14:57:13 <RRSAgent> RRSAgent has joined #BioRDF
14:57:13 <RRSAgent> logging to http://www.w3.org/2007/08/27-BioRDF-irc
14:57:20 <ericP> Zakim, this will be BioRDF
14:57:20 <Zakim> ok, ericP; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 3 minutes
14:58:29 <matthiassamwald> matthiassamwald has joined #biordf
14:58:34 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
14:58:42 <Zakim> +Don_Doherty
14:59:13 <Zakim> +??P14
15:00:13 <ericP> agenda + URI note - Jonathan [Susie]
15:00:16 <ericP> agenda?
15:00:38 <ericP> agenda+ Demo extensions - Alan [Susie]
15:00:50 <ericP> agenda+ Documentation of SenseLab conversion - Kei [Susie]
15:01:06 <ericP> agenda+ Use cases - All [Susie]
15:01:18 <ericP> agenda+ AOB [Susie]
15:01:23 <Zakim> +Susie
15:01:33 <Zakim> +??P19
15:02:06 <Zakim> +EricP
15:02:50 <matthiassamwald> p14 is me
15:02:52 <ericP> Zakim, who is here?
15:02:52 <Zakim> On the phone I see Don_Doherty, ??P14, Susie, ??P19, EricP
15:02:53 <Zakim> On IRC I see matthiassamwald, RRSAgent, Zakim, Don, ericP
15:03:03 <ericP> Zakim, ??P14 is matthiassamwald 
15:03:03 <Zakim> +matthiassamwald; got it
15:03:14 <Zakim> +Alan
15:03:46 <Zakim> +Kei_Cheung
15:03:53 <Zakim> +Scott_Marshall
15:04:00 <ericP> Zakim, ??P19 is DanielRuben
15:04:00 <Zakim> +DanielRuben; got it
15:04:16 <ericP> chair: Susie
15:04:21 <ericP> scribe: ericP
15:04:30 <ericP> agenda?
15:05:01 <ericP> agenda+ text mining [Scott_Marshall]
15:06:28 <ericP> ACTION: Susie to ask Johnathan what he needs for TAG access
15:06:52 <mscottm> mscottm has joined #biordf
15:06:55 <ericP> ericP: not sure what more direct access there could be
15:07:05 <ericP> Zakim, take up agendum 2
15:07:05 <Zakim> agendum 2. "Demo extensions - Alan" taken up [from Susie via ericP]
15:07:15 <ericP> Zakim, take up agendum 4
15:07:15 <Zakim> agendum 4. "Use cases - All" taken up [from Susie via ericP]
15:07:17 <ericP> Zakim, take up agendum 3
15:07:17 <Zakim> agendum 3. "Documentation of SenseLab conversion - Kei" taken up [from Susie via ericP]
15:07:47 <ericP> Kei: we have created a wiki page documenting the senslab conversion
15:07:59 <matthiassamwald> http://esw.w3.org/topic/HCLS/Senselab_Conversion
15:08:38 <ericP> Kei: we converted NeuronDB to RDF and later to OWL
15:08:56 <ericP> ... in this, we learned ontology design features
15:09:28 <ericP> ... was focused on the NeuronDB database structure
15:09:49 <alanr> alanr has joined #biordf
15:09:53 <ericP> ... matthiassamwald joined the team and helped convert to a more generic OWL structure
15:10:15 <ericP> ... that data was used in the Banff demo
15:10:52 <ericP> ... contents of Senelab's native DB change from time to time
15:11:00 <ericP> ... working out how to reflect in RDF
15:11:09 <ericP> ... considering two-step approach:
15:11:21 <ericP> ... - syntactic conversion to RDF
15:11:35 <ericP> ... ... automated
15:11:47 <ericP> ... - semantic conversion to OWL
15:11:57 <ericP> ... ... needs human intervention
15:11:59 <ericP> ... .
15:12:43 <ericP> ... had a meeting with some HCLS folks about conversion process
15:13:12 <ericP> ... want to make sure we follow best practices and that we track the demo ontology changes
15:13:23 <ericP> Susie: what's the goal, W3C note?
15:13:37 <ericP> Kei: not sure. this is just an initial version
15:13:43 <ericP> ... want feedback from more people
15:13:48 <ericP> ... suggestions?
15:14:27 <ericP> Susie: given that you are grappling with modeling/data/ontology changes, can you call it finished in say, a month?
