More MRI study support (#423)

* Check existence of n-back and add note * Add MRI study-related file formats * Update * Rebuild NF.jsonld, json --------- Co-authored-by: nf-osi[bot] <[email protected]>
nf-osi · Apr 11, 2024 · caa6382 · caa6382
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diff --git a/NF.jsonld b/NF.jsonld
@@ -5880,6 +5880,8 @@
       "@id" : "bts:dockerimage"
     }, {
       "@id" : "bts:dup"
+    }, {
+      "@id" : "bts:edat3"
     }, {
       "@id" : "bts:excel"
     }, {
@@ -5950,6 +5952,8 @@
       "@id" : "bts:powerpoint"
     }, {
       "@id" : "bts:pzfx"
+    }, {
+      "@id" : "bts:psydat"
     }, {
       "@id" : "bts:raw"
     }, {
@@ -14662,6 +14666,17 @@
     },
     "sms:displayName" : "miRNAenrichment",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:edat3",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "edat3",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "edat3",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:VillanovaUniversity",
     "@type" : "rdfs:Class",
@@ -16466,6 +16481,17 @@
     },
     "sms:displayName" : "nerves",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:psydat",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "psydat",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "psydat",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:NewMexicoStateUniversity",
     "@type" : "rdfs:Class",

diff --git a/modules/Assay/Assay.yaml b/modules/Assay/Assay.yaml
@@ -386,6 +386,8 @@ enums:
       n-back task:
         description: A task in which items (e.g., letters) are presented one at a time and participants must identify each item that repeats relative to the item that occurred "n" items before its onset.
         meaning: https://www.cognitiveatlas.org/task/id/tsk_4a57abb949bcd/
+        notes:
+        - There are variants such as verbal n-back and visuospatial n-back; currently we do not go into that level of granularity.
       neuropsychological assessment:
         description: Evaluation for cognitive impairment by assessing the neuropsychological domains.
         meaning: http://purl.obolibrary.org/obo/MAXO_0009018

diff --git a/modules/Data/FileFormat.yaml b/modules/Data/FileFormat.yaml
@@ -135,7 +135,10 @@ enums:
         meaning: http://edamontology.org/format_3973
       dup:
         description: output of the Picard MarkDuplicates tool.
-        meaning: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.4.0/picard_sam_markduplicates_MarkDuplicates.php
+        source: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.4.0/picard_sam_markduplicates_MarkDuplicates.php
+      edat3:
+        description: The .edat3 proprietary format is used to store experiment data that can be analyzed in E-DataAid.
+        source: https://support.pstnet.com/hc/en-us/articles/229354727-INFO-E-Prime-file-extensions-18091
       excel:
         description: Microsoft Excel spreadsheet format
       fasta:
@@ -228,6 +231,7 @@ enums:
       ome-tiff:
         description: OME-TIFF is a preferred open image format
         meaning: http://edamontology.org/format_3727
+
       pdf:
         description: Portable Document Format
         meaning: http://edamontology.org/format_3508
@@ -242,6 +246,11 @@ enums:
       pzfx:
         description: A PZFX file is a Prism project created by GraphPad Prism, a scientific application used to analyze and graph data. It contains project data including graphs and layouts, notes, and tables.
         meaning: https://fileinfo.com/extension/pzfx
+      psydat:
+        description: TrialHandler or StairHandler object that has been saved to disk with the python cPickle module, ideal for batch analysis and plotting with Python.
+        source: https://www.psychopy.org/general/dataOutputs.html
+        notes:
+        - Not in EDAM as of April 2024. 
       raw:
         description: Proprietary file format for mass spectrometry data from Thermo Scientific
         meaning: http://edamontology.org/format_3712