Changes between Version 47 and Version 48 of PhenotypeImportExportFormats


Ignore:
Timestamp:
Sep 9, 2013, 3:24:03 PM (7 years ago)
Author:
gomidori
Comment:

--

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  • PhenotypeImportExportFormats

    v47 v48  
    1313==== User submissions - single file ====
    1414|| ||'''Contents'''||'''Example'''||'''Cardinality'''||
    15 ||1||Gene systematic ID||SPBC11B10.09||1,>1 See ^3||
     15||1||Gene systematic ID||SPBC11B10.09||1,>1 (See ^1)||
    1616||2||FYPO ID||FYPO:0000000||1||
    17 ||3||Allele description||G146D See ^4||1,>1 See ^3||
    18 ||4||Genotype name/description||h- ura4-D18 leu1-32 See ^1||0,1||
    19 ||5||Strain background||972 h- See ^2||1||
    20 ||6||Gene name||cdc2||0,1,>1 See ^3||
    21 ||7||Allele name|| cdc2-1w||0,1,>1 See ^3||
    22 ||8||Allele synonym||cdc2-1W See ^5||0,1,>1||
    23 ||9||Allele type|| amino acid substitution|| ?||
    24 ||10||Evidence||ECO:0000000 See ^6||1||
    25 ||11||Condition||PECO:0000004 See ^7||1,>1||
    26 ||12||Penetrance|| %, range%, or small CV ('high', 'medium', or 'low')||0,1||
    27 ||13||Expressivity|| integer + units, allowing ranges, or small CV ('high' (synonym: strong), 'medium', or 'low' (synonym: weak))||0,1||
    28 ||14||Extension||annotation_extension=assayed_using(PomBase:SPBC582.03)||0,1,>1||
    29 ||15||Reference||1||
    30 ||16||taxon||1||
    31 ||17||Date||20120101||1||
     17||3||Allele description||G146D (See ^2)||1,>1 (See ^1)||
     18||4||Expression||endogenous (See ^3)||1,>1 See ^1||
     19||5||Parental strain||972 h- (See ^4)||1||
     20||6||Strain name (background)||SP286 (See ^5)||0,1||
     21||7||Genotype description||h- ura4-D18 leu1-32 ade6-M210 (See ^6)||0,1||
     22||8||Gene name||cdc2||0,1,>1 (See ^7)||
     23||9||Allele name|| cdc2-1w||0,1,>1 (See ^7)||
     24||10||Allele synonym||cdc2-1W (See ^1)||0,1,>1||
     25||11||Allele type|| amino acid substitution||1 (See ^8)||
     26||12||Evidence||ECO:0000000 (See ^9)||1||
     27||13||Condition||PECO:0000004 (See ^10)||1,>1||
     28||14||Penetrance|| %, range%, or small CV ('high', 'medium', or 'low', or corresponding FYPO_EXT ID)||0,1||
     29||15||Expressivity|| integer + units, allowing ranges, or small CV ('high' (synonym: strong), 'medium', or 'low' (synonym: weak), or corresponding FYPO_EXT ID)||0,1||
     30||16||Extension||annotation_extension=assayed_using(PomBase:SPBC582.03)||0,1,>1||
     31||17||Reference||PMID:23697806||1||
     32||18||taxon||4896||1||
     33||19||Date||20120101||1||
    3234
    3335==== Internal use and output -- separate entity and annotation files ====
     
    3739||'''Contents'''||'''Example'''||'''Cardinality'''||
    3840||Database||!PomBase||1||
    39 ||Allele systematic ID||SPBC11B10.09-01 See ^8||1||
    40 ||Allele name||cdc2-1w||0,1||
    41 ||Allele synonym||cdc2-1W See ^5||0,1,>1||
     41||Allele systematic ID||SPBC11B10.09-01||1||
     42||Allele name||cdc2-1w (See ^7)||0,1||
     43||Allele synonym||cdc2-1W||0,1||
    4244||Allele description||G146D||1||
    4345||Gene systematic ID||SPBC11B10.09||1||
     
    5052||Database||!PomBase||1||
    5153||Genotype ID||123456||1||
    52 ||Genotype name/description||h- ura4-D18 leu1-32 See ^1||1||
    53 ||Allele systematic ID||SPBC11B10.09-01 See ^4||1,>1||
     54||Genotype name/description||h- ura4-D18 leu1-32 (See ^7)||1||
     55||Allele systematic ID||SPBC11B10.09-01 (See ^11)||1,>1||
    5456||Strain background||972 h- (OR strain ID, if we house them in the db)||1||
    5557
     
