Updated GNOme database

snijderlab · Sep 13, 2024 · 84564d3 · 84564d3
1 parent 8e3ac3c
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Showing 8 changed files with 33 additions and 38 deletions.
diff --git a/proforma_grammar.md b/proforma_grammar.md
diff --git a/rustyms-imgt-generate/src/combine.rs b/rustyms-imgt-generate/src/combine.rs
@@ -10,7 +10,7 @@ use crate::imgt_gene::IMGTGene;
 use crate::structs::DataItem;
 
 use crate::shared::{
-    AnnotatedSequence, Annotation, ChainType, Constant, Gene, GeneType, Germline, Germlines,
+    AnnotatedSequence, Annotation, Gene, Germline, Germlines,
     Species,
 };
 use crate::structs::SingleSeq;

diff --git a/rustyms/Cargo.toml b/rustyms/Cargo.toml
@@ -11,7 +11,7 @@ repository = "https://github.com/snijderlab/rustyms"
 readme = "README.md"
 include = [
     "src/**/*",
-    "databases/**/*",
+    "databases/**/*.gz",
     "README.md",
     "build.rs",
     "benches/**/*",

diff --git a/rustyms/README.md b/rustyms/README.md
@@ -78,3 +78,26 @@ It has multiple features which allow you to slim it down if needed (all are enab
 * `rand` - allows the generation of random peptides.
 * `rayon` - enables parallel iterators using rayon, mostly for `imgt` but also in consecutive align.
 * `mzdata` - enables integration with [mzdata](https://github.com/mobiusklein/mzdata) which has more advanced raw file support.
+
+## Sources for the downloaded files
+
+- PSI-MOD: https://github.com/HUPO-PSI/psi-mod-CV (2021-06-13 v1.031.6)
+- Unimod: http://www.unimod.org/obo/unimod.obo (2024-08-12 11:33)
+- RESID: ftp://ftp.proteininformationresource.org/pir_databases/other_databases/resid/ (2018-04-31 RESIDUES.XML)
+- XL-MOD: https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo (2021-03-23 1.1.12)
+- GNO: http://purl.obolibrary.org/obo/gno.obo (2024-05-21) structures: https://glycosmos.org/download/ ('List of all GlyCosmos Glycans data.') (downloaded 2024-07-02)
+  - To save space (crates.io has a hard limit on crate size) the unused columns of the structures csv are remove (only 0 and 1 are kept) and the `gno.obo` is trimmed using the following regex: `(property_value: GNO:00000(022|023|041|042|101|102) .*$\n)|(def: .*$\n)|(synonym: .*$\n)|(name: [^ ]*$\n)` (any matching line is removed) and the following replacement regex `(is_a: [^ ]*) ! .*\n` with `$1\n`.
+  - The structures csv file has only the first two columns kept for the same reason, also remove the two lines starting with `"`
+- Isotopic atomic masses: https://ciaaw.org/data/IUPAC-atomic-masses.csv (2021-03-17)
+
+## Ontologies
+
+| Name    | Modifications | Numbered | Rules | Diagnostic ions / neutral losses | Description / synonyms / cross ids |
+| ------- | ------------- | -------- | ----- | -------------------------------- | ---------------------------------- |
+| Unimod  | Yes           | Yes      | Yes   | Yes                              | Yes                                |
+| PSI-MOD | Yes           | Yes      | Yes   | NA                               | Yes                                |
+| RESID   | Yes           | Yes      | Yes   | NA                               | Yes                                |
+| XL-MOD  | Yes           | Yes      | Yes   | Yes                              | Yes                                |
+| GNO     | Yes           | NA       | NA    | NA (solved for all glycans)      | NA                                 |
+
+Note some modifications that do not fit the assumptions of rustyms might be missing from the ontologies. Examples of these are cross-links with more then 2 positions from XL-MOD and RESID, and modifications with different diff_formulas based on which location they bound from RESID. Additionally only the Glycans of a specific mass or with a structure.
diff --git a/rustyms/databases/GNOme.obo.gz b/rustyms/databases/GNOme.obo.gz
diff --git a/rustyms/databases/glycosmos_glycans_list.csv.gz b/rustyms/databases/glycosmos_glycans_list.csv.gz
diff --git a/rustyms/src/build/gnome.rs b/rustyms/src/build/gnome.rs
@@ -52,18 +52,15 @@ fn parse_gnome(_debug: bool) -> HashMap<String, GNOmeModification> {
             continue;
         }
         // name: glycan of molecular weight 40.03 Da
-        let name = &obj.lines["name"][0];
         let mut modification = GNOmeModification {
             code_name: obj.lines["id"][0][4..].to_lowercase(),
-            is_a: obj.lines["is_a"][0]
-                .split_once('!')
-                .map(|(a, _)| a.trim()[4..].to_lowercase())
-                .unwrap(),
-            mass: if name.len() > 30 {
-                name[27..name.len() - 3].parse::<f64>().ok()
-            } else {
-                None
-            },
+            is_a: obj.lines["is_a"][0].trim()[4..].to_lowercase(),
+            mass: obj
+                .lines
+                .get("name")
+                .map(|e| &e[0])
+                .filter(|n| n.len() > 30)
+                .and_then(|name| name[27..name.len() - 3].parse::<f64>().ok()),
             ..GNOmeModification::default()
         };
 

diff --git a/rustyms/src/lib.rs b/rustyms/src/lib.rs
@@ -11,6 +11,7 @@
     clippy::suboptimal_flops,
     clippy::too_many_lines
 )]
+#![recursion_limit = "256"]
 
 #[cfg(feature = "align")]
 /// Only available with feature `align`.