Changes between Version 6 and Version 7 of xQTLUserReview


Ignore:
Timestamp:
2011-11-26T23:56:41+01:00 (13 years ago)
Author:
jvelde
Comment:

--

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  • xQTLUserReview

    v6 v7  
     1== Datamodel enhancements for Panacea ==
     2
     3Genes [List] '''-> xQTL entity: Gene'''[[BR]]
     4Contains all the identified genes in a certain Wormbase release. It is a list with the main identifier the Wormbase ID (WBgene00000001). Furthermore it will contain the sequence name, common name, splice variants, start position, end position and (in a later version) can include information like intron, exon and promotor position.
     5
     6|| Needed field || Example value || xQTL field ||
     7|| Wormbase ID || WBgene00000912 || name ||
     8|| Common name || daf-16 || description ||
     9|| Sequence name || R13H8.1 || alias ||
     10|| Splice variant || R13H8.1a || symbol ||
     11|| Chromosome || I || chromosome_name ||
     12|| Start Position || 10750332 || bpstart ||
     13|| End Position || 10776689 || bpend ||
     14
     15Platforms [List] '''-> xQTL entity: !OntologyTerm'''[[BR]]
     16List with a micro-array platform identifier and a description about the micro-array platform
     17
     18|| Needed field || Example value || xQTL field ||
     19|| PlatformID || WUR_Agilent || name ||
     20|| Info || 4*44K array || description ||
     21
     22Platform info [List] '''-> xQTL entity: Probe'''[[BR]]
     23This is a list per micro-array platform that contains all the info about the spots on the micro array. Spot ID, Gene ID, splice variant, probe sequence, probe position on the genome, etc.
     24
     25|| Needed field || Example value || xQTL field ||
     26|| Spot ID || WUR_AGI_00001 || name ||
     27|| Wormbase ID || WBgene00000912 || description ||
     28|| Splice variant || R13H8.1a || symbol ||
     29|| Probe sequence || ### || seq ||
     30|| Probe Chromosome || I || chromosome_name ||
     31|| Probe position || ### || bpstart ||
     32|| Unambiguous || ### || mismatch ||
     33
     34Samples [List] '''-> xQTL entity: Sample'''[[BR]]
     35List of samples. Sample ID, genotype, experiment
     36
     37|| Needed field || Example value || xQTL field ||
     38|| Sample ID || Sample000001 || name ||
     39|| Genotype || WN001 || ??? ||
     40|| Experiment || TEMP16_EXP || ??? ||
     41|| Remarks || ### || description ||
     42
     43Experiments [List] '''-> xQTL entity: ???'''[[BR]]
     44List of experiments, Experiment ID, what was measured, conditions, etc…
     45
     46|| Needed field || Example value || xQTL field ||
     47|| Experiment ID || TEMP16_EXP || name ||
     48|| Measured || Gene expression || ??? ||
     49|| Platform || WSU || ??? ||
     50|| Growing temperature || 16 || ??? ||
     51|| Stage || L4 || ??? ||
     52|| Hours || ### || ??? ||
     53|| Treatment || No || ??? ||
     54|| Remarks || ### || description ||
     55
     56Projects [List] '''-> xQTL entity: ???'''[[BR]]
     57List 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.
     58
     59|| Needed field || Example value || xQTL field ||
     60|| Project ID || GROW_TEMP || name ||
     61|| Experiment ID || TEMP16_EXP || ??? ||
     62|| Publications || Li etal 2006 || ??? ||
     63|| Remarks || ### || description ||
     64
     65Datasets [List] '''-> xQTL entity: Data'''[[BR]]
     66List of datasets. Contains information like, belongs to experiment, normalization, mapping models etc.
     67
     68|| Needed field || Example value || xQTL field ||
     69|| Dataset ID || DATA_TEMP16 || name ||
     70|| Type || Gene expression || ontologyreference_name ||
     71|| Unit || Log 2 intensities || ??? ||
     72|| Processed || Normalized || ??? ||
     73|| Experiment ID || TEMP16_EXP || investigation?? ||
     74|| Remarks || ### || description ||
     75
     76Polymorphisms [List] '''-> xQTL entity: ???'''[[BR]]
     77List 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.   
     78
     79|| Needed field || Example value || xQTL field ||
     80|| SNP ID || SNP_a000001 || name ||
     81|| Chromosome || I || chromosome_name ||
     82|| Status || Confirmed || ??? ||
     83|| Position || 2312245 || ??? ||
     84|| Reference || A || ??? ||
     85|| A || N2 || ??? ||
     86|| T ||  || ??? ||
     87|| C || CB4856 || ??? ||
     88|| G ||  || ??? ||
     89|| Remarks || description || ??? ||
     90
     91Markers [List] '''-> xQTL entity: Marker'''[[BR]]
     92List of marker IDs. Should contain the position and type, etc.
     93
     94|| Needed field || Example value || xQTL field ||
     95|| Marker ID || Marker_00001 || name ||
     96|| Other Name || pkI067 || symbol ||
     97|| Type || PCR || ontologyreference_name ||
     98|| Chromosome || I || chromosome_name ||
     99|| Position || 2312245 || bpstart ||
     100|| SNP ID || SNP_a000001 || ??? ||
     101|| Remarks || ### || description ||
     102
     103Mapping populations [List] '''-> xQTL entity: ???'''[[BR]]
     104List of available mapping populations and their description. Many more mapping population will become available in the near future. Some are already developed and genotyped.
     105
     106|| Needed field || Example value || xQTL field ||
     107|| Population ID || Pop_001 || name ||
     108|| Parental strains || N2, CB4856 || strain_name ||
     109|| Type || RIL || ontologyreference_name ||
     110|| Number of Genotypes || 200 || ??? ||
     111|| Publication || ### || ??? ||
     112|| Remarks || ### || description ||
     113
     114Strains [List] '''-> xQTL entity: Strain'''[[BR]]
     115List of wild-type strains and their description. Isolation site, etc
     116
     117|| Needed field || Example value || xQTL field ||
     118|| Strain_ID || N2 || name ||
     119|| Isolation site || Bristol || ??? ||
     120|| Description || ### || description ||
     121|| Sequenced || ### || ??? ||
     122
     123
     124
    1125== Report builder feedback 18 nov 2011 ==
    2126Yang: