Changes between Version 17 and Version 18 of xQTLUserReview


Ignore:
Timestamp:
2011-12-01T10:52:34+01:00 (13 years ago)
Author:
jvelde
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • xQTLUserReview

    v17 v18  
    2424|| Needed field || Example value || xQTL field ||
    2525|| Wormbase ID || WBgene00000912 || name ||
    26 || Common name || daf-16 || alternativeIdentifiers ||
    27 || Sequence name || R13H8.1 || alternativeIdentifiers ||
    28 || Splice variant || R13H8.1a || Transcript.gene(xref->Gene) ||
     26|| Common name || daf-16 || Use: 'Alternative identifiers', MREF to 'AlternateId' table (NEW) ||
     27|| Sequence name || R13H8.1 || Use: 'Alternative identifiers', MREF to 'AlternateId' table (NEW) ||
     28|| Splice variant || R13H8.1a || Use: XREF in 'Transcript' table pointing to 'Gene' (NEW) ||
    2929|| Chromosome || I || chromosome_name ||
    3030|| Start Position || 10750332 || bpstart ||
    … …  
    4343|| Needed field || Example value || xQTL field ||
    4444|| Spot ID || WUR_AGI_00001 || name ||
    45 || Wormbase ID || WBgene00000912 || gene(xref->Gene) ||
    46 || Splice variant || R13H8.1a || transcript(xref->Transcript) ||
     45|| Wormbase ID || WBgene00000912 || Use: 'ReportsFor' XREF pointing to a 'Gene' (NEW) ||
     46|| Splice variant || R13H8.1a || Use: the existing 'Transcript' to 'Gene' XREF ||
    4747|| Probe sequence ||  || seq ||
    4848|| Probe Chromosome || I || chromosome_name ||
    … …  
    5252Samples [List] '''-> xQTL entity: Sample'''[[BR]]
    5353List of samples. Sample ID, genotype, experiment.
    54 Sample properties == genotype matrix OF phenotype matrix
     54Sample properties == genotype matrix OR phenotype matrix
    5555
    5656|| Needed field || Example value || xQTL field ||
    5757|| Sample ID || Sample000001 || name ||
    58 || Genotype || WN001 || via Data (Measurement(name=Genotype), ObservedValue(value=WN001, feature=Genotype, target=Sample000001))||
    59 || Experiment || TEMP16_EXP || via Data ||
     58|| Genotype || WN001 || Use: a 'Data' matrix of Sample x DerivedTrait instead. For example: Measurement(name=Genotype), ObservedValue(value=WN001, feature=Genotype, target=Sample000001))||
     59|| Experiment || TEMP16_EXP || Use: a 'Data' matrix, this is the name of the matrix. ||
    6060|| Remarks ||  || description ||
    6161
    … …  
    6666
    6767|| Needed field || Example value || xQTL field ||
    68 || Experiment ID || TEMP16_EXP || name of ProtocolApplication/Data ||
    69 || Measured || Gene expression || tag of data set ||
    70 || Platform || WSU || phenotype of each sample in the set ||
    71 || Growing temperature || 16 || phenotype of each sample in the set ||
    72 || Stage || L4 || phenotype of each sample in the set ||
    73 || Hours ||  || phenotype of each sample in the set ||
    74 || Treatment || No || phenotype of each sample in the set ||
    75 || Remarks ||  || description of ProtocolApplication/Data ||
    76 
    77 Projects [List] '''-> xQTL entity: ???'''[[BR]]
     68|| Experiment ID || TEMP16_EXP || Use: Name of a 'Data' matrix (= 'ProtocolApplication') ||
     69|| Measured || Gene expression || Use: Tags of a 'Data' matrix (= 'ProtocolApplication') ||
     70|| Platform || WSU || Use: matrix data, phenotype of each sample in the set ||
     71|| Growing temperature || 16 || Use: matrix data, phenotype of each sample in the set ||
     72|| Stage || L4 || Use: matrix data, phenotype of each sample in the set ||
     73|| Hours ||  || Use: matrix data, phenotype of each sample in the set ||
     74|| Treatment || No || Use: matrix data, phenotype of each sample in the set ||
     75|| Remarks ||  || Use: Description of a 'Data' matrix (= 'ProtocolApplication') ||
     76
     77Projects [List] '''-> xQTL entity: OntologyTerm'''[[BR]]
    7878List to link experiments together, because multiple experiments under different conditions can belong to one project. Might also be a way to give access to the different groups of data.
