regen for v7.7.1

microbiomedata · Jun 27, 2023 · 5c26ae7 · 5c26ae7
1 parent d25229c
commit 5c26ae7
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Showing 18 changed files with 12,170 additions and 40,059 deletions.
diff --git a/examples/output/Database-biosample-exhasutive.ttl b/examples/output/Database-biosample-exhasutive.ttl
@@ -591,9 +591,9 @@ nmdc:bsm-99-dtTMNb a nmdc:Biosample ;
     MIXS:0000650 [ a nmdc:QuantityValue ;
             nmdc:has_raw_value "xxx" ] ;
     MIXS:0000652 [ a nmdc:TextValue ;
-            nmdc:has_raw_value "mercury;0.09 micrograms per gram" ],
+            nmdc:has_raw_value "arsenic;0.09 micrograms per gram" ],
         [ a nmdc:TextValue ;
-            nmdc:has_raw_value "arsenic;0.09 micrograms per gram" ] ;
+            nmdc:has_raw_value "mercury;0.09 micrograms per gram" ] ;
     MIXS:0000653 [ a nmdc:QuantityValue ;
             nmdc:has_raw_value "xxx" ] ;
     MIXS:0000656 [ a nmdc:QuantityValue ;

diff --git a/examples/output/Database-functional-annotations.ttl b/examples/output/Database-functional-annotations.ttl
@@ -2,33 +2,33 @@
 
 [] a nmdc:Database ;
     nmdc:functional_annotation_set [ a nmdc:FunctionalAnnotation ;
+            nmdc:has_function "KEGG.REACTION:R00100" ],
+        [ a nmdc:FunctionalAnnotation ;
+            nmdc:has_function "SUPFAM:SSF57615" ],
+        [ a nmdc:FunctionalAnnotation ;
+            nmdc:has_function "MetaNetX:MNXR101574" ],
+        [ a nmdc:FunctionalAnnotation ;
+            nmdc:has_function "CATH:1.10.10.200" ],
+        [ a nmdc:FunctionalAnnotation ;
             nmdc:has_function "TIGRFAM:TIGR00010" ],
         [ a nmdc:FunctionalAnnotation ;
-            nmdc:has_function "KEGG.REACTION:R00100" ],
+            nmdc:has_function "KEGG_PATHWAY:rsk00410" ],
         [ a nmdc:FunctionalAnnotation ;
-            nmdc:has_function "GO:0032571" ],
+            nmdc:has_function "EGGNOG:veNOG12876" ],
         [ a nmdc:FunctionalAnnotation ;
             nmdc:has_function "KEGG.ORTHOLOGY:K00001" ],
         [ a nmdc:FunctionalAnnotation ;
-            nmdc:has_function "EGGNOG:veNOG12876" ],
+            nmdc:has_function "RHEA:12345" ],
         [ a nmdc:FunctionalAnnotation ;
             nmdc:has_function "PANTHER.FAMILY:PTHR12345" ],
         [ a nmdc:FunctionalAnnotation ;
-            nmdc:has_function "PFAM:PF11779" ],
+            nmdc:has_function "GO:0032571" ],
         [ a nmdc:FunctionalAnnotation ;
             nmdc:has_function "SEED:Biotin_biosynthesis" ],
         [ a nmdc:FunctionalAnnotation ;
             nmdc:has_function "EC:1.1.1.1" ],
         [ a nmdc:FunctionalAnnotation ;
             nmdc:has_function "MetaCyc:RXN-14904" ],
         [ a nmdc:FunctionalAnnotation ;
-            nmdc:has_function "CATH:1.10.10.200" ],
-        [ a nmdc:FunctionalAnnotation ;
-            nmdc:has_function "SUPFAM:SSF57615" ],
-        [ a nmdc:FunctionalAnnotation ;
-            nmdc:has_function "RHEA:12345" ],
-        [ a nmdc:FunctionalAnnotation ;
-            nmdc:has_function "MetaNetX:MNXR101574" ],
-        [ a nmdc:FunctionalAnnotation ;
-            nmdc:has_function "KEGG_PATHWAY:rsk00410" ] .
+            nmdc:has_function "PFAM:PF11779" ] .
 
