go BP

docs/go_BP.md

@@ -9,9 +9,7 @@ hide:
     * A **Biological Process** is a series of events accomplished by one or more ordered assemblies of molecular functions. Some examples are "cell cycle regulation", "ion transport", or "signal transduction".
     * It can be difficult to distinguish between a biological process and a molecular function, but the general rule is that a process must have more than one distinct step.
     * Gene products may be annotated with multiple biological process terms.
-    * Because GO annotation describes the wild-type functions of genes, a phenotype that perturbs a certain biological process is not sufficient to annotate a gene to a molecular process. For instance, the fact that deleting a gene perturbs spindle assembly assembly is not sufficient evidence to annotate that gene to the biological process "spindle assembly", or even "regulation of spindle assembly".
-    * Experiment with mutants can be used to support a GO annotation, but they must show direct involvement of the gene in the process.
-
+    * Phenotypes can be used to support a GO annotation, but they must show direct involvement of the gene in the process, because GO describes the wild-type roles of gene products. For instance, the isolated fact that deleting a gene perturbs spindle assembly is not sufficient to annotate that gene to the biological process "spindle assembly", or even "regulation of spindle assembly". However, combined with further genetic and localization experiments, it can support a GO annotation.
 
 ## Video summary
 
@@ -21,5 +19,22 @@ hide:
     </div>
 </div>
 
-## Evidence required
+On the `Quick Links` list, click on `GO biological process` to open a window that requires you to indicate:
 
+* **Gene:** the gene that participates in a biological process. See [how to add genes](./genotype_management.md#adding-genes-info).
+* **Term name:** a GO term describing the biological process.
+    * Start typing a molecular function in the search box. If you do not find the precise function you are looking for, choose a broad term (e.g. cell cycle, transport) that can be refined later.
+    * Click the chosen term, and verify that the displayed definition describes the phenotype you want to annotate. There is sometimes a "Comment" section with extra tips for annotation.
+    * If the blue button reads `Next`, click it and see if you can find a more specific term that the one you originally selected. If so, select it and do as before.
+    * Otherwise, click `Finish`.
+    * If you do not find the term you require, select a broader term, and request a new one clicking on `Suggest a new term` on the right side of the text box.
+* **Annotation extension:** this field appears once you have selected a GO term. Always click the `Add` button to see if you can specify:
+    * **Links to gene products:** extensions such as `targets`, `processes`, `transports`, etc. link the a biological process with the gene product targeted by that process.
+    * **Links to biological processes:** `happens during` can be used to indicate that the biological process takes place during a cell cycle phase or cellular response to stimulus . For example, the transcription factor atf1 participates in "positive regulation of transcription by RNA polymerase II" during "cellular response to oxidative stress".
+    * **Links to a cellular component:** `occurs in` can be used to connect a few processes like endocytosis can be linked to the cellular location where they take place.
+    * **Links to sequence ontology terms**: `occurs at` indicates the type of DNA region where the process happens. For example, the "positive regulation of transcription by RNA polymerase II" by ste11 transcription factor occurs at promoters with TR boxes.
+    * You can make several annotations with the same biological process and gene, with different extensions:
+        * To link it to several gene products (e.g. different substrates of a kinase).
+        * To indicate that a gene is involved in the same biological process during different cellular responses to stimuli.
+* **Evidence code:** the type of experiment where the phenotype was observed.
+* **Comment:** it's very useful for us if you indicate the figure or table where this phenotype comes from.

docs/go_MF.md

@@ -8,20 +8,22 @@ hide:
     * Gene Ontology (GO) annotations are used to describe the normal (wild type) functions, processes and cellular components or locations of a gene product (protein or RNA).
     * **Molecular Function** is the basic activity performed by a gene product, such as "protein serine/threonine kinase activity", "transporter" or any other activity that occurs at the molecular level. As a general rule, molecular functions correspond to single step activities performed by individual gene products. A gene can have multiple molecular functions.
     * Gene products may be annotated with multiple molecular function terms.
-    * Whenever possible, we want to connect the molecular function of a gene to the other types of GO terms through annotation extensions:
-        * The cellular component where that function happens (e.g. the cytoskeletal protein-membrane anchor activity of cdc12 takes place at the medial cortex).
-        * The biological process in which this molecular function is involved (e.g. that cdc12 activity is involved in the mitotic actomyosin ring assembly).
+    * Whenever possible, we want to connect the molecular function of a gene to other GO terms or gene products through annotation extensions:
+        * The cellular component where that function happens (e.g. the cytoskeletal protein-membrane anchor activity of cdc15 takes place at the medial cortex).
+        * The biological process in which this molecular function is involved (e.g. that cdc15 activity is involved in the mitotic actomyosin ring assembly).
+        * The cell cycle phase during which it occurs (Cell cycle phases are also GO biological processes).
+        * The gene products targeted by the molecular function (all the proteins that Cdc15 anchors)
             <div markdown style="max-width: 800px">
-              ![](assets/go_mf_cdc12.png)
+              ![](assets/go_mf_cdc15.png)
             </div>
-        * The cell cycle phase during which it occurs (Cell cycle phases are also GO biological processes).
         * The cellular response to stimulus in which that molecular function is involved (e.g. hsf1 is a heat-shock transcription factor, so we can connect its "transcription regulatory region nucleic acid binding" molecular function to the "cellular response to heat")
-        * GO is very rich and has many term-specific extensions. For instance, in the example below we connect the DNA binding activity of the transcription factor with HSE (Heat Shock Element, a term from the Sequence Ontology) to indicate the type of sequences where dna binding happens.
+        * The DNA region where a gene product binds. For instance, in the example below we connect the DNA binding activity of the transcription factor with HSE (Heat Shock Element, a term from the Sequence Ontology) to indicate the type of sequences where DNA binding happens.
             <div markdown style="max-width: 500px">
               ![](assets/go_mf_hsf1.png)
             </div>
 
 
+
 ## Video summary
 
 <div class="video-sizer">
@@ -32,19 +34,22 @@ hide:
 
 ## Making an annotation
 
+On the `Quick Links` list, click on `GO molecular function` to open a window that requires you to indicate:
+
 * **Gene:** the gene that shows the molecular function. See [how to add genes](./genotype_management.md#adding-genes-info).
 * **Term name:** a GO term describing the molecular function.
     * Start typing a molecular function in the search box. If you do not find the precise function you are looking for, choose a broad term (e.g. catalytic activity, molecular adaptor, transporter) that can be refined later.
     * Click the chosen term, and verify that the displayed definition describes the phenotype you want to annotate. There is sometimes a "Comment" section with extra tips for annotation.
     * If the blue button reads `Next`, click it and see if you can find a more specific term that the one you originally selected. If so, select it and do as before.
     * Otherwise, click `Finish`.
     * If you do not find the term you require, select a broader term, and request a new one clicking on `Suggest a new term` on the right side of the text box.
-* **Annotation extension:** this field appears once you have selected a term describing the phenotype, always click the `Add` button to see if you can specify:
+* **Annotation extension:** this field appears once you have selected a GO term. Always click the `Add` button to see if you can specify:
     * **Links to gene products:** extensions such as `anchors`, `transports`, `phosphorylates`, etc. link the molecular function of a gene with the gene products that are substrates of that activity. Some gene products should be linked to themselves (e.g. pom1 `phosphorylates` pom1)
     * **Links to biological processes:**
         * `involved in biological process` to indicate that the function takes part in a particular cellular process.
         * `happens during` to indicate that the function occurs during a cell cycle phase or cellular response to stimulus.
     * **Links to a cellular component:** `physical location` to indicate that the function occurs at a specific location or protein complex.
+    * **Links to sequence ontology terms**: to indicate the type of transcript or DNA regions a gene product binds to.
     * You can make several annotations with the same molecular function and gene, with different extensions:
         * To link it to several gene products (e.g. different substrates of a kinase).
         * To indicate that a gene kinase activity  phosphorylates a protein inside the nucleus during mitosis, and a different one in the cytoplasm during interphase.

docs/javascript/did_you_know.js → docs/javascript/extra.js

@@ -1,3 +1,4 @@
+
 // A simple script that displays a random did you know message at the footer
 
 const allMessages = [
@@ -17,3 +18,11 @@ const message = document.createElement('p')
 message.innerHTML = '<strong>Did you know?</strong> 🤔 ' + randomMessage
 
 footer.appendChild(message)
+
+// The template is a bit limited in what it allows you to edit, so this
+// is a simple workaround to replace the icon by a button with text
+
+const editIcon = document.querySelector('a[title="Edit this page"]')
+const editMessage = document.createElement('span')
+editMessage.textContent = 'Found a mistake? Fix it in on GitHub!'
+editIcon.insertBefore(editMessage, editIcon.firstChild)

docs/phenotypes.md

@@ -24,7 +24,7 @@ On the `Quick Links` list, click on `Phenotype` to open a window that requires y
       * If the blue button reads `Next`, click it and see if you can find a more specific term that the one you originally selected. If so, select it and do as before.
       * Otherwise, click `Finish`.
       * If you do not find the term you require, select a broader term, and request a new one clicking on `Suggest a new term` on the right side of the text box.
-  * **Annotation extension:** this field appears once you have selected a term describing the phenotype, always click the `Add` button to see if you can specify:
+  * **Annotation extension:** this field appears once you have selected a phenotype term. Always click the `Add` button to see if you can specify:
       * **Penetrance:** proportion of cells in the population that show the phenotype, can be a qualitative value or a percentage.
       * **Severity:** qualitative value to capture the strength of the phenotype. This is specially useful when several mutants show the same phenotype with different strength (e.g. cells being elongated).
       * **Others:** certain terms allow for other extensions. In general they are self-explaining, but here some important clarifications:

mkdocs.yml

@@ -24,7 +24,7 @@ markdown_extensions:
 extra_css:
   - stylesheets/extra.css
 extra_javascript:
-  - javascript/did_you_know.js
+  - javascript/extra.js
 
 plugins:
   - search