address comments on NXsubstance

FAIRmat-NFDI · Feb 7, 2025 · 6180f23 · 6180f23
1 parent 910d0d4
commit 6180f23
Showing 1 changed file with 51 additions and 38 deletions.
diff --git a/contributed_definitions/NXsubstance.nxdl.xml b/contributed_definitions/NXsubstance.nxdl.xml
@@ -38,40 +38,56 @@
              Molecular mass of the substance
         </doc>
     </field>
-    <field name="cas_number">
-        <doc>
-             Unique numeric CAS REGISTRY number of the sample chemical content
-             For further information, see https://www.cas.org/.
-        </doc>
-    </field>
-    <field name="cas_name">
+    <field name="molecular_formula_hill">
         <doc>
-             CAS REGISTRY name of the sample chemical content
+             The chemical formula specified using CIF conventions.
+             Abbreviated version of CIF standard:107
+             This is the *Hill* system used by Chemical Abstracts.
+
+             * Only recognized element symbols may be used.
+             * Each element symbol is followed by a 'count' number. A count of '1' may be omitted.
+             * A space or parenthesis must separate each cluster of (element symbol + count).
+             * Where a group of elements is enclosed in parentheses, the multiplier for the
+               group must follow the closing parentheses. That is, all element and group
+               multipliers are assumed to be printed as subscripted numbers.
+             * Unless the elements are ordered in a manner that corresponds to their chemical
+               structure, the order of the elements within any group or moiety depends on
+               whether or not carbon is present.
+             * If carbon is present, the order should be:
+               - C, then H, then the other elements in alphabetical order of their symbol.
+               - If carbon is not present, the elements are listed purely in alphabetic order of their symbol.
         </doc>
     </field>
     <field name="identifier_cas">
         <doc>
-             CAS REGISTRY URI
+             Unique CAS REGISTRY URI.
+             For further information, see https://www.cas.org/.
         </doc>
-        <attribute name="type" type="NX_CHAR">
+        <attribute name="type">
             <enumeration>
                 <item value="URL"/>
             </enumeration>
         </attribute>
-    </field>
+        <attribute name="cas_number">
+            <doc>
+                Numeric CAS REGISTRY number associated with this identifier.
+            </doc>
+        </attribute>
+        <attribute name="cas_name">
+            <doc>
+                CAS REGISTRY name associated with this identifier.
+            </doc>
+        </attribute>
+    </field>     
     <group name="cas_image" type="NXnote">
         <doc>
              CAS REGISTRY image
         </doc>
     </group>
-    <field name="cas_synonyms">
-        <doc>
-             Synonyms in the CAS system.
-        </doc>
-    </field>
     <field name="identifier_inchi_str">
         <doc>
-             String InChi identifier.
+             Standard string InChi identifier" (as per v1.02).
+
              The InChI identifier expresses chemical structures in terms of atomic connectivity,
              tautomeric state, isotopes, stereochemistry and electronic charge in order to
              produce a string of machine-readable characters unique to the respective molecule.
@@ -84,41 +100,38 @@
              Hashed version of the full InChI (using the SHA-256 algorithm).
         </doc>
     </field>
-    <field name="iupac_name">
+    <field name="identifier_iupac_name">
         <doc>
              Name according to the IUPAC system (standard).
              For further information, see https://iupac.org/.
         </doc>
     </field>
-    <field name="smile">
+    <field name="identifier_smiles">
         <doc>
              Identifier in the SMILES (Simplified Molecular Input Line Entry System) system
              For further information, see https://www.daylight.com/smiles/.
         </doc>
     </field>
-    <field name="canonical_smile">
+    <field name="identifier_canonical_smiles">
         <doc>
-             Canonical version of the smiles identifier
+             Canonical version of the SMILES identifier
         </doc>
     </field>
-    <field name="molecular_formula_hill">
+    <field name="identifier_pub_chem">
         <doc>
-             The chemical formula specified using CIF conventions.
-             Abbreviated version of CIF standard:107
-             This is the *Hill* system used by Chemical Abstracts.
-
-             * Only recognized element symbols may be used.
-             * Each element symbol is followed by a 'count' number. A count of '1' may be omitted.
-             * A space or parenthesis must separate each cluster of (element symbol + count).
-             * Where a group of elements is enclosed in parentheses, the multiplier for the
-               group must follow the closing parentheses. That is, all element and group
-               multipliers are assumed to be printed as subscripted numbers.
-             * Unless the elements are ordered in a manner that corresponds to their chemical
-               structure, the order of the elements within any group or moiety depends on
-               whether or not carbon is present.
-             * If carbon is present, the order should be:
-               - C, then H, then the other elements in alphabetical order of their symbol.
-               - If carbon is not present, the elements are listed purely in alphabetic order of their symbol.
+            Standard PubChem identifier (CID).
+
+            The PubChem Compound Identifier (CID) is a unique numerical identifier assigned to 
+            a compound in the PubChem database, which contains information on the biological activities
+            of small molecules. The CID allows users to access detailed data about compounds, including 
+            their chemical structure, molecular formula, and biological properties.
+
+            For further information, see https://pubchem.ncbi.nlm.nih.gov/.
         </doc>
+         <attribute name="pub_chem_link">
+            <doc>
+                CAS REGISTRY name associated with this identifier.
+            </doc>
+        </attribute>
     </field>
 </definition>