all sections added

docs/go_BP.md

@@ -23,7 +23,7 @@ On the `Quick Links` list, click on `GO biological process` to open a window tha
 
 * **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.
+    * Start typing a process in the search box. If you do not find the precise process 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`.
@@ -33,6 +33,7 @@ On the `Quick Links` list, click on `GO biological process` to open a window tha
     * **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.
+    * **Modified form:** sometimes, only a certain modified form of the gene product (e.g. phosphorylated) participates in the biological process. This is very valuable information, but requires a PR ontology term to exist for the modified version of the protein, which is rare. You can include this information in the comment section (e.g. write: "phosphorylated form").
     * 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.

docs/go_CC.md

@@ -3,13 +3,35 @@ hide:
   - toc
 ---
 
-<!-- Syntax to include an external file here -->
-{% include 'go_disclaimer.md' %}
+??? warning "Before you make a GO annotation"
+
+    * 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).
+    * **Cellular components** represent subcellular structures and macromolecular complexes, such as nucleus, nuclear inner membrane, nuclear pore, and proteasome complex.
+    * Generally, a gene product is located in or is a subcomponent of a particular cellular component.
+    * Gene products may be annotated with multiple cellular component terms.
+
 
 ## Video summary
 
 <div class="video-sizer">
     <div class="video-wrapper">
     <iframe src="https://www.youtube.com/embed/KY7ev8IEG00" frameborder="0" allowfullscreen></iframe>
     </div>
-</div>
+</div>
+
+On the `Quick Links` list, click on `GO cellular component` to open a window that requires you to indicate:
+
+* **Gene:** the gene that is located in a cellular component. See [how to add genes](./genotype_management.md#adding-genes-info).
+* **Term name:** a GO term describing the cellular component.
+    * Start typing a cellular component in the search box. If you do not find the precise component you are looking for, choose a broad term (e.g. cytoskeleton, mitochondrion) 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 biological processes:** `observed in this location during` can be used to indicate that gene product localizes to the cellular component during a cell cycle phase or cellular response to stimulus. For example, med7 localizes to euchromatin during "mitotic M phase".
+    * **Links to sequence ontology terms**: `found at genomic region` indicates the type of DNA region for terms describing chromatin or chromosome regions. For example, man1 locates to the cellular component "heterochromatin" at "long terminal repeat" genomic regions.
+    * **Links to genes:** similarly, `found at genomic region` can also specify the genes within the cellular component. For example, epe1 localizes to heterochromatin at the swi6 gene.
+    * **Modified form:** sometimes, only a certain modified form of the gene product (e.g. phosphorylated) localizes in the cellular component. This is very valuable information, but requires a PR ontology term to exist for the modified version of the protein, which is rare. You can include this information in the comment section (e.g. write: "phosphorylated form").
+* **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

@@ -50,6 +50,7 @@ On the `Quick Links` list, click on `GO molecular function` to open a window tha
         * `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.
+    * **Modified form:** sometimes, only a certain modified form of the gene product (e.g. phosphorylated) exhibits the activity. This is very valuable information, but requires a PR ontology term to exist for the modified version of the protein, which is rare. You can include this information in the comment section (e.g. write: "phosphorylated form").
     * 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/index.md

@@ -22,8 +22,6 @@ This site contains a step-by-step video and text guide for curating a paper usin
 
     <img src="assets/activate_advanced_mode.png" alt="activating advanced mode by clicking on the top right gear icon">
 
-* If you are unfamiliar with what annotation means, and how ontology terms are used for this, visit our [brief intro to annotation](./intro_annotation.md).
-
 ## Creating annotations
 
 Depending on the publication, you may be able to add different types of annotations, follow the links below to see videos and text showing how to do it:

docs/request_curation_session.md

@@ -1,5 +1,12 @@
-If you have not received a link from the PomBase team to curate a publication, you can easily send a request and we will send you an email with a link shortly.
+---
+hide:
+  - toc
+---
 
-If the publication is in PubMed, you can search for it in the PomBase searchbar, and request to curate that publication (see animation below). If the publication is not in PomBase, send an email to [[email protected]](mailto:[email protected]) indicating the title of the publication you want to curate.
+If you have not received a link from the PomBase team to curate a publication, you can easily send a request and we will send you an email with a link shortly:
 
-<img src="/assets/request_curation_session.gif" alt="video showing how to find a publication in PomBase and request a session link">
+* If the publication is in PubMed, you can search for it in the PomBase search bar, and request to curate that publication (see animation below).
+* If the publication is not in PomBase, send an email to [[email protected]](mailto:[email protected]) indicating the title of the publication you want to curate.
+<div style="margin-top: 1em;" markdown>
+![](assets/request_curation_session.gif)
+</div>

mkdocs.yml

@@ -51,7 +51,6 @@ nav:
     - 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
     - Productivity tricks: productivity.md
     - Describing alleles: describing_alleles.md