diff --git a/docs/genes_alleles_genotypes.md b/docs/genes_alleles_genotypes.md index 2dbea76..3e8f523 100644 --- a/docs/genes_alleles_genotypes.md +++ b/docs/genes_alleles_genotypes.md @@ -6,7 +6,7 @@ hide:
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## Adding genes to a session diff --git a/docs/genetic_interaction.md b/docs/genetic_interaction.md index 00122f7..2d8d488 100644 --- a/docs/genetic_interaction.md +++ b/docs/genetic_interaction.md @@ -11,7 +11,7 @@ hide:
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diff --git a/docs/go_BP.md b/docs/go_BP.md index c015708..3b836f1 100644 --- a/docs/go_BP.md +++ b/docs/go_BP.md @@ -9,7 +9,7 @@ hide:
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diff --git a/docs/go_CC.md b/docs/go_CC.md index c5e72b6..5cf6ef6 100644 --- a/docs/go_CC.md +++ b/docs/go_CC.md @@ -9,6 +9,6 @@ hide:
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diff --git a/docs/phenotypes.md b/docs/phenotypes.md index 4bf283b..01c2149 100644 --- a/docs/phenotypes.md +++ b/docs/phenotypes.md @@ -9,20 +9,21 @@ hide:
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## Making an annotation -On the `Quick Links` list, click on `Phenotype`, it should open a window that requires you to indicate: - - * **Genotype:** you can choose from the previously created genotypes (see [how to add genotypes](./genes_alleles_genotypes.md)). You can click on the magnifying glass on the right to use a search box instead of a drop-down menu. +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 what you are looking for, choose a broad term (e.g. abnormal spindle). - * Click the chosen term, and verify that the displayed definition describes the phenotype you want to annotate. There might be a "Comment" section with extra tips for annotation. + * 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. + * 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 canspecify: * **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). @@ -37,4 +38,5 @@ On the `Quick Links` list, click on `Phenotype`, it should open a window that re * **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:** 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. + * **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. diff --git a/docs/physical_interaction.md b/docs/physical_interaction.md index d783ca6..d74a755 100644 --- a/docs/physical_interaction.md +++ b/docs/physical_interaction.md @@ -6,6 +6,6 @@ hide:
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