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berkeleybop · Mar 29, 2024 · 4a53218 · 4a53218
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diff --git a/aio-base.json b/aio-base.json
@@ -16,9 +16,9 @@
         "val" : "Artificial Intelligence Ontology"
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2024-03-28"
+        "val" : "2024-03-29"
       } ],
-      "version" : "http://purl.obolibrary.org/obo/aio/releases/2024-03-28/aio-base.json"
+      "version" : "http://purl.obolibrary.org/obo/aio/releases/2024-03-29/aio-base.json"
     }
   } ]
 }
diff --git a/aio-base.obo b/aio-base.obo
@@ -1,9 +1,9 @@
 format-version: 1.2
-data-version: aio/releases/2024-03-28/aio-base.owl
+data-version: aio/releases/2024-03-29/aio-base.owl
 ontology: aio/aio-base
 property_value: http://purl.org/dc/elements/1.1/type IAO:8000001
 property_value: http://purl.org/dc/terms/description "None" xsd:string
 property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
 property_value: http://purl.org/dc/terms/title "Artificial Intelligence Ontology" xsd:string
-property_value: owl:versionInfo "2024-03-28" xsd:string
+property_value: owl:versionInfo "2024-03-29" xsd:string
 
diff --git a/aio-base.owl b/aio-base.owl
@@ -9,12 +9,12 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:dcterms="http://purl.org/dc/terms/">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/aio/aio-base.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aio/releases/2024-03-28/aio-base.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aio/releases/2024-03-29/aio-base.owl"/>
         <dce:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
         <dcterms:description>None</dcterms:description>
         <dcterms:license rdf:resource="https://creativecommons.org/licenses/unspecified"/>
         <dcterms:title>Artificial Intelligence Ontology</dcterms:title>
-        <owl:versionInfo>2024-03-28</owl:versionInfo>
+        <owl:versionInfo>2024-03-29</owl:versionInfo>
     </owl:Ontology>
 
 

diff --git a/aio-full.json b/aio-full.json
@@ -13,9 +13,9 @@
         "val" : "Artificial Intelligence Ontology"
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2024-03-28"
+        "val" : "2024-03-29"
       } ],
-      "version" : "http://purl.obolibrary.org/obo/aio/releases/2024-03-28/aio-full.json"
+      "version" : "http://purl.obolibrary.org/obo/aio/releases/2024-03-29/aio-full.json"
     },
     "nodes" : [ {
       "id" : "http://purl.obolibrary.org/obo/IAO_0000002",
@@ -16674,29 +16674,6 @@
           "val" : "physical reasoning"
         } ]
       }
-    }, {
-      "id" : "https://w3id.org/aio/GenerativeLanguageCircuit",
-      "lbl" : "Generative Language Circuit",
-      "type" : "CLASS",
-      "meta" : {
-        "definition" : {
-          "val" : "A generative language circuit is a type of LLM that learns to generate programs or code by training on input-output pairs, effectively learning the underlying \"program\" that maps inputs to outputs.",
-          "xrefs" : [ "TBD" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "GLC"
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Generative Language Circuit"
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "analogy circuit"
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "program synthesis"
-        } ]
-      }
     }, {
       "id" : "https://w3id.org/aio/GenerativeLanguageInterface",
       "lbl" : "Generative Language Interface",
@@ -21651,10 +21628,6 @@
       "sub" : "https://w3id.org/aio/GenerativeCommonsenseLLM",
       "pred" : "is_a",
       "obj" : "https://w3id.org/aio/ApplicationFocus"
-    }, {
-      "sub" : "https://w3id.org/aio/GenerativeLanguageCircuit",
-      "pred" : "is_a",
-      "obj" : "https://w3id.org/aio/ModelArchitecture"
     }, {
       "sub" : "https://w3id.org/aio/GenerativeLanguageInterface",
       "pred" : "is_a",

diff --git a/aio-full.obo b/aio-full.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: aio/releases/2024-03-28/aio-full.owl
+data-version: aio/releases/2024-03-29/aio-full.owl
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
@@ -10,7 +10,7 @@ ontology: aio/aio-full
 property_value: http://purl.org/dc/terms/description "None" xsd:string
 property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
 property_value: http://purl.org/dc/terms/title "Artificial Intelligence Ontology" xsd:string
-property_value: owl:versionInfo "2024-03-28" xsd:string
+property_value: owl:versionInfo "2024-03-29" xsd:string
 
 [Term]
 id: APOLLO_SV:00000008
@@ -3115,16 +3115,6 @@ synonym: "Generative Commonsense LLM" EXACT []
 synonym: "physical reasoning" RELATED []
 is_a: https://w3id.org/aio/ApplicationFocus ! Application Focus
 
