|
+ Variant type + |
+
+ Example + |
+|
|
+ Wild type + |
+
+ ase1+ + |
+|
|
+ Knockout / deletion + |
+
+ ase1Δ + |
+|
|
+ Partial deletion + |
+
+ Indicate what’s left + |
+
+ ase1(1-35) +ase1(1-35, 40-700) + |
+
|
+ Indicate what’s missing + |
+
+ ase1Δ(114-120) +ase1Δ(114-120,150-200) + |
+|
|
+ Residue insertion + |
+
+ ase1-P114PVPAL + |
+|
|
+ Substitution or deletion-insertion + |
+
+ Single residues + |
+
+ ase1-P114A,Q117A +ase1-P114* + |
+
|
+ Consecutive residues + |
+
+ ase1-PLI114AAA +ase1-PLI114LAVKK + |
+|
|
+ Combinations of the above + |
+
+ ase1Δ(10-20)-P114A,Q117A + |
+|
|
+ Forward genetics, variant unknown + |
+
+ ase1-35 (must be unique) + |
+|
|
+ CTD + |
+
+ All repeats mutated + |
+
+ rpb1-CTD-Y1F + |
+
|
+ Some repeats mutated + |
+
+ rpb1-CTD-Y1F(r1-r12) + |
+|
|
+ Some repeats deleted + |
+
+ rpb1-CTD-Δ(r11-r29) + |
+|
|
+ Motifs mutated every 2 repeats, from repeat 1 to 29. + |
+
+ rpb1-CTD-Y1F(r1-r29-2) + |
+|
|
+ Combinations of the above + |
+
+ rpb1-CTD-S5A(r1-r12)Δ(r13-r29) + |
+|
|
+ CTD and non-CTD mutations + |
+
+ rpb1-N494D-CTD-Δ(r11-r29) + |
+|
+ + \ No newline at end of file diff --git a/docs/faqs.md b/docs/faqs.md new file mode 100644 index 0000000..70e55e2 --- /dev/null +++ b/docs/faqs.md @@ -0,0 +1,28 @@ + +## Phenotype annotations + +### How do I indicate that a mutation or deletion is viable? + +Annotate a genotype including that allele to `viable vegetative cell population`. Viability can depend on conditions and other alleles present on the genotype. See [phenotypes](./phenotypes.md) + +### How do I indicate that a mutation or deletion is lethal? + +Annotate a genotype including that allele to `inviable vegetative cell population`. Lethality can depend on conditions and other alleles present on the genotype. See [phenotypes](./phenotypes.md) + +### How do I indicate that an allele is thermosensitive? + +Annotate a genotype including that allele to `inviable vegetative cell population`, including `high temperature` or `low temperature` as a condition. See [phenotypes](./phenotypes.md) + +## Genotype management + +### What's the difference between "Wild type product level" and "Not assayed"? + +Historically, `Wild type product level` and `Not assayed` have been used interchangeably when a non-wild type allele is expressed from the endogenous locus. We recommend `Not assayed` if you have not measured expression. See [Genotype management](./genotype_management.md) + +### What to do when control strains over-express the wild-type allele, or express it from a plasmid? + +PomBase does not capture the difference between strains expressing an allele from a plasmid or the native locus in phenotype annotations. Similarly, we do not have a way to capture the fact that the control of an experiments is over-expressing the wild-type allele. Therefore, if both the wild-type (control) and mutant allele are over-expressed / knocked-down, ???. See [Genotype management](./genotype_management.md) + +### What if the wild-type copy is still present in a mutant strain? + +Multi-loci phenotype can be used to indicate that the wild-type allele is still present in a strain expressing an allele of that gene. For example, a strain that bears both the wild type _cdc25_ and the mutant allele _cdc25-22_. For this purpose, you can create a wild-type allele with expression level `Wild type product level`. See [Genotype management](./genotype_management.md) \ No newline at end of file diff --git a/docs/genes_alleles_genotypes.md b/docs/genes_alleles_genotypes.md deleted file mode 100644 index 3e8f523..0000000 --- a/docs/genes_alleles_genotypes.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -hide: - - toc ---- -## Video summary - -
+
* 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
diff --git a/docs/javascript/did_you_know.js b/docs/javascript/did_you_know.js
new file mode 100644
index 0000000..47a6f42
--- /dev/null
+++ b/docs/javascript/did_you_know.js
@@ -0,0 +1,19 @@
+// A simple script that displays a random did you know message at the footer
+
+const allMessages = [
+ 'Canto has ways to save time during curation, visit our productivity page.',
+ 'You can submit high-throughput datasets of genetic and physical interactions to BioGrid, and they will appear in PomBase.',
+ 'You can submit high-throughput annotations of GO, phenotype, modification, or gene expression data, visit our data submission documentation.',
+ 'You can submit sequence-linked data, and they will appear in PomBase genome browser. Visit our data submission documentation.'