15:14:49 <ericP> ... and then release future [coherent] versions
15:14:51 <ericP> Kei: seems reasonable
15:15:59 <ericP> ericP: let me know if you'd like to publish it as a SPARQL interface to your database
15:16:09 <ericP> Kei: may be easier with a complete RDF dump
15:16:36 <ericP> ... but some folks may wish to access the DB directly [with queries]
15:16:46 <ericP> Susie: senselab is in Oracle?
15:17:34 <ericP> ... could publish in MySQL and use mapping stuff we're working on [SPASQL]
15:17:51 <ericP> Kei: yes, interested in working on mapping
15:18:14 <ericP> zakim, take up agendum 2
15:18:14 <Zakim> agendum 2. "Demo extensions - Alan" taken up [from Susie via ericP]
15:18:47 <ericP> Don: not on extension yet; still working on installation
15:18:57 <ericP> ... ran into glitch on loading DBs
15:19:40 <ericP> ... we have Virtuoso installed
15:19:43 <ericP> ... running into problem with perl script
15:19:49 <ericP> ... AlanR is helping
15:19:58 <ericP> Susie: any progress on the poster?
15:20:22 <ericP> Don: will be ready to talk about poster in about two weeks
15:21:07 <ericP> ... want to dive into matthiassamwald's poster and target to a neuroscience audience
15:22:20 <ericP> matthiassamwald: will upload my demo to a server and send a pointer to public-semweb-lifesci
15:22:52 <ericP> Susie: AlanR is working with DERI to install DB
15:23:05 <ericP> alanr: DERI has machine back up
15:23:24 <ericP> ... not sure if they've installed Virtuoso
15:23:39 <ericP> ... considering hiring someone to write install scripts
15:23:50 <ericP> ... my schedule should be more calm now
15:23:59 <ericP> ... expect progress in next couple weeks
15:24:10 <ericP> Susie: hosted at MIT in the interim?
15:24:28 <ericP> alanr: yes. dunno if we will always host it
15:25:03 <ericP> Susie: EricN is working on UI
15:25:27 <ericP> ... we considered working with UI experts, but seems we don't want to do that now
15:25:53 <ericP> alanr: I have an idea for a UI; am looking for an implementor
15:26:07 <ericP> ... idea: wiki page with queries
15:26:32 <ericP> ... ... fill in a form to tailor the queries on the wiki
15:27:10 <ericP> ... ... and an interface to add specific predicates and structures for say, MESH
15:27:13 <ericP> ... .
15:27:58 <ericP> ScottM: very interested, but don't want to commit to time
15:28:50 <ericP> matthiassamwald: I will be starting in DERI in october/november
15:29:16 <ericP> alanr: would like an auto-completer like for google search in firefox
15:29:45 <matthiassamwald> http://neuroscientific.net/leeet/
15:30:16 <ericP> [ discussion of related libraries, including leeet and a Sesame-tailored completion engine ]
15:30:33 <ericP> Susie: noting everyone is on vacation, any progress on data conversion?
15:30:38 <ericP> alanr: nope
15:30:41 <matthiassamwald> "Leeet is a Semantic Web application that allows rapid and intuitive creation, editing and querying of Semantic Web content and annotations". It features an autocomplete mechanism based on Sparql queries.
15:30:57 <ericP> ... talked to a fellow from EBI who is interested in expression data
15:31:07 <ericP> ... Marco Brandisi (SP?)
15:32:38 <ericP> Susie: would be interesting to work on DrugDB. will prod people who volunteered
15:33:07 <ericP> ... may be some folks at Lilly who can contribute
15:33:42 <ericP> s/can/will want to /
15:34:37 <alanr> 1) Representing the information about the samples, experiment, protocols leading to the hybridization, technical aspects of the hybridization, etc.
15:34:39 <alanr> 2) Representing what the computed intensity of the spots on an array, as well as how those were computed (e.g. MAS5, rma, d-chip, etc)
15:34:40 <alanr> 3) Representing which genes are thought to be relatively highly expressed by interpreting the intensity of the spots as amount of expression of certain genes.
15:35:21 <ericP> Zakim, take up agendum 4
15:35:21 <Zakim> agendum 4. "Use cases - All" taken up [from Susie via ericP]
15:35:42 <ericP> DanielD: was interested in a use case involving images
15:36:01 <ericP> ... want to work with extending images with semantic annotations
15:36:15 <ericP> susie: we are working on Use Cases in SWEO
15:37:53 <ericP> DanielD: there was a discussion of a hemograph use case
15:38:23 <ericP> s/hemo/mamma/
15:38:37 <ericP> ScottM: I have been working on a mammