Re: BioRDF Telcon
Today's minutes are available at: http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/10-04_Conference_Call Thanks to Lena for scribing. M. Scott Marshall is now the new chair of BioRDF!! He will announce the next BioRDF call. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, October 4 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, October 4, 2010 * Time of Call: 11:00 am Eastern Time (5 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction * Revision of ISWC'10/SWPM-2010 paper * Next phase of BioRDF
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, October 4 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, October 4, 2010 * Time of Call: 11:00 am Eastern Time (5 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction * Revision of ISWC'10/SWPM-2010 paper * Next phase of BioRDF
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, September 27 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, September 27, 2010 * Time of Call: 11:00 am Eastern Time (5 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction * Presentation on Rat Genome Database (Simon Twigger) * Update ( ISWC'10/SWPM-2010 paper was accetped, but revisions are needed) * Possibility of submitting another paper
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, September 13 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, September 13, 2010 * Time of Call: 11:00 am Eastern Time (5 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction * Update (paper was submitted to ISWC'10/SWPM-2010) * Follow up and next steps
Re: BioRDF Telcon
Today's minutes are available at: http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/08-30_Conference_Call Thanks to Matthias for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, August 30 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, August 30, 2010 * Time of Call: 11:00 am Eastern Time (5 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction * Paper submission to ISWC'10/SWPM-2010
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, August 30 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, August 30, 2010 * Time of Call: 11:00 am Eastern Time (5 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction * Paper submission to ISWC'10/SWPM-2010
Re: BioRDF Telcon
Today's minutes are available at: http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/08-23_Conference_Call Thanks to Matthias for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, August 23 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, August 23, 2010 * Time of Call: 11:00 am Eastern Time (5 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction (Kei) * Gene list RDF representation (Lena, Satya, Michael, Jun, and Scott) * Paper submission to ISWC'10/SWPM-2010 (All)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, August 23 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, August 23, 2010 * Time of Call: 11:00 am Eastern Time (5 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction (Kei) * Gene list RDF representation (Lena, Satya, Michael, Jun, and Scott) * Paper submission to ISWC'10/SWPM-2010 (All)
Re: BioRDF Telcon
The minutes for today's call are available at: http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/08-16_Conference_Call Thanks to Jun for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, August 16 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, August 16, 2010 * Time of Call: 11:00 am Eastern Time (5 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction (Kei) * Gene list RDF representation (Lena, Satya, Michael, Jun, and Scott) * Paper submission to ISWC'10/SWPM-2010 (All)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, August 16 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, August 16, 2010 * Time of Call: 11:00 am Eastern Time (5 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction (Kei) * Gene list RDF representation (Lena, Satya, Michael, Jun, and Scott) * Paper submission to ISWC'10/SWPM-2010 (All)
Re: Fwd: RDF from Atlas
One thing for all of us to think about is how to increase expressivity without introducing too much complexity. Just my two cents. Cheers, -Kei Christoph Grabmueller wrote: Scott, I don't mind at all if you CC this to the HCLS mailing list. I am aware though that a full representation of ArrayExpress/Atlas would require a significant increase in graph complexity. Cheers, Christoph M. Scott Marshall wrote: Note to BioRDF members: Christoph Grabmeuller provided us with example microarray RDF from Rebholz's text mining group at EBI using EFO (see below). Notice that Christoph would like feedback and guidance. It could be informative to compare our approaches. Christoph, [Would you mind if I CC the HCLS mailing list HCLS public-semweb-lifesci@w3.org ? There are many others in HCLS that would like to know about this work and could contribute advice/opinions.] Thanks for your example RDF. It looks like a good start. The teleconference that Jun and Lena and I had with James was very useful, but several in the BioRDF task force couldn't attend (I organized it during my vacation but several others including Kei were travelling). I'm looking forward to helping each other find a satisfying approach to microarray data in RDF and hopefully arriving at a consensus that results in similar RDF being served directly from ArrayExpress and GEO. It would then be possible to perform some basic bioinformatics work in SPARQL without having to create special ontologies and namespaces. Maybe this link will help you to understand what we are doing: http://esw.w3.org/HCLSIG_BioRDF_Subgroup/QueryFederation2 Any questions you may have will help us to improve our wiki page. Some of our latest work is being 'staged' in DropBox at the moment but should be available from the wiki soon.. Cheers, Scott
BioRDF telcon call
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, August 9 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, August 9, 2010 * Time of Call: 11:00 am Eastern Time (5 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction (Kei) * Gene list RDF representation (Lena, Satya, Michael, Jun, and Scott) * Paper submission to ISWC'10/SWPM-2010 (All)
Re: BioRDF Telcon
Today's minutes are available at: http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/08-02_Conference_Call Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, August 2 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, August 2, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei * Scribe: to-be-determined ==Agenda== * Introduction (Kei) * Gene list RDF representation (Lena, Satya, Michael, Jun, and Scott) * Publication opportunities (e.g., ISWC'10: http://wiki.knoesis.org/index.php/SWPM-2010)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, August 2 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, August 2, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei * Scribe: to-be-determined ==Agenda== * Introduction (Kei) * Gene list RDF representation (Lena, Satya, Michael, Jun, and Scott) * Publication opportunities (e.g., ISWC'10: http://wiki.knoesis.org/index.php/SWPM-2010)
Re: BioRDF Telcon
Thanks for correcting that, Scott. I'm still not quite out of my Asian time zone. :-) -Kei is M. Scott Marshall wrote: Hi Kei, I think that 11AM EDT = 5PM CET. Cheers, Scott On Jul 31, 2010 8:26 AM, Kei Cheung kei.che...@yale.edu mailto:kei.che...@yale.edu wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, August 2 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, August 2, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Nice, France) * Dial-In #: +44.203.318.0479 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org http://irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei * Scribe: to-be-determined ==Agenda== * Introduction (Kei) * Gene list RDF representation (Lena, Satya, Michael, Jun, and Scott) * Publication opportunities (e.g., ISWC'10: http://wiki.knoesis.org/index.php/SWPM-2010)
Re: BioRDF minutes
Hi Jun, Yes, I think it'd be better if we postpone it to August 2. Cheers, -Kei Jun Zhao wrote: Hi Kei, Welcome back! I thought we agreed that (before you left for the holiday) there would be a biordf call on July 26, chaired by you. I didn't announce it on the mailing list yet. Would you rather postpone it to August 2? cheers, Jun Kei Cheung wrote: Hi Jun et al, Thanks a lot for keeping things going while I was away. I just got back from Hong Kong and am recovering from the trip. Let's plan on having the next call on Aug. 2. This will give me some time to recuperate and catch up on things. Best, -Kei Jun Zhao wrote: Dear all, The minutes of Monday's call is available at http://www.w3.org/2010/07/19-hcls-minutes.html. Thanks for Scott for the scribing. -- Jun
Re: BioRDF minutes
Hi Jun et al, Thanks a lot for keeping things going while I was away. I just got back from Hong Kong and am recovering from the trip. Let's plan on having the next call on Aug. 2. This will give me some time to recuperate and catch up on things. Best, -Kei Jun Zhao wrote: Dear all, The minutes of Monday's call is available at http://www.w3.org/2010/07/19-hcls-minutes.html. Thanks for Scott for the scribing. -- Jun
Re: BioRDF Telcon
the rigours of ontology engineer. ... NCBO is a community place. scott: i suppose that some of the data released in september will also contain the data that was annotated jeff: yes scott: you could also make that data available from NCBO kei: another topic: gene lists. a number of us have been working on how to represent gene lists. ... we could look at Neurolex to see which neuroscience terms we can extract form these endpoints that would be relevant for annotation. ... matthias has also been working with aTags, used NCBO resources. ... we need an iterated process of debugging, based on use-cases ... i will be away, jun will convene some of the calls stephen: we would be happy to receive feedback, suggestions for links. scott: one potential use-case would be EHRs, helping clinicians with certain tasks through integrated information. *Excerpts End*** Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, June 14 (see details below). Jeff Grethe and Stephen Larson will join the call to talk to us ahout NIF SPARQL endpoints. Cheers, -Kei == Conference Details == * Date of Call: Monday, June 14, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei * Scribe: to-be-determined ==Agenda== * Introduction (Kei) * NIF SPARQL endpoints (Jeff, Stephen) * Gene list RDF representation (Lena, Satya, Jun, Scott)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, June 14 (see details below). Jeff Grethe and Stephen Larson will join the call to talk to us ahout NIF SPARQL endpoints. Cheers, -Kei == Conference Details == * Date of Call: Monday, June 7, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei * Scribe: to-be-determined ==Agenda== * Introduction (Kei) * NIF SPARQL endpoints (Jeff, Stephen) * Gene list RDF representation (Lena, Satya, Jun, Scott)
Re: BioRDF Telcon
Chris Baker's presentation (ppt and pdf) is available at: https://transfer.med.yale.edu/upload/data/39YObdi808qV4ftL3FY1588AL5AAC2AKLpS/Baker_-_BioRDF_-_W3C_-_HCLS_Lipid-Ontology_and_Reuse_Cases.pptx https://transfer.med.yale.edu/upload/data/39YObdi808qV4ftL3FY1588AL5AAC2AKLpS/Baker_-_BioRDF_-_W3C_-_HCLS_Lipid-Ontology_and_Reuse_Cases.pdf Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, June 7 (see details below). As part of the agenda, Chris Baker will give a presentation on Lipid Ontology Cheers, -Kei == Conference Details == * Date of Call: Monday, June 7, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei * Scribe: to-be-determined ==Agenda== * Introduction * Lipid ontology presentation (Chris Baker) * Gene list RDF representation (Lena, Satya, Jun, Scott)
Re: BioRDF Telcon
Today's minutes are available at: http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/06-07_Conference_Call -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, June 7 (see details below). As part of the agenda, Chris Baker will give a presentation on Lipid Ontology Cheers, -Kei == Conference Details == * Date of Call: Monday, June 7, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei * Scribe: to-be-determined ==Agenda== * Introduction * Lipid ontology presentation (Chris Baker) * Gene list RDF representation (Lena, Satya, Jun, Scott)
Re: BioRDF Telcon
Hi Michael, mdmiller wrote: hi kei, What do we mean by differentially expressed genes? One definition is that differentially expressed genes are genes with significantly different expression in two samples/conditions/experimental factors/dimensions (e.g., treated vs. untreated, disease vs, normal, time point1 vs. time point 2) of microarray experiments. yes, this was my meaning. this is to differentiate between a gene that is always expressed under normal conditions because it is part of an essential pathway that is always running, that gene is only interesting if its expression level changes--similarly for a normally unexpressed gene. Thanks for confirming. A consensus definition (even it's broad) is important to our gene list representation. There are a variety of methods (e.g., statistical tests) that can be used to identify a list of differentially expressed genes in two different groups. That's Scott's point about the importance of capturing as part of the genelist context what methods have been used for detecting differentially expressed genes. I hope the use case can help convince the community the need/use of a common vocabulary for describing such methods. How to measure or infer gene expression (e.g., from mRNA) is a whole complex question that may be beyond the scope of our use case. yes, which i think was scott's point in his reply. in fact, for the BioRDF use case, initially at least, it is probably sufficient that the authors of the paper state that a gene is part of the significant gene list. Just want to clarify that what I meant was that it might be beyond the scope of our use case to accurately, comprehensively, and precisely define what gene expression really mean given the degree of complexity involved. Cheers, -Kei cheers, michael - Original Message - From: Kei Cheung kei.che...@yale.edu To: mdmiller mdmille...@comcast.net Cc: M. Scott Marshall marsh...@science.uva.nl; HCLS public-semweb-lifesci@w3.org Sent: Tuesday, May 25, 2010 8:52 PM Subject: Re: BioRDF Telcon Hi Michael et al, What do we mean by differentially expressed genes? One definition is that differentially expressed genes are genes with significantly different expression in two samples/conditions/experimental factors/dimensions (e.g., treated vs. untreated, disease vs, normal, time point1 vs. time point 2) of microarray experiments. How to measure or infer gene expression (e.g., from mRNA) is a whole complex question that may be beyond the scope of our use case. Cheers, -Kei mdmiller wrote: hi scott, i think you, jim and lena are doing a great job moving the technical aspect of this work forward. i'm looking forward to seeing the end results. cheers, michael - Original Message - From: M. Scott Marshall marsh...@science.uva.nl To: mdmiller mdmille...@comcast.net Cc: Kei Cheung kei.che...@yale.edu; HCLS public-semweb-lifesci@w3.org Sent: Tuesday, May 25, 2010 10:21 AM Subject: Re: BioRDF Telcon Hi Michael, Thanks for the clarification. I also explained those concepts during the BioRDF teleconference but it is difficult for the scribe to capture such details accurately from a phone conversation. Just knowing that a gene has changed (either up or down) already gives us something to work with. Since we started with the microarray use case, we have aimed to focus on the list of differentially expressed genes as our entry point into related molecular information, phenotypes, pathways, diseases, etc. In addition to the gene list and experimental factors, there is some data provenance information that characterizes the origins of the gene list, such as the type of significant analysis or technique that was performed (ANOVA, LIMMA, ..) and p-value cutoff for the list discussed in the associated article(s), software packages used (specific R package from BioConductor, GeneSpring, NextBio, ..). It would be handy if there was a common vocabulary for this type of information (URI's for statistical techniques and software packages). I think that some related resources have been described by myGrid/myExperiment. However, lacking a complete vocabulary, it is still possible to make use of the gene list without such a fine grained description of its provenance. Cheers, Scott On Tue, May 25, 2010 at 9:35 AM, mdmiller mdmille...@comcast.net wrote: hi all, sorry i ended up not being able to make the call. P value The probability (ranging from zero to one) that the results observed in a study could have occurred by chance if the null hypothesis was true. A P value of ? 0.05 is often used as a threshold to indicate statistical significance. (1) the exact meaning of p-value depends on what is being measured. also, sometimes it isn't so important that a gene is up or down regulated but whether its expression changes from up or down regulated over the experimental factors, e.g. if you increase the dose of the drug do the target genes
Re: BioRDF Telcon