+]
+
+const randomMessage = allMessages[Math.floor(Math.random() * allMessages.length)]
+
+// Set the initial message
+
+const footer = document.getElementsByClassName('md-footer-meta__inner')[0]
+
+const message = document.createElement('p')
+message.innerHTML = 'Did you know? 🤔 ' + randomMessage
+
+footer.appendChild(message)
diff --git a/docs/phenotypes.md b/docs/phenotypes.md
index 01c2149..1beb10d 100644
--- a/docs/phenotypes.md
+++ b/docs/phenotypes.md
@@ -16,7 +16,7 @@ hide:
## Making an annotation
On the `Quick Links` list, click on `Phenotype` to open a window that requires you to indicate:
-****
+
* **Genotype:** you can choose from the genotypes added to the session from a dropdown (see [how to add genotypes](./genes_alleles_genotypes.md)). Click on the magnifying glass on the right to use a search box instead of a drop-down menu.
* **Term name:** a FYPO term describing the phenotype associated with the genotype you selected above.
* Start typing a phenotype in the search box. If you do not find the precise phenotype you are looking for, choose a broad term (e.g. abnormal spindle) that can be refined later.
@@ -34,9 +34,11 @@ On the `Quick Links` list, click on `Phenotype` to open a window that requires y
* **Catalytic activity phenotypes:** similarly, if a mutation in enzyme X affects its activity, still specify gene X in `assayed enzyme`, and if X auto-phosphorylates, indicate it in `assayed substrate`. A mutation in gene X may also affect catalytic activity of Y, then use Y in `assayed enzyme`
* **Interaction phenotypes:** Indicate always two gene products. Mutation in gene X may affect interaction of proteins Z and Y, or of protein X with Y. If a mutation affects a protein/RNA interaction with itself, add the same protein twice.
* **Assayed region extension:** depending on the phenotype, you will be able to select from either:
- * **Genes:** e.g. to indicate that a mutation gene X causes "abnormal chromatin organization" in the region of gene Y, you select `assayed region or gene` with gene Y. If several genes are affected, create multiple annotations.
- * **Sequence ontology term:** to indicate that the phenotype affects a type of sequence (e.g. `centromeric repeat`).
+ * **Genes:** e.g. to indicate that a mutation gene X causes "abnormal chromatin organization" in the region of gene Y, you select `assayed region or gene` with gene Y. If several genes are affected, create multiple annotations.
+ * **Sequence ontology term:** to indicate that the phenotype affects a type of sequence (e.g. `centromeric repeat`).
* **Evidence code:** the type of experiment where the phenotype was observed.
* **Conditions:** Conditions are aspects of the experimental setup that are **independent of what cells, strain, organism, etc. are used**. Type and select from the autocomplete options. Several conditions can be added, and capture the medium or temperature used, presence of chemicals, agar plates or liquid culture, etc.
* **Comment:** it's very useful for us if you indicate the figure or table where this phenotype comes from.
+
+!!! question "These are just the basics, more info and edge cases can be found in the [FAQs](faqs.md#phenotype-annotations)"
\ No newline at end of file
diff --git a/docs/physical_interaction.md b/docs/physical_interaction.md
index d74a755..712c48a 100644
--- a/docs/physical_interaction.md
+++ b/docs/physical_interaction.md
@@ -8,4 +8,8 @@ hide: