Add new data processing terms for zero intensity trimming (#460)

* add new data processing terms for zero intensity trimming

* revise description

* restore lost terms post merge

* version bump

* restore another lost term

* fix term ordering, add automation to detect and flag

* add python config

Author: mobiusklein

.github/workflows/validate-obo.yml

@@ -27,3 +27,10 @@ jobs:
     # Runs a single command using the runners shell
     - name: Validate OBO file
       run: fastobo-validator --duplicates psi-ms.obo
+    - uses: actions/setup-python@v6
+      with:
+          python-version: '3.10'
+    - name: Check sorting
+      run: |
+        python -m pip install fastobo
+        python scripts/check_sorted.py psi-ms.obo

psi-ms.obo

@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: 4.1.227
+data-version: 4.1.228
 date: 02:12:2025 11:00
 saved-by: Joshua Klein
 default-namespace: MS
@@ -24933,18 +24933,6 @@ name: secondary electrospray ionization
 def: "Secondary electrospray ionization (SESI) is an atmospheric pressure ionization (API) technique that uses a primary nano-electrospray plume of solvent ions to ionize neutral gaseous molecules in the gas phase via efficient proton transfer reactions. Operating at atmospheric pressure, SESI allows for the sensitive and real-time detection of volatile organic compounds (VOCs) and vapors with minimal sample preparation, making it ideal for applications like breath analysis and environmental monitoring." [PSI:MS]
 is_a: MS:1000240 ! atmospheric pressure ionization
 
-[Term]
-id: MS:1003800
-name: TSQ Certis
-def: "Thermo Scientific TSQ Certis Triple Quadrupole MS." [PSI:PI]
-is_a: MS:1000494 ! Thermo Scientific instrument model
-
-[Term]
-id: MS:1003801
-name: AccurateMassSearch
-def: "OpenMS TOPP tool to assemble metabolite features from singleton mass traces." [PSI:MS]
-is_a: MS:1000752 ! TOPP software
-
 [Term]
 id: MS:1003780
 name: zstd compression
@@ -24981,6 +24969,30 @@ name: MS-Numpress short logged float compression followed by zstd compression
 def: "Compression using MS-Numpress short logged float compression and Zstandard." [PSI:MS, https://github.com/ms-numpress/ms-numpress]
 is_a: MS:1000572 ! binary data compression type
 
+[Term]
+id: MS:1003800
+name: TSQ Certis
+def: "Thermo Scientific TSQ Certis Triple Quadrupole MS." [PSI:PI]
+is_a: MS:1000494 ! Thermo Scientific instrument model
+
+[Term]
+id: MS:1003801
+name: AccurateMassSearch
+def: "OpenMS TOPP tool to assemble metabolite features from singleton mass traces." [PSI:MS]
+is_a: MS:1000752 ! TOPP software
+
+[Term]
+id: MS:1003901
+name: zero intensity point trimming
+def: "Apply an algorithm to remove excess zero intensity value data points from a spectrum. Data may be retained for interperatbility such as retaining only zeros that flank non-zero intensity value data points from a profile spectrum.." [PSI:MS]
+is_a: MS:1000543 ! data processing action
+
+[Term]
+id: MS:1003902
+name: zero intensity point trimming interpolation
+def: "A zero intensity point trimming algorithm that interpolates the m/z coordinate values from the local data or an estimated model." [PSI:MS]
+is_a: MS:1003901 ! zero intensity point trimming
+
 [Term]
 id: MS:4000000
 name: PSI-MS CV Quality Control Vocabulary

scripts/check_sorted.py

@@ -0,0 +1,31 @@
+import sys
+
+import fastobo
+
+cv = fastobo.load(sys.argv[1])
+
+terms = list(cv)
+in_order = True
+last = None
+conflicts = []
+for i, t in enumerate(terms):
+    if isinstance(t, fastobo.term.TermFrame):
+        if t.id.prefix == 'NCIT':
+            continue
+        if last is None:
+            last = t.id
+        elif t.id.prefix != last.prefix:
+            last = t.id
+        else:
+            if int(t.id.local) < int(last.local):
+                conflicts.append((t.id, last, i))
+                print(f"{t.id} is lower than {last}")
+                in_order = False
+            last = t.id
+
+if in_order:
+    print("All MS terms in order")
+    sys.exit(0)
+else:
+    print(conflicts)
+    sys.exit(1)