Hi Michael, Our use case is considered a pilot project for exploring how to use semantic web to represent some of the information about microarray experiments including co-expressed/differentially expressed genes and the context of how such genes are identified (as described in papers). While keeping things simple and well defined (based on a limited number of examples), we hope to demonstrate how such information/knowledge on the semantic web can help researchers locate microarray datasets more easily. For example, users may be interested in collecting (from different databases) raw datasets belonging to different microarray experiments using a particular microarray platform (e.g., Affymetrix) to study Alzheimer Disease (AD) for particular neural cell types and brain regions, Such a collection may help researchers (biostatisticians) perform meta analysis to identify biomarkers for a given stage of AD, for example. Also, please see my response below. Michael Liebman wrote: I usually monitor this group and don't contribute but seeing the recent exchanges about Gene expression, I feel a need to put things into a better perspective than the one currently Being shared I'm glad you contribute. My experience comes from many years overseeing bioinformatics (and gene expression, proteomics And clinical data) at Wyeth, Roche, UPenn and with a DOD center at Windber- There appear to be several issues that are not being realistically addressed in the current discussion Thanks for the introduction. 1. there is significant experimental variability across individual studies, published or not- Because of variation in tissue/cell handling/storage/preparation, experimental variability in The experiment and significant variability in the data analysis. i.e. experimental reproducibility Inter-lab is poor and even intra-lab can be a major challenge I agree with you on the challenge of variability inherent in microarray and other high-throughput technologies. 2. the measurement that is usually referred to as up or down gene expression/regulation refers to The comparison between 2 experiments (sample under 2 different conditions) but typically does not Adequately correct for individual experimental variability other than simple scaling. We have shown That this is inadequate. Yes, that’s why more sophisticated normalization methods have been developed to address some of the variability issues. 3. leaving the interpretation to the author is significantly limited as it tends to reflect the bias of The author to observe/confirm what they are looking for in many of these studies- i.e. a biostatistician Will tell you that these experiments are extremely under-powered to reveal the true statistically significant Results they would like to achieve We're not agreeing or disagreeing with the authors. We just want to capture the information as described in the paper. We'll let others judge the validity of the results presented in the paper. 4. human nature looks to favor the big differences as being most significant- unfortunately nature doesn't Work this way- many of the largest differences are not functionally relevant but reflect the fact that biological Control of these specific genes may not be critical to function and so large variability can be observed and should Not be interpreted, all of the time, as being most significant. In fact, we have developed analytical methods to Look at large libraries of gene expression studies and evaluate the overall stability/variability of individual Genes (and probes) to establish a significance in difference between states based on how much variation should be Expected vs how much is observed, especially in genes that show extremely small levels of expression overall and which Would not be considered by typical approaches to data analysis It sounds like your group is developing new methodologies to tackle the problem of determing the significance of gene expression. Sorry to interrupt the exchange but I believe that it is critical, when considering the development of systems to Represent, store, exchange, model data, that an understanding of the specifics and uniqueness of the underlying Data and analytical approaches must be considered beyond simple statistics. No problem. Thanks for the input. Best, -Kei Michael Michael N. Liebman, PhD President/Managing Director Strategic Medicine, Inc 231 Deepdale Drive Kennett Square, PA 19348 (814) 659 5450 mobile m.lieb...@strategicmedicine.com www.strategicmedicine.com -Original Message- From: public-semweb-lifesci-requ...@w3.org [mailto:public-semweb-lifesci-requ...@w3.org] On Behalf Of mdmiller Sent: Wednesday, May 26, 2010 1:47 PM To: Kei Cheung Cc: HCLS Subject: Re: BioRDF Telcon hi kei, Just want to clarify that what I meant was that it might be beyond the scope of our use case to accurately, comprehensively, and precisely define what gene
Re: BioRDF Telcon
Today's minutes are available at: http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/05-24_Conference_Call Thanks to Matthias for scribing. Cheers, -Kei mdmiller wrote: hi kei, look forward to joining the call, michael - Original Message - From: Kei Cheung kei.che...@yale.edu To: mdmiller mdmille...@comcast.net; HCLS public-semweb-lifesci@w3.org Sent: Saturday, May 22, 2010 12:10 PM Subject: Re: BioRDF Telcon Hi Michael, Yes, May 24 was what I meant. It was a typo. Thanks, -Kei mdmiller wrote: hi kei, do you mean monday (may 24)? cheers, michael - Original Message - From: Kei Cheung kei.che...@yale.edu To: JunZhao jun.z...@zoo.ox.ac.uk Cc: public-semweb-lifesci@w3.org Sent: Friday, May 21, 2010 2:28 PM Subject: Re: BioRDF Telcon Since there were only Jun and Scott who attended the last BioRDF call (I was not able to attend due to some emergency meetings), we decided to have the next BioRDF call on the coming Monday (May 21) at 11 am (EDT). The agenda will be the same (see below). Cheers, -Kei JunZhao wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, May 17 (see details below). Cheers, -Jun == Conference Details == * Date of Call: Monday, May 17, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Jun * Scribe: to-be-determined ==Agenda== * Introduction * Gene list RDF representation * iPhone demo
Re: BioRDF Telcon
Hi Michael, Yes, May 24 was what I meant. It was a typo. Thanks, -Kei mdmiller wrote: hi kei, do you mean monday (may 24)? cheers, michael - Original Message - From: Kei Cheung kei.che...@yale.edu To: JunZhao jun.z...@zoo.ox.ac.uk Cc: public-semweb-lifesci@w3.org Sent: Friday, May 21, 2010 2:28 PM Subject: Re: BioRDF Telcon Since there were only Jun and Scott who attended the last BioRDF call (I was not able to attend due to some emergency meetings), we decided to have the next BioRDF call on the coming Monday (May 21) at 11 am (EDT). The agenda will be the same (see below). Cheers, -Kei JunZhao wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, May 17 (see details below). Cheers, -Jun == Conference Details == * Date of Call: Monday, May 17, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Jun * Scribe: to-be-determined ==Agenda== * Introduction * Gene list RDF representation * iPhone demo
Re: BioRDF Telcon
Since there were only Jun and Scott who attended the last BioRDF call (I was not able to attend due to some emergency meetings), we decided to have the next BioRDF call on the coming Monday (May 21) at 11 am (EDT). The agenda will be the same (see below). Cheers, -Kei JunZhao wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, May 17 (see details below). Cheers, -Jun == Conference Details == * Date of Call: Monday, May 17, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Jun * Scribe: to-be-determined ==Agenda== * Introduction * Gene list RDF representation * iPhone demo
Re: BioRDF Telcon
Today's minutes are available at: http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/05-03_Conference_Call Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, May 3 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, May 3, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * Gene list RDF representation (Jun, Satya, Lena, Scott, Jim) * iPhone demo (Don)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, May 3 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, May 3, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * Gene list RDF representation (Jun, Satya, Lena, Scott, Jim) * iPhone demo (Don)
Re: Monday evening get-together at WWW2010
Thanks a lot for arranging this, John. -Kei John Madden wrote: Hi all, Just to update you all (even though I know Andrea's flight was cancelled, but who knows)...we now have a venue for our get together on Monday evening in Raleigh. I've made patio reservations at 6:00 pm for 10 people -- but they tell me that 6:00 pm is early enough that they will happily expand to however many show up. Bu-ku Restaurant website http://bukuraleigh.com/buku/, map http://bit.ly/am1onV, 110 East Davie Street, Raleigh, NC (919) 834-6963 This is a restaurant that has rave reviews, with a wide variety of menu items from tapas-style to full dinners, a style of cuisine that is very eclectic (billed as global street food), lots of great beers and cocktails available and plenty of tolerance for diners who like to linger. It is located about 2 blocks from the Convention Center. Outdoor patio seating is under a roof, so even if it is rainy we should do okay. Hope to see you there, and feel free to invite others!! John
Re: BioRDF Telcon
Jim McCusker's presentation is available at: http://prezi.com/pr7qkiw_5yk2/ -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, April 19 (see details below). Jun Zhao will convene this telcon call. Cheers, -Kei == Conference Details == * Date of Call: Monday, April 19, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. (Please see the IRC update forwarded by Scott Marshall to the HCLS list) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Jun Zhao * Scribe: to-be-determined ==Agenda== * Introduction: Jun * MAGE-TAB/MGED ontology mapping (Jim McCusker) * Gene list RDF representation (Jun, Satya, Lena, Scott) * iPhone demo (Don)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, April 19 (see details below). Jun Zhao will convene this telcon call. Cheers, -Kei == Conference Details == * Date of Call: Monday, April 19, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. (Please see the IRC update forwarded by Scott Marshall to the HCLS list) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Jun Zhao * Scribe: to-be-determined ==Agenda== * Introduction: Jun * MAGE-TAB/MGED ontology mapping (Jim McCusker) * Gene list RDF representation (Jun, Satya, Lena, Scott) * iPhone demo (Don)
Re: BioRDF Telcon
Today's BioRDF telcon minutes are available at: http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/04-05_Conference_Call Thanks to Jun for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, April 5 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, April 5, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * Microarray use case -- RDF structure of genelists + experiments + provenance (All) * Collaboration with Sci. Discourse based on microarray use case (Jun, Sudeshna, Satya, Scott) * IPhone app (Don)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, April 5 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, April 5, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * Microarray use case -- RDF structure of genelists + experiments + provenance (All) * Collaboration with Sci. Discourse based on microarray use case (Jun, Sudeshna, Satya, Scott) * IPhone app (Don)
Re: BioRDF Telcon
Don has created an initial wiki page for describing the iphone app (see the link below). http://esw.w3.org/HCLSIG_BioRDF_Subgroup_iPhone_App_Use_Case#iPhone_App_Use_Case Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, March 22 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, March 22, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * IPhone app (Don) * Microarray use case -- RDF structure of genelists + experiments + provenance (All) * Collaboration with Sci. Discourse based on microarray use case (Jun, Sudeshna, Satya, Scott)
Re: BioRDF Telcon
Today's BioRDF meeting minutes are available at: http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/03-22_Conference_Call Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, March 22 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, March 22, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * IPhone app (Don) * Microarray use case -- RDF structure of genelists + experiments + provenance (All) * Collaboration with Sci. Discourse based on microarray use case (Jun, Sudeshna, Satya, Scott)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (4 pm CET) on Monday, March 22 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, March 22, 2010 * Time of Call: 11:00 am Eastern Time (4 pm CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * IPhone app (Don) * Microarray use case -- RDF structure of genelists + experiments + provenance (All) * Collaboration with Sci. Discourse based on microarray use case (Jun, Sudeshna, Satya, Scott)
Re: BioRDF Telcon
Today's BioRDF minutes are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2010/03-03_Conference_Call Thanks to Matthias for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, March 8 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, March 8, 2010 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * IPhone app demo (Don) * Microarray use case -- RDF structure of genelists + experiments + provenance (All) * Cross-task and cross-community activities (All)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, March 8 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday, March 8, 2010 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * IPhone app demo (Don) * Microarray use case -- RDF structure of genelists + experiments + provenance (All) * Cross-task and cross-community activities (All)
Re: BioRDF Telcon
The minutes for today's BioRDF telcon are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2010/02-22_Conference_Call Thanks to Jun for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, February 8 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday February 8, 2010 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * HCLS KB (Matthias, Adrian) * Microarray use case -- RDF structure of genelists + experiments (Lena, Satya, Jun) * Query federation demos (e.g., iPhone app -- Don)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, February 22 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday February 22, 2010 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * Biohackathon update (Matthias) * Microarray use case -- RDF structure of genelists + experiments (Lena, Satya, Jun) * Query federation demos (e.g., iPhone app -- Don) * BioRDF presentation at CSHALS2010/HCLS tutorial (All)
Re: URIs for UMLS
May be a related question, for gene information, should be use entrez gene id or umls id (cui)? Cheers, -Kei Matthias Samwald wrote: Sorry for asking such a seemingly simple question. Establishing URIs for UMLS entities has now been discussed for years. What is the current status of this development? Do we have somehow useful, acccepted, possibly linked-data friendly entities for UMLS IDs by now? I seem to be unable to find any documentation of such a thing, only proposals in research papers. Cheers, Matthias
Re: BioRDF Telcon
The minutes for today's BioRDF telcon call are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2010/02-08_Conference_Call Thanks to Don for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, February 8 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday February 8, 2010 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * HCLS KB (Matthias, Adrian) * Microarray use case -- RDF structure of genelists + experiments (Lena, Satya, Jun) * Query federation demos (e.g., iPhone app -- Don)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, February 8 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday February 8, 2010 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * HCLS KB (Matthias, Adrian) * Microarray use case -- RDF structure of genelists + experiments (Lena, Satya, Jun) * Query federation demos (e.g., iPhone app -- Don)
Re: BioRDF Telcon
The minutes for yesterday's BioRDF telcon are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2010/01-25_Conference_Call Thanks to Lena for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, January 25 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday January 25, 2010 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * Microarray use case -- explore RDF structure based on some sample queries (All) * Applications/demos (All)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, January 25 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday January 25, 2010 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * Microarray use case -- explore RDF structure based on some sample queries (All) * Applications/demos (All)
BioRDF Telcon Postponed
In observance of the Martin Luther King Day, the BioRDF call is postponed to the following Monday on January 25 at 11 am (EDT). Agenda will be announced later. Best, -Kei
Call for papers: Semantic Web for Chinese Medicine
[Apologies for cross-posting] Call for Papers (A Thematic Series in Chinese Medicine) Semantic Web for Chinese Medicine: Harmonizing Data and Information of Chinese Medicine and Western Medicine Submission deadline: 31 January, 2010 Guest editors: Kei-Hoi Cheung (1) and Huajun Chen (2) (1) Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut, USA. (kei.che...@yale.edu) (2) College of Computer Science, Zhejiang University, Hangzhou, China. (huajun...@zju.edu.cn) Scope of the thematic series As the use of Chinese Medicine (CM) is growing, the question of how to relate CM and western medicine becomes increasingly important. Semantic relationships are to be discovered, established, explored, and reasoned with the help of computers, as large amounts and diversities of data and information about CM and western medicine have been collected digitally. While digital data are available, harmonizing such data is a challenging informatics problem due to differences in data formats, data models, and ontologies. The cultural and language differences present an additional challenge. This thematic series focuses on the use of Semantic Web technologies to help harmonize CM data and biomedical data. These technologies include RDF, RDFS, OWL, SPARQL, triplestores, linked data, ontologies, semantic web services, semantic rule engines, reasoners, and so on. Example topics The following are a few examples of potential topics for your contribution to this thematic series: 1.Semantic mashup/integration of existing resources/services to create new resources/services allowing CM data and other types of data including molecular, clinical, and pharmaceutical data to be combined for integrative or translational research. 2.Creation of data warehouses or data federation systems. 3.Construction and use of ontologies in the CM domain with links to other biomedical domains. 4.Biomedical network integration and analysis. 5.Approaches to facilitating cross-cultural and/or multilingual collaboration (e.g., cross-cultural knowledge integration and information retrieval). 6.Semantic merge between databases and literature (e.g., ontology mining from text literature). You are invited to submit your latest research on either topic for publication in a special issue; review and commentary articles are also welcome. All submitted manuscripts will be immediately entered into a peer review process. The submission deadline is 31 January, 2010 while some peer-reviewed and accepted papers can be published online earlier. About the journal -- Chinese Medicine (http://www.cmjournal.org/), the official journal of the International Society for Chinese Medicine, aims to provide a forum for the dissemination of high quality research. All articles in the journal are open access and fully peer-reviewed. Submit your research to Chinese Medicine and take advantage of an efficient online submission process, a high quality peer-review service, and high visibility for your article. There are no color charges and no limits on the number of figures or text. The published version of your article will be immediately placed in PubMed Central and other freely accessible full-text repositories. This complies with the open access policies of many funders including those of the Howard Hughes Medical Institute, NIH, and Wellcome Trust. Online submission --- Please submit your manuscript via our online submission system (http://www.cmjournal.org/manuscript/). For more information about the journal, contact the Editorial Office (cmjour...@gmail.com) or visit our instructions for authors (http://www.cmjournal.org/info/instructions/).
