OMERO.editor Where next

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OMERO.editorWhere next?

• (After Beta3)

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Goal of Editor? (1)

• To record a complete description of the
  experiment. Like a lab notebook that someone else
  can understand! (Not just the protocol
  description)?

Fix and Stain Cells Prepare formaldehyde by
dissolving 1.85g powder in 10mls PBS. Warm in
fume cupboard till solution is clear. Filter
through 0.2uM filter. This is 37 solution
Lab note-book
Word documents, Spreadsheets etc
Web sites http//lamondlab.com/f7immunostainprotoc
ol.htm
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Goal of Editor? (2)

• To make a nice UI for viewing protocols (text /
  tables etc) within insight?

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Goal of Editor? (3)

• To develop a data-model for an experiment or at
  least a format for recording an experiment?

• Eg usefulchem(wiki)
• Experiment
• Objective
• Procedure
• Results
• Discussion
• Conclusion

e.g. MAGE-TAB
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Goal of Editor? (4)

• To be an electronic lab notebook? (The experiment
  is the home, link to the data)

UsefulChem http//usefulchem.wikispaces.com/ Chem
Tools http//chemtools.chem.soton.ac.uk/projects/b
log/ eCAT http//www.axiope.com
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What Editor does now(Should it continue to do
these?)

• Separates Experimental variables from Protocol
  description
• Clear fields, load defaults etc.
• Easy to view the important metadata
• Hierarchy
• Simple data types (Text, number, table, date,
  time, link, image, Ontology term, checkbox,
  drop-down menu)

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Problems

• Protocols and Experiments in Editor dont look
  like biologists expect Experimental variables
  not in context.
• Editor files not nicely displayed by other
  software.
• Editor files not understood by other software.

Which of these should I aim to solve? Solving any
of these requires a change in OMERO.editor file
format
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File Format Options?

• MAGE-TAB
• Protocols with parameters
• Software can understand format (although
  protocols are free-text)
• Easy to edit in other software (Excel)
• Other reasons for using Tabs are not applicable
  to OMERO.editor
• MAGE-TAB document consists of several TAB files
  1 for protocols, the others describe microarray
  set-up and workflow.
• Wiki / semantic wiki
• Semantic wiki is an overkill?
• Could use markup to identify parameters.
• Save as html / database?

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File Format Options?

• XML
• This is current format.
• Can include other XML with no changes.
• Difficult to read without OMERO.editor
• Reading imported XML is dependent on the format
  of the XML. Some easy (eg OME-XML), most are much
  harder (eg GelML, MAGE-ML etc).

GelML in OMERO.editor
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File Format Options?

• XHTML
• All the advantages of XML, but can be displayed
  by any browser.
• Can place parameters in context within text.
• Supports tables, hierarchy etc.

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Mapping MAGE-TAB to editor/XML
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