-[Term]
-id: https://w3id.org/aio/GenerativeLanguageCircuit
-name: Generative Language Circuit
-def: "A generative language circuit is a type of LLM that learns to generate programs or code by training on input-output pairs, effectively learning the underlying \"program\" that maps inputs to outputs." [TBD] {type="owl:Axiom"}
-synonym: "analogy circuit" RELATED []
-synonym: "Generative Language Circuit" EXACT []
-synonym: "GLC" EXACT []
-synonym: "program synthesis" RELATED []
-is_a: https://w3id.org/aio/ModelArchitecture ! Model Architecture
-
 [Term]
 id: https://w3id.org/aio/GenerativeLanguageInterface
 name: Generative Language Interface

diff --git a/aio-full.owl b/aio-full.owl
@@ -18,11 +18,11 @@
      xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/aio/aio-full.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aio/releases/2024-03-28/aio-full.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aio/releases/2024-03-29/aio-full.owl"/>
         <dcterms:description>None</dcterms:description>
         <dcterms:license rdf:resource="https://creativecommons.org/licenses/unspecified"/>
         <dcterms:title>Artificial Intelligence Ontology</dcterms:title>
-        <owl:versionInfo>2024-03-28</owl:versionInfo>
+        <owl:versionInfo>2024-03-29</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -9079,26 +9079,6 @@ class labels for these objects. The resulting predictor can be used to attach cl
 
 
 
-    <!-- https://w3id.org/aio/GenerativeLanguageCircuit -->
-
-    <owl:Class rdf:about="https://w3id.org/aio/GenerativeLanguageCircuit">
-        <rdfs:subClassOf rdf:resource="https://w3id.org/aio/ModelArchitecture"/>
-        <obo:IAO_0000115>A generative language circuit is a type of LLM that learns to generate programs or code by training on input-output pairs, effectively learning the underlying &quot;program&quot; that maps inputs to outputs.</obo:IAO_0000115>
-        <oboInOwl:hasExactSynonym>GLC</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Generative Language Circuit</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasRelatedSynonym>analogy circuit</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasRelatedSynonym>program synthesis</oboInOwl:hasRelatedSynonym>
-        <rdfs:label>Generative Language Circuit</rdfs:label>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="https://w3id.org/aio/GenerativeLanguageCircuit"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget>A generative language circuit is a type of LLM that learns to generate programs or code by training on input-output pairs, effectively learning the underlying &quot;program&quot; that maps inputs to outputs.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref>TBD</oboInOwl:hasDbXref>
-    </owl:Axiom>
-
-
-
     <!-- https://w3id.org/aio/GenerativeLanguageInterface -->
 
     <owl:Class rdf:about="https://w3id.org/aio/GenerativeLanguageInterface">

diff --git a/aio-src.csv b/aio-src.csv
@@ -398,7 +398,6 @@ Neuro-Symbolic LLM,AIO:Neuro-SymbolicLLM,Model,Neuro-Symbolic LLM,knowledge reas
 Causal LLM,AIO:CausalLLM,Model,Causal LLM,unidirectional|autoregressive,"A causal LLM only attends to previous tokens in the sequence when generating text, modeling the probability distribution autoregressively from left-to-right or causally.",TBD,,AIO:InterpretabilityandEthics
 Ordinal LLM,AIO:OrdinalLLM,Model,Ordinal LLM,ranking|preference modeling,"An ordinal LLM is trained to model ordinal relationships and rank outputs, rather than model probability distributions over text sequences directly.",TBD,,AIO:InterpretabilityandEthics
 Differentiable LLM,AIO:DifferentiableLLM,Model,Differentiable LLM,end-to-end training|fully backpropagable,"A differentiable LLM has an architecture amenable to full end-to-end training via backpropagation, without relying on teacher forcing or unlikelihood training objectives.",TBD,,AIO:ModelArchitecture
-Generative Language Circuit,AIO:GenerativeLanguageCircuit,Model,GLC|Generative Language Circuit,analogy circuit|program synthesis,"A generative language circuit is a type of LLM that learns to generate programs or code by training on input-output pairs, effectively learning the underlying ""program"" that maps inputs to outputs.",TBD,,AIO:ModelArchitecture
 Unsupervised LLM,AIO:UnsupervisedLLM,Model,Unsupervised LLM,self-supervised,"An unsupervised LLM is trained solely on unlabeled data using self-supervised objectives like masked language modeling, without any supervised fine-tuning.",TBD,,AIO:LearningParadigms
 Semi-Supervised LLM,AIO:Semi-SupervisedLLM,Model,Semi-Supervised LLM,self-training,A semi-supervised LLM combines self-supervised pretraining on unlabeled data with supervised fine-tuning on labeled task data.,TBD,,AIO:LearningParadigms
 Multilingual LLM,AIO:MultilingualLLM,Model,Multilingual LLM,cross-lingual transfer,"A multilingual LLM is trained on text from multiple languages, learning shared representations that enable zero-shot or few-shot transfer to new languages.",TBD,,AIO:LearningParadigms

