See also: IRC log
<jun> I can scribe
<kei> scribenick lena
<kei> io-informatics.com
sorry... my internet connection was lost
IO informatics is moving towards integration of biomedical data;
mscottm: data sharing in bioinformatics
(sorry... who is talking?)
<mscottm> That was Chuck Raffi (sp?) from IO Informatics
kei: been working on data
integration using rdf/owl to standardize in machine
understandable way
... provennace, data used to describe experiments; how to link
to existing ontologies
<matthias_samwald> lena, you are causing noise while typing.
(thaks, just mutted myself :-) )
kei: could recommend best
practices to facilitate data integration
... could be applied to microaray data but to other datasets as
well
... capture the relationships to support semantic queries
... finalizing the genelist as soon as possible due to deadline
submission approaching
<jun> I think I should talk after Lena
kei: introduction almost
complete
... possible link to other ontologies (provenir?) that our
structure could be related to
jun: provenance information is
quite rich
... looking at what used to generate the samples
kei: capture the version of software
satya: have not modified the ontology
jun: doap ( ?) has been used to
describe software
... makes sense to start with the queries and decide how the
rdf representation of the data looks like and then represent in
the ontology
<jun> http://usefulinc.com/ns/doap#
kei: our work should be in line
with other existing efforts
... examples are array express or mged group
ssahoo2 (breaking up): ncbo and obi ontologies
ssahoo2: making sure we are not
re-inventing the wheel
... nci thesaurus and other ontologies, need to be careful to
avoid re-creating the ontologies
mscottm: in contact with EBI who
have said that they have not done this yet
... software ontologies have been used
kei: look at the rdf structure
and see how well the queries can be answered
... decide what are the unique things that we have contributed
and how can we link to other groups work
<mscottm> http://bioportal.bioontology.org/ontologies/42036
<mscottm> http://www.ebi.ac.uk/efo/swo
kei: other potential datasets
that we can integrate with (pathway/protein/diseasome)
... scott mentions uniprot dataset
mscottm: uniprot has its own rdf
representation - not in hcls kb because it is very large
... we can integrate relevant parts of the uniprot datasets
kei: interesting to integrate genomics and proteomics
mscottm: uniprot datasets behind
a sparql endpoint has been done (but used their own flavor of
rdf structure)
... sticky point is coordination with others in the
community
... is there a way to coordinate with bio2rdf?
... while we are at it, why not integrate shared
vocabularies?
... use some of the information in the protein records
<mscottm> http://www.stanford.edu/~coulet/material/ontology/phare.owl
mscottm: another source of rdf
it's a pharma ontology about genes, drugs and diseases
... put together at ncbo by Adrian Cullet (?)
... the source of information is nlp techniques
<mscottm> http://sparql.bioontology.org/webui
mscottm: (not a text miner)
<mscottm> http://www.stanford.edu/~coulet/material/sparql_queries
mscottm: already behind a sparql endpoint
scott agreed to coordinate with other sparql endpoints
matthias_samwald: annotating some
of the text associated with the microarray studies
... need to know which kinds of studies did we chose
mscottm: use void
... void statement can be inserted into the graph itself
... can also put the statement in the second graph
... use void to refer to who created a particular statement
<ssahoo2> to follow up on Scott's idea - should we treat Lena's RDF file and Jun's RDF file as two separate sources?
satya - they are not separate representations, they are follow ups
the name at the end of the files is not its owner but the latest person who made the modifications
mscottm: idea is coming up with interesting provenance information
<ssahoo2> right - we add distinct named graph ids with each of the ttl files and issue a federated SPARQL query directed to each named graph
<mscottm> yes
<ssahoo2> ok
http://ibl.mdanderson.org/~mhdeus/sparql_federation/endpoint2.php
<jun> yes, sure
<ssahoo2> yes
matthias_samwald: if we focus on some example it is easier to connect to other sources
kei: think about some example queries that will give broader integration with other types of data
mscottm: will look into how niff
is doing relatively to its work with microarrays
... problem is our focus queries are too directed to the
neurosciences, but not so much towards provenance
kei: jun is adding the provenance dimension to the paper
mscottm: if we know where the
genelist came from and the microarray experiment, we can come
up with the experiments as results from previous provenance
queries
... we can build a query that preceeds the selection of the 3
datasets
kei: all the examples are affy
platforms, but different statistical approachas
... main tasks - get the examples working!
<mscottm> mscottmarshall@gmail.com
This is scribe.perl Revision: 1.135 of Date: 2009/03/02 03:52:20 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) Succeeded: s/about/after/ No ScribeNick specified. Guessing ScribeNick: Lena Inferring Scribes: Lena WARNING: No "Present: ... " found! Possibly Present: Chuck IPcaller Kei_Cheung LenaDeus P3 P6 aaaa aabb aacc inserted jun kei matthias_samwald mscottm satya ssahoo2 You can indicate people for the Present list like this: <dbooth> Present: dbooth jonathan mary <dbooth> Present+ amy WARNING: No meeting title found! You should specify the meeting title like this: <dbooth> Meeting: Weekly Baking Club Meeting WARNING: No meeting chair found! You should specify the meeting chair like this: <dbooth> Chair: dbooth Got date from IRC log name: 09 Aug 2010 Guessing minutes URL: http://www.w3.org/2010/08/09-hcls-minutes.html People with action items: WARNING: Input appears to use implicit continuation lines. You may need the "-implicitContinuations" option.[End of scribe.perl diagnostic output]