    7979
    … …  
    8888
    8989|| Needed field || Example value || xQTL field ||
    90 || Project ID || GROW_TEMP || use Data.ontologyReference ||
    91 || Experiment ID || TEMP16_EXP || use Data.ontologyReference ||
    92 || Publications || Li etal 2006 || ??? TODO ||
    93 || Remarks ||  || description ||
     90|| Project ID || GROW_TEMP || Use: Tags of a 'Data' matrix (= 'ProtocolApplication') ||
     91|| Experiment ID || TEMP16_EXP || Use: Tags of a 'Data' matrix (= 'ProtocolApplication') ||
     92|| Publications || Li etal 2006 ||Use: 'Publication' table ||
     93|| Remarks ||  || Use: Description of the 'tag' used (OntologyTerm) for Project/Experiment ||
    9494
    9595Datasets [List] '''-> xQTL entity: Data'''[[BR]]
    … …  
    9797
    9898|| Needed field || Example value || xQTL field ||
    99 || Dataset ID || DATA_TEMP16 || name ||
    100 || Type || Gene expression || ontologyreference_name ||
    101 || Unit || Log 2 intensities || tag ||
    102 || Processed || Normalized || tag ||
    103 || Experiment ID || TEMP16_EXP || tag ||
    104 || Remarks ||  || description ||
    105 
    106 Polymorphisms [List] '''-> xQTL entity: ???'''[[BR]]
     99|| Dataset ID || DATA_TEMP16 || Use: Name field ||
     100|| Type || Gene expression || Use: Tags field ||
     101|| Unit || Log 2 intensities || Use: Tags field ||
     102|| Processed || Normalized || Use: Tags field ||
     103|| Experiment ID || TEMP16_EXP || Use: Tags field ||
     104|| Remarks ||  || Use: Description field ||
     105
     106Polymorphisms [List] '''-> xQTL entity: SNP (NEW)'''[[BR]]
    107107List of polymorphisms, probably only SNPs first, although up to 500 deleted genes are known between CB and N2. The position and base pair change, probable AA change and gene features like intron, exon, promotor etc. can be included. More-over it should indicate which parental strains/wild isolates contain which basepair at the SNP position. Sequences of a dozen wild-isolates will become available in 2012.   
    108108
    109109|| Needed field || Example value || xQTL field ||
    110 || SNP ID || SNP_a000001 || name ||
    111 || Chromosome || I || chromosome_name ||
    112 || Status || Confirmed || ??? ||
    113 || Position || 2312245 || ??? ||
    114 || Reference || A || ??? ||
    115 || A || N2 || ??? ||
    116 || T ||  || ??? ||
    117 || C || CB4856 || ??? ||
    118 || G ||  || ??? ||
    119 || Remarks ||  || description ||
     110|| SNP ID || SNP_a000001 || Use: Name field ||
     111|| Chromosome || I || Use: Chromosome_name field ||
     112|| Status || Confirmed || Use: Status field ||
     113|| Position || 2312245 || bpstart ||
     114|| Reference || A || Use: MREF of 'SNP' to 'Polymorphism' (NEW) ||
     115|| A || N2 || Use: MREF of 'SNP' to 'Polymorphism' (NEW) ||
     116|| T ||  || Use: MREF of 'SNP' to 'Polymorphism' (NEW) ||
     117|| C || CB4856 || Use: MREF of 'SNP' to 'Polymorphism' (NEW) ||
     118|| G ||  || Use: MREF of 'SNP' to 'Polymorphism' (NEW) ||
     119|| Remarks ||  || Use: Description field ||
    120120
    121121Markers [List] '''-> xQTL entity: Marker'''[[BR]]
    … …  
    128128|| Chromosome || I || chromosome_name ||
    129129|| Position || 2312245 || bpstart ||
    130 || SNP ID || SNP_a000001 || ??? ||
     130|| SNP ID || SNP_a000001 || Use: 'ReportsFor' field (NEW) ||
    131131|| Remarks ||  || description ||
    132132