example metadata

Example metadata

The following flat-files describe the metadata input for the exemplar merging pipeline. They are required in order to identify the variable and observations within the input files so that appropriate statistical analysis can be applied. They are also important for the metadata required in the MzQuantML XML export.

Arabidopsis thaliana dataset

[Dataset]
name: Comparison of sodium dodecyl sulfate vs octyl glucoside
[Organisation]
name: SynthSys
address: SynthSys, University of Edinburgh, Waddington Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JD, UK
url: http://www.synthsys.ed.ac.uk
[Organisation]
name: ISMB
address: Institute of Structural and Molecular Biology, University of Edinburgh, Edinburgh, UK
url: http://www.ed.ac.uk/schools-departments/biology/structural-molecular-biology
[Author]
id: JK
fistname: Johanna
surname: Krahmer
email: J.Krahmer@sms.ed.ac.uk
affiliation: SynthSys
affiliation: ISMB
[Experiment]
#.* means everything is part of the same experiment (it matches everything)
pattern: .*
name: SDS vs OG
description: A comparison of sodium dodecyl sulfate vs octyl glucoside
author: JK
[Variable]
#regular expression matches the letters before the final replicate tag see http://www.regexplanet.com/advanced/java/index.html
pattern: _([a-zA-Z0-9]+)_\d$
id: treatment
name: treatment
description: treatment
class: java.lang.String
[Replicates]
# $ is the end of the header and () is the area to match...so this pattern matches everything that is after the _ and before the end of the header
pattern: _(\d+)$
[Headers]
3702_EthylAcetate_OGeth_1
3702_EthylAcetate_OGeth_2
3702_EthylAcetate_OGeth_3
3702_EthylAcetate_OGeth_4
3702_EthylAcetate_OGeth_5
3702_EthylAcetate_SDSeth_1
3702_EthylAcetate_SDSeth_2
3702_EthylAcetate_SDSeth_3
3702_EthylAcetate_SDSeth_4
3702_EthylAcetate_SDSeth_5

Ostreococcus tauri dataset

[Dataset]
name: IC261
[Organisation]
name: SynthSys
address: SynthSys, University of Edinburgh, Waddington Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JD, UK
url: http://www.synthsys.ed.ac.uk
[Organisation]
name: ISMB
address: Institute of Structural and Molecular Biology, University of Edinburgh, Edinburgh, UK
url: http://www.ed.ac.uk/schools-departments/biology/structural-molecular-biology
[Author]
id: TLB
fistname: Thierry
surname: Le Bihan
email: thierry.lebihan@ed.ac.uk
affiliation: SynthSys
affiliation: ISMB
[Author]
id: SFM
fistname: Sarah
initials: F
surname: Martin
email: Sarah.Martin@ed.ac.uk
affiliation: SynthSys
[Author]
id: GVO
fistname: Gerben
initials: 
surname: van Ooijen
email: Gerben.vanOoijen@ed.ac.uk
affiliation: SynthSys
[Experiment]
#.* means everything is part of the same experiment (it matches everything)
pattern: .*
name: IC261
description: IC261
author: GVO, SFM, TLB
[Variable]
#matches the letters before the final replicate tag see http://www.regexplanet.com/advanced/java/index.html
pattern: _([a-zA-Z0-9]+)_\d$
id: treatment
name: treatment
description: treatment
class: java.lang.String
[Replicates]
# $ is the end of the header and () is the area to match...so this pattern matches everything that is after the _ and before the end of the header
pattern: _(\d+)$
[Headers]
120905_o1_04_ph120831_ot_CCAI_3
120905_o1_05_ph120831_ot_CCAI_2
120905_o1_08_ph120831_ot_CCAI_4
120906_o1_02_ph120831_ot_CCAI_5
120906_o1_06_ph120831_ot_CCAI_1
120905_o1_03_ph120831_ot_IC261_5
120905_o1_07_ph120831_ot_IC261_2
120906_o1_03_ph120831_ot_IC261_3
120906_o1_07_ph120831_ot_IC261_4
120906_o1_09_ph120831_ot_IC261_1

Mus musculus dataset

The following metadata describes the experiment by Docherty (2010) and is required for the import of MaxQuant and Progenesis files into the merging workflow.

[Dataset]
name: MusPhospho
[Organisation]
name: SynthSys
address: SynthSys, University of Edinburgh, Waddington Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JD, UK
url: http://www.synthsys.ed.ac.uk
[Organisation]
name: ISMB
address: Institute of Structural and Molecular Biology, University of Edinburgh, Edinburgh, UK
url: http://www.ed.ac.uk/schools-departments/biology/structural-molecular-biology
[Author]
id: TLB
firstname: Thierry
surname: Le Bihan
email: thierry.lebihan@ed.ac.uk
affiliation: SynthSys
affiliation: ISMB
[Experiment]
#the regular expression “.*” means everything is part of the same experiment (it matches everything)
pattern: .*
name: MusPhospho
description: MusPhospho
author: TLB
[Variable]
# the regular expression matches the letters before the final replicate tag see http://www.regexplanet.com/advanced/java/index.html
pattern: _([a-z])\d$
id: slice
name: slice
description: slice
class: java.lang.String
[Replicates]
# $ is the end of the header and “()” is the area to match. This pattern matches everything that is after the _ and before the end of the header
pattern: _[a-z](\d+)$
[Headers]
090319_o1_02_so090213ph_mo_c1
090319_o1_03_so090213ph_mo_c2
090319_o1_04_so090213ph_mo_s1
090319_o1_05_so090213ph_mo_s2