added collapse use cases

qiyunzhu · Aug 3, 2021 · 347301f · 347301f
1 parent 634535d
commit 347301f
Showing 1 changed file with 12 additions and 10 deletions.
diff --git a/doc/collapse.md b/doc/collapse.md
@@ -19,16 +19,18 @@ woltka tools collapse -i input.biom -m mapping.txt -o output.biom
 
 With this tool one can achieve the following goals:
 
-1. Translate feature IDs into names or descriptions.
-   - Example: Translate taxonomic IDs to taxon names.
-   - Example: Translate [UniRef](https://www.uniprot.org/help/uniref) IDs to protein names, while **merging** same names.
-
-2. Group lower features into higher categories.
-   - Example: Convert genera to families.
-
-3. Convert lower features into higher ones, where each lower feature may correspond to **multiple** higher features.
-   - Example: Convert KEGG [orthologs](https://www.genome.jp/kegg/ko.html) to [pathways](https://www.genome.jp/kegg/pathway.html).
-   - Example: Convert [GO](http://geneontology.org/docs/ontology-documentation/) terms to [GO Slim](http://www-legacy.geneontology.org/GO.slims.shtml) terms.
+1. Translate feature IDs into names or descriptions. Examples:
+   - Translate taxonomic IDs to taxon names.
+   - Translate ORF IDs to gene IDs, while **dropping** the unannotated.
+   - Translate [UniRef](https://www.uniprot.org/help/uniref) IDs to protein names, while **merging** same names.
+
+2. Group lower features into higher categories. Examples:
+   - Group genera into families, then into orders.
+   - Group chemical structures by chemical ontology.
+
+3. Convert lower features into higher ones, where each lower feature may correspond to **multiple** higher features. Examples:
+   - Convert KEGG [orthologs](https://www.genome.jp/kegg/ko.html) to [pathways](https://www.genome.jp/kegg/pathway.html).
+   - Convert [GO](http://geneontology.org/docs/ontology-documentation/) terms to [GO Slim](http://www-legacy.geneontology.org/GO.slims.shtml) terms.
 
 The last usage is an important complement to the main classification workflow, which currently relies on a tree structure and does not support one-to-many mapping. This can be achieved by using the profile collapsing function (although one can only move up one level per run).