" RELATED [ChEBI]
@@ -10436,9 +10439,10 @@ is_a: CHEBI:52209 ! aetiopathogenetic role
 id: CHEBI:50909
 name: nephrotoxic agent
 namespace: chebi_ontology
-def: "A role played by a chemical compound exihibiting itself through the ability to induce damage to the kidney in animals." []
+def: "A role played by any chemical compound (natural or synthetic) exhibiting itself through the ability to induce damage to the kidneys." []
 subset: 3_STAR
 synonym: "agente nefrotoxico" RELATED [ChEBI]
+synonym: "nephrotoxic agents" RELATED [ChEBI]
 synonym: "nephrotoxicant" RELATED [ChEBI]
 is_a: CHEBI:52209 ! aetiopathogenetic role
 
@@ -10834,7 +10838,7 @@ synonym: "N-acylamino acid" RELATED [ChEBI]
 synonym: "N-acylamino acids" RELATED [ChEBI]
 is_a: CHEBI:33575 ! carboxylic acid
 is_a: CHEBI:37622 ! carboxamide
-is_a: CHEBI:83821 ! amino acid derivative
+is_a: CHEBI:83821 ! amino-acid derivative
 relationship: has_functional_parent CHEBI:33709 ! amino acid
 
 [Term]
@@ -11011,7 +11015,7 @@ synonym: "(2S)-2-ammonio-3-phenylpropanoate" RELATED [IUPAC]
 synonym: "L-phenylalanine" RELATED [UniProt]
 synonym: "phenylalanine" RELATED [ChEBI]
 xref: MetaCyc:PHE
-is_a: CHEBI:35238 ! amino acid zwitterion
+is_a: CHEBI:35238 ! amino-acid zwitterion
 relationship: is_enantiomer_of CHEBI:57981 ! D-phenylalanine zwitterion
 relationship: is_tautomer_of CHEBI:17295 ! L-phenylalanine
 
@@ -11142,7 +11146,7 @@ def: "Zwitterionic form of an L-alpha-amino acid having an anionic carboxy group
 subset: 3_STAR
 synonym: "an L-alpha-amino acid" RELATED [UniProt]
 synonym: "L-alpha-amino acid zwitterions" RELATED [ChEBI]
-is_a: CHEBI:78608 ! alpha-amino acid zwitterion
+is_a: CHEBI:78608 ! alpha-amino-acid zwitterion
 relationship: is_tautomer_of CHEBI:15705 ! L-alpha-amino acid
 
 [Term]
@@ -11153,7 +11157,7 @@ def: "Zwitterionic form of a D-alpha-amino acid having an anionic carboxy group
 subset: 3_STAR
 synonym: "a D-alpha-amino acid" RELATED [UniProt]
 synonym: "D-alpha-amino acid zwitterions" RELATED [ChEBI]
-is_a: CHEBI:35238 ! amino acid zwitterion
+is_a: CHEBI:35238 ! amino-acid zwitterion
 relationship: is_tautomer_of CHEBI:16733 ! D-alpha-amino acid
 
 [Term]
@@ -11296,16 +11300,6 @@ synonym: "D-alpha-amino carboxylate" RELATED [ChEBI]
 is_a: CHEBI:33558 ! alpha-amino-acid anion
 relationship: is_conjugate_base_of CHEBI:16733 ! D-alpha-amino acid
 
-[Term]
-id: CHEBI:61015
-name: nephrotoxin
-namespace: chebi_ontology
-def: "A poison that interferes with the function of the kidneys." []
-subset: 3_STAR
-synonym: "nephrotoxins" RELATED [ChEBI]
-is_a: CHEBI:50909 ! nephrotoxic agent
-is_a: CHEBI:64909 ! poison
-
 [Term]
 id: CHEBI:61120
 name: nucleobase-containing molecular entity
@@ -11360,7 +11354,7 @@ namespace: chebi_ontology
 def: "Zwitterionic form of a polar amino acid having an anionic carboxy group and a protonated amino group." []
 subset: 2_STAR
 synonym: "a polar amino acid" RELATED [UniProt]
-is_a: CHEBI:35238 ! amino acid zwitterion
+is_a: CHEBI:35238 ! amino-acid zwitterion
 relationship: is_tautomer_of CHEBI:26167 ! polar amino acid
 
 [Term]
@@ -11665,7 +11659,6 @@ synonym: "amino-acid anion residue" RELATED [ChEBI]
 synonym: "amino-acid anion residues" RELATED [ChEBI]
 synonym: "anionic amino acid residue" RELATED [ChEBI]
 synonym: "anionic amino acid residues" RELATED [ChEBI]
-synonym: "anionic amino-acid residues" RELATED [ChEBI]
 is_a: CHEBI:64775 ! organic anionic group
 relationship: is_conjugate_base_of CHEBI:33708 ! amino-acid residue
 
