protein modification

docs/physical_interaction.md

@@ -11,6 +11,7 @@ To create a physical interaction, on the `Quick Links` list, click on `Physical
 
 * The two genes that show the physical interaction in `Gene` and `Interacting Gene`.
 * The `Interaction type` (the type of experiment that supports the physical interaction).
+* In the `Comment`, it's very useful for us if you indicate the figure or table where this interaction comes from.
 
 When making an annotation consider that:
 
@@ -25,4 +26,4 @@ When making an annotation consider that:
     * For `binds to peptide`, `Gene` should be the protein that can bind to a peptide from the `Interacting Gene`.
     * For `binds to RNA`, `Gene` should be the protein that can bind to the RNA of the `Interacting Gene`.
 * If you perform asymmetric experiments both ways (A affinity-captures B and B affinity-captures A), you should include two physical interaction annotations.
-* It can be laborious to 
+* If you have to add many interactions, there are ways to do this quickly, see our [productivity page](./productivity.md#transferring-physical-interactions).

docs/productivity.md

@@ -9,4 +9,10 @@ hide:
     <div class="video-wrapper">
     <iframe src="https://www.youtube.com/embed/KY7ev8IEG00" frameborder="0" allowfullscreen></iframe>
     </div>
-</div>
+</div>
+
+
+
+
+
+### Transferring physical interactions

docs/protein_modification.md

@@ -3,10 +3,27 @@ hide:
   - toc
 ---
 
-## Video summary
+To create a protein modification annotation, on the `Quick Links` list, click on `Protein modification` to open a window that requires you to indicate:
+
+* **Gene**: gene of which the protein is modified.
+* **Term name**: a term from the MOD ontology to represent the modification. Some can be tricky to find, see [below](#modifications-that-are-tricky-to-find).
+* **Annotation extensions**: available once a term is selected. Most are self-explaining, but some clarifications:
+    * Extensions that contain `during`, allow you to specify:
+        * A cell cycle phase (e.g. `removed during` anaphase)
+        * A cellular response to a stress (e.g. `present during` cellular response to heat)
+    * Extensions that contain `in presence of` allow to add a chemical, drug or metabolite (e.g. galactose or hydroxyurea).
+    * Extension `in absence of` allows you to indicate that the modification is exist when a certain gene is missing (e.g. deletion of gene X leads to the phosphorylation of protein Y).
+    * For proteins that modify themselves, use `added by` with the same gene as the `Gene` field of the modification.
+    * You can use `position modified` to indicate the affected residue or residues (comma-separated).
+* **Evidence code**: this can only be `Inferred from Direct Assay`.
+* **Comment**: it's very useful for us if you indicate the figure or table where this interaction comes from.
+
+### Modifications that are tricky to find
+
+* **Phosphorylation:**  below the term names and their MOD codes, which can be used in the `Term name` field.
+    * Serine:    O-phospho-L-serine (MOD:00046)
+    * Threonine: O-phospho-L-threonine (MOD:00047)
+    * Tyrosine:  O4'-phospho-L-tyrosine (MOD:00048)
+* **Methylation:** there are many terms, we recommend starting from "methylated residue" (MOD:00427), and iterate towards more specific terms.
+* **Glycosilation:** there are more specific terms, but "N-glycosylated residue" (MOD:00006) or "O-glycosylated residue" (MOD:00396) are often sufficient.
 
-<div class="video-sizer">
-    <div class="video-wrapper">
-    <iframe src="https://www.youtube.com/embed/KY7ev8IEG00" frameborder="0" allowfullscreen></iframe>
-    </div>
-</div>

docs/stylesheets/extra.css

@@ -112,3 +112,13 @@ main {
     display: none;
   }
 }
+
+.md-typeset ul {
+  margin-bottom: 0;
+  margin-top: 0;
+}
+
+.md-typeset p {
+  margin-block-end: 0;
+  margin-block-start: 0;
+}

mkdocs.yml

@@ -40,15 +40,15 @@ nav:
   - Home: index.md
   - How to annotate:
     - Genotype management: genotype_management.md
-    - GO Biological Process: go_BP.md
-    - GO Cellular Component: go_CC.md
-    - GO Molecular Function: go_MF.md
     - Phenotypes: phenotypes.md
-    - Physical Interaction: physical_interaction.md
     - Genetic Interaction: genetic_interaction.md
+    - Physical Interaction: physical_interaction.md
     - Protein modification: protein_modification.md
     - Protein sequence feature/motif: protein_sequence_feature.md
     - RNA or protein level: rna_protein_level.md
+    - GO Molecular Function: go_MF.md
+    - GO Biological Process: go_BP.md
+    - GO Cellular Component: go_CC.md
   - Other:
     - Introduction to annotation: intro_annotation.md
     - Requesting to curate a paper: request_curation_session.md

readme.md

@@ -4,6 +4,8 @@ A static site with canto documentation for users to get started with Canto. The
 
 ## Run locally
 
+For Val, if you have not added poetry to the path, use `.local/bin/poetry` instead of poetry.
+
 ### Install dependencies
 
 To install the dependencies, we used poetry (see [poetry installation instructions](https://python-poetry.org/docs/)). In the source directory run: