Merge branch 'master' into 1803_mouth_rinse_specimen

obi-ontology · Aug 26, 2024 · b89f5c5 · b89f5c5
2 parents b8f9e8a + 0da1d20
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diff --git a/src/ontology/OntoFox_inputs/ChEBI_input.txt b/src/ontology/OntoFox_inputs/ChEBI_input.txt
@@ -6,6 +6,7 @@ CHEBI
 
 [Low level source term URIs]
 http://purl.obolibrary.org/obo/CHEBI_23367
+http://purl.obolibrary.org/obo/CHEBI_4431 # deoxyribonucleotide
 http://purl.obolibrary.org/obo/CHEBI_4705
 http://purl.obolibrary.org/obo/CHEBI_15377
 http://purl.obolibrary.org/obo/CHEBI_15956
@@ -25,6 +26,7 @@ http://purl.obolibrary.org/obo/CHEBI_31624
 http://purl.obolibrary.org/obo/CHEBI_31642
 http://purl.obolibrary.org/obo/CHEBI_31643
 http://purl.obolibrary.org/obo/CHEBI_31991
+http://purl.obolibrary.org/obo/CHEBI_32875 # methyl group
 http://purl.obolibrary.org/obo/CHEBI_33359
 http://purl.obolibrary.org/obo/CHEBI_33375
 http://purl.obolibrary.org/obo/CHEBI_33376
@@ -124,6 +126,8 @@ http://purl.obolibrary.org/obo/CHEBI_39124 # calcium ion
 [Top level source term URIs and target direct superclass URIs]
 http://purl.obolibrary.org/obo/CHEBI_23367
 subClassOf http://purl.obolibrary.org/obo/BFO_0000040
+http://purl.obolibrary.org/obo/CHEBI_4431 # deoxyribonucleotide
+subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 # molecular entity
 http://purl.obolibrary.org/obo/CHEBI_4705
 subClassOf http://purl.obolibrary.org/obo/CHEBI_16991
 http://purl.obolibrary.org/obo/CHEBI_15377
@@ -162,6 +166,8 @@ http://purl.obolibrary.org/obo/CHEBI_31643
 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
 http://purl.obolibrary.org/obo/CHEBI_31991
 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
+http://purl.obolibrary.org/obo/CHEBI_32875 # methyl group
+subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 # molecular entity
 http://purl.obolibrary.org/obo/CHEBI_33359
 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
 http://purl.obolibrary.org/obo/CHEBI_33375

diff --git a/src/ontology/OntoFox_inputs/GO_input.txt b/src/ontology/OntoFox_inputs/GO_input.txt
@@ -47,7 +47,6 @@ http://purl.obolibrary.org/obo/GO_0005694
 http://purl.obolibrary.org/obo/GO_0005739 # mitochondrion
 http://purl.obolibrary.org/obo/GO_0006006
 http://purl.obolibrary.org/obo/GO_0006260
-http://purl.obolibrary.org/obo/GO_0006306
 http://purl.obolibrary.org/obo/GO_0006338
 http://purl.obolibrary.org/obo/GO_0006909
 http://purl.obolibrary.org/obo/GO_0006955
@@ -66,7 +65,6 @@ http://purl.obolibrary.org/obo/GO_0015925 # galactosidase activity
 http://purl.obolibrary.org/obo/GO_0016064
 http://purl.obolibrary.org/obo/GO_0016160 # amylase activity
 http://purl.obolibrary.org/obo/GO_0016231 # beta-N-acetylglucosaminidase activity
-http://purl.obolibrary.org/obo/GO_0016570 # histone modification
 http://purl.obolibrary.org/obo/GO_0016788 #hydrolase activity, acting on ester bonds
 http://purl.obolibrary.org/obo/GO_0019814
 http://purl.obolibrary.org/obo/GO_0019815
@@ -139,7 +137,6 @@ http://purl.obolibrary.org/obo/GO_0042611
 http://purl.obolibrary.org/obo/GO_0043227
 http://purl.obolibrary.org/obo/GO_0043316
 http://purl.obolibrary.org/obo/GO_0043565
-http://purl.obolibrary.org/obo/GO_0044030
 http://purl.obolibrary.org/obo/GO_0044807 # macrophage migration inhibitory factor production
 http://purl.obolibrary.org/obo/GO_0044808 # Oncostatin M production
 http://purl.obolibrary.org/obo/GO_0044809 # chemokine (C-C motif) ligand 17 production
@@ -398,8 +395,6 @@ http://purl.obolibrary.org/obo/GO_0043316
 subClassOf http://purl.obolibrary.org/obo/GO_0001906
 http://purl.obolibrary.org/obo/GO_0043565 
 subClassOf http://purl.obolibrary.org/obo/OBI_0001588
-http://purl.obolibrary.org/obo/GO_0044030 
-subClassOf http://purl.obolibrary.org/obo/GO_0008150
 http://purl.obolibrary.org/obo/GO_0048869 
 subClassOf http://purl.obolibrary.org/obo/GO_0008150
 http://purl.obolibrary.org/obo/GO_0050896 
@@ -458,10 +453,6 @@ http://purl.obolibrary.org/obo/GO_0097391
 subClassOf http://purl.obolibrary.org/obo/GO_0032602
 http://purl.obolibrary.org/obo/GO_0097392 
 subClassOf http://purl.obolibrary.org/obo/GO_0032602
-http://purl.obolibrary.org/obo/GO_0006306
-subClassOf http://purl.obolibrary.org/obo/GO_0008150
-http://purl.obolibrary.org/obo/GO_0016570
-subClassOf http://purl.obolibrary.org/obo/GO_0008150
 http://purl.obolibrary.org/obo/GO_0005739
 subClassOf http://purl.obolibrary.org/obo/GO_0043227
 http://purl.obolibrary.org/obo/GO_0140730

