<michael> will call in soon

<mscottm2> Michel: Bio2RDF (not BioRDF) is looking at github to share esp. RDF conversion source code

<mscottm2> Scott: Sounds like an important move to provide provenance for RDF and repeatability.

<mscottm2> Scott: Do you have an approach to versioning of scripts yet?

<mscottm2> Michel: Not yet, but that's in the cards.

https://github.com/bio2rdf/bio2rdf-scripts

scott: note - results of expression studies (microarray/NGS) from arrayexpress/GEO - give them examples to follow; reassurance of a good RDF representation
... last paper talks about multiple representations;
... objective 2 - how to make use of the representation; jason etchelman (sp?) python script mageml to rdf; jim mccusker r-script tool to generate rdf with provenance

<egombocz> Jason Eshleman will porvide script code

scott: note is not quite ready; eric suggests we put it out as a draft over the next 2 months; time to work comments into the document

michael: generate a todo list;

scott: semantic gap - be nice to have a nice OWL representation, beyond the RDF representation

<egombocz> I think he also was suggestiing this to be able to merge nicely with NCBO's ontologies (or parts thereof)

<egombocz> Maybe he could put a short note about what he said in the chat box here

scott: for linked data - basic information retrieval with sparql - differentially expressed genes with pathways, drug compounds, snps, diseases, etc
... how do we fit an OWL representation into this?
... with stronger semantics in OWL, we can make very clear the semantics from MAGE-OM

michael: MAGE-tab to MAGE-RDF would be complete (?)

scott: add item to to-do list

<mscottm2> https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C&hl=en_US&authkey=CK-y8Y8C

<egombocz> 415-740-9416 is egombocz

<michael> sorry about the communication gap, i'm traveling. scott got my points across well.

<Lena> per eric's request

<ericP> http://www.ebi.ac.uk/~tomasz/pub/rdf_graph.png

<mscottm2> Scott: Ideally, IO Informatics would be able to use our W3C note to produce the 'consensus version' of RDF that it suggests

<michael> eric, what's the link?

<ericP> http://www.ebi.ac.uk/~tomasz/pub/rdf_graph.png

<mscottm2> Erich: I will talk about this with Jason tomorrow.

<ericP> www.ebi.ac.uk/~tomasz/pub/rdf_graph.png

<mscottm2> Eric: Maybe just a small group could talk about this in a teleconference. Jason and perhaps someone who understands the HCLS ontologies better than I do.

<Lena> https://www.dropbox.com/home/bioRDF%40HCLS?select=JBI-11-222R1.pdf

<Lena> https://dl-web.dropbox.com/get/bioRDF%40HCLS/JBI-11-222R1.pdf?w=5833e759&dl=1

<ericP> Lena: in table 1, we prefer GXA terms over blood genomics terms

<Lena> in table 1 also, when there are no GXA terms (empty cells), we use blood genomics terms

<mscottm2> Because today is MLK day in the U.S.: A petition to save his old church from foreclosure: http://act.rebuildthedream.com/sign/is-nothing-sacred?source=FBS

<mscottm2> MLK's famous Vietnam speech: http://www.youtube.com/watch?v=b80Bsw0UG-U

<egombocz> egombocz@io-informatics.com

<michael> by all!

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