Creating data sheet template for 'omics data (snapshot 1)

This investigation contains spreadsheet templates and examples for SEEK users to download and use for structuring experimental data. These templates were developed by the SysMO-DB team and the SysMO PALs

DOI: 10.15490/seek.1.investigation.1.1

Created at: 21st Dec 2015 at 17:30

Contents

Creating template for metabolomics data

These templates can be used for a selection of metabolomics data types. There is a MASTER template for general use and adaptation as well as several more specific templates for particular types of experiment (e.g. HPLC), or specific assay types (e.g glucose pulse)

Metabolomics Master 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.

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

Creating Templates for Transcriptomics

Here you will find guidelines for creating MAGE-TAB compliant transcriptomics data files as well as examples and links to online tools and resources.

General Transcriptomics Templates

Some generic examples of transcriptomics templates that conform to the MAGE-TAB specification. These templates were created and modified from templates produced by ArrayExpress and GEO.
These templates are generic and non-specific for any particular array platform.

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

Affy Transcriptomics Templates

Some examples of transcriptomics templates for Affymetrix data that conform to the MAGE-TAB specification. These templates were 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.

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

A example of an RT-PCR Excel template. RT-PCR is Reverse Transcriptase PCR (NOT to be confused with Real Time PCR, which is normally referred to as qPCR)

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 templates will mean easier submission to public databases on publication and greater consistency of data in SEEK.

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

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.

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

NimbleGen Transcriptomics Templates

Some examples of transcriptomics templates for NimbleGen data that conform to the MAGE-TAB specification. These templates were 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 templates will mean easier submission to GEO/ArrayExpress upon publication and greater consistency of data in SEEK for easier searching and comparing.

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

Creating Templates for Proteomics

Here you will find guidelines for creating MIAPE compliant proteomics data files as well as examples and links to online tools and resources

Proteomics Templates (Mass spectrometry)

Some examples of proteomics templates for Mass Spectrometry data that conform to the MIAPE specification

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 Template (gel electrophoresis)

Examples of proteomics templates for gele electrophoresis data that conform to the MIAPE-GE specification

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
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Citation
Krebs, O. (2015). Creating data sheet template for 'omics data. SEEK. http://doi.org/10.15490/seek.1.investigation.1.1
Snapshots
Snapshot 2 (22nd Dec 2015)
Snapshot 1 (21st Dec 2015) DOI
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