diff --git a/aio.json b/aio.json
@@ -13,9 +13,9 @@
         "val" : "Artificial Intelligence Ontology"
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2024-03-28"
+        "val" : "2024-03-29"
       } ],
-      "version" : "http://purl.obolibrary.org/obo/aio/releases/2024-03-28/aio.json"
+      "version" : "http://purl.obolibrary.org/obo/aio/releases/2024-03-29/aio.json"
     },
     "nodes" : [ {
       "id" : "http://purl.obolibrary.org/obo/IAO_0000002",
@@ -16674,29 +16674,6 @@
           "val" : "physical reasoning"
         } ]
       }
-    }, {
-      "id" : "https://w3id.org/aio/GenerativeLanguageCircuit",
-      "lbl" : "Generative Language Circuit",
-      "type" : "CLASS",
-      "meta" : {
-        "definition" : {
-          "val" : "A generative language circuit is a type of LLM that learns to generate programs or code by training on input-output pairs, effectively learning the underlying \"program\" that maps inputs to outputs.",
-          "xrefs" : [ "TBD" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "GLC"
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Generative Language Circuit"
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "analogy circuit"
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "program synthesis"
-        } ]
-      }
     }, {
       "id" : "https://w3id.org/aio/GenerativeLanguageInterface",
       "lbl" : "Generative Language Interface",
@@ -21651,10 +21628,6 @@
       "sub" : "https://w3id.org/aio/GenerativeCommonsenseLLM",
       "pred" : "is_a",
       "obj" : "https://w3id.org/aio/ApplicationFocus"
-    }, {
-      "sub" : "https://w3id.org/aio/GenerativeLanguageCircuit",
-      "pred" : "is_a",
-      "obj" : "https://w3id.org/aio/ModelArchitecture"
     }, {
       "sub" : "https://w3id.org/aio/GenerativeLanguageInterface",
       "pred" : "is_a",

diff --git a/aio.obo b/aio.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: releases/2024-03-28
+data-version: releases/2024-03-29
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
@@ -10,7 +10,7 @@ ontology: aio
 property_value: http://purl.org/dc/terms/description "None" xsd:string
 property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
 property_value: http://purl.org/dc/terms/title "Artificial Intelligence Ontology" xsd:string
-property_value: owl:versionInfo "2024-03-28" xsd:string
+property_value: owl:versionInfo "2024-03-29" xsd:string
 
 [Term]
 id: APOLLO_SV:00000008
@@ -988,8 +988,8 @@ name: regulatory agency
 def: "A regulatory agency is a organization that has responsibility over or for  the legislation (acts and regulations) for a given sector of the government." []
 is_a: OBI:0000245 ! organization
 intersection_of: OBI:0000245 ! organization
-intersection_of: RO:0000087 OBI:0000014 ! has_role regulator role
-relationship: RO:0000087 OBI:0000014 ! has_role regulator role
+intersection_of: RO:0000087 OBI:0000014 ! has role regulator role
+relationship: RO:0000087 OBI:0000014 ! has role regulator role
 property_value: IAO:0000111 "regulatory agency" xsd:string
 property_value: IAO:0000112 "The US Environmental Protection Agency" xsd:string
 property_value: IAO:0000114 IAO:0000122
@@ -1212,7 +1212,7 @@ id: OBI:0000835
 name: manufacturer
 def: "A person or organization that has a manufacturer role" []
 is_a: BFO:0000040 ! material entity
-relationship: RO:0000087 OBI:0000571 ! has_role manufacturer role
+relationship: RO:0000087 OBI:0000571 ! has role manufacturer role
 property_value: IAO:0000111 "manufacturer" xsd:string
 property_value: IAO:0000114 IAO:0000123
 
