Add or update terms based on GitHub issue suggestions (#779)

* Add or update terms based on GitHub issue suggestions

Completed with AI assistance from Claude Code
✅ Issue #757 - Sphere Formation Assay

  - Added "sphere formation" as a new term in modules/Assay/Assay.yaml:827-834
  - Added "tumor spheroid formation assay" as an alias
  - Linked with cross-references to related terms ("in vitro tumorigenesis" and "Matrigel-based tumorigenesis assay")
  - Updated "Matrigel-based tumorigenesis assay" description to reference "sphere formation"

  ✅ Issue #662 - Weight Assay

  - Added "weight" with EFO:0004338 in modules/Assay/Assay.yaml:546-548
  - Placed in ClinicalBehavioralAssayEnum section

  ⏭️ Issue #646 - Cancer Diagnosis

  - Skipped - Determined "cancer" is too broad/vague for this specialized NF metadata dictionary
  - Existing specific cancer/tumor types are more appropriate

  ✅ Issue #185 - Mouse Models

  - Added "Nf1-MET" to modules/Sample/AnimalModelManual.yaml:20-21
  - Added "Nf1-P53" to modules/Sample/AnimalModelManual.yaml:26-27
  - Both follow existing naming conventions

  All changes maintain alphabetical ordering and follow the existing file structure conventions.

* Update Assay.yaml

Remove similar assays from see_also to resolve error 'sphere formation is not a valid URI or CURIE' since 'see_also field should only contain URLs/URIs, not references to other terms in the schema'
Completed with AI assistance from Claude Code

* Consolidate tumorigenesis assay terms

Completed with AI assistance from Claude Code

* Remove mRNA counts assay term and move NanoString nCounter from assay to platform

Completed with AI assistance from Claude Code
Fixes #704 - mRNA Counts Confusion

  - Removed "mRNA counts" from Assay.yaml (was data output, not an assay type)
  - Removed "NanoString nCounter Analysis System" from Assay.yaml (was misplaced - it's a platform, not an assay)
  - Added "NanoString nCounter Analysis System" to modules/Assay/Platform.yaml:133-139 in ArrayPlatformEnum
  - Aliases for backwards compatibility: NanoString, NanoString nCounter, Nanostring Counter

* Add titles

Add titles to hopefully make terms more user-friendly to fix #770

* Move title after notes for 'Germline Mutation'

* Add key for number of PCR cycles for library

Fixes #631 . Completed with AI assistance from Claude Code

* Change 'meaning' to 'slot_uri' to resolve bug

---------

Co-authored-by: Anh Nguyet Vu <32753274+anngvu@users.noreply.github.com>

Author: BelindaBGarana

modules/Assay/Assay.yaml

@@ -543,6 +543,9 @@ enums:
       six-minute walk test:
         description: The six-minute walk test (6MWT) is a simple, standardized functional assay of exercise capacity that measures how far the human subject can walk within a 6-minute duration; used to to evaluate lung and heart conditions.
         source: https://www.ncbi.nlm.nih.gov/books/NBK576420/
+      weight:
+        description: An assay or measurement that quantifies the mass or weight of a subject, specimen, or sample. Commonly used in clinical assessments, biosample characterization, and longitudinal health monitoring.
+        meaning: EFO:0004338
       word recognition score:
         description: Assays how well a person can understand speech by repeating a list of words. The WRS is a percentage of words correctly repeated. It's a more functional measure because it predicts whether hearing loss can be improved with amplification.
   CellBasedAssayEnum:
@@ -587,19 +590,9 @@ enums:
 
           '
         meaning: NCIT:C16434
-      Matrigel-based tumorigenesis assay:
-        description: An assay in which tumor cells are loaded into a Matrigel matrix and measured for tumor formation characteristics
-        see_also:
-        - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230200/
       Migration Assay:
         description: An in vitro assay in which cultured cells are monitored and analyzed for their ability to move into an acellular area of a culture material.
         source: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C19425
-      NanoString nCounter Analysis System:
-        aliases:
-        - NanoString
-        - NanoString nCounter
-        description: A proprietary molecular analysis system for single molecule detection with no amplification. It uses unique fluorescent barcodes for direct, digital detection and copy number quantitation of hundreds of different target molecules in a single run. It requires only nanoscale amounts of RNA and has a detection sensitivity down to 1 copy per cell.
-        meaning: NCIT:C198498
       STR profile:
         aliases:
         - Short Tandem Repeat Profile
@@ -729,7 +722,12 @@ enums:
       in silico synthesis:
         description: Synthesis of molecules and compounds (e.g. drug candidates) via simulation or other system outside of a live biological system.
       in vitro tumorigenesis:
-        description: An in vitro assay devised to measure tumor formation
+        aliases:
+        - sphere formation
+        - tumor spheroid formation assay
+        - Matrigel-based tumorigenesis assay
+        description: An in vitro assay devised to measure tumor formation, including sphere formation assays where cells form three-dimensional spherical structures (spheroids) to assess tumor-initiating capacity, stem cell properties, and self-renewal capability. Includes Matrigel-based and other matrix-based approaches.
+        source: https://pmc.ncbi.nlm.nih.gov/articles/PMC6121836/
       in vivo PDX viability:
         description: Assay to assess viability using PDX model.
       in vivo tumor growth:
@@ -751,8 +749,6 @@ enums:
         - LTP
         description: A measure of the persistent robust synaptic response induced by synchronous stimulation of pre- and postsynaptic cells.
         meaning: VT:0002207
-      mRNA counts:
-        description: A mRNA profiling assay using digital molecular barcoding technology to quantify target mRNA molecules without the need for amplification.
       massively parallel reporter assay:
         description: An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences.
         meaning: OBI:0002675

modules/Assay/Platform.yaml

@@ -130,8 +130,13 @@ enums:
         source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18224
       NanoString Human nCounter PanCancer IO360 Panel:
         source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL32069
-      Nanostring Counter:
-        description: ''
+      NanoString nCounter Analysis System:
+        aliases:
+        - NanoString
+        - NanoString nCounter
+        - Nanostring Counter
+        description: A proprietary molecular analysis system for single molecule detection with no amplification. It uses unique fluorescent barcodes for direct, digital detection and copy number quantitation of hundreds of different target molecules in a single run. It requires only nanoscale amounts of RNA and has a detection sensitivity down to 1 copy per cell.
+        meaning: NCIT:C198498
       Perlegen 300Karray:
         description: ''
       10x Visium Spatial Gene Expression:

modules/Sample/AnimalModelManual.yaml

@@ -17,10 +17,14 @@ enums:
         description: Nf1-C383X/Flox
       Nf1-C848R/Flox:
         description: Nf1-C848R/Flox
+      Nf1-MET:
+        description: Mouse model with NF1 and MET alterations
       Nf1-OPG:
         description: Nf1-OPG
       Nf1-OPG-Arg816:
         description: Nf1-OPG-Arg816
+      Nf1-P53:
+        description: Mouse model with NF1 and P53 alterations
       Nf1-R681X/Flox:
         description: Nf1-R681X/Flox
       Nf1flox/flox: