Creating data sheet template for 'omics data

Metabolomics Master Excel Template

This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.

• MASTER_exampleBlank2.xls

Transcriptomics Template (ArrayExpress Format)

An example template for MAGE-TAB compliant transcriptomics data. This example only covers the Investigation Description Format (IDF) and the Sample and Data Relationship Format (SDRF) worksheets (i.e. the metadata from a microarray experiment).
This template was generated automatically using the ArrayExpress submission help tool (http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi)

• microarray_example_newformat.xls

Transcriptomics Template Guidelines

An overview of creating MAGE-TAB compliant spreadsheets for transcriptomics data in SysMO SEEK

• TranscriptomicsGuidelines.doc

3' or Whole Gene Expression Array Template (Affymetrix)

This Excel template is for use with affy transcriptomics data in Matrix table format. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.

• GA_affy_SEEKJERM.xls

Chip-chip Array Template (Affymetrix)

This Excel template is for use with affy Chip-chip data where the results of the primary analysis are reported in BAR and BED files. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.

• GA_affy_genomic_BAR_SEEKJERM.xls

Transcriptomics Template Guidelines

An overview of creating MAGE-TAB compliant spreadsheets for transcriptomics data in SysMO SEEK

• TranscriptomicsGuidelines.doc

RT-PCR Excel Template

An example of a JERM-compliant template for RT-PCR data

This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.

• GA_RT-PCR_SEEKJERM.xls

Transcriptomics Template Guidelines

An overview of creating MAGE-TAB compliant spreadsheets for transcriptomics data in SysMO SEEK

• TranscriptomicsGuidelines.doc

Chip-chip Excel template example

This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model).
Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.

• GA_ChIP_chip_w_platf_SEEKJERM.xls

Transcriptomics Template Guidelines

An overview of creating MAGE-TAB compliant spreadsheets for transcriptomics data in SysMO SEEK

• TranscriptomicsGuidelines.doc

Transcriptomics Gene Expression Excel Template (NimbleGen)

This template is for recording gene expression data from the NimbleGen platform.
This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.
Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

• GA_NG_genex_plat_SEEKJERM.xls

Genomic Data Submission Excel Template (NimbleGen)

This template is for recording genome data from the NimbleGen platform.
This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.
Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

• GA_NG_genomic_plat_SEEKJERM.xls

Proteomics Template from PRIDE

An example of a completed data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of a MIAPE compliant data format taken from the PRIDE website (http://www.ebi.ac.uk/pride).

• PRIDE_template_example.xls

Proteomics Template (empty) from PRIDE

An example of a blank data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of MIAPE compliant data.

The shreadsheet contains macros to help you annotate your data with terms from controlled vocabularies and ontologies

• PRIDE_template_empty.xls

Proteomics Mass Spec Template (SysMO JERM)

This is an Excel template for Mass Spec data that contains all the necessary MIAPE metadata fields. It was derived from examples on the PRIDE website (PRoteomics IDEntifications database http://www.ebi.ac.uk/pride/)

• JERM_priderf_SEEKJERM.xls

Proteomics Gel Electrophoresis Excel Template

This template is a JERM compliant spreadsheet for use with gel electrophoresis data. It is in the style of the JERM MASTER template with worksheets for metadata, organism_sample, instrument and data. To conform to MIAPE-GE all worksheets are mandatory.
A detailed description of MIAPE-GE is available from http://www.psidev.info/miape/MIAPE_GE_1_4.pdf

• JERM_2DGel_SEEKJERM.xls

Template for proteomics (2D gel)

MIAPE based Gel Electrophoresis Data Entry Worksheet

• Exampledata_PROTEOMICS (1).xls