@@ -1579,7 +1579,7 @@ id: OBI:0002989
 name: material supplier
 def: "A person or organization that provides material supplies to other people or organizations." []
 is_a: BFO:0000040 ! material entity
-relationship: RO:0000087 OBI:0000018 ! has_role material supplier role
+relationship: RO:0000087 OBI:0000018 ! has role material supplier role
 property_value: IAO:0000111 "material supplier" xsd:string
 property_value: IAO:0000114 IAO:0000123
 property_value: IAO:0000117 "Rebecca Jackson" xsd:string
@@ -1611,8 +1611,8 @@ name: specimen
 def: "A material entity that has the specimen role." []
 is_a: BFO:0000040 ! material entity
 intersection_of: BFO:0000040 ! material entity
-intersection_of: RO:0000087 OBI:0000112 ! has_role specimen role
-relationship: RO:0000087 OBI:0000112 ! has_role specimen role
+intersection_of: RO:0000087 OBI:0000112 ! has role specimen role
+relationship: RO:0000087 OBI:0000112 ! has role specimen role
 property_value: IAO:0000111 "specimen" xsd:string
 property_value: IAO:0000112 "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen." xsd:string
 property_value: IAO:0000114 IAO:0000122
@@ -1866,14 +1866,14 @@ id: SWO:0000396
 name: software developer organization
 def: "An organization or legal entity (including single person) that is responsible for developing software. Developing includes aspects of design, coding and testing." []
 is_a: OBI:0000245 ! organization
-relationship: RO:0000087 SWO:0000392 ! has_role software developer role
+relationship: RO:0000087 SWO:0000392 ! has role software developer role
 
 [Term]
 id: SWO:0000397
 name: software publisher organization
 def: "An organization or legal entity (including single person) that is responsible for publishing software. Publishing here includes tasks such as designing and producing physical products, technical customer support, licensing arrangements and marketing." []
 is_a: OBI:0000245 ! organization
-relationship: RO:0000087 SWO:0000260 ! has_role publisher role
+relationship: RO:0000087 SWO:0000260 ! has role publisher role
 
 [Term]
 id: UO:0000001
@@ -3115,16 +3115,6 @@ synonym: "Generative Commonsense LLM" EXACT []
 synonym: "physical reasoning" RELATED []
 is_a: https://w3id.org/aio/ApplicationFocus ! Application Focus
 
-[Term]
-id: https://w3id.org/aio/GenerativeLanguageCircuit
-name: Generative Language Circuit
-def: "A generative language circuit is a type of LLM that learns to generate programs or code by training on input-output pairs, effectively learning the underlying \"program\" that maps inputs to outputs." [TBD] {type="owl:Axiom"}
-synonym: "analogy circuit" RELATED []
-synonym: "Generative Language Circuit" EXACT []
-synonym: "GLC" EXACT []
-synonym: "program synthesis" RELATED []
-is_a: https://w3id.org/aio/ModelArchitecture ! Model Architecture
-
 [Term]
 id: https://w3id.org/aio/GenerativeLanguageInterface
 name: Generative Language Interface
@@ -5321,7 +5311,7 @@ property_value: IAO:0000116 "A role inheres in its bearer at all times for which
 property_value: IAO:0000118 "is role of" xsd:string
 property_value: IAO:0000118 "role_of" xsd:string
 is_a: RO:0000052 ! inheres in
-inverse_of: RO:0000087 ! has_role
+inverse_of: RO:0000087 ! has role
 
 [Typedef]
 id: RO:0000085

diff --git a/aio.owl b/aio.owl
@@ -18,11 +18,11 @@
      xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/aio.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aio/releases/2024-03-28/aio.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aio/releases/2024-03-29/aio.owl"/>
         <dcterms:description>None</dcterms:description>
         <dcterms:license rdf:resource="https://creativecommons.org/licenses/unspecified"/>
         <dcterms:title>Artificial Intelligence Ontology</dcterms:title>
-        <owl:versionInfo>2024-03-28</owl:versionInfo>
+        <owl:versionInfo>2024-03-29</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -9079,26 +9079,6 @@ class labels for these objects. The resulting predictor can be used to attach cl
 
 
 
-    <!-- https://w3id.org/aio/GenerativeLanguageCircuit -->
-
-    <owl:Class rdf:about="https://w3id.org/aio/GenerativeLanguageCircuit">
-        <rdfs:subClassOf rdf:resource="https://w3id.org/aio/ModelArchitecture"/>
-        <obo:IAO_0000115>A generative language circuit is a type of LLM that learns to generate programs or code by training on input-output pairs, effectively learning the underlying &quot;program&quot; that maps inputs to outputs.</obo:IAO_0000115>
-        <oboInOwl:hasExactSynonym>GLC</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Generative Language Circuit</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasRelatedSynonym>analogy circuit</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasRelatedSynonym>program synthesis</oboInOwl:hasRelatedSynonym>
-        <rdfs:label>Generative Language Circuit</rdfs:label>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="https://w3id.org/aio/GenerativeLanguageCircuit"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget>A generative language circuit is a type of LLM that learns to generate programs or code by training on input-output pairs, effectively learning the underlying &quot;program&quot; that maps inputs to outputs.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref>TBD</oboInOwl:hasDbXref>
-    </owl:Axiom>
-
-
-
     <!-- https://w3id.org/aio/GenerativeLanguageInterface -->
 
     <owl:Class rdf:about="https://w3id.org/aio/GenerativeLanguageInterface">