    7173||Database||!PomBase||1||
    7274||Genotype ID||123456||1||
    73 ||FYPO ID||FYPO:0000000||1||Yes||
    74 ||Evidence||ECO:0000000 See ^7||1||Yes||
     75||Expression||endogenous (See ^3) Also see Outstanding Issues||1||
     76||FYPO ID||FYPO:0000000||1||
     77||Evidence||ECO:0000000 (See ^9)||1||
    7578||Reference||PMID:3502942||1||
    76 ||Condition|| at high temperature See ^8||0,1||No||
    77 ||Penetrance|| %, range%, or small CV ('high', 'medium', or 'low')||0,1||No||
    78 ||Expressivity|| integer + units, allowing ranges, or small CV ('high' (synonym: strong), 'medium', or 'low' (synonym: weak))||0,1||No||
    79 ||Extension||occurs_in(CL:0002674)||0,1,>1||
    80 ||Date||20120101||1||Yes||
     79||Condition|| at high temperature See ^10||0,1||
     80||Penetrance|| Penetrance|| %, range%, or small CV ('high', 'medium', or 'low', or corresponding FYPO_EXT ID)||0,1||
     81||Expressivity||integer + units, allowing ranges, or small CV ('high' (synonym: strong), 'medium', or 'low' (synonym: weak), or corresponding FYPO_EXT ID)||0,1||
     82||Extension||annotation_extension=assayed_using(PomBase:SPBC582.03)||0,1,>1||
     83||Date||20120101||1||
    8184
    8285==== Table footnotes: ====
    8386
    84 1. Derived from background strain plus allele designation (allele name if available; otherwise allele systematic ID)
     871. Cardinality is one for single genes, >1 for multiple genes (double mutants, triple mutants, etc.). Also see Outstanding Issues.
    8588
    86 2. In a substantial majority of cases, the background will be 972 h-, so these will be the defaults in the curation tool. Users will be able to change h- to h90 or h+ upon entering allele details, and can contact curators if they have anything non-standard. Status as at 2012-01-25 curator meeting: After discussing options -- e.g. gathering selectable marker or other background details --  we have decided to use the defaults noted above, and try to capture "nutritional" or other marker alleles only when they are "of interest" in an experiment (e.g. when having particular markers present makes a difference to a phenotype, or when a phenotype is only relevant in one mating type). Also see "older notes" below.
     892. May include 'deletion' or residue description (see https://sourceforge.net/apps/trac/pombase/wiki/DescribingResidues); may also have SO ID; see Outstanding Issues.
     90
     913. Allowable values: 'overexpression', 'knockdown', 'endogenous', 'null', 'not specified'. Deletions should always have 'null' expression. (Added in 2013-09-09 update)
     92
     934. This column is for the An entry in this column is mandatory, but "unknown" will be an allowable value, in case submitters don't actually know the background. In a substantial majority of cases, the parental background will be 972 h-, so these will be the defaults in the curation tool. Users will be able to change h- to h90 (968) or h+ (975) upon entering allele details, and can contact curators if they have anything non-standard. Status as at 2012-01-25 curator meeting: After discussing options -- e.g. gathering selectable marker or other background details --  we have decided to use the defaults noted above, and try to capture "nutritional" or other marker alleles only when they are "of interest" in an experiment (e.g. when having particular markers present makes a difference to a phenotype, or when a phenotype is only relevant in one mating type). Also see "older notes" below. Update 2013-09-09: added bit about allowing "unknown"; clarified split between this and new column 3, i.e. that this is for the ancestral lab background, usually 972 h- or the isogenic H+ or h90.
     94
     955. Use this column for a lab's in-house name/ID/designation for the background strain (i.e. the derivative of the parental strain that has selectable marker alleles etc.). (Split from column 2 in 2013-09-09 update)
     96
     976. List of alleles present in the background strain, such as selectable marker alleles (don't include the "allele(s) of interest). If no name is used for an allele in the literature (should be rare for background alleles), can use allele systematic ID in this column.
     98
     997. If no name is used for an allele in the literature, can use allele systematic ID in this column. Cardinality is one for single genes, >1 for multiple genes (double mutants, triple mutants, etc.). Also see Outstanding Issues.
     100
     1018. Supported allele types: 'wild type', 'deletion', 'mutation of single amino acid residue', 'mutation of multiple amino acid residues', 'partial deletion, amino acid', 'partial deletion, nucleotide', 'mutation of a single nucleotide', 'nonsense mutation', 'other', 'unknown'.
     102
     1039. ECO subset (note: waiting for ECO additions)
     104
     10510. Phenotype Experimental Conditions Ontology (PECO) ID(s)
     106
     10711. Derived from gene systematic ID; assigned consecutively
     108
     109++-- old numbering --++
     1101. Names of alleles (as in note 3) present in the background genotype
     111
     1122. An entry in this column is mandatory, but "unknown" will be an allowable value, in case submitters don't actually know the background. In a substantial majority of cases, the parental background will be 972 h-, so these will be the defaults in the curation tool. Users will be able to change h- to h90 (968) or h+ (975) upon entering allele details, and can contact curators if they have anything non-standard. Status as at 2012-01-25 curator meeting: After discussing options -- e.g. gathering selectable marker or other background details --  we have decided to use the defaults noted above, and try to capture "nutritional" or other marker alleles only when they are "of interest" in an experiment (e.g. when having particular markers present makes a difference to a phenotype, or when a phenotype is only relevant in one mating type). Also see "older notes" below.
    87113
    881143. If no name used in literature, can use allele systematic ID in this column. Cardinality is one for single genes, >1 for multiple genes (double mutants, triple mutants, etc.). Also see Outstanding Issues.
    89115
    90 4. May include 'deletion', 'overexpression', or residue description (see https://sourceforge.net/apps/trac/pombase/wiki/DescribingResidues); may also have SO ID; see Outstanding Issues.
     1164. May include 'deletion', or residue description (see https://sourceforge.net/apps/trac/pombase/wiki/DescribingResidues); may also have SO ID; see Outstanding Issues.
    91117
    921185. If the user wants to submit an alternative name for an allele
     
    97123
    981248. Derived from gene systematic ID (assigned consecutively)
     125
     126++-- end old numbering --++
    99127
    100128==== Older notes on strain background ====
     
    110138  * For output, we'll have allele IDs, so what goes in the description column is just for convenience and can be incomplete if necessary
    111139  * For user submissions, what should we collect? Not realistic to expect SO ids ...
     140 * How to handle expression in multiple-file scenario? Have put it with the annotation format for now, but that doesn't really capture which allele(s) the expression refers to. Don't think it belongs in the allele table, though, because expression isn't inherent in allele features (except for complete deletions). Maybe in genotype file somehow? (2013-09-09)
    112141
    113142Additional questions:
     
    125154||1||Database||!PomBase||0,1||1||No||
    126155||2||Genotype ID||123456||0,1||1||No||
    127 ||3||Genotype name/description||972h-,ade10-1 See ^1||0,1||1||No||
    128 ||4||Strain bacground||972 h- See ^2||1||1||Yes||
    129 ||5||Gene systematic ID||SPCPB16A4.03c||1,>1 See ^3||1,>1||Yes||
    130 ||6||Gene name||ade10||0,1,>1 See ^3||1,>1||No||
    131 ||7||Allele systematic ID||SPCPB16A4.03c-01 See ^4||0,1,>1 See ^3||1,>1||No||
    132 ||8||Allele name|| ade10-1||0,1,>1 See ^3||1,>1||No||
    133 ||9||Allele description||deletion See ^5||1,>1 See ^3||1,>1||Yes||
    134 ||10||Allele synonym||ade101 See ^6||0,1,>1||0,1,>1||No||
     156||3||Genotype name/description||972h-,ade10-1||0,1||1||No||
     157||4||Strain background||972 h- See ^4||1||1||Yes||
     158||5||Gene systematic ID||SPCPB16A4.03c||1,>1 See ^1||1,>1||Yes||
     159||6||Gene name||ade10||0,1,>1 See ^7||1,>1||No||
     160||7||Allele systematic ID||SPCPB16A4.03c-01 See ^11||0,1,>1 See ^1||1,>1||No||
     161||8||Allele name|| ade10-1||0,1,>1 See ^7||1,>1||No||
     162||9||Allele description||deletion See ^2||1,>1 See ^1||1,>1||Yes||
     163||10||Allele synonym||ade101 See ^7||0,1,>1||0,1,>1||No||
    135164||11||FYPO ID||FYPO:0000000||1||1||Yes||
    136 ||12||Evidence||ECO:0000000 See ^7||1||1||Yes||
    137 ||13||Condition|| at high temperature See ^8||0,1||0,1||No||
     165||12||Evidence||ECO:0000000 See ^9||1||1||Yes||
     166||13||Condition|| at high temperature See ^10||0,1||0,1||No||
    138167||14||Penetrance|| %, range%, or small CV ('high', 'medium', or 'low')||0,1||0,1||No||
    139168||15||Expressivity|| integer + units, allowing ranges, or small CV ('high' (synonym: strong), 'medium', or 'low' (synonym: weak))||0,1||0,1||No||
    140169||16||Date||20120101||1||1||Yes||
    141170
    142 Note: footnotes same as in tables for newer drafts above
     171Note: footnotes same as in tables for newer drafts above (updated 2013-09-09)
    143172
    144173Note: forgot to include reference in this draft!!