diff --git a/src/ontology/OntoFox_inputs/NCBITaxon_input.txt b/src/ontology/OntoFox_inputs/NCBITaxon_input.txt
@@ -30,7 +30,6 @@ http://purl.obolibrary.org/obo/NCBITaxon_11676
 http://purl.obolibrary.org/obo/NCBITaxon_11709
 http://purl.obolibrary.org/obo/NCBITaxon_388799
 http://purl.obolibrary.org/obo/NCBITaxon_10407
-http://purl.obolibrary.org/obo/NCBITaxon_11103
 http://purl.obolibrary.org/obo/NCBITaxon_10376
 http://purl.obolibrary.org/obo/NCBITaxon_10358
 http://purl.obolibrary.org/obo/NCBITaxon_160
@@ -41,6 +40,7 @@ http://purl.obolibrary.org/obo/NCBITaxon_33208 #Metazoa
 http://purl.obolibrary.org/obo/NCBITaxon_784
 http://purl.obolibrary.org/obo/NCBITaxon_12637 #Dengue
 http://purl.obolibrary.org/obo/NCBITaxon_37124 #Chikungunya
+http://purl.obolibrary.org/obo/NCBITaxon_3052230 # Hepacivirus hominis
 
 
 [Top level source term URIs and target direct superclass URIs]

diff --git a/src/ontology/OntoFox_outputs/CLO_imports.owl b/src/ontology/OntoFox_outputs/CLO_imports.owl
@@ -56,18 +56,11 @@
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CLO_0000001">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001866"/>
         <obo:IAO_0000111>cell line cell</obo:IAO_0000111>
-        <obo:IAO_0000111 xml:lang="en">cell line cell</obo:IAO_0000111>
-        <obo:IAO_0000111 xml:lang="zh">细胞系细胞</obo:IAO_0000111>
         <obo:IAO_0000115 xml:lang="en">A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture</obo:IAO_0000115>
         <obo:IAO_0000115>A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
-</obo:IAO_0000115>
-        <obo:IAO_0000115>一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分</obo:IAO_0000115>
-        <obo:IAO_0000115>一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分
 </obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/clo.owl"/>
         <rdfs:label>cell line cell</rdfs:label>
-        <rdfs:label xml:lang="en">cell line cell</rdfs:label>
-        <rdfs:label xml:lang="zh">细胞系细胞</rdfs:label>
     </owl:Class>
 
 
@@ -77,14 +70,9 @@
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CLO_0000018">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CLO_0000001"/>
         <obo:IAO_0000111>mortal cell line cell</obo:IAO_0000111>
-        <obo:IAO_0000111 xml:lang="en">mortal cell line cell</obo:IAO_0000111>
-        <obo:IAO_0000111 xml:lang="zh">非永生细胞系细胞</obo:IAO_0000111>
         <obo:IAO_0000115>A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence.</obo:IAO_0000115>
-        <obo:IAO_0000115 xml:lang="en">A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/clo.owl"/>
         <rdfs:label>mortal cell line cell</rdfs:label>
-        <rdfs:label xml:lang="en">mortal cell line cell</rdfs:label>
-        <rdfs:label xml:lang="zh">非永生细胞系细胞</rdfs:label>
     </owl:Class>
 
 
@@ -94,15 +82,9 @@
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CLO_0000019">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CLO_0000001"/>
         <obo:IAO_0000111>immortal cell line cell</obo:IAO_0000111>
-        <obo:IAO_0000111 xml:lang="en">immortal cell line cell</obo:IAO_0000111>
-        <obo:IAO_0000111 xml:lang="zh">永生细胞系细胞</obo:IAO_0000111>
         <obo:IAO_0000115>A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.</obo:IAO_0000115>
-        <obo:IAO_0000115 xml:lang="en">A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.</obo:IAO_0000115>
-        <obo:IAO_0000115>预期能够进行无限次分裂的细胞系细胞，作为永生细胞系一部分，能够支持体外无限增殖。</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/clo.owl"/>
         <rdfs:label>immortal cell line cell</rdfs:label>
-        <rdfs:label xml:lang="en">immortal cell line cell</rdfs:label>
-        <rdfs:label xml:lang="zh">永生细胞系细胞</rdfs:label>
     </owl:Class>
 
 
@@ -112,16 +94,11 @@
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CLO_0000031">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001905"/>
         <obo:IAO_0000111 xml:lang="en">cell line</obo:IAO_0000111>
-        <obo:IAO_0000111 xml:lang="zh">细胞系</obo:IAO_0000111>
         <obo:IAO_0000115 xml:lang="en">A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). </obo:IAO_0000115>
         <obo:IAO_0000115>A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).  
-</obo:IAO_0000115>
-        <obo:IAO_0000115 xml:lang="zh">一个培养细胞群体，其代表具有共同增殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。</obo:IAO_0000115>
-        <obo:IAO_0000115>培养的细胞群体代表具有共同繁殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 
 </obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/clo.owl"/>
         <rdfs:label xml:lang="en">cell line</rdfs:label>
-        <rdfs:label xml:lang="zh">细胞系</rdfs:label>
     </owl:Class>