diff --git a/examples/output/Database-mags-activities.ttl b/examples/output/Database-mags-activities.ttl
@@ -17,6 +17,17 @@ nmdc:wfmag-99-5MiDJM a nmdc:MagsAnalysisActivity ;
     nmdc:input_contig_num 169782 ;
     nmdc:low_depth_contig_num 0 ;
     nmdc:mags_list [ a nmdc:MagBin ;
+            nmdc:bin_name "bins.2" ;
+            nmdc:bin_quality "LQ" ;
+            nmdc:completeness "51.25"^^xsd:float ;
+            nmdc:contamination "10.34"^^xsd:float ;
+            nmdc:gene_count 2548 ;
+            nmdc:num_16s 0 ;
+            nmdc:num_23s 0 ;
+            nmdc:num_5s 1 ;
+            nmdc:num_t_rna 26 ;
+            nmdc:number_of_contig 426 ],
+        [ a nmdc:MagBin ;
             nmdc:bin_name "bins.1" ;
             nmdc:bin_quality "LQ" ;
             nmdc:completeness "11.42"^^xsd:float ;
@@ -37,18 +48,7 @@ nmdc:wfmag-99-5MiDJM a nmdc:MagsAnalysisActivity ;
             nmdc:num_23s 0 ;
             nmdc:num_5s 0 ;
             nmdc:num_t_rna 1 ;
-            nmdc:number_of_contig 11 ],
-        [ a nmdc:MagBin ;
-            nmdc:bin_name "bins.2" ;
-            nmdc:bin_quality "LQ" ;
-            nmdc:completeness "51.25"^^xsd:float ;
-            nmdc:contamination "10.34"^^xsd:float ;
-            nmdc:gene_count 2548 ;
-            nmdc:num_16s 0 ;
-            nmdc:num_23s 0 ;
-            nmdc:num_5s 1 ;
-            nmdc:num_t_rna 26 ;
-            nmdc:number_of_contig 426 ] ;
+            nmdc:number_of_contig 11 ] ;
     nmdc:name "MAGs activiity 1781_86101" ;
     nmdc:started_at_time "2021-01-10T00:00:00+00:00" ;
     nmdc:too_short_contig_num 159810 ;
@@ -71,26 +71,26 @@ nmdc:wfmag-99-VOgM5i a nmdc:MagsAnalysisActivity ;
     nmdc:input_contig_num 78376 ;
     nmdc:low_depth_contig_num 0 ;
     nmdc:mags_list [ a nmdc:MagBin ;
-            nmdc:bin_name "bins.1" ;
+            nmdc:bin_name "bins.2" ;
             nmdc:bin_quality "LQ" ;
-            nmdc:completeness "25.86"^^xsd:float ;
+            nmdc:completeness "0.0"^^xsd:float ;
             nmdc:contamination "0.0"^^xsd:float ;
-            nmdc:gene_count 401 ;
+            nmdc:gene_count 383 ;
             nmdc:num_16s 0 ;
             nmdc:num_23s 0 ;
             nmdc:num_5s 0 ;
-            nmdc:num_t_rna 4 ;
+            nmdc:num_t_rna 5 ;
             nmdc:number_of_contig 74 ],
         [ a nmdc:MagBin ;
-            nmdc:bin_name "bins.2" ;
+            nmdc:bin_name "bins.1" ;
             nmdc:bin_quality "LQ" ;
-            nmdc:completeness "0.0"^^xsd:float ;
+            nmdc:completeness "25.86"^^xsd:float ;
             nmdc:contamination "0.0"^^xsd:float ;
-            nmdc:gene_count 383 ;
+            nmdc:gene_count 401 ;
             nmdc:num_16s 0 ;
             nmdc:num_23s 0 ;
             nmdc:num_5s 0 ;
-            nmdc:num_t_rna 5 ;
+            nmdc:num_t_rna 4 ;
             nmdc:number_of_contig 74 ],
         [ a nmdc:MagBin ;
             nmdc:bin_name "bins.3" ;