| 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. |
| 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 == |
| | 46 | == Annotation extensions == |
| | 47 | Phenotype 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 | |
| 39 | | === Relations used in S. pombe FYPO annotations === |
| | 76 | === FYPO annotation extension relations === |
| | 77 | These 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" |