Re: BioRDF Telcon
Today's minutes are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2010/01-04_Conference_Call Cheers, -Kei Kei Cheung wrote: Happy 2010! This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, January 4 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday January 4, 2010 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * Microarray use case -- explore RDF structure based on some sample queries (All)
Re: BioRDF Telcon
Hi Don, When I sent out the meeting announcement over the weekend, I didn't realize that I accidentally sent it to myself instead of the HCLS list. My apologies to you and others. Today we focused on discussing the initial structure. As we discussed in the last biordf call of 2009, it'd be interesting as part of the demo if your iphone app can demontrate that some queries can be performed based on the structure. Please join the next meeting, which will be in two weeks. Cheers, -Kei Donald Doherty wrote: Oops! Sorry to have missed the meeting Kei. Somehow I didn't see the meeting announcement. An action item is waiting for me... Happy New Year! Don On Jan 4, 2010, at 3:42 PM, Kei Cheung wrote: Today's minutes are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2010/01-04_Conference_Call Cheers, -Kei Kei Cheung wrote: Happy 2010! This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, January 4 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday January 4, 2010 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * Microarray use case -- explore RDF structure based on some sample queries (All)
Re: Microarray use case
Thanks! Neuroscientists do use iPhone :-) . Maryann Martone wrote: Yes that's correct. The vta is next to the sn Sent from my iPhone On Dec 23, 2009, at 8:56 AM, Kei Cheung kei.che...@yale.edu wrote: Thanks for confirming. I also found in neurolex the following: Ventral tegmental area dopamine neuron. That means dopamine neuron (or dopaminergic cell) can be found in more than one brain region. As far as the substantia nigra is concerned, dopamine neuron is only found in its subregion pars compacta. -Kei Maryann Martone wrote: Yes On Dec 22, 2009, at 6:42 PM, Kei Cheung wrote: Thanks, Maryann. In other words, dopamine (or dopaminergic) neurons are found only in the pars cmpacta portion of the substantia nigra. -Kei Maryann Martone wrote: Yes, they are same as the dopaminergic neurons are in the pars compacta. On Dec 22, 2009, at 6:36 PM, Kei Cheung wrote: I'm posting the following question to the neurolex group in the hope of getting some neuroscience domain expert input to our microarray use case (http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/ QueryFederation2 ). One of the microarray experiments mentions substantia nigra dopamine neuron. I searched neurolex and found the following: substantia nigra pars compacta dopaminergic cell. Are they the same? As I understand it, pars compacta is a portion of substantia nigra Thanks, -Kei -- You received this message because you are subscribed to the Google Groups neurolex group. To post to this group, send email to neuro...@googlegroups.com. To unsubscribe from this group, send email to neurolex+unsubscr...@googlegroups.com . For more options, visit this group at http://groups.google.com/group/neurolex?hl=en . Maryann Martone, Ph. D. Professor-in-Residence Department of Neuroscience University of California, San Diego San Diego, CA 92093-0446 858-822-0745 Maryann Martone, Ph. D. Professor-in-Residence Department of Neuroscience University of California, San Diego San Diego, CA 92093-0446 858-822-0745 -- You received this message because you are subscribed to the Google Groups neurolex group. To post to this group, send email to neuro...@googlegroups.com. To unsubscribe from this group, send email to neurolex+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/neurolex?hl=en.
Microarray use case
I'm posting the following question to the neurolex group in the hope of getting some neuroscience domain expert input to our microarray use case (http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 ). One of the microarray experiments mentions substantia nigra dopamine neuron. I searched neurolex and found the following: substantia nigra pars compacta dopaminergic cell. Are they the same? As I understand it, pars compacta is a portion of substantia nigra Thanks, -Kei
Re: BioRDF Telcon
The minutes for today's BioRDF call are available at the following: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/12-21_Conference_Call As we discussed during the call, I updated both the microarray use case wiki page [1] and the provenance wiki page [2] with several example queries to move forward. Thanks to Scott for scribing. Wish you all Happy Holidays! Cheers, -Kei [1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 [2] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, December 21 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday December 21, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * HCLS KB update (Matthias, Adrian) * Microarray use case (All) * Possible application(s)/demo(s) (All)
Re: Health Care and Life Sciences SemanticWb on iPhone and iPod touch
Forgot to cc the list. -Kei Kei Cheung wrote: Hi Don, Donald Doherty wrote: Hi Kei, Great to hear from you and the podcast idea is excellent. I wonder, is there any effort to have semantics attached to the podcasts? That'd be cool to have triples indicating content. Check out the Neuropod feeds at: http://feeds.nature.com/nature/podcast/neuropod?format=xml These feeds (XML format) describe different neuroscience podcasts. One can choose to listen to podcasts relating to dopamine neuron, Alzheimer disesae, etc. The semantic web and podcasts can make neuroscience music to our ears. Have fun! -Kei The main difficulty with making an iPhone app work with multiple SPARQL endpoints, from my perspective, is due to 1) differing coverage and content, 2) differing structures, and 3) differing URIs. Number 3 is the easiest to deal with. An application that goes straight to the endpoints without using a server to do translation, aggregation, etc. across endpoints must either do all of this itself (too much for an iPhone app) or get its full content from the endpoint it uses. Detailed PubMed information, for instance, is a very important feature to scientists. Only the Bio2RDF endpoints provide details including abstracts in RDF. All endpoints seem to have the authors associated with a particular paper but a big limitation of every endpoint is that it is impossible to reconstruct the order of the authors. (At least I haven't found a way.) Don On Dec 17, 2009, at 3:26 PM, Kei Cheung wrote: Hi Don, Donald Doherty wrote: Scott Marshall suggested that people on the HCLS list would have fun with my SemanticWb iPhone and iPod touch app (www.actionpotential.com ). Mobile neuroscience sounds an interesting concept. You may also want to use it to play the neuroscience podcasts of interest. It's one of many technologies I play around with to test the potential (and current limits) of the Semantic Web and Semantic Web technologies (for instance, see my site using MIT Simile technology at www.historicshadyside.org). Currently SemanticWb is using Bio2RDF endpoints. I'm working to make it possible for the user to select from a number of SPARQL endpoints but it's unfortunately non-trivial. Is it because of the bandwidth issue? I think it'd be nice if it can also access other endpoints like the HCLS KB's. That reminds me that Scott had mentioned to me recently that the HCLS KB endpoint at Berlin could not be accessible. I wonder if it has been fixed yet. Cheers, -Kei Enjoy! And I'll be happy to talk about lessons learned. Donald Doherty, Ph.D. donald.dohe...@actionpotential.com
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, December 21 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday December 21, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * HCLS KB update (Matthias, Adrian) * Microarray use case (All) * Possible application(s)/demo(s) (All)
Re: magetab2magerdf
Hi Susanna, Thanks for the information. If I understand it correctly, ISA-TAB can be used for different types of experiments (e.g., microarray, deep sequencing, and mass spectrometry), while MAGE-TAB is designed for microarray experiments only. However, if people are doing micorarray experiments only, MAGE-TAB and ISA-TAB are essentially the same. I may have missed something. Best, -Kei Susanna Sansone wrote: Hi Kei, isa-tab (how does this differ from mage-tab?) ISA-Tab is a superset of MAGE-Tab and serves to report multi-omics (and in general, multi-assays) studies. Please, see: http://isatab.sf.net and details in the ISA-Tab specification. Regards, Susanna
Re: Health Care and Life Sciences SemanticWb on iPhone and iPod touch
Hi Don, Donald Doherty wrote: Scott Marshall suggested that people on the HCLS list would have fun with my SemanticWb iPhone and iPod touch app (www.actionpotential.com). Mobile neuroscience sounds an interesting concept. You may also want to use it to play the neuroscience podcasts of interest. It's one of many technologies I play around with to test the potential (and current limits) of the Semantic Web and Semantic Web technologies (for instance, see my site using MIT Simile technology at www.historicshadyside.org). Currently SemanticWb is using Bio2RDF endpoints. I'm working to make it possible for the user to select from a number of SPARQL endpoints but it's unfortunately non-trivial. Is it because of the bandwidth issue? I think it'd be nice if it can also access other endpoints like the HCLS KB's. That reminds me that Scott had mentioned to me recently that the HCLS KB endpoint at Berlin could not be accessible. I wonder if it has been fixed yet. Cheers, -Kei Enjoy! And I'll be happy to talk about lessons learned. Donald Doherty, Ph.D. donald.dohe...@actionpotential.com
Re: Microarray Experiment Context
Hi Satya, Jun et al, I added to the list of provenance terms another a list of terms extracted from the abstracts of the 4 microarray experiments listed in [1]. The terms were automatically extracted from the abstracts using the NCBO Annotator (http://bioportal.bioontology.org/annotator) with NIFSTD being the ontology (one can also input multiple ontologies). We can prune this list and combine with your list and to see what sort of relationships exist among them. We can also go deeper into each paper to see what additional terms/relationships we can find (e.g., at the level of gene list). Based on these terms and relationships, we can start to explore the type of semantic queries that can be answered as part of the next step. I found a couple of interesting issues using the Annotator. 1. It picked up the term neurofibrillary tangle but not its plural form neurofibrillary tangles. So it would be nice to include synonyms even if these synonyms may not be included in the input ontology. 2. It didn't pick up temporal and prefrontal cortex even though temporal cortex and prefrontal cortex are defined in NIFSTD I wonder if tools like atag can help address these issues (what happens if atags are applied to the abstracts). There are terms like dopamine neuron that doesn't seem to be found in NIFSTD. I'll need to look into it more and may check with the NeuroLex group on this. Cheers, -Kei [1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Kei Cheung wrote: Hi Satya et al, Thanks for creating the wiki page. I think it's a good start. I hope our use case can help facilitate some of the ontology alignment effort. You already listed a few to start. Other might include: NIFSTD, SenseLab, SWAN, TMO, etc. You can also add my name to the contact for the page if you want. Cheers, -Kei Satya Sahoo wrote: Hi all, I have created a wiki page to collect provenance related terms describing experiment conditions and protocols used to generate microarray data [1]. The page also lists a set of queries that rely on the provenance information associated with gene expression data. Please add additional terms required to better describe the experiment context, such as the statistical tools or process used to obtain gene list (published in literature) from raw experiment data. -- thanks to Jun for the wiki page edit rights :) cheers, Satya Kno.e.sis http://knoesis.wright.edu/researchers/satya [1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext
BioRDF: Microarray use case
I have updated the description of the microarray use case at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 As part of the update, new examples are provided. Also included are the main concepts/terms extracted from the examples (abstracts). Cheers, -Kei
Re: BioRDF Telcon
Hi Michael, Thanks for pointing to MSigDB. I inlucded this in the related links section of the microarray use case description (http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2). Also please see my response below. Cheers, -Kei mdmiller wrote: hi all, here is he link to Molecular Signatures Database (MSigDB): [1]: http://www.broadinstitute.org/gsea/msigdb/ cheers, michael - Original Message - From: mdmiller mdmille...@comcast.net To: Kei Cheung kei.che...@yale.edu Cc: Jim McCusker james.mccus...@yale.edu; Helena Deus helenad...@gmail.com; HCLS public-semweb-lifesci@w3.org Sent: Thursday, December 10, 2009 6:49 AM Subject: Re: BioRDF Telcon hi kei, To me, ontologies can be used to facilitate integrated semantic queries across experiments/datasets. yes, and this is starting to become a reality. this effort, along with other HCLS initiatives are helping to pave the way. While some of the protocols are standardized, the data protocols for obtaining things like gene lists vary a lot. One of my questions is that can such data analysis protocols be somehow entered into mage-tab. yes it can be, along with the gene list, but in practice this is not done by the submitter. after the Derived Array Data representing the normalized data, like CHP files, there can be one or more Protocol REF columns describing the analysis to obtain the gene list followed by a Derived Array Data Matrix File that is the gene list with its signature. perhaps MIAME needs to be extended to state this. it's something i'll be bringing up with the MGED board. it's just now that this has become something of value to be machine readable. besides GeneSigDB, there is another effort, MSiqDB [1], that is also curating gene lists. so the community is beginning to see the value of this. Yes, for these gene lists to be of value to researchers, rich annotation is key. The challenge here is that it's quite tedious to enter the custom data analysis protocols in a structured way by hand. At least for now, I don't think we need to convert the huge primary data files (e.g., CEL file) into RDF. For the time being, we are more focused on the processed gene lists that may be associated with more biological meanings. perhaps its worthwhile considering using an ontology 'raw data' class for raw data that contains a reference to the data file. one could then use appropriate analysis tools to produce normalized data which could then also be referenced by a 'normalized data' class. It seems to make sense. cheers, michael - Original Message - From: Kei Cheung kei.che...@yale.edu To: mdmiller mdmille...@comcast.net Cc: Jim McCusker james.mccus...@yale.edu; Helena Deus helenad...@gmail.com; HCLS public-semweb-lifesci@w3.org Sent: Monday, December 07, 2009 7:32 AM Subject: Re: BioRDF Telcon mdmiller wrote: hi jim and lena, great progress! this will be a nice tool. a couple of comments. 1) i think ProtocolApplication is based seen as an individual instance of the Protocol class. quite often there are arguments whether ontologies should have individuals or be simply classes. to me, that doesn't apply here where real world objects are being connected to ontologies. the BioSource is realized as the 'Source Name' column in MAGE-TAB and those entries represent real people in studies, mice or rats in non-clinical studies, etc., and the characteristics values like age represent real individual instances of age. in the same way, the values in the Protocol REF column of MAGE-TAB are real wet-lab or analysis individual instances of protocols, called protocol applications in MAGE-OM. It sounds like we need to look at how to map column names and entries to classes, instances, and relationships appropriately. failure to make this distinction, to me, has obscured how much value ontologies can have in the real world. too often i see ontologies seen in and of themselves, which has its own value certainly, but not for the use cases i have dealing with real biological data. To me, ontologies can be used to facilitate integrated semantic queries across experiments/datasets. 2) the usefulness, for this use case, of the information between the 'Source Name' and its characteristics and the 'Derived Array Data Matrix File' or 'Derived Array Data File' has limited usefulness, error correction and normalization can make some difference but if the provider of the MAGE-TAB is trusted, all that is pretty routine these days. the above combined with experimental factors and experiment design info is probably 95% to 99.9% the worthwhile information from the MAGE-TAB. if one notices a difference in the final gene set between two experiments that look the same, only then it might be worthwhile going into more detail. and has been noted the MAGE-TAB information needs to be supplemented with the information on the final gene set, its
Re: magetab2magerdf
Hi Jim, Michael,
The following paper describes how to convert mage-tab and isa-tab (how
does this differ from mage-tab?) into DAG for visualization purposes.
http://www.biomedcentral.com/1471-2105/10/133
Why not DAG for machine readability as well?
Cheers,
-Kei
mdmiller wrote:
hi jim,
looks like you're making great progress. i have a few comments
in-line below.
cheers,
michael
- Original Message - From: Jim McCusker
james.mccus...@yale.edu
To: w3c semweb HCLS public-semweb-lifesci@w3.org
Sent: Tuesday, December 08, 2009 6:05 AM
Subject: magetab2magerdf
I'm distinguishing between magetab2rdf (raw conversion of magetab into
an RDF structure) and magetab2magerdf (conversion of magetab into an
RDF-based MAGE-OM structure) here. My purposes and goals require a
magetab2magerdf approach, so that's what I've been working on.
I have checked in code for magetab2magerdf at the googlecode project
http://magetab2rdf.googlecode.com. The code can be checked out from:
http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/
and example RDF is in:
http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/examples/E-MEXP-986/
I currently load the IDF-related entities into the RDF. I'm beginning
work on SDRF next.
http://magetab2rdf.googlecode.com/svn/trunk/ontologies/mage-om.owl
contains the additional properties and classes needed to support an
RDF-based MAGE-OM on top of the MGED Ontology.
A few notes on E-MEXP-986:
The URI for the MGED Ontology is
http://mged.sourceforge.net/ontologies/MGEDontology.owl, but has been
set to http://mged.sourceforge.net/ontologies/MGEDontology.php in the
IDF. The actual Term Source name is The MGED Ontology.
A common practice seems to be to refer to MGED Ontology without
reference to its URI.
as you probably noticed,
http://mged.sourceforge.net/ontologies/MGEDontology.php allows
appending #{class name} to go directly to the definition of the
term, so in a sense it is indeed a valid URI, that is a URL. it also
came before the owl format. can th epowl format be reached into over
he net to extract simply the class definition or does it need to be
downloaded and processed locally? my understanding is that a site
would have to have some sort of query, hopefully sparql, mechanism on
top to enable this.
Since I have to import the MGED ontology already for it's classes and
properties, I have already imported it under the correct URI. I have
added a kludge where if the term source name contains the string MGED
Ontology, the code assumes you mean the MGED Ontology, and sets the
URI appropriately. However, this is a one-off solution.
think of it as same as
I went back and forth about importing the Term Source ontologies.
However, this particular experiment has used the ArrayExpress term
source using the URI http://www.ebi.ac.uk/arrayexpress/; which
doesn't correspond to an available ontology, but is technically a term
source.
yes, and it does support a query mechinism, albeit a one off for that
site. i believe they plan on adding support for a sparql endpoint but
aren't sure if or when.
I'm considering attempting to import the ontology if it's available
and validate if it is, but if it fails to resolve to a document the
validation will not happen against that term source.
A note on Limpopo:
The IDF Comment didn't seem to import on this experiment. I'm not sure
if it's a format problem or something else.
i ran into this also, the implementation assumes
Comment[type]\ttext\ttext... to coresspond to the format of the
other fields in the IDF. the MAGE-TAB 1.0 spec doesn't address, my
assumption was that it was simply Comment[type]text but that's not
what the parser expects. we'll be discussing this for the MAGE-TAB
1.1 spec to clarify it one way or another, possibly updating the
parser before that.
Thoughts and feedback are greatly appreciated.
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu
PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mcc...@cs.rpi.edu
http://tw.rpi.edu
Re: BioRDF Telcon
Hi Lena, Thanks for finding the IDF and SDRF files corresponding to the experiment (E-GEOD-4757). It looks like the SDRF file contains richer metadata that can support richer semantic queries across experiments (e.g., finding experiments that involve the same cell types for the same/related brain regions for the same species). I noticed in the SDRF file that there are 20 samples (10 normal and 10 AD with neurofibriallary tangle). According to the abstract of the paper (http://www.ncbi.nlm.nih.gov/pubmed/16242812?dopt=Abstract), it says the following: ... we compared gene expression profiles of NFT-bearing entorhinal cortex neurons from 19 AD patients, adjacent non-NFT-bearing entorhinal cortex neurons from the same patients, and non-NFT-bearing entorhinal cortex neurons from 14 non-demented, histopathologically normal controls (ND). If I understand it correctly, there should be a total of 33 samples (19 AD and 14 normal). This may be more of a curation question for the ArrayExpress team. Maybe I missed something. Cheers, -Kei Helena Deus wrote: Hi Kei, Furtunatelly arrayexpress provides both the IDF and SDRF for that acession number, at http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-GEOD-4757 I have a small RDF document of that IDF at http://magetab2rdf.googlecode.com/svn/trunk/E-GEOD-4757.idf.rdf Thanks Lena On Tue, Dec 1, 2009 at 9:20 PM, Kei Cheung kei.che...@yale.edu mailto:kei.che...@yale.edu wrote: Hi Lena, Helena Deus wrote: @Kei, When you said data structure, did you mean the RDF structure For now, all I have is the java object returned by parser. I've been using Limpopo, which creates an object that I can then parse to RDF uing Jena. The challenge, though, has been coming up with the predicates to formalize the relationships between the various elements. I'm using the XML structures fir IDF/SDRF etc. at http://magetab-om.sourceforge.net to automatically generate the structure that will contain the data. My plan is to then create the RDF triples that use the attributes described in those documents and populate them with the data from the MAGE-TAB java object created by Limpopo. Thanks for the pointer and explaining your strategy. We might not need to convert everything from mage-tab for our purposes. Right now all I have is a very raw RDF/XML document describing the relationships in the IDF structure: http://magetab2rdf.googlecode.com/svn/trunk/magetabpredicates.rdf The triples for that had to be encoded manually using Jena by reading the model. I think IDF is a good start. For a real example for our use case, I wonder if any mage-tab file is available for experiment E-GEOD-4757 (transcription profiling of human neurons with and without neurofibriallary tangles from Alzheimer's patients). Helen may know. Cheers, -Kei @Satya and Jun I would very much like to be involved in that effort, do you already have a URL that I can look at? Thanks Lena On Tue, Nov 24, 2009 at 2:19 PM, Kei Cheung kei.che...@yale.edu mailto:kei.che...@yale.edu mailto:kei.che...@yale.edu mailto:kei.che...@yale.edu wrote: Hi Lena et al, When you said data structure, did you mean the RDF structure. If so, is a pointer to the structure that we can look at? As discussed during yesterday's call, Jun and Satya will help create a wiki page for listing some of the requirements for provenance/workflow in the context of gene lists, perhaps we should also use it to help coordinate some of the future activities (people also brought up Taverna during the call yesterday). Please coordinate with Satya and Jun. Cheers, -Kei Helena Deus wrote: Hi all, I apologize for missing the call yesterday! It seems you had a pretty interesting discussion! :-) If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into RDF would result in obtaining only the raw and processed data files but not the mechanism used to process it nor the resulting gene list. That's also what I concluded after looking at the data structure created by Tony Burdett's Limpopo parser. However, having the raw data as linked data is already a great start! Kei, should I be looking into Taverna in order to reprocessed the raw files with a traceable analysis workflow? Thanks! Lena On Tue, Nov 24, 2009 at 9:59 AM, mdmiller mdmille
Re: BioRDF Telcon
mdmiller wrote: hi jim and lena, great progress! this will be a nice tool. a couple of comments. 1) i think ProtocolApplication is based seen as an individual instance of the Protocol class. quite often there are arguments whether ontologies should have individuals or be simply classes. to me, that doesn't apply here where real world objects are being connected to ontologies. the BioSource is realized as the 'Source Name' column in MAGE-TAB and those entries represent real people in studies, mice or rats in non-clinical studies, etc., and the characteristics values like age represent real individual instances of age. in the same way, the values in the Protocol REF column of MAGE-TAB are real wet-lab or analysis individual instances of protocols, called protocol applications in MAGE-OM. It sounds like we need to look at how to map column names and entries to classes, instances, and relationships appropriately. failure to make this distinction, to me, has obscured how much value ontologies can have in the real world. too often i see ontologies seen in and of themselves, which has its own value certainly, but not for the use cases i have dealing with real biological data. To me, ontologies can be used to facilitate integrated semantic queries across experiments/datasets. 2) the usefulness, for this use case, of the information between the 'Source Name' and its characteristics and the 'Derived Array Data Matrix File' or 'Derived Array Data File' has limited usefulness, error correction and normalization can make some difference but if the provider of the MAGE-TAB is trusted, all that is pretty routine these days. the above combined with experimental factors and experiment design info is probably 95% to 99.9% the worthwhile information from the MAGE-TAB. if one notices a difference in the final gene set between two experiments that look the same, only then it might be worthwhile going into more detail. and has been noted the MAGE-TAB information needs to be supplemented with the information on the final gene set, its expression values, and the higher-level level analysis that was used, that is buried in the paper usually. While some of the protocols are standardized, the data protocols for obtaining things like gene lists vary a lot. One of my questions is that can such data analysis protocols be somehow entered into mage-tab. 3) i'm not sure if there was a desire to capture the raw data in the RDF. that will be, for affymetrix, a million to six million probes in the CEL file, even the processed data in the CHP file would have 20,000 to 60,000 probe sets. i'm not sure if that is the best way to represent that. At least for now, I don't think we need to convert the huge primary data files (e.g., CEL file) into RDF. For the time being, we are more focused on the processed gene lists that may be associated with more biological meanings. Cheers, -Kei cheers, michael Michael Miller mdmille...@comcast.net - Original Message - From: Jim McCusker james.mccus...@yale.edu To: Helena Deus helenad...@gmail.com Cc: Kei Cheung kei.che...@yale.edu; mdmiller mdmille...@comcast.net; HCLS public-semweb-lifesci@w3.org Sent: Monday, November 30, 2009 8:19 AM Subject: Re: BioRDF Telcon I'm following a similar strategy, but have been folowing the MGED ontology where possible. I've finished aligning the IDF portion, and have started on SDRF. MGED ontology is missing a property and class for what is often termed as ProtocolApplication, which usually serves as an edge between derived from and derived nodes, while linking to the protocol used for the derivation. I am planning on creating this link in a MAGE extensions ontology, but would like to vet the structure here: ProtocolApplication is a class. New properties: has_derivation_source has_derivative And then ProtocolApplication would have the restrictions: has_protocol some Protocol I don't put, domains, etc. on the derived properties to allow use in directly describing derivations if people so choose. There is no superclass for all nodes that can be derived or derived from, so I'm not bothering with restrictions for those, although I could add a union restriction to it. If this structure us acceptable to people, I can publish the ontology for general use pretty quickly, and let us work from the same data structure. I would appreciate any feedback. Jim On Monday, November 30, 2009, Helena Deus helenad...@gmail.com wrote: @Kei, When you said data structure, did you mean the RDF structure For now, all I have is the java object returned by parser. I've been using Limpopo, which creates an object that I can then parse to RDF uing Jena. The challenge, though, has been coming up with the predicates to formalize the relationships between the various elements. I'm using the XML structures fir IDF/SDRF etc. at http://magetab-om.sourceforge.net to automatically generate the structure
Re: Microarray Experiment Context
Hi Satya et al, Thanks for creating the wiki page. I think it's a good start. I hope our use case can help facilitate some of the ontology alignment effort. You already listed a few to start. Other might include: NIFSTD, SenseLab, SWAN, TMO, etc. You can also add my name to the contact for the page if you want. Cheers, -Kei Satya Sahoo wrote: Hi all, I have created a wiki page to collect provenance related terms describing experiment conditions and protocols used to generate microarray data [1]. The page also lists a set of queries that rely on the provenance information associated with gene expression data. Please add additional terms required to better describe the experiment context, such as the statistical tools or process used to obtain gene list (published in literature) from raw experiment data. -- thanks to Jun for the wiki page edit rights :) cheers, Satya Kno.e.sis http://knoesis.wright.edu/researchers/satya [1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, December 7 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday December 7, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined ==Agenda== * Introduction: Kei * Mage-tab parsing: Lena, Jim, Michael, Helen * Provenance and workflow: Satya, Jun, Yolanda * Next steps: All
Re: BioRDF Telcon
Hi Satya, I think Eric (cc'ed) can grant you edit right to the page(s) you want to edit. Please check with him. Best, -Kei Satya Sahoo wrote: Hi all, michael wrote: what is usually missing from those documents, along with the final gene list, is how that gene list was obtained, what higher level analysis was used, that is generally only in the paper unfortunately. Could you list some specific terms that describe how gene list was obtained and higher level of analysis? - we can include these in the list of provenance terms I am compiling to describe the experiment context. An initial list of provenance terms from a MAGE-ML file [1] is located at [2]. lena: I am trying to get edit rights for the wiki pages (I believe my username SatyaSahoo needs to be added to a list according to the new W3C wiki policy). I will send out an update and link once I get access. Best, satya Kno.e.sis center, WSU http://knoesis.wright.edu/researchers/satya [1] http://np2.ctrl.ucla.edu/np2/mage/mageml.jsp [2] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2?action=AttachFiledo=gettarget=NeuroscienceMicroarrayConsortium_ProvenanceTerms.txt http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2?action=AttachFiledo=gettarget=NeuroscienceMicroarrayConsortium_ProvenanceTerms.txt On Tue, Nov 24, 2009 at 9:59 AM, mdmiller mdmille...@comcast.net mailto:mdmille...@comcast.net wrote: hi all, (from the minutes) Yolanda/Kei/Scott: semantic annotation/description of workflow would enable the retrieval of data relevant to that workflow (i.e.. data that could be used to populate that workflow for a different experimental scenario) what is typically in a MAGE-TAB/MAGE-ML document are the protocols for how the source was processed into the extract then how the hybridization, feature extraction, error and normalization were performed. these are interesting and different protocols can cause differences at this level but it is pretty much a known art and usually not of too much interest or variability. what is usually missing from those documents, along with the final gene list, is how that gene list was obtained, what higher level analysis was used, that is generally only in the paper unfortunately. cheers, michael . - Original Message - From: Kei Cheung kei.che...@yale.edu mailto:kei.che...@yale.edu To: HCLS public-semweb-lifesci@w3.org mailto:public-semweb-lifesci@w3.org Sent: Monday, November 23, 2009 1:27 PM Subject: Re: BioRDF Telcon Today's BioRDF minutes are available at the following: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call Thanks to Rob for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, November 23 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday November 23, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org http://irc.w3.org port 6665 channel #
