<scribe> scribenick: matthias_samwald

kei: deadline for paper is 27., last week we had an extra meeting, over the weekend i revised introduction and abstract of the article, also added more references.
... i also added acknowledgements.
... jun, maybe you can give us an update?

jun: i had a look at the paper this morning, i did not manage to do work over weekend
... lena said she managed to give example for level 2 and level 3 provenance data
... i looked into MIAME protocols

<jun> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5281

jun: i found one for the second paper
... we can use tool by (?) from RPI which can transform XML into RDF

kei: our focus has been the processed, relevant gene list

<jun> James McCuster

michael: this is based on MAGE-ML, not MAGE-TAB

<mscottm> sorry - technical difficulties

kei: anyways, these data are not containing gene lists in that sense.

<mscottm> joined now

jun: i hope to finish this work by tomorrow and describe it in the google doc.

kei: it is a bit confusing that there are so many ontologies describing diseases
... scott mentioned the disease ontology, which seems to be quite comprehensive

scott: diesease ontology is indeed comprehensive. if we know which ontology is used to described diseases, that helps us to do automated federation
... if you have a purl ID, then you can add statements about the graph to the graph itself.
... lena told us that that she needs help with that approach
... this could also be an example of using provenance for federation

kei: eric and lena worked together on query federation.
... about the VOID data... jun, can you help lena use the VOID vocabulary?
... lena's e-mail said she will be away, i don't know what her availability is during that time.
... we should still aim to submit the paper on 27.

scott: will be moving back to netherlands soon, that might limit my ability to work on the paper.

kei: we need to finalize the decision on which examples and datasets we will show in the paper.

jun: lena shared the SPARQL endpoint, i can identify other examples while she is away.

kei: i think the RDF representation is very close to final
... based on that gene list representation we could come up with some examples

scott: queries could be restricted based on projects and consortiums

jun: maybe scott could write these down (e.g. in the motivation section)

scott: also basic information such as "how many statements are in the graph" etc.

kei: maybe we could have an extra call
... whoever can join an extra call later this week (e.g. wed/thur) would help

scott: i can make it on those days

michael: i can make some comments

jun: maximum number of pages is 6
... maybe we can delete some of the figures if the page number is exceeded
... we can discuss on call later this week
... feel free to cut my text if needed.

__ the group agrees to have another teleconference on thursday 26. __

scott: is all the data in the dropbox?

eric: i believe so.

scott: simon twigger has done some very good work for microarrays, he is part of NCBO, gave presentation at C-SHALS
... close to the work we are doing, but we haven't gotten to the level of exchanging RDF graphs

michael: could you please add this to the discussion section?

scott: i will.

<scribe> Scribe: Matthias Samwald

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