University of Manchester

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Oct 2, 2013 (3 years and 10 months ago)

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NERC Environmental

Bioinformatics Centre

Loading annotated spreadsheets into maxdLoad2

NERC Environmental

Bioinformatics Centre


The maxdLoad2 database

Browse

Edit

Load

NERC Environmental

Bioinformatics Centre

Worksheets with experiment data in maxdLoad2 format

NERC Environmental

Bioinformatics Centre

Spreadsheet overview

NERC Environmental

Bioinformatics Centre

Comment boxes are available on
each worksheet to display help text

maxdLoad2
attribute name

Field Data Requirement
describes the format of
the data and if it is a
compulsory field within
maxdLoad2

Name of table
within maxdLoad2

The number with dollar
prefix is used to match the
data to the table fields
within maxdLoad2

Worksheet layout

NERC Environmental

Bioinformatics Centre

Using “presets” to load spreadsheets into maxdLoad2

Data can be entered into
maxdLoad2 by one of two
methods .




Entering data directly into


the database using the


“Create” option.




Loading data from a text


file or Excel spreadsheet


using the “Load” option.



NERC Environmental

Bioinformatics Centre

The Load option allows data from
worksheets and text files to be entered
in a batch format.


The preset file adds a dollar prefixed
number into each attribute field of the
maxdLoad2 table that corresponds to
a column of data in the worksheet.

NERC Environmental

Bioinformatics Centre

A single worksheet can
be selected from a
spreadsheet and loaded
into the database.

The data from the worksheet can be previewed prior
to upload to ensure the data is correct.

NERC Environmental

Bioinformatics Centre

After loading the
worksheet, the
data can be viewed
using the Browse
function.


In this example,
only the Name and
Title have been
loaded from the
worksheet.

Browsing the loaded data

NERC Environmental

Bioinformatics Centre

We recommend
that the data
tables are
loaded in the
following
order:
-

Sample

Treated Sample

Extract

Labelled Extract

Array

Order of loading

Source

Sampling Protocol

Treatment Protocol

Extraction Protocol

Labelling Protocol

Hybridisation Protocol

Scanning Protocol

Image Analysis Protocol


Hybridisation

Image

Measurement

Submitter

Experiment

NERC Environmental

Bioinformatics Centre



Fast to annotate experiments




Annotate to MIAME or MIAME/Env standards




Simple auto
-
naming generation of samples (making the


experiment and relationships of samples easy to follow)




Incorporates data fields for lab
-
specific id's




Easy to up
-
load into maxdLoad2




Easy to customize

Benefits of using the spreadsheet

NERC Environmental

Bioinformatics Centre

NEBC Oxford

Dawn Field

Bela Tiwari

Tim Booth

Stewart Houten

Ashley Morley


NEBC Manchester

Andy Brass

Dave Hancock

Norman Morrison

University of Cardiff

Pete Kille


University of Manchester

Kevin Garwood

Giles Velarde