Re: BioRDF Telcon
Hi Lena, Helena Deus wrote: @Kei, When you said data structure, did you mean the RDF structure For now, all I have is the java object returned by parser. I've been using Limpopo, which creates an object that I can then parse to RDF uing Jena. The challenge, though, has been coming up with the predicates to formalize the relationships between the various elements. I'm using the XML structures fir IDF/SDRF etc. at http://magetab-om.sourceforge.net to automatically generate the structure that will contain the data. My plan is to then create the RDF triples that use the attributes described in those documents and populate them with the data from the MAGE-TAB java object created by Limpopo. Thanks for the pointer and explaining your strategy. We might not need to convert everything from mage-tab for our purposes. Right now all I have is a very raw RDF/XML document describing the relationships in the IDF structure: http://magetab2rdf.googlecode.com/svn/trunk/magetabpredicates.rdf The triples for that had to be encoded manually using Jena by reading the model. I think IDF is a good start. For a real example for our use case, I wonder if any mage-tab file is available for experiment E-GEOD-4757 (transcription profiling of human neurons with and without neurofibriallary tangles from Alzheimer's patients). Helen may know. Cheers, -Kei @Satya and Jun I would very much like to be involved in that effort, do you already have a URL that I can look at? Thanks Lena On Tue, Nov 24, 2009 at 2:19 PM, Kei Cheung kei.che...@yale.edu mailto:kei.che...@yale.edu wrote: Hi Lena et al, When you said data structure, did you mean the RDF structure. If so, is a pointer to the structure that we can look at? As discussed during yesterday's call, Jun and Satya will help create a wiki page for listing some of the requirements for provenance/workflow in the context of gene lists, perhaps we should also use it to help coordinate some of the future activities (people also brought up Taverna during the call yesterday). Please coordinate with Satya and Jun. Cheers, -Kei Helena Deus wrote: Hi all, I apologize for missing the call yesterday! It seems you had a pretty interesting discussion! :-) If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into RDF would result in obtaining only the raw and processed data files but not the mechanism used to process it nor the resulting gene list. That's also what I concluded after looking at the data structure created by Tony Burdett's Limpopo parser. However, having the raw data as linked data is already a great start! Kei, should I be looking into Taverna in order to reprocessed the raw files with a traceable analysis workflow? Thanks! Lena On Tue, Nov 24, 2009 at 9:59 AM, mdmiller mdmille...@comcast.net mailto:mdmille...@comcast.net mailto:mdmille...@comcast.net mailto:mdmille...@comcast.net wrote: hi all, (from the minutes) Yolanda/Kei/Scott: semantic annotation/description of workflow would enable the retrieval of data relevant to that workflow (i.e. data that could be used to populate that workflow for a different experimental scenario) what is typically in a MAGE-TAB/MAGE-ML document are the protocols for how the source was processed into the extract then how the hybridization, feature extraction, error and normalization were performed. these are interesting and different protocols can cause differences at this level but it is pretty much a known art and usually not of too much interest or variability. what is usually missing from those documents, along with the final gene list, is how that gene list was obtained, what higher level analysis was used, that is generally only in the paper unfortunately. cheers, michael . - Original Message - From: Kei Cheung kei.che...@yale.edu mailto:kei.che...@yale.edu mailto:kei.che...@yale.edu mailto:kei.che...@yale.edu To: HCLS public-semweb-lifesci@w3.org mailto:public-semweb-lifesci@w3.org mailto:public-semweb-lifesci@w3.org mailto:public-semweb-lifesci@w3.org Sent: Monday, November 23, 2009 1:27 PM Subject: Re: BioRDF Telcon Today's BioRDF minutes are available at the following: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call Thanks to Rob for scribing. Cheers, -Kei Kei Cheung wrote
Re: BioRDF Telcon
Hi Jim, It sounds like you and Lena can share experiences with each other. It'd be great if you two can coordinate on mage-tab parsing using some examples. Cheers, -Kei Jim McCusker wrote: I'm following a similar strategy, but have been folowing the MGED ontology where possible. I've finished aligning the IDF portion, and have started on SDRF. MGED ontology is missing a property and class for what is often termed as ProtocolApplication, which usually serves as an edge between derived from and derived nodes, while linking to the protocol used for the derivation. I am planning on creating this link in a MAGE extensions ontology, but would like to vet the structure here: ProtocolApplication is a class. New properties: has_derivation_source has_derivative And then ProtocolApplication would have the restrictions: has_protocol some Protocol I don't put, domains, etc. on the derived properties to allow use in directly describing derivations if people so choose. There is no superclass for all nodes that can be derived or derived from, so I'm not bothering with restrictions for those, although I could add a union restriction to it. If this structure us acceptable to people, I can publish the ontology for general use pretty quickly, and let us work from the same data structure. I would appreciate any feedback. Jim On Monday, November 30, 2009, Helena Deus helenad...@gmail.com wrote: @Kei, When you said data structure, did you mean the RDF structure For now, all I have is the java object returned by parser. I've been using Limpopo, which creates an object that I can then parse to RDF uing Jena. The challenge, though, has been coming up with the predicates to formalize the relationships between the various elements. I'm using the XML structures fir IDF/SDRF etc. at http://magetab-om.sourceforge.net to automatically generate the structure that will contain the data. My plan is to then create the RDF triples that use the attributes described in those documents and populate them with the data from the MAGE-TAB java object created by Limpopo. Right now all I have is a very raw RDF/XML document describing the relationships in the IDF structure: http://magetab2rdf.googlecode.com/svn/trunk/magetabpredicates.rdf The triples for that had to be encoded manually using Jena by reading the model. @Satya and Jun I would very much like to be involved in that effort, do you already have a URL that I can look at? ThanksLena On Tue, Nov 24, 2009 at 2:19 PM, Kei Cheung kei.che...@yale.edu wrote: Hi Lena et al, When you said data structure, did you mean the RDF structure. If so, is a pointer to the structure that we can look at? As discussed during yesterday's call, Jun and Satya will help create a wiki page for listing some of the requirements for provenance/workflow in the context of gene lists, perhaps we should also use it to help coordinate some of the future activities (people also brought up Taverna during the call yesterday). Please coordinate with Satya and Jun. Cheers, -Kei Helena Deus wrote: Hi all, I apologize for missing the call yesterday! It seems you had a pretty interesting discussion! :-) If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into RDF would result in obtaining only the raw and processed data files but not the mechanism used to process it nor the resulting gene list. That's also what I concluded after looking at the data structure created by Tony Burdett's Limpopo parser. However, having the raw data as linked data is already a great start! Kei, should I be looking into Taverna in order to reprocessed the raw files with a traceable analysis workflow? Thanks! Lena On Tue, Nov 24, 2009 at 9:59 AM, mdmiller mdmille...@comcast.net mailto:mdmille...@comcast.net wrote: hi all, (from the minutes) Yolanda/Kei/Scott: semantic annotation/description of workflow would enable the retrieval of data relevant to that workflow (i.e. data that could be used to populate that workflow for a different experimental scenario) what is typically in a MAGE-TAB/MAGE-ML document are the protocols for how the source was processed into the extract then how the hybridization, feature extraction, error and normalization were performed. these are interesting and different protocols can cause differences at this level but it is pretty much a known art and usually not of too much interest or variability. what is usually missing from those documents, along with the final gene list, is how that gene list was obtained, what higher level analysis was used, that is generally only in the paper unfortunately. cheers, michael . - Original Message - From: Kei Cheung kei.che...@yale.edu mailto:kei.che...@yale.edu To: HCLS public-semweb-lifesci@w3.org mailto:public-semweb-lifesci@w3.org Sent: Monday, November 23, 2009 1:27 PM Subject: Re: BioRDF Telcon Today's BioRDF minutes
Re: BioRDF Telcon
Hi Michael et al, Thanks for pointing out the kind of metadata captured in MAGE-TAB. Yes, we have discussed what kind of semantic information might be needed for describing gene lists. In addition to recording how the gene lists were obtained, we might need to keep track of how these gene lists might be used by other people (beyond the paper). Cheers, -Kei mdmiller wrote: hi all, (from the minutes) Yolanda/Kei/Scott: semantic annotation/description of workflow would enable the retrieval of data relevant to that workflow (i.e. data that could be used to populate that workflow for a different experimental scenario) what is typically in a MAGE-TAB/MAGE-ML document are the protocols for how the source was processed into the extract then how the hybridization, feature extraction, error and normalization were performed. these are interesting and different protocols can cause differences at this level but it is pretty much a known art and usually not of too much interest or variability. what is usually missing from those documents, along with the final gene list, is how that gene list was obtained, what higher level analysis was used, that is generally only in the paper unfortunately. cheers, michael . - Original Message - From: Kei Cheung kei.che...@yale.edu To: HCLS public-semweb-lifesci@w3.org Sent: Monday, November 23, 2009 1:27 PM Subject: Re: BioRDF Telcon Today's BioRDF minutes are available at the following: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call Thanks to Rob for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, November 23 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday November 23, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined == Agenda == * Roll call introduction (Kei) * RDF representation of microarray experiment and data (All) * Provenance and workflow (All)
Re: Differentially Expressed Gene Lists
Hi Misha and All, I believe there is a complementary relationship between paper-based gene lists and the gene lists produced by Atlas. Different methods may produce different lists of genes (there should be some overlap though) for the same experiment. It's good to consider the possibility of integrating GeneSigDB and Atlas. I also believe SDA is complementary to the paper-based approach and database approach. It is a practice/framework recommended for authors/editors to enter things like gene lists in a machine readable format. FEBS Letters (published by Elsevier) has experimented with SDA. That's why I wonder if a similar experiment can be done for gene lists. Cheers -Kei Misha Kapushesky wrote: Hi, Just to add to what Michael said, I will be in Boston around Christmas and one of the goals of this visit is to talk to the GeneSigDB guys about integrating it somehow with our Atlas, as gene list/signature curation is something a lot of our users demand frequently. Cheers, Misha On Mon, Nov 23, 2009 at 9:08 PM, Kei Cheung kei.che...@yale.edu wrote: Since there seems to be an interest in exploring how to represent differentially expressed gene list, I'm cc'ing this to the HCLS list (Scott also suggested doing this). In addition to Michael's suggestion (see below), the following is a reference to Structured Digital Abstract (SDA) for those who are interested. http://www.nature.com/nature/journal/v447/n7141/full/447142a.html Cheers, -Kei mdmiller wrote: hi all, SDA does sound useful but it still has the hurdle that the writers of the abstract need to be aware and care to use such structures or someone else needs to add such structure afterwards. as i mentioned at the F2F, there is GeneSigDB [1] hosted at dana farber, which is curating gene lists from papers. this is very useful in that it pulls out into a structured database the genes of interest from papers but has the limitation that it doesn't provide the signatures of interest. there is also the matter of the algorithm that, given a new gene expression profile, provides a score as to inclusion or exclusion from the biomarker. i'm not a bioinformaticists but my understanding is such algorithms may depend on more than just the signatures, they might depend on the values of some higher level algorithm, i.e. there may not be one size fits all algorithms to determine membership. i also won't be able to make the call. cheers, michael [1]: http://compbio.dfci.harvard.edu/genesigdb/ Michael Miller mdmille...@comcast.net - Original Message - From: Helen Parkinson parkin...@ebi.ac.uk To: Kei Cheung kei.che...@yale.edu Cc: marsh...@science.uva.nl; mdmiller mdmille...@comcast.net; Misha Kapushesky osto...@ebi.ac.uk; Eric Prud'hommeaux e...@w3.org; Matthias Samwald samw...@gmx.at Sent: Monday, November 23, 2009 5:58 AM Subject: Re: Differentially Expressed Gene Lists I should have read the spec for the SDA. Sounds useful. Kei Cheung wrote: Helen Parkinson wrote: I've been wondering how structured digital abstract (SDA) can be applied to gene lists. There has been a pilot application of SDA by FEBS in terms of interactions with links to MINT. Perhaps, a similar thing can be done for gene lists with links to databases like ArrayExpress and GEO. Mark Gerstein and I are working on a paper describing some extension of SDA (Matthias is also a co-author). Gene lists don't really appear in abstracts either often, one or two genes of interest are mentioned. I'd be happy to take a look at a subset of papers though to confirm/deny this. If that would help Many people misunderstood that structured digital abstract applies only to abstracts (I know the name is misleading unforunately), it can be applied to representing key findings described in the paper. The abstract I'm looking at is the following: http://www.ncbi.nlm.nih.gov/pubmed/16242812 It mentions explicitly that one of the key findings is a differently gene list of 225 genes across different conditions. Four of the validated genes are also mentioned in the abstract: apolipoprotein J, interleukin-1 receptor-associated kinase 1, tissue inhibitor of metalloproteinase 3, and casein kinase 2, beta. The job of creating an OWL/RDF representation of microarray experiement results should *start* with differentially expressed genes and experimental conditions. I would hope that it doesn't start with text mining ill-defined text sources (such as figures). On the bright side, if the experiment of interest is included in Gene Expression Atlas, we are all set, right? We just need a way to export the RDF. I'm planning to give a short presentation including an example during the BioRDF call tomorrow. I'll miss this unfortunately, as will Misha. Yes, if the experiment is in Atlas we can now export rdf and we have a prototype working. Look forward to seeing
Re: BioRDF Telcon
Hi Lena et al, When you said data structure, did you mean the RDF structure. If so, is a pointer to the structure that we can look at? As discussed during yesterday's call, Jun and Satya will help create a wiki page for listing some of the requirements for provenance/workflow in the context of gene lists, perhaps we should also use it to help coordinate some of the future activities (people also brought up Taverna during the call yesterday). Please coordinate with Satya and Jun. Cheers, -Kei Helena Deus wrote: Hi all, I apologize for missing the call yesterday! It seems you had a pretty interesting discussion! :-) If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into RDF would result in obtaining only the raw and processed data files but not the mechanism used to process it nor the resulting gene list. That's also what I concluded after looking at the data structure created by Tony Burdett's Limpopo parser. However, having the raw data as linked data is already a great start! Kei, should I be looking into Taverna in order to reprocessed the raw files with a traceable analysis workflow? Thanks! Lena On Tue, Nov 24, 2009 at 9:59 AM, mdmiller mdmille...@comcast.net mailto:mdmille...@comcast.net wrote: hi all, (from the minutes) Yolanda/Kei/Scott: semantic annotation/description of workflow would enable the retrieval of data relevant to that workflow (i.e. data that could be used to populate that workflow for a different experimental scenario) what is typically in a MAGE-TAB/MAGE-ML document are the protocols for how the source was processed into the extract then how the hybridization, feature extraction, error and normalization were performed. these are interesting and different protocols can cause differences at this level but it is pretty much a known art and usually not of too much interest or variability. what is usually missing from those documents, along with the final gene list, is how that gene list was obtained, what higher level analysis was used, that is generally only in the paper unfortunately. cheers, michael . - Original Message - From: Kei Cheung kei.che...@yale.edu mailto:kei.che...@yale.edu To: HCLS public-semweb-lifesci@w3.org mailto:public-semweb-lifesci@w3.org Sent: Monday, November 23, 2009 1:27 PM Subject: Re: BioRDF Telcon Today's BioRDF minutes are available at the following: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call Thanks to Rob for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, November 23 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday November 23, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org http://irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined == Agenda == * Roll call introduction (Kei) * RDF representation of microarray experiment and data (All) * Provenance and workflow (All)
Re: BioRDF Telcon
mdmiller wrote: hi all, the MAGE-TAB also can have (and often does) good phenotypic information on the sources (patients, mice, etc) of the samples used plus the experimental factors. I think it's also important for EFO to be harmonized with existing ontologies like the one in NCBO. Cheers, -Kei it does typically have the method to process from the raw to the processed data but what i meant was the information on how the normalized processed data was reduced to the gene list. cheers, michael - Original Message - *From:* Helena Deus mailto:helenad...@gmail.com *To:* mdmiller mailto:mdmille...@comcast.net *Cc:* Kei Cheung mailto:kei.che...@yale.edu ; HCLS mailto:public-semweb-lifesci@w3.org *Sent:* Tuesday, November 24, 2009 10:06 AM *Subject:* Re: BioRDF Telcon Hi all, I apologize for missing the call yesterday! It seems you had a pretty interesting discussion! :-) If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into RDF would result in obtaining only the raw and processed data files but not the mechanism used to process it nor the resulting gene list. That's also what I concluded after looking at the data structure created by Tony Burdett's Limpopo parser. However, having the raw data as linked data is already a great start! Kei, should I be looking into Taverna in order to reprocessed the raw files with a traceable analysis workflow? Thanks! Lena On Tue, Nov 24, 2009 at 9:59 AM, mdmiller mdmille...@comcast.net mailto:mdmille...@comcast.net wrote: hi all, (from the minutes) Yolanda/Kei/Scott: semantic annotation/description of workflow would enable the retrieval of data relevant to that workflow (i.e. data that could be used to populate that workflow for a different experimental scenario) what is typically in a MAGE-TAB/MAGE-ML document are the protocols for how the source was processed into the extract then how the hybridization, feature extraction, error and normalization were performed. these are interesting and different protocols can cause differences at this level but it is pretty much a known art and usually not of too much interest or variability. what is usually missing from those documents, along with the final gene list, is how that gene list was obtained, what higher level analysis was used, that is generally only in the paper unfortunately. cheers, michael . - Original Message - From: Kei Cheung kei.che...@yale.edu mailto:kei.che...@yale.edu To: HCLS public-semweb-lifesci@w3.org mailto:public-semweb-lifesci@w3.org Sent: Monday, November 23, 2009 1:27 PM Subject: Re: BioRDF Telcon Today's BioRDF minutes are available at the following: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call Thanks to Rob for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, November 23 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday November 23, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org http://irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined == Agenda == * Roll call introduction (Kei) * RDF representation of microarray experiment and data (All) * Provenance and workflow (All)
Re: Differentially Expressed Gene Lists
Since there seems to be an interest in exploring how to represent differentially expressed gene list, I'm cc'ing this to the HCLS list (Scott also suggested doing this). In addition to Michael's suggestion (see below), the following is a reference to Structured Digital Abstract (SDA) for those who are interested. http://www.nature.com/nature/journal/v447/n7141/full/447142a.html Cheers, -Kei mdmiller wrote: hi all, SDA does sound useful but it still has the hurdle that the writers of the abstract need to be aware and care to use such structures or someone else needs to add such structure afterwards. as i mentioned at the F2F, there is GeneSigDB [1] hosted at dana farber, which is curating gene lists from papers. this is very useful in that it pulls out into a structured database the genes of interest from papers but has the limitation that it doesn't provide the signatures of interest. there is also the matter of the algorithm that, given a new gene expression profile, provides a score as to inclusion or exclusion from the biomarker. i'm not a bioinformaticists but my understanding is such algorithms may depend on more than just the signatures, they might depend on the values of some higher level algorithm, i.e. there may not be one size fits all algorithms to determine membership. i also won't be able to make the call. cheers, michael [1]: http://compbio.dfci.harvard.edu/genesigdb/ Michael Miller mdmille...@comcast.net - Original Message - From: Helen Parkinson parkin...@ebi.ac.uk To: Kei Cheung kei.che...@yale.edu Cc: marsh...@science.uva.nl; mdmiller mdmille...@comcast.net; Misha Kapushesky osto...@ebi.ac.uk; Eric Prud'hommeaux e...@w3.org; Matthias Samwald samw...@gmx.at Sent: Monday, November 23, 2009 5:58 AM Subject: Re: Differentially Expressed Gene Lists I should have read the spec for the SDA. Sounds useful. Kei Cheung wrote: Helen Parkinson wrote: I've been wondering how structured digital abstract (SDA) can be applied to gene lists. There has been a pilot application of SDA by FEBS in terms of interactions with links to MINT. Perhaps, a similar thing can be done for gene lists with links to databases like ArrayExpress and GEO. Mark Gerstein and I are working on a paper describing some extension of SDA (Matthias is also a co-author). Gene lists don't really appear in abstracts either often, one or two genes of interest are mentioned. I'd be happy to take a look at a subset of papers though to confirm/deny this. If that would help Many people misunderstood that structured digital abstract applies only to abstracts (I know the name is misleading unforunately), it can be applied to representing key findings described in the paper. The abstract I'm looking at is the following: http://www.ncbi.nlm.nih.gov/pubmed/16242812 It mentions explicitly that one of the key findings is a differently gene list of 225 genes across different conditions. Four of the validated genes are also mentioned in the abstract: apolipoprotein J, interleukin-1 receptor-associated kinase 1, tissue inhibitor of metalloproteinase 3, and casein kinase 2, beta. The job of creating an OWL/RDF representation of microarray experiement results should *start* with differentially expressed genes and experimental conditions. I would hope that it doesn't start with text mining ill-defined text sources (such as figures). On the bright side, if the experiment of interest is included in Gene Expression Atlas, we are all set, right? We just need a way to export the RDF. I'm planning to give a short presentation including an example during the BioRDF call tomorrow. I'll miss this unfortunately, as will Misha. Yes, if the experiment is in Atlas we can now export rdf and we have a prototype working. Look forward to seeing the protoype. SDA can be seen as a bridge between databases and literature. It fits both bottom-up and top-down approach. BTW, I've pasted Kei's reminder below for the next BioRDF call (tomorrow). It would be great if you could call in and help us to figure this out. Apologies, I have 30 days holiday to use before the end of the year, so I won't make this. Have a good vacation. -Kei Cheers, Scott n.b. Does anybody mind if I post this to the mailing list? It's fine with me if people think nothing is controversal or premature here. :-) Cheers, -Kei - This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, November 23 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday November 23, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS
Re: BioRDF Telcon
Today's BioRDF minutes are available at the following: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call Thanks to Rob for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, November 23 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday November 23, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined == Agenda == * Roll call introduction (Kei) * RDF representation of microarray experiment and data (All) * Provenance and workflow (All)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, November 23 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday November 23, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung * Scribe: to-be-determined == Agenda == * Roll call introduction (Kei) * RDF representation of microarray experiment and data (All) * Provenance and workflow (All)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, November 9 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday November 9, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665channel=%23hcls for IRC access. * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call introduction (Kei) * BioRDF breakout update (Kei) * Follow up (All)
BioRDF breakout at F2F
For those who join the BioRDF breakout remotely, please use the following information: Topic: BioRDF task break out Date: Tuesday, November 3, 2009 Time: 9:00 am, Pacific Standard Time (San Francisco, GMT-08:00) WebEx Meeting Number: 922 391 470 WebEx Meeting Password: ncbomeeting Dial-In #: +1.617.761.6200 (Cambridge, MA) Dial-In #: +33.4.89.06.34.99 (Nice, France) Dial-In #: +44.117.370.6152 (Bristol, UK) Participant Access Code: 42571 (HCLS1) --- To join the online meeting (Now from iPhones too!) --- 1. Go to https://stanford.webex.com/stanford/j.php?ED=123758442UID=1139021767PW=NMDAwNDQyZTVlRT=MiM0 https://stanford.webex.com/stanford/j.php?ED=123758442UID=1139021767PW=NMDAwNDQyZTVlRT=MiM0 2. Enter your name and email address. 3. Enter the meeting password: ncbomeeting 4. Click Join Now. To view in other time zones or languages, please click the link: https://stanford.webex.com/stanford/j.php?ED=123758442UID=1139021767PW=NMDAwNDQyZTVlORT=MiM0 https://stanford.webex.com/stanford/j.php?ED=123758442UID=1139021767PW=NMDAwNDQyZTVlORT=MiM0
Re: Action Items from call today
Hi Jun et al, The following gene list: http://public.tgen.org/tgen.org/supplementarydata/neurogenomics/supplementarydata/brain_regions/PCA1_0_98_correlation.xls was gereated using the Principal components analysis (PCA). It is an annotated list of 102 genes showing at least a 0.98 correlation to PCA1 (first principal component). This is part of the following paper: http://www.ncbi.nlm.nih.gov/pubmed/17077275?dopt=Abstract I'm airport t to the airport now ... Cheers, -Kei Jun Zhao wrote: Hello Michael, Sorry I didn't see this email from you since I have been traveling. I am aware of the scovo vocabulary. Actually scovo is used in the voiD [1] vocabulary to describe statistics about data and I am one member of the voiD working group. Although scovo is a well-designed model to serve its purpose, we have found that it is quite difficult to query for datasets using this vocabulary. Hence, in the current voiD working group, proposing an alternative model to describe statistics of datasets has been a high priority. We are planning to release voiD2.0 including a new statistics model around Christmas. It would be nice if I can gather more user requirements from you and people on this list.:) [1] http://rdfs.org/ns/void-guide Best, Jun mdmiller wrote: hi all, on a different HCLS thread i saw this proposal from jeni tennison for specifying a generic dataset, it might be a useful way to encode a list of differentially expressed genes. it looks like one could do this encoding on the fly, so that the data itself at the source could be in whatever format is natural. http://sw.joanneum.at/scovo/schema.html cheers, michael Michael Miller mdmille...@comcast.net - Original Message - From: Kei Cheung kei.che...@yale.edu To: Helen Parkinson parkin...@ebi.ac.uk Cc: HCLS public-semweb-lifesci@w3.org; Tony Burdett tburd...@ebi.ac.uk Sent: Wednesday, October 14, 2009 7:03 PM Subject: Re: Action Items from call today Thanks, Helen. To make it more concrete. I've been thinking about some example queries that I hope can be answered by the RDF data once converted. I wonder if the following example quereis can be answered: Retrieve a list of differentially expressed genes between different brain regions (e.g., hippocampus and entorhinal cortex) for normally aged human subjects. Retrieve a list of differentially expressed genes for the same brain region of normal human subjects and AD patients. Using these lists of genes one can issue (federated) queries to retrieve addtional information about the genes for various types of analyses (e.g., GO term enrichment). Just a thought. Cheers, -Kei Helen Parkinson wrote: Hi here are my action items from the call today 1. MAGE-TAB-RDF, Lena requested details. Code here: https://sourceforge.net/projects/limpopo/ Java Parser for MAGE-TAB developed by EBI, used by several groups. Contact Tony Burdett tburd...@ebi.ac.uk for details. Tony estimates for a simple RDF dump a few days work. Lena if you are interested in working on this java code please contact Tony as he's already designed with rdf export in mind 2. MAGE-TAB-MAGE-ML - code from Junmin Liu at UPenn https://sourceforge.net/projects/tab2mage/files/ - see mage2tab Pretty much all public MAGE-ML comes from AE and is available from Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's mage-ml importer, and non public data 3. EBI experimental factor ontology (EFO) slides, attached see also www.ebi.ac.uk/efo 4. Noted that an RDF dump of atlas data and triple store access will be useful, we'll announce when these are available thanks Helen
Re: F2F Teleconference access code: 42571 (42572 for TMO call)
Thanks, Eric. Do we have a projector during the breakout on Tuesday? -Kei Eric Prud'hommeaux wrote: I've changed the teleconfrence bridge reservation access codes because long ones don't always work. The HCLS F2F meeting will have an access code of 42571 (HCLS1) both Monday and Tuesday, 08:00 - 18:00PDT (16:00-02:00Z). The folks working on TMO will meet on 42572 (HCLS2) on Tuesday.