@@ -12107,7 +12100,7 @@ def: "An amino acid zwitterion obtained by transfer of a proton from the carboxy
 subset: 3_STAR
 synonym: "an aromatic amino-acid" RELATED [UniProt]
 synonym: "aromatic amino-acid zwitterions" RELATED [ChEBI]
-is_a: CHEBI:35238 ! amino acid zwitterion
+is_a: CHEBI:35238 ! amino-acid zwitterion
 relationship: is_tautomer_of CHEBI:33856 ! aromatic amino acid
 
 [Term]
@@ -12587,13 +12580,16 @@ is_a: CHEBI:52208 ! biophysical role
 
 [Term]
 id: CHEBI:78608
-name: alpha-amino acid zwitterion
+name: alpha-amino-acid zwitterion
 namespace: chebi_ontology
 alt_id: CHEBI:83409
-def: "An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3." []
+def: "An amino acid-zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3." []
 subset: 3_STAR
+synonym: "alpha-amino acid zwitterion" RELATED [ChEBI]
+synonym: "alpha-amino acid zwitterions" RELATED [ChEBI]
+synonym: "alpha-amino-acid zwitterions" RELATED [ChEBI]
 synonym: "an alpha-amino acid" RELATED [UniProt]
-is_a: CHEBI:35238 ! amino acid zwitterion
+is_a: CHEBI:35238 ! amino-acid zwitterion
 relationship: is_tautomer_of CHEBI:33704 ! alpha-amino acid
 
 [Term]
@@ -12709,7 +12705,7 @@ synonym: "canonical amino-acid derivatives" RELATED [ChEBI]
 synonym: "proteinogenic amino acid derivatives" RELATED [ChEBI]
 synonym: "proteinogenic amino-acid derivative" RELATED [ChEBI]
 synonym: "proteinogenic amino-acid derivatives" RELATED [ChEBI]
-is_a: CHEBI:83821 ! amino acid derivative
+is_a: CHEBI:83821 ! amino-acid derivative
 relationship: has_functional_parent CHEBI:83813 ! proteinogenic amino acid
 
 [Term]
@@ -12721,7 +12717,7 @@ subset: 3_STAR
 synonym: "non-canonical amino acid derivative" RELATED [ChEBI]
 synonym: "non-canonical amino-acid derivatives" RELATED [ChEBI]
 synonym: "non-proteinogenic amino-acid derivatives" RELATED [ChEBI]
-is_a: CHEBI:83821 ! amino acid derivative
+is_a: CHEBI:83821 ! amino-acid derivative
 
 [Term]
 id: CHEBI:83813
@@ -12757,12 +12753,14 @@ is_a: CHEBI:33709 ! amino acid
 
 [Term]
 id: CHEBI:83821
-name: amino acid derivative
+name: amino-acid derivative
 namespace: chebi_ontology
 alt_id: CHEBI:25359
 def: "Any derivative of an amino acid resulting from reaction at an amino group, carboxy group, side-chain functional group, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing amino acid residues." []
 subset: 3_STAR
+synonym: "amino acid derivative" RELATED [ChEBI]
 synonym: "amino acid derivatives" RELATED [ChEBI]
+synonym: "amino-acid derivatives" RELATED [ChEBI]
 synonym: "modified amino acids" RELATED [ChEBI]
 is_a: CHEBI:35352 ! organonitrogen compound
 

flybase_controlled_vocabulary.obo

@@ -1,14 +1,13 @@
 format-version: 1.2
-data-version: 2024-10-17
-date: 17:10:2024 15:25
+data-version: 2024-12-05
+date: 05:12:2024 13:42
 subsetdef: camcur "camcur"
 subsetdef: common_tool_use "Terms to summarize typical use of a gene from one organism that is introduced into another organism primarily for use an experimental tool, rather than to study the function of the gene"
 subsetdef: do_not_annotate "Term not to be used for direct annotation"
 subsetdef: do_not_manually_annotate "Term not to be used for direct manual annotation"
 subsetdef: fbcvsubset_mgiribbons "MGI ribbon terms"
 subsetdef: lethal_phase "lethal phase terms"
 default-namespace: FlyBase miscellaneous CV
-idspace: dc http://purl.org/dc/elements/1.1/ 
 idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# 
 idspace: terms http://purl.org/dc/terms/ 
 ontology: fbcv/fbcv-simple

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for fbcv
 # Generated using ontology-development-kit
-# ODK Version: v1.5.2
+# ODK Version: v1.5.4
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use fbcv.Makefile instead
 
@@ -46,7 +46,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by dc-properties 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.5.2
+ODK_VERSION_MAKEFILE =      v1.5.4
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')