14:52:59 <RRSAgent> RRSAgent has joined #hcls
14:52:59 <RRSAgent> logging to http://www.w3.org/2010/08/16-hcls-irc
14:53:09 <kei> Zakim, this will be BioRDF
14:53:09 <Zakim> ok, kei; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 7 minutes
14:53:31 <kei> agenda+ introduction [Kei]
14:54:09 <kei> agenda+ genelist rdf representation [Lena, Satya, Jun, Michael, Scott]
14:54:48 <kei> agenda+ paper submission to ISWC/SWPM-2010 [All[
14:55:06 <kei> Zakim, take up next agendum
14:55:06 <Zakim> agendum 1. "introduction" taken up [from Kei]
14:55:14 <kennyluck> kennyluck has left #hcls
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14:59:04 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
14:59:11 <Zakim> + +1.510.387.aaaa
14:59:59 <ericP> Zakim, pleae dial ericP-office
14:59:59 <Zakim> I don't understand 'pleae dial ericP-office', ericP
15:00:07 <ericP> Zakim, please dial ericP-office
15:00:07 <Zakim> ok, ericP; the call is being made
15:00:08 <Zakim> +EricP
15:01:27 <Zakim> -EricP
15:01:30 <Zakim> +Kei_Cheung
15:01:33 <ericP> Zakim, please dial ericP-office
15:01:33 <Zakim> ok, ericP; the call is being made
15:01:34 <Zakim> +EricP
15:02:41 <Zakim> +[IPcaller]
15:02:43 <jun> jun has joined #hcls
15:03:19 <Zakim> + +1.832.386.aabb
15:04:04 <LenaDeus> LenaDeus has joined #hcls
15:04:53 <Zakim> + +1.650.319.aacc
15:05:14 <mscottm> Zakim, +1.650.319.aacc is mscottm
15:05:14 <Zakim> +mscottm; got it
15:06:17 <mscottm> Zakim, who is here?
15:06:17 <Zakim> On the phone I see +1.510.387.aaaa, EricP, Kei_Cheung, [IPcaller], +1.832.386.aabb, mscottm
15:06:19 <Zakim> On IRC I see LenaDeus, jun, mscottm, RRSAgent, Zakim, kei, egonw_, ericP
15:06:40 <kei> scribenick jun
15:07:47 <jun> topic: RDF gene expression representation and the provenance paper
15:11:00 <jun> Kei: let's start with the RDF structure of the gene list
15:12:16 <jun> Kei: last time, we agreed to let Lena to try some queries with the current structure
15:12:27 <kei> http://esw.w3.org/HCLSIG_BioRDF_Subgroup/QueryFederation2
15:12:31 <jun> Lena: I tried the queries shared in the google doc
15:13:04 <jun> Lena: Which gene is overexpressed in the brain region "Entorhinal cortex"? 
15:13:42 <jun> Lena: we can't do the first query, Find experiments involving the same disease/phenotype, brain region, and species
15:14:19 <jun> Kei: we do have experiments sharing the same condition or experimental context, such as brain regions
15:15:00 <jun> Kei: it's true that it's hard to find genes that are commonly expressed in different brain regions
15:19:39 <Chuck> Chuck has joined #hcls
15:20:15 <michael> michael has joined #hcls
15:22:38 <jun> Scott: will try to find some queries along the line of provenance information
15:22:38 <Zakim> + +1.206.605.aadd
15:31:30 <jun> michael: the different array design 1, 2 would lead to different probe ids
15:32:28 <jun> michale: agree with Lena that by the time they get to the gene list, the different versions of probe design wouldn't matter any more
15:32:52 <jun> Kei: they may only need to go back to the raw datasets when they want to repeat the experiments themselves
15:34:55 <jun> michael: people have done analysis over the process of experiment and realised that the process was not good
15:38:22 <michael> not so much the process as the actual oligos used for the probe set not matching the target gene
15:40:19 <jun> Scott: it could be easy to use provenance to demonstrate how we can choose which dataset is more recent than another.
15:40:36 <jun> Jun: we have published this use case in ipaw 2010
15:41:35 <jun> Lena: I have played with the javascript library for query federation
15:43:16 <jun> Lena: how can we publish a voiD description for the gene lists?
15:45:55 <jun> Lena: I have added the example queries in the google doc
15:47:23 <ericP> SPARQL -npq \
15:47:32 <ericP>   -M '<r12> CONSTRUCT { ?s <p1> ?o1 ; <p2> ?o2 } WHERE { SERVICE <S12> { ?s <p1> ?o1 ; <p2> ?o2 } }' \
15:47:39 <ericP>   -M '<r23> CONSTRUCT { ?s <p2> ?o2 ; <p3> ?o3 } WHERE { SERVICE <S23> { ?s <p2> ?o2 ; <p3> ?o3 } }' \
15:47:48 <ericP>   -e 'SELECT * WHERE { ?x1 <p1> ?n1 ; <p2> ?n2 ; <p3> ?n3 }'
15:54:30 <jun> Kei: can voiD help with decomposing the query
15:54:55 <jun> Eric: I am only using my rules in my implementation
15:56:22 <jun> Kei: could Lena incorporate the query federation and voiD part for the paper demo?
