Changes between Initial Version and Version 1 of PhenotypeAnnotationGuidelines


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Timestamp:
Jan 29, 2015, 4:42:26 PM (6 years ago)
Author:
vw253
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  • PhenotypeAnnotationGuidelines

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     3== Phenotype ==
     4 * A guideline from Maria at SGD: "in summary, we annotate phenotypes that represent the effects of mutations on the organism as a whole, rather than the effects on the product of the gene that is mutated. For example, if a particular mutation blocks the in vitro activity of an enzyme, we might annotate that with GO but would not make a phenotype annotation. However, if the same mutation causes the inability of yeast to utilize a certain nutrient, then we would capture that as a phenotype annotation."
     5 * Another thought from Midori: direct involvement or effects can usually be captured with GO terms, whereas indirect effects are better as phenotypes
     6  * example: tad3 subunit of tRNA adenosine deaminase - GO term for adenosine-to-inosine conversion; phenotype annotations for cell cycle arrest (PMID:17875641)
     7 * [https://sourceforge.net/p/pombase/fission-yeast-phenotype/ phenotype tracker] to request new terms
     8 * NOTE, at present we can't capture phenotypes of double/triple mutants. The ability to do this will be added to the curation tool in the future. To capture an allele for a double/triple mutant you will need to create an entry on the wiki. If the phenotype is "synthetic lethal" this is explicit in the BioGRID evidence code and can be inferred later from the evidence, but we'll still need to capture the alleles (on the wiki for now).
     9 * If there is no relevant evidence code, then find one in [https://evidenceontology.googlecode.com/svn/trunk/eco-edit.obo] and request it for inclusion by Kim.
     10 * If it doesn't exist request one from the evidence ontology: see http://code.google.com/p/evidenceontology/issues/list
     11 * Naming alleles
     12  * wild type is yfg1+
     13  * if paper names it, use that name; otherwise:
     14   * deletions are named yfg1delta by default
     15   * if a deletion also has a marker inserted, you can use the name yfg1delta::ura4+
     16   * a disruption (different from a deletion, in that gene sequence, esp. coding, is still present) is yfg1::ura4+
     17   * everything else will just default to "noname"
     18  * Additonal note: allele systematic ids will be gene systematic id dash integer, e.g. SPBC4.04c-2 SPBC4.04c-1, etc.  won't encode any details in identifier; stuff that info in properties, description, etc.
     19 * Phenotype annotations can have extensions to capture:
     20  * gene or protein used in an assay
     21   * e.g. annotation_extension=assayed_using(PomBase:SPAC30D11.10)
     22   * also see additional [wiki:ProteinBindingPhenotypeExtensions notes on extensions with protein binding terms]
     23  * expressivity (usually only used for high-throughput)
     24   * e.g. annotation_extension=has_expressivity(25%) or annotation_extension=has_expressivity(FYPO_EXT:0000003) (note: FYPO_EXT:0000003 = low)
     25  * penetrance (usually only used for high-throughput)
     26   * e.g. annotation_extension=has_penetrance(25%) or annotation_extension=has_penetrance(FYPO_EXT:0000003)
     27 * [http://pombase.svn.sourceforge.net/viewvc/pombase/phenotype_ontology/supplemental_files/fypo_extension_relations.obo phenotype extension relations] are in a small obo file in SVN
     28=== Conditions ===
     29 * Describes the experimental conditions which may or definitely affect the phenotype. Includes things such as:
     30  * Type of medium: rich medium, minimal medium, growth on agar plates, growth in liquid culture, glucose medium, sporulation medium etc
     31  * Chemicals added to the assay which are 'normally' not included in the medium, or which are added to the medium in a higher than normal concentration. This includes a wide range of substances: glutamate, cyclosporin A, calcium, hydrogen peroxide.
     32  * Chemicals added in a limiting amount (perhaps enough to get things going) but is then rapidly depleted by the cells. For instance adding 5 mg/L of adenine to the medium instead of 100 mg/L.
     33  * The temperature at which the cells were grown. Currently split into 3 categories; low, medium and high.
     34  * Sequential growth conditions, in which cells were subjected to a series of different conditions such as nitrogen starvation and recovery or heat shock and recovery.
     35 * Conditions live in a small in-house [http://pombase.svn.sourceforge.net/viewvc/pombase/phenotype_ontology/peco.obo ontology] in svn
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