Re: Action Items from call today
Hi Michael et al, Thanks for pointing to this generic approach of RDF representation of datasets. A list of differentially expressed genes may be associated with values such as P-values, fold-change, gene symbols, etc. Also, it's important to capture metadata/provenance associated with the gene list. This may include the type of statistical test (e.g., ANOVA) and the array platform employed (e.g., Affymetrix U133A). This may be an interesting discussion topic at the F2F meeting. Cheers, -Kei mdmiller wrote: hi all, on a different HCLS thread i saw this proposal from jeni tennison for specifying a generic dataset, it might be a useful way to encode a list of differentially expressed genes. it looks like one could do this encoding on the fly, so that the data itself at the source could be in whatever format is natural. http://sw.joanneum.at/scovo/schema.html cheers, michael Michael Miller mdmille...@comcast.net - Original Message - From: Kei Cheung kei.che...@yale.edu To: Helen Parkinson parkin...@ebi.ac.uk Cc: HCLS public-semweb-lifesci@w3.org; Tony Burdett tburd...@ebi.ac.uk Sent: Wednesday, October 14, 2009 7:03 PM Subject: Re: Action Items from call today Thanks, Helen. To make it more concrete. I've been thinking about some example queries that I hope can be answered by the RDF data once converted. I wonder if the following example quereis can be answered: Retrieve a list of differentially expressed genes between different brain regions (e.g., hippocampus and entorhinal cortex) for normally aged human subjects. Retrieve a list of differentially expressed genes for the same brain region of normal human subjects and AD patients. Using these lists of genes one can issue (federated) queries to retrieve addtional information about the genes for various types of analyses (e.g., GO term enrichment). Just a thought. Cheers, -Kei Helen Parkinson wrote: Hi here are my action items from the call today 1. MAGE-TAB-RDF, Lena requested details. Code here: https://sourceforge.net/projects/limpopo/ Java Parser for MAGE-TAB developed by EBI, used by several groups. Contact Tony Burdett tburd...@ebi.ac.uk for details. Tony estimates for a simple RDF dump a few days work. Lena if you are interested in working on this java code please contact Tony as he's already designed with rdf export in mind 2. MAGE-TAB-MAGE-ML - code from Junmin Liu at UPenn https://sourceforge.net/projects/tab2mage/files/ - see mage2tab Pretty much all public MAGE-ML comes from AE and is available from Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's mage-ml importer, and non public data 3. EBI experimental factor ontology (EFO) slides, attached see also www.ebi.ac.uk/efo 4. Noted that an RDF dump of atlas data and triple store access will be useful, we'll announce when these are available thanks Helen
Re: Action Items from call today
Hi Jim, Helen, et al, If Limpopo has been used by multiple microarray data providers, it should be more robust and useful to the microarray use case. -Kei Helen Parkinson wrote: Jim Stanford are now using the limpopo parser as well, the cannonical one has been replaced by this. Limpopo is used by at least 3 groups EBI, SMD, and MeV and is tested, I'd go with this, thanks Helen Jim McCusker wrote: Hi all, I have a quick bit of input about MAGE-TAB-RDF (which is something that I'm rather interested in). On Tue, Oct 13, 2009 at 1:00 AM, Helen Parkinson parkin...@ebi.ac.uk mailto:parkin...@ebi.ac.uk wrote: here are my action items from the call today 1. MAGE-TAB-RDF, Lena requested details. Code here: https://sourceforge.net/projects/limpopo/ Java Parser for MAGE-TAB developed by EBI, used by several groups. Contact Tony Burdett tburd...@ebi.ac.uk mailto:tburd...@ebi.ac.uk for details. Tony estimates for a simple RDF dump a few days work. Lena if you are interested in working on this java code please contact Tony as he's already designed with rdf export in mind I have been experimenting with ftp://smd-ftp.stanford.edu/smd/transfers/magetab/, which is the canonical magetab parser, and includes an object model. I have been attempting to annotate the data model with Sesame Elmo annotations to produce a useful RDF graph from the parsed object graph. I have only made some progress on this, as the its use of custom collection subclasses confuses the Elmo mapping code. If Limpopo is separate from the parser that I'm working on, and has an easier-to-work-with object model, I can possibly make some good progress on this in a short period of time. Glancing at the code from Limpopo, the object model seems very different, and can possibly be used by Elmo to generate RDF. If I use this route, is this something that would be interesting to the group? Jim -- Jim McCusker Programmer Analyst Krauthammer Lab, Pathology Informatics Yale School of Medicine james.mccus...@yale.edu mailto:james.mccus...@yale.edu | (203) 785-6330 http://krauthammerlab.med.yale.edu PhD Student Tetherless World Constellation Rensselaer Polytechnic Institute mcc...@cs.rpi.edu mailto:mcc...@cs.rpi.edu http://tw.rpi.edu
Re: Action Items from call today
Hi Michael, Thanks for sharing your experience with your GWAS project. The thing with marker identification and prediction is that it involves a series of possibly iteratirve analyses. The resulting gene lists are really the products of these analyses. Therefore, it is important to capture the context of these gene lists. See you and others at the F2F. Cheers, -Kei dmiller wrote: hi kei, yes, the proposal for specifying the dataset seemed to allow rich annotation, one reason i liked it. the piece i find missing is this. not being a biologist or statistician i can't offer much help (my strength is software). once a large group of individuals have been part of a GWAS (perhaps as part of a clinical trial) and a marker based on a gene expression signature over n genes has been determined, presumably that would be published as the set of n genes and some averaged measure of up regulation or down regulation per gene based on averaging that group of individuals and an outcome such as bad prognosis or good prognosis associated with the marker. now if a new individual has a gene expression profile, how will the expression of this individual's genes be compared against the marker to determine which group the individual falls into? (there are other scenarios, such as multiple markers associated with different outcomes but the above seems the simplest case.) look forward to meeting you and the others at the F2F next week. cheers, michael Michael Miller mdmille...@comcast.net - Original Message - From: Kei Cheung kei.che...@yale.edu To: mdmiller mdmille...@comcast.net Cc: Helen Parkinson parkin...@ebi.ac.uk; HCLS public-semweb-lifesci@w3.org; Tony Burdett tburd...@ebi.ac.uk Sent: Thursday, October 29, 2009 1:43 PM Subject: Re: Action Items from call today Hi Michael et al, Thanks for pointing to this generic approach of RDF representation of datasets. A list of differentially expressed genes may be associated with values such as P-values, fold-change, gene symbols, etc. Also, it's important to capture metadata/provenance associated with the gene list. This may include the type of statistical test (e.g., ANOVA) and the array platform employed (e.g., Affymetrix U133A). This may be an interesting discussion topic at the F2F meeting. Cheers, -Kei mdmiller wrote: hi all, on a different HCLS thread i saw this proposal from jeni tennison for specifying a generic dataset, it might be a useful way to encode a list of differentially expressed genes. it looks like one could do this encoding on the fly, so that the data itself at the source could be in whatever format is natural. http://sw.joanneum.at/scovo/schema.html cheers, michael Michael Miller mdmille...@comcast.net - Original Message - From: Kei Cheung kei.che...@yale.edu To: Helen Parkinson parkin...@ebi.ac.uk Cc: HCLS public-semweb-lifesci@w3.org; Tony Burdett tburd...@ebi.ac.uk Sent: Wednesday, October 14, 2009 7:03 PM Subject: Re: Action Items from call today Thanks, Helen. To make it more concrete. I've been thinking about some example queries that I hope can be answered by the RDF data once converted. I wonder if the following example quereis can be answered: Retrieve a list of differentially expressed genes between different brain regions (e.g., hippocampus and entorhinal cortex) for normally aged human subjects. Retrieve a list of differentially expressed genes for the same brain region of normal human subjects and AD patients. Using these lists of genes one can issue (federated) queries to retrieve addtional information about the genes for various types of analyses (e.g., GO term enrichment). Just a thought. Cheers, -Kei Helen Parkinson wrote: Hi here are my action items from the call today 1. MAGE-TAB-RDF, Lena requested details. Code here: https://sourceforge.net/projects/limpopo/ Java Parser for MAGE-TAB developed by EBI, used by several groups. Contact Tony Burdett tburd...@ebi.ac.uk for details. Tony estimates for a simple RDF dump a few days work. Lena if you are interested in working on this java code please contact Tony as he's already designed with rdf export in mind 2. MAGE-TAB-MAGE-ML - code from Junmin Liu at UPenn https://sourceforge.net/projects/tab2mage/files/ - see mage2tab Pretty much all public MAGE-ML comes from AE and is available from Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's mage-ml importer, and non public data 3. EBI experimental factor ontology (EFO) slides, attached see also www.ebi.ac.uk/efo 4. Noted that an RDF dump of atlas data and triple store access will be useful, we'll announce when these are available thanks Helen
BioRDF (no telcon call on Oct 26)
As many people will be attending ISWC 2009, there will be no BioRDF telcon call on the coming Monday. The next call will be on Nov 9. Cheers, -Kei
Re: Call For Papers: Semantic Web for Chinese Medicine
Since some of you have asked, the authors don't need to pay for the publication costs for papers published in the BMC Chinese Medicine journal (http://www.cmjournal.org/), which is open access. Also, the journal just announced its impact factor of 2.35 (tracked by Thomson Reuters (ISI)). Cheers, -Kei Kei Cheung wrote: Call for Papers (A Thematic Series in CHINESE MEDICINE) Semantic Web for Chinese Medicine: Harmonizing Data and Information of Chinese Medicine and Western Medicine Guest editors: Kei-Hoi Cheung (1) and Huajun Chen (2) (1) Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut, USA. (2) College of Computer Science, Zhejiang University, Hangzhou, China. Scope of the thematic series As the use of Chinese Medicine (CM) is growing, the question of how to relate CM and western medicine becomes increasingly important. Semantic relationships are to be discovered, established, explored, and reasoned with the help of computers, as large amounts and diversities of data and information about CM and western medicine have been collected digitally. While digital data are available, harmonizing such data is a challenging informatics problem due to differences in data formats, data models, and ontologies. The cultural and language differences present an additional challenge. This thematic series focuses on the use of Semantic Web technologies to help harmonize CM data and biomedical data. These technologies include RDF, RDFS, OWL, SPARQL, triplestores, linked data, ontologies, semantic web services, semantic rule engines, reasoners, and so on. Example topics The following are a few examples of potential topics for your contribution to this thematic series: 1.Semantic mashup/integration of existing resources/services to create new resources/services allowing CM data and other types of data including molecular, clinical, and pharmaceutical data to be combined for integrative or translational research. 2.Creation of data warehouses or data federation systems. 3.Construction and use of ontologies in the CM domain with links to other biomedical domains. 4.Biomedical network integration and analysis. 5.Approaches to facilitating cross-cultural and/or multilingual collaboration (e.g., cross-cultural knowledge integration and information retrieval). 6.Semantic merge between databases and literature (e.g., ontology mining from text literature). You are invited to submit your latest research on either topic for publication in a special issue next year; review and commentary articles are also welcome. All submitted manuscripts will be immediately entered into a peer review process. The submission deadline is 31 January, 2010 while some peer-reviewed and accepted papers can be published online earlier. About the journal -- Chinese Medicine (http://www.cmjournal.org/), the official journal of the International Society for Chinese Medicine, aims to provide a forum for the dissemination of high quality research. All articles in the journal are open access and fully peer-reviewed. Submit your research to Chinese Medicine and take advantage of an efficient online submission process, a high quality peer-review service, and high visibility for your article. There are no color charges and no limits on the number of figures or text. The published version of your article will be immediately placed in PubMed Central and other freely accessible full-text repositories. This complies with the open access policies of many funders including those of the Howard Hughes Medical Institute, NIH, and Wellcome Trust. Online submission --- Please submit your manuscript via our online submission system (http://www.cmjournal.org/manuscript/). For more information about the journal, contact the Editorial Office (cmjour...@gmail.com) or visit our instructions for authors (http://www.cmjournal.org/info/instructions/).
Re: Action Items from call today
Thanks, Helen. To make it more concrete. I've been thinking about some example queries that I hope can be answered by the RDF data once converted. I wonder if the following example quereis can be answered: Retrieve a list of differentially expressed genes between different brain regions (e.g., hippocampus and entorhinal cortex) for normally aged human subjects. Retrieve a list of differentially expressed genes for the same brain region of normal human subjects and AD patients. Using these lists of genes one can issue (federated) queries to retrieve addtional information about the genes for various types of analyses (e.g., GO term enrichment). Just a thought. Cheers, -Kei Helen Parkinson wrote: Hi here are my action items from the call today 1. MAGE-TAB-RDF, Lena requested details. Code here: https://sourceforge.net/projects/limpopo/ Java Parser for MAGE-TAB developed by EBI, used by several groups. Contact Tony Burdett tburd...@ebi.ac.uk for details. Tony estimates for a simple RDF dump a few days work. Lena if you are interested in working on this java code please contact Tony as he's already designed with rdf export in mind 2. MAGE-TAB-MAGE-ML - code from Junmin Liu at UPenn https://sourceforge.net/projects/tab2mage/files/ - see mage2tab Pretty much all public MAGE-ML comes from AE and is available from Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's mage-ml importer, and non public data 3. EBI experimental factor ontology (EFO) slides, attached see also www.ebi.ac.uk/efo 4. Noted that an RDF dump of atlas data and triple store access will be useful, we'll announce when these are available thanks Helen
Re: BioRDF Telcon
The minutes for today's BioRDF call are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/10-12_Conference_Call Thanks to Matthias for scribing. Also, thanks to Helen for giving an informative update on Gene Expression Atlas. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, October 12 (see details below). Helen Parkinson from EBI will give a presentation on Gene Expression Atlas. The description of the microarray use case is available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Cheers, -Kei == Conference Details == * Date of Call: Monday October 12, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call introduction (Kei) * HCLS KB update (Matthias, Adrian) * Gene Expression Atlas (Helen) * Discussion (All)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, October 12 (see details below). Helen Parkinson from EBI will give a presentation on Gene Expression Atlas. The description of the microarray use case is available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Cheers, -Kei == Conference Details == * Date of Call: Monday October 12, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call introduction (Kei) * HCLS KB update (Matthias, Adrian) * Gene Expression Atlas (Helen) * Discussion (All)
Re: Jena as RDF Adapter
The paper outlines 3 approaches to query federation: Receptor Explorer (Rob), AIDA (Scott), and FeDeRate (Eric). While the first two approaches involve querying RDF/OWL datasets (converted from different data sources), the third approach involves mapping SPARQL to SQL using SWObjects. I don't think any of these approaches use Jena adapter to map to relational databases. I may have missed something. If so, the developers of these approaches can chime in. -Kei Oliver Ruebenacker wrote: Hello, Very nice! And this woks by implementing Jena's Graph interface? Take care Oliver On Thu, Oct 1, 2009 at 8:31 AM, Kei Cheung kei.che...@yale.edu wrote: Andrea Splendiani wrote: Hi, do you have a link to some docs ? (other than the paper that should come out tomorrow ?) The special issue just came out: http://www.biomedcentral.com/1471-2105/10?issue=S10 The paper is accessible at: http://www.biomedcentral.com/1471-2105/10/S10/S10 It provides links to the following supplemental materials: AIDA Toolkit: The software is available at http://www.adaptivedisclosure.org/aida and may be freely downloaded under the Apache license. FeDeRate: The data and software are available at https://sourceforge.net/projects/swobjects and may be freely downloaded and used with no license requirements. HCLS KB hosted by DERI, Galway, Ireland http://hcls.deri.org/sparql HCLS KB hosted by the Freie Universitaet Berlin: http://www.corporate-semantic-web.de/hcls.html Cheers, -Kei ciao, Andrea On 30 Sep 2009, at 23:45, M. Scott Marshall wrote: Hi Oliver, Are you aware of SWObjects http://sourceforge.net/projects/swobjects/ from Eric Prud'hommeaux? We've used it in a few demo's now: http://hcls.deri.org/coi/demo/ http://www.w3.org/2009/08/7tmdemo Kei-Hoi Cheung, H. Robert Frost, M. Scott Marshall, Eric Prud'hommeaux, Matthias Samwald, Jun Zhao, Adrian Paschke, A Journey to Semantic Web Query Federation in Life Sciences, BMC Bioinformatics Volume 10 Supplement 10, Oct 2009. Cheers, Scott -- M. Scott Marshall Leiden University Medical Center / University of Amsterdam http://staff.science.uva.nl/~marshall Oliver Ruebenacker wrote: Hello, On http://esw.w3.org/topic/RDFImportersAndAdapters it is said that: Jena Framework: Jena's Graph interface could be used to implement adapters. [...] D2RQ is an example of an adapter implemented as a Jena graph. Do we know of any implementations other than adapters to relational databases (such as D2RQ)? While I am convinced above statement is true, it would be nice to have a citation to convince others, too. Do you know any? Thanks! Take care Oliver --- Andrea Splendiani Senior Bioinformatics Scientist Rothamsted Research, Harpenden, UK andrea.splendi...@bbsrc.ac.uk +44(0)1582 763133 ext 2004
Re: Jena as RDF Adapter
Andrea Splendiani wrote: Hi, do you have a link to some docs ? (other than the paper that should come out tomorrow ?) The special issue just came out: http://www.biomedcentral.com/1471-2105/10?issue=S10 The paper is accessible at: http://www.biomedcentral.com/1471-2105/10/S10/S10 It provides links to the following supplemental materials: AIDA Toolkit: The software is available at http://www.adaptivedisclosure.org/aida and may be freely downloaded under the Apache license. FeDeRate: The data and software are available at https://sourceforge.net/projects/swobjects and may be freely downloaded and used with no license requirements. HCLS KB hosted by DERI, Galway, Ireland http://hcls.deri.org/sparql HCLS KB hosted by the Freie Universitaet Berlin: http://www.corporate-semantic-web.de/hcls.html Cheers, -Kei ciao, Andrea On 30 Sep 2009, at 23:45, M. Scott Marshall wrote: Hi Oliver, Are you aware of SWObjects http://sourceforge.net/projects/swobjects/ from Eric Prud'hommeaux? We've used it in a few demo's now: http://hcls.deri.org/coi/demo/ http://www.w3.org/2009/08/7tmdemo Kei-Hoi Cheung, H. Robert Frost, M. Scott Marshall, Eric Prud'hommeaux, Matthias Samwald, Jun Zhao, Adrian Paschke, A Journey to Semantic Web Query Federation in Life Sciences, BMC Bioinformatics Volume 10 Supplement 10, Oct 2009. Cheers, Scott -- M. Scott Marshall Leiden University Medical Center / University of Amsterdam http://staff.science.uva.nl/~marshall Oliver Ruebenacker wrote: Hello, On http://esw.w3.org/topic/RDFImportersAndAdapters it is said that: Jena Framework: Jena's Graph interface could be used to implement adapters. [...] D2RQ is an example of an adapter implemented as a Jena graph. Do we know of any implementations other than adapters to relational databases (such as D2RQ)? While I am convinced above statement is true, it would be nice to have a citation to convince others, too. Do you know any? Thanks! Take care Oliver --- Andrea Splendiani Senior Bioinformatics Scientist Rothamsted Research, Harpenden, UK andrea.splendi...@bbsrc.ac.uk +44(0)1582 763133 ext 2004
Re: HCLS Telcon reminder
I apologize for missing today's HCLS call due to conflict in my schedule. The following are some updates on BioRDF: 1. The two HCLS KB's are in the process of being upgraded in terms of hardware and software. 2. As Susie suggested, I added the query federation paper to the list under the heading 'Semantic Web Documents' on the HCLS IG wiki page (http://esw.w3.org/topic/HCLSIG). 3. We continue to explore the query federation use case in the context of integrating neuroscience microarray data with other types of data. This may help serve as a use case for new SPARQL features. 4. Helen (at EBI) informed me that a new version of Gene Expression Atlas (with links to NIFSTD) might be released soon. Cheers, -Kei Marshall, M.S. wrote: Here's the reminder for Thursday's HCLS call. See http://esw.w3.org/topic/HCLSIG/Meetings/2009-10-01_Conference_Call for up-to-date details, snapshot pasted below. New participants please see http://esw.w3.org/topic/HCLSIG and http://esw.w3.org/topic/HTML/Teleconferences and info about mibbit at the end of this message. Cheers, Scott Conference Details * Date of Call: Thursday October 1, 2009 * Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 17:00 Central European Time (CET) * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS). * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC) * Duration: ~1h * Convener: Scott * Scribe: TBD Agenda * News Updates by BioRDF, COI, LODD, Pharma Ontology, Scientific Discourse, Terminology - All * Next F2F - All * Collecting use cases for new SPARQL features * Provenance Incubator Group - Scott * SKOS testimonial from HCLS * Semantic Web Applications and Tools for the Life Sciences Workshop, Abstracts due: Oct. 5 - Scott * AOB IRC * If you do not have an IRC client installed on your computer, you can get one of the many free one (search irc client and your platform), or you can use a web-based client. One possible web-based client you might try is Mibbit (http://www.mibbit.com/chat/). If you use mibbit, fill out the blanks like this: you need to click on Server (highlighted in red in attached image) to reveal the Server address field. NOTE: this meeting will use the hcls channel. (Note that I suggest using port 80 from mibbit. The W3C irc server supports this, and it neatly bypasses enterprise firewall issues that many users seem to be having with port 6667.)
Re: BioRDF Telcon
The minutes for yesterday's BioRDF call are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/09-28_Conference_Call Thanks to Eric for scribing and Huajun for giving an informative presentation on TCM and Semantic Web. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held on Monday, September 28 (see details below). This time the call will be held at 10 am EDT (4 pm CET) instead of the regular time (11 am EDT/5pm CET) because our guest speaker (Huajun Chen) is located in a time zone that is 12 hours ahead of the EDT. Therefore, we decided to make some accommodation to meet earlier this time. I also edited the BioRDF part the google calendar that Eric had created: http://www.google.com/calendar/embed?src=w3.hcls%40gmail.com Thanks to Eric for creating this shared calendar. We should think about how to use more web 2.0 ways to help facilitate/coordinate HCLS activities. Cheers, -Kei == Conference Details == * Date of Call: Monday September 28, 2009 * Time of Call: 10:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call introduction (Kei) * HCLS KB update (Matthias, Adrian) * F2F meeting (All) * Semantic Web Development for Traditional Chinese Medicine: a Report for Current Status (Huajun) * QA (All)
Re: BioRDF Telcon
We're currently resolving a technical issue with Zakim. In the meantime, Huajun's slides can be downloaded via the following: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup?action=AttachFiledo=gettarget=W3C-Group.ppt -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held on Monday, September 28 (see details below). This time the call will be held at 10 am EDT (4 pm CET) instead of the regular time (11 am EDT/5pm CET) because our guest speaker (Huajun Chen) is located in a time zone that is 12 hours ahead of the EDT. Therefore, we decided to make some accommodation to meet earlier this time. I also edited the BioRDF part the google calendar that Eric had created: http://www.google.com/calendar/embed?src=w3.hcls%40gmail.com Thanks to Eric for creating this shared calendar. We should think about how to use more web 2.0 ways to help facilitate/coordinate HCLS activities. Cheers, -Kei == Conference Details == * Date of Call: Monday September 28, 2009 * Time of Call: 10:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call introduction (Kei) * HCLS KB update (Matthias, Adrian) * F2F meeting (All) * Semantic Web Development for Traditional Chinese Medicine: a Report for Current Status (Huajun) * QA (All)
Re: BioRDF Telcon
Instead of using the regular code 4257 please use 26632 (followed by the # sign). -Kei Kei Cheung wrote: We're currently resolving a technical issue with Zakim. In the meantime, Huajun's slides can be downloaded via the following: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup?action=AttachFiledo=gettarget=W3C-Group.ppt -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon call will be held on Monday, September 28 (see details below). This time the call will be held at 10 am EDT (4 pm CET) instead of the regular time (11 am EDT/5pm CET) because our guest speaker (Huajun Chen) is located in a time zone that is 12 hours ahead of the EDT. Therefore, we decided to make some accommodation to meet earlier this time. I also edited the BioRDF part the google calendar that Eric had created: http://www.google.com/calendar/embed?src=w3.hcls%40gmail.com Thanks to Eric for creating this shared calendar. We should think about how to use more web 2.0 ways to help facilitate/coordinate HCLS activities. Cheers, -Kei == Conference Details == * Date of Call: Monday September 28, 2009 * Time of Call: 10:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call introduction (Kei) * HCLS KB update (Matthias, Adrian) * F2F meeting (All) * Semantic Web Development for Traditional Chinese Medicine: a Report for Current Status (Huajun) * QA (All)
BioRDF Telcon
This is a reminder that the next BioRDF telcon call will be held on Monday, September 28 (see details below). This time the call will be held at 10 am EDT (4 pm CET) instead of the regular time (11 am EDT/5pm CET) because our guest speaker (Huajun Chen) is located in a time zone that is 12 hours ahead of the EDT. Therefore, we decided to make some accommodation to meet earlier this time. I also edited the BioRDF part the google calendar that Eric had created: http://www.google.com/calendar/embed?src=w3.hcls%40gmail.com Thanks to Eric for creating this shared calendar. We should think about how to use more web 2.0 ways to help facilitate/coordinate HCLS activities. Cheers, -Kei == Conference Details == * Date of Call: Monday September 28, 2009 * Time of Call: 10:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call introduction (Kei) * HCLS KB update (Matthias, Adrian) * F2F meeting (All) * Semantic Web Development for Traditional Chinese Medicine: a Report for Current Status (Huajun) * QA (All)
Re: BioRDF Telcon
Hi Helen, Thanks for circulating the link to EFO and the associated mapping application. For annotating neuroscience microarray experiments, for example, we need a rich-enough collection of neuroscience concepts and relationships. I hope your interaction with the neurolex group will help in this regard. Best, -Kei Helen Parkinson wrote: One of my action items following the call was to circulate a link to a text-ontology mapping application https://sourceforge.net/projects/efo/files/ It's a perl implementation of the metaphone algorithm and we use it to map free text values entered via our older annotation tools to ontology terms vs an OWL or OBO format ontology. The performance depends largely on how well the ontology is aligned with the input data, for this reason we developed our own ontology. It's being used in EBI and also by colleagues at UPenn Comments and questions welcome, Tomasz Adamusiak is the developer and cc'd if there are any questions thanks Helen Kei Cheung wrote: The minutes of today's BioRDF call are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/08-31_Conference_Call Thanks to: Helen for giving a report on neuroscience mciroarray data curation; Sudeshna for giving an informative presentation; Lena for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon. call will be held at 11 am EDT (5 pm CET) on Monday, August 31 (see details below). The description of the microarray use case is available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Cheers, -Kei == Conference Details == * Date of Call: Monday August 31, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call and introduction (Kei) * HCLS KB update (Matthias, Adrian) * Update on neuroscience microarray data curation (Helen) * Presentation: Semantic Annotation of Genomics Experiments (Sudeshna) * QA and discussion (All)
Re: BioRDF Telcon
Nigam Shah wrote: On Tue, Sep 1, 2009 at 6:37 AM, Helen Parkinson parkin...@ebi.ac.uk mailto:parkin...@ebi.ac.uk wrote: The performance depends largely on how well the ontology is aligned with the input data, for this reason we developed our own ontology. This is very true. However, if there is already an existing ontology that matches the input data well (e.g. the NCI Thesaurus in case of Tissue Microarray Annotations in TMAD (http://tma.stanford.edu/) .. then its possible to use the annotator tool at NCBO (http://bioportal.bioontology.org/annotate). Regards, Nigam. I notice that EFO is accessible through BioPortal. As the Neurolex group is in the process of updating NIFSTD, perhaps the new version of NIFSTD may also be made accessible through BioPortal when it's ready. Thanks, -Kei
Re: BioRDF Telcon
Thanks for letting us know, Maryann. -Kei Maryann Martone wrote: It is already. On Sep 1, 2009, at 11:58 AM, Kei Cheung wrote: Nigam Shah wrote: On Tue, Sep 1, 2009 at 6:37 AM, Helen Parkinson parkin...@ebi.ac.uk mailto:parkin...@ebi.ac.uk wrote: The performance depends largely on how well the ontology is aligned with the input data, for this reason we developed our own ontology. This is very true. However, if there is already an existing ontology that matches the input data well (e.g. the NCI Thesaurus in case of Tissue Microarray Annotations in TMAD (http://tma.stanford.edu/) .. then its possible to use the annotator tool at NCBO (http://bioportal.bioontology.org/annotate). Regards, Nigam. I notice that EFO is accessible through BioPortal. As the Neurolex group is in the process of updating NIFSTD, perhaps the new version of NIFSTD may also be made accessible through BioPortal when it's ready. Thanks, -Kei Maryann Martone Professor-In-Residence Dept of Neurosciences University of California, San Diego San Diego, CA 92093-0446 Tel: 858 822 0745 Fax: 858 246 0644
Re: BioRDF Telcon
The minutes of today's BioRDF call are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/08-31_Conference_Call Thanks to: Helen for giving a report on neuroscience mciroarray data curation; Sudeshna for giving an informative presentation; Lena for scribing. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon. call will be held at 11 am EDT (5 pm CET) on Monday, August 31 (see details below). The description of the microarray use case is available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Cheers, -Kei == Conference Details == * Date of Call: Monday August 31, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call and introduction (Kei) * HCLS KB update (Matthias, Adrian) * Update on neuroscience microarray data curation (Helen) * Presentation: Semantic Annotation of Genomics Experiments (Sudeshna) * QA and discussion (All)
BioRDF Telcon
This is a reminder that the next BioRDF telcon. call will be held at 11 am EDT (5 pm CET) on Monday, August 31 (see details below). The description of the microarray use case is available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Cheers, -Kei == Conference Details == * Date of Call: Monday August 31, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call and introduction (Kei) * HCLS KB update (Matthias, Adrian) * Update on neuroscience microarray data curation (Helen) * Presentation: Semantic Annotation of Genomics Experiments (Sudeshna) * QA and discussion (All)
Re: BioRDF Telcon
The minutes for today's BioRDF telcon are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009-08-17_Conference_Call Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF telcon. call will be held at 11 am EDT (5 pm CET) on Monday, August 17 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday August 17, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call and introduction (Kei) * TCM data update (Jun) * Microarray use case discussion (All)
BioRDF Telcon
This is a reminder that the next BioRDF telcon. call will be held at 11 am EDT (5 pm CET) on Monday, August 17 (see details below). Cheers, -Kei == Conference Details == * Date of Call: Monday August 17, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call and introduction (Kei) * TCM data update (Jun) * Microarray use case discussion (All)
