<Tomasz> Erik, how do you define Mapped Data?

<mscottm> https://groups.google.com/forum/?fromgroups=#!topic/expressionrdf/j5I8Tqwr3Dc

<mscottm> https://docs.google.com/drawings/d/1ZFA72YBEcc6BQp31GsAJI1L6WK0mPuNltIkpp8WMcSk/edit

<mscottm> https://docs.google.com/drawings/d/1ZFA72YBEcc6BQp31GsAJI1L6WK0mPuNltIkpp8WMcSk/edit

michel, do you have an SVG of this image?

<michel> Basic idea is that experiments are composed of a number of steps (e.g. sample preparation, bioassay, data processing) each of which have inputs and outputs

i'd like to play with it a bit to change the direction and label of the has_input arcs so you can visually see a data flow

<michel> you can save it as svg

<James> in general output is used to model processes and things they produce

<James> has_output that is

authoritative version is google?

<James> what type of thing is experiment michel?

<mscottm> SIO diagram (refines last one) https://docs.google.com/drawings/d/1pn86hwXfF87oz2tQr2r5pb95CB_Q-kmCMe2AGs3dxHw/edit

<michel> james -> an experimetn is a process

<James> ok tnx

<jupp> http://wwwdev.ebi.ac.uk/fgpt/efosemweb.html

<James> so every gene list is generared using pairwise comparisons

<jupp> http://www.ebi.ac.uk/gxa/experiment/E-GEOD-1659

<James> the other thing to say is that this will change with the new stats for atlas

michel, what's the relationship between "has input" and "is source of" (latter connecting "test sample" and "gene expression value" to "test-control differential gene expression value"

)

<michel> 'has input' is between a process and an object

ahh, it runs through "gene expression value", but the the actual terminus is the "control sample"

<michel> 'is source of' is between an object to another object

<James> i'd agree michel - we're sold on the pattern

created a multi-color version of michel's figure: https://docs.google.com/drawings/d/1xIvQzFPWYbioqs-k9-u8veP7zmW1_b6RRFE1FMbKS1Q/edit

in an effort to track the flow of material and data, i reversed some arrows and changed their labels: s/has input/input for/ and s/is derived from/material for/

of course, this favors user comprehension over accurately conveying the ontology

<mscottm> https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C&authkey=CK-y8Y8C#

<mscottm> expression RDF note draft: https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C&authkey=CK-y8Y8C#

michael, it's left as an exercise for the reader

like fermat's last theorum

michel, (noting that you are viewing the image i created) should the material channel (the blue at the bottom) be a different color from the process channel?

like maybe blood red?

<James> sorry i have to run as have call at 5

<mscottm> [michel, all]Discussion of cleaning up tables of key concepts and their mappings.

<mscottm> michel: <proposes new demo that employs OWL mappings analog of SWObjects>

<mscottm> Scott: wary of adding new items before shipping the note

<mscottm> Eric: You can always version it.

<mscottm> Scott: Would prefer to version it. Time is right to publish what we've discussed. But maybe it's possible to put the demo together by the time the rest of the doc is ready.

<mscottm> Michel: What will the note look like?

<mscottm> Scott: The way it does now + rewrite + some of the GXA specifics that have recently been settled.

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