Changes between Version 3 and Version 4 of PhenotypeAnnotationGuidelines


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Timestamp:
Apr 10, 2015, 4:55:58 PM (6 years ago)
Author:
mah79
Comment:

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  • PhenotypeAnnotationGuidelines

    v3 v4  
    11
    22
    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
     3= Phenotype Curation Guide =
     4== FYPO ==
     5 * Basic [wiki:FissionYeastPhenotypeOntology documentation] on wiki
     6 * Use the [https://sourceforge.net/p/pombase/fission-yeast-phenotype/ FYPO SourceForge tracker] to request new terms
     7
     8== Scope of phenotype curation ==
     9... especially when to curate phenotype, GO, or both
     10 * SGD's criteria (from Maria): "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."
     11 * General !PomBase attitude: direct involvement or effects can usually be captured with GO terms, whereas indirect effects are better as phenotypes. We can pretty much always annotate an observed phenotype, but only a subset of phenotypes effectively support IMP-evidenced GO annotations.
    612  * 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
     13
     14== Alleles ==
     15=== Names ===
    1216  * wild type is yfg1+
    1317  * if paper names it, use that name; otherwise:
     
    1519   * if a deletion also has a marker inserted, you can use the name yfg1delta::ura4+
    1620   * 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 ===
     21   * everything else will just default to "noname" (displayed as "unnamed" on gene pages)
     22  * Additonal note: allele systematic ids will be gene systematic id dash integer, e.g. SPBC4.04c-2 SPBC4.04c-1, etc. and won't encode any details in identifier; stuff that info in properties, description, etc.
     23
     24=== Descriptions ===
     25 * See the built-in Canto hints and the [wiki:DescribingResidues page on describing residues] for how to specify allele descriptions
     26 * Choose "unknown" option in Canto if the change isn't described in the paper you're curating
     27  * If a description is entered in any Canto session, it will override an "unknown" description for the same allele name in any other session.
     28  * On gene pages, just the allele name will appear, with "unknown" in a mouseover
     29
     30== Evidence ==
     31 * If there is no relevant evidence code, then find one in [https://evidenceontology.googlecode.com/svn/trunk/eco-edit.obo] and ask Kim to add it to the allowed list (affects Chado and the Canto interface).
     32 * If it doesn't exist request one from the evidence ontology: see http://code.google.com/p/evidenceontology/issues/list
     33 * If you use the "other" evidence code, you can put some specifics in a comment on the annotation.
     34
     35
     36== Conditions ==
    2937 * Describes the experimental conditions which may or definitely affect the phenotype. Includes things such as:
    3038  * Type of medium: rich medium, minimal medium, growth on agar plates, growth in liquid culture, glucose medium, sporulation medium etc
     
    3341  * The temperature at which the cells were grown. Currently split into 3 categories; low, medium and high.
    3442  * 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
    36   
     43 * Conditions live in a small in-house [http://pombase.svn.sourceforge.net/viewvc/pombase/phenotype_ontology/peco.obo ontology] in svn. Request new condition terms on the [https://sourceforge.net/p/pombase/fission-yeast-phenotype/ FYPO tracker].
     44 * Also see the [wiki:PrePostComposePhenotype page on pre- vs. post-composed FYPO terms]
    3745
     46== Annotation extensions ==
     47Phenotype annotations can have extensions to capture expressivity (severity), penetrance, and genes, transcripts or proteins used in an assay. Expressivity and penetrance can use qualitative values from the FYPO_EXT mini-ontology (in svn at pombe-embl/mini-ontologies/fypo_extension.obo), or penetrance can be specified quantitatively as a percent (I haven't run into any quantitative expressivity as of 2015-04-10 -mah).
     48 * Expressivity is usually qualitative, e.g. has_expressivity(FYPO_EXT:0000003) (note: FYPO_EXT:0000003 = low)
     49 * Penetrance
     50  * Qualitative e.g. FYPO:0000821
     51  * Quantitative e.g. has_penetrance(25%)
     52 * Specifying what was assayed
     53  * 'Binding' phenotype terms
     54   * Binding to DNA, chromatin, small molecules
     55    * DNA binding FYPO:0000653 and descendants
     56     * assayed_using(geneA) strongly recommended; assumed if omitted
     57     * assayed_using(SO:nnnnnnn) optional, but recommended where possible
     58    * chromatin binding FYPO:0001093 - assayed_using(geneA) strongly recommended; assumed if omitted
     59    * small molecule binding, e.g. GTP binding FYPO:0001528 and descendants - assayed_using(geneA) strongly recommended; assumed if omitted
     60   * Protein binding - this is a special case because all of the things involved are gene products. Annotation extensions should therefore name both/all of the interacting proteins, whether or not that includes the mutated gene product. Canto should eventually require that each assayed_using() extension contains two or more gene/protein IDs. A check is run with each Chado load to flag any protein binding annotations that don't have two extensions (part of the chado_checks log). The Chado load also allows duplicated extensions specifically for the protein binding terms, in case a protein binding to itself is assayed.
     61    * mutation in geneA affects binding of protein A to protein B
     62     * assayed_using(geneA,geneB)
     63    * mutation in geneA affects binding of protein B to protein C
     64     * assayed_using(geneB,geneC)
     65    * mutation in geneA affects binding of protein A to protein B and protein C (three-way interaction)
     66     * assayed_using(geneA,geneB,geneC)
     67  * 'Catalytic activity' phenotype terms
     68   * Use assayed_enzyme
     69   * Use assayed_substrate to capture the substrate
     70   * A catalytic activity phenotype annotation may have either or both of assayed_enzyme and assayed_substrate. It's less useful if the annotation has neither extension.
     71   * assayed_enzyme and assayed_substrate introduced March-April 2015. We've decided not to be too bothered about retrofitting extensions made with assayed_using prior to adding the new extension relations, because they're not wrong, they're just a bit less specific than is now possible.
     72  * Everything else (e.g. protein localization, protein level, RNA level, etc.) - assayed_using
     73   * e.g. assayed_using(PomBase:SPAC30D11.10)
     74 
    3875
    39  === Relations used in S. pombe FYPO annotations ===
     76=== FYPO annotation extension relations ===
     77These are in an [https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/supplemental_files/fypo_extension_relations.obo OBO file in svn]. As of 2015-04-09:
     78 * has_expressivity - see above
     79 * has_penetrance - see above
     80 * assayed_using - see above
     81  * assayed_enzyme - see above
     82  * assayed_substrate - see above
     83 * occurs_in - rarely used; use with biological process phenotypes, usually with a Cell Ontology ID to capture when a phenotype is seen in one mating type but not the other
     84  * e.g. FYPO:0000821 occurs_in(CL:0002675)
     85 * is_bearer_of - rarely used, and a terrible kludge; use with colony pigmentation phenotypes to capture the colour
     86  * e.g. FYPO:0000741 is_bearer_of(PATO:0000322), where PATO:0000322 is "red"
    4087
    41 These are in an [https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/supplemental_files/fypo_extension_relations.obo OBO file in svn].
     88== Additional notes ==
     89 * The [http://curation.pombase.org/pombe/docs/fypo_annotation Canto documentation on phenotype curation] has more information and examples.
     90 * Canto changes to capture phenotypes of double/triple mutants are in the testing phase now. In the meantime, we're alleles, phenotypes, etc. on the wiki or in files. Note: If the phenotype is "synthetic lethal" this is explicit in the BioGRID evidence code and can be inferred later from the interaction evidence, but we'll still need to make a note of the alleles.