15:56:40 <jun> Lena: Lena will work on this with Eric offline
15:57:54 <jun> Kei: summarize the paper status: 1) we should add new authors if appropriate; 2) I completed the introduction section and need to polish it;
15:58:58 <jun> ... 3) we should continue to work on the google doc in parallel, including the method and implementation sections, and finalize the demo examples;
15:59:22 <jun> ... 4) we can schedule additional calls for this week
16:01:09 <jun> Eric: maybe Lena and I could spend some time together and let the rest of the group know about our findings
16:01:50 <Zakim> - +1.510.387.aaaa
16:04:30 <mscottm> I have to go to the Terminology call - bye!
16:04:36 <Zakim> -mscottm
16:04:52 <michael> what is the URL for the go0ogle doc? thanks
16:05:37 <jun> we will have an intermediate call this Friday, 12:00 EST, using the hcls line
16:06:37 <ericP> eric+google@w3.org
16:06:52 <Zakim> -Kei_Cheung
16:06:54 <Zakim> - +1.206.605.aadd
16:06:55 <Zakim> -[IPcaller]
16:07:22 <kei> RRSAgent, please draft minutes
16:07:22 <RRSAgent> I have made the request to generate http://www.w3.org/2010/08/16-hcls-minutes.html kei
16:07:32 <kei> RRSAgent, please make log world-visible
16:15:54 <ericP> SELECT *  WHERE { { SERVICE <S12> { ?x1 <p1> ?n1 . ?x1 <p2> ?n2 . }
16:15:54 <ericP>                     SERVICE <S23> { ?x1 <p2> ?_r23_0_o2 . ?x1 <p3> ?n3 . } }
16:15:54 <ericP>             UNION { SERVICE <S12> { ?x1 <p1> ?n1 . ?x1 <p2> ?_r12_1_o2 . }
16:15:54 <ericP>                     SERVICE <S23> { ?x1 <p2> ?n2 . ?x1 <p3> ?n3 . } } }
16:17:51 <LenaDeus> SELECT * WHERE {   ?gene rdf:type :gene .   ?gene rdfs:label ?geneName .  SERVICE <http://hcls.deri.org/sparql> { ?diseasomeGene rdfs:label ?geneName .  ?disease diseasome:associatedGene ?diseasomeGene.  ?disease rdfs:label ?diseaseName . }  }
16:18:33 <LenaDeus> SELECT * WHERE {   SERVICE <http://ibl.mdanderson.org/~mhdeus/sparql_federation/endpoint2.php> { ?gene rdf:type :gene .   ?gene rdfs:label ?geneName .  } SERVICE <http://hcls.deri.org/sparql> { ?diseasomeGene rdfs:label ?geneName .  ?disease diseasome:associatedGene ?diseasomeGene.  ?disease rdfs:label ?diseaseName . }  }
16:21:04 <michael> quit
16:22:00 <ericP> http://sourceforge.net/projects/swobjects/
16:32:42 <ericP> chmod +x SPARQL11
16:34:02 <ericP> ./SPARQL -e '...'
16:35:20 <ericP> ./SPARQL11 --help
16:36:08 <ericP> ./SPARQL11 --debug 1 -e ...
16:39:49 <Zakim> - +1.832.386.aabb
16:39:52 <Zakim> -EricP
16:39:53 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:39:55 <Zakim> Attendees were +1.510.387.aaaa, EricP, Kei_Cheung, [IPcaller], +1.832.386.aabb, mscottm, +1.206.605.aadd
16:41:00 <egonw_> egonw_ has joined #hcls
16:44:01 <ericP> LenaDeus, feel free to type progress reports here; i'll read back when i return
17:25:32 <LenaDeus> hi Eric, here is my code: ./SPARQL11 -e 'PREFIX : <http://purl.org/net/biordfmicroarray/ns#>  PREFIX diseasome: <http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT * WHERE { SERVICE <http://ibl.mdanderson.org/~mhdeus/sparql_federat
17:25:43 <LenaDeus> damn... I'll use paste bin
17:31:11 <LenaDeus> here is the input: http://pastebin.org/559155
17:31:19 <LenaDeus> and the output: http://pastebin.org/559384
17:32:05 <LenaDeus> It tells me that host of "http://ibl.mdanderson.org/~mhdeus/sparql_federation/endpoint2.php" is not found
17:32:15 <LenaDeus> is there anything that I could be doing wrong?
17:39:12 <ericP> LenaDeus, will check in 5 mins
17:39:41 <ericP> (on android now)
17:48:55 <ericP> LenaDeus, nice timing; looks like pastebin is down
17:53:00 <LenaDeus> really?
17:53:16 <LenaDeus> over here it seems to be working...
17:54:53 <ericP> ahh, back now
17:55:09 <Lena> Lena has joined #hcls
17:56:54 <ericP> i see we are less formal now
17:57:05 <Lena> >(
17:57:10 <Lena> :)
17:57:16 <Lena> this is linux-lena
17:58:13 <ericP> ahh, easier to paste, i bet
17:58:19 <Lena> yep
17:58:23 <ericP> http://pastebin.org/559155 gave me http://pastebin.org/559695
17:59:11 <Lena> that is exactly what I was expecting! how did you do that?!?
17:59:22 <ericP> which demonstrates a certain challenge in dealing with what virtuos is willing to parse
17:59:58 <Lena> could it be something in the configuration?
18:00:13 <ericP> eric@ubu:~/checkouts/swobjects/bin$ sum ./SPARQL11
18:00:13 <ericP> 28887 21195
18:00:32 <ericP> (to test that we're playing with the same executable)
18:00:49 <ericP> i don't see how any configuration could creep into this
18:02:56 <Lena> 09042  5689
18:03:07 <Lena> different version...?
18:03:45 <ericP> try downloading again from sourceforge
18:03:51 <ericP> who knows how old the one you got was
18:03:57 <ericP> also, you can try ./SPARQL11 --service http://ibl.mdanderson.org/~mhdeus/sparql_federation/endpoint2.php -e 'PREFIX : <http://purl.org/net/biordfmicroarray/ns#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT * WHERE { ?gene a :gene .  ?gene rdfs:label ?geneName . }'
18:04:30 <Lena> I noticed you released a new sparql11 on sourceforge
18:04:50 <ericP> yeah, that's the one i was uploading as we were talking
18:05:05 <Lena> Host not found (authoritative)
18:05:12 <ericP> the above query gives me 562 answers.
18:05:20 <ericP> weird
18:05:27 <Lena> I'll try with that version
18:07:01 <Lena> now sum returns the same as yours...
18:07:10 <Lena> but still giving me Host not found (authoritative)
18:09:01 <ericP> try prepending with strace -fo mdanderson.org.strace ./SPARQL11...
18:09:53 <Lena> same thing 
18:10:17 <Lena> also said [ Process PID=2650 runs in 32 bit mode. ]
18:10:38 <ericP> now you should have a file called mdanderson.org.strace which tells a bit about what library calls were made
18:11:01 <Lena> where can I find those?
18:11:32 <ericP> let me switch to a more formal command notation: using $(cmd) to signify typing "cmd" on the command line
18:11:59 <ericP> can you $(wc mdanderson.org.strace) ?
18:12:13 <ericP> actually, can you $(telnet ibl.mdanderson.org 80) ? that might tell us a lot
18:12:53 <Lena> Trying 143.111.251.220... Connected to dqspub1.mdacc.tmc.edu. Escape character is '^]'.
18:14:56 <ericP> ok, let's look at the strace output
18:16:02 <ericP> $(wc mdanderson.org.strace)
18:16:16 <ericP> or maybe paste it into pastebin
18:17:07 <Lena> wc: mdanderson.org.strace: No such file or directory
18:17:31 <ericP> odd, $(strace -fo mdanderson.org.strace ./SPARQL11...) should have created such a file
18:17:56 <ericP> and we know it worked 'cause you saw [ Process PID=2650 runs in 32 bit mode. ]
18:17:57 <Lena> (this is ubuntu, if that's any help...)
18:18:28 <ericP> it's apparently a 64bit machine; i wonder if that confuses things
18:18:32 <Lena> i'll try again 
18:19:24 <ericP> to be more clear, i mean $(strace -fo mdanderson.org.strace ./SPARQL11 --service http://ibl.mdanderson.org/~mhdeus/sparql_federation/endpoint2.php -e 'PREFIX : <http://purl.org/net/biordfmicroarray/ns#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT * WHERE { ?gene a :gene .  ?gene rdfs:label ?geneName . }')
18:22:14 <Lena> ok, now the file is there
18:22:16 <Lena> opening it
18:22:41 <ericP> if you dump it in pastebin, i'll compare it to mine
18:23:10 <Lena> http://pastebin.org/560695
18:23:15 <ericP> tx
18:23:51 <Lena> ups... I have to go
18:24:10 <Lena> are you around tomorrow so we can continue this? :)
18:24:44 <Lena> I will leave irc on
18:26:14 <Lena> worse case scenario you send me the output of the query and we put that in the paper ;-)
18:26:58 <ericP> yeah, but that seems so anticlimactic
18:27:04 <ericP> sure, i'll be here tomorrow
18:27:23 <Lena> thanks, talk to you tomorrow
18:27:25 <ericP> i'll try to get my morning work done tonight so we can geek some in the am
18:27:29 <ericP> ciao
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