Merge pull request #249 from microbiomedata/2174-add-aliases-mappings…

…-annotations-for-gold-platform-model-cv

Updates to InstrumentModelEnum

assets/misc/gold_seqMethod_to_nmdc_instrument_set.tsv

@@ -0,0 +1,11 @@
+GOLD SeqMethod	NMDC instrument_set id
+Illumina HiSeq	nmdc:inst-14-79zxap02
+Illumina HiSeq 2500	nmdc:inst-14-nn4b6k72
+Illumina HiSeq 2500-1TB	nmdc:inst-14-nn4b6k72
+Illumina HiSeq 2500-Rapid	nmdc:inst-14-nn4b6k72
+Illumina NextSeq 550	nmdc:inst-14-xz5tb342
+Illumina NovaSeq	nmdc:inst-14-xx07be40
+Illumina NovaSeq 6000	nmdc:inst-14-mr4r2w09
+Illumina NovaSeq S2	nmdc:inst-14-mr4r2w09
+Illumina NovaSeq S4	nmdc:inst-14-mr4r2w09
+Illumina NovaSeq SP	nmdc:inst-14-mr4r2w09

src/schema/basic_classes.yaml

@@ -665,89 +665,162 @@ enums:
       vortex_genie_2:
         aliases:
           - VortexGenie2
+
       novaseq:
         aliases:
           - NovaSeq
+          - Illumina NovaSeq
+
       novaseq_6000:
         aliases:
           - NovaSeq 6000
+          - Illumina NovaSeq 6000
         meaning: OBI:0002630
+        comments: Possible flowcell versions are SP, S1, S2, S4.
+        see_also: 
+         - https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html
+        structured_aliases:
+          Illumina NovaSeq S2:
+            contexts:
+            -  https://gold.jgi.doe.gov/
+            predicate: NARROW_SYNONYM
+          Illumina NovaSeq S4:
+            contexts:
+            -  https://gold.jgi.doe.gov/
+            predicate: NARROW_SYNONYM    
+          Illumina NovaSeq SP:
+            contexts:
+            -  https://gold.jgi.doe.gov/
+            predicate: NARROW_SYNONYM                
+
+      novaseq_x:
+        aliases:
+          - Illumina NovaSeq X
+          - Illumina NovaSeq X Plus 
+        comments: Possible flowcell versions are 1.5B, 10B, 25B. Only difference between X and X Plus is 2 flowcells for X Plus versus 1 flowcell for X.
+        see_also: 
+          - https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus/specifications.html
+
       hiseq:
         aliases:
           - Illumina HiSeq
+
       hiseq_1000:
         aliases:
           - Illumina HiSeq 1000
         meaning: OBI:0002022
+
       hiseq_1500:
         aliases:
           - Illumina HiSeq 1500
         meaning: OBI:0003386
+
       hiseq_2000:
         aliases:
           - Illumina HiSeq 2000
         meaning: OBI:0002001
+
       hiseq_2500:
         aliases:
           - Illumina HiSeq 2500
         meaning: OBI:0002002
+        structured_aliases:
+          Illumina HiSeq 2500-1TB:
+            contexts:
+            -  https://gold.jgi.doe.gov/
+            predicate: NARROW_SYNONYM
+          Illumina HiSeq 2500-Rapid:
+            contexts:
+            -  https://gold.jgi.doe.gov/
+            predicate: NARROW_SYNONYM    
+
       hiseq_3000:
         aliases:
           - Illumina HiSeq 3000
         meaning: OBI:0002048
+
       hiseq_4000:
         aliases:
           - Illumina HiSeq 4000
         meaning: OBI:0002049
+
       hiseq_x_ten:
         aliases:
           - Illumina HiSeq X Ten
         meaning: OBI:0002129
+
       miniseq:
         aliases:
           - Illumina MiniSeq
         meaning: OBI:0003114
-      nextseq_1000:
-        aliases:
-          - Illumina NextSeq 1000
-        meaning: OBI:0003606
+
       miseq:
         aliases:
           - MiSeq
           - Illumina MiSeq
         meaning: OBI:0002003
+
+      nextseq_1000:
+        aliases:
+          - Illumina NextSeq 1000
+        meaning: OBI:0003606
+
+      nextseq:
+        aliases:
+          - NextSeq
+          - Illumina NextSeq
+        structured_aliases:
+          Illumina NextSeq-HO:
+           contexts:
+            -  https://gold.jgi.doe.gov/
+           predicate: NARROW_SYNONYM
+          Illumina NextSeq-MO:
+            contexts:
+            -  https://gold.jgi.doe.gov/
+            predicate: NARROW_SYNONYM              
+
       nextseq_500:
         aliases:
           - NextSeq 500
+          - Illumina NextSeq 500
         meaning: OBI:0002021
+
       nextseq_550:
         aliases:
           - NextSeq 550
+          - Illumina NextSeq 550
         meaning: OBI:0003387
+
       gridion:
         aliases:
           - Oxford Nanopore GridION Mk1
         meaning: OBI:0002751
+
       minion:
         aliases:
           - Oxford Nanopore MinION
         meaning: OBI:0002750
+
       promethion:
         aliases:
           - Oxford Nanopore PromethION
         meaning: OBI:0002752
+
       rs_II:
         aliases:
           - PacBio RS II
         meaning: OBI:0002012
+
       sequel:
         aliases:
           - PacBio Sequel
         meaning: OBI:0002632
+
       sequel_II:
         aliases:
           - PacBio Sequel II
         meaning: OBI:0002633
+
       revio:
         aliases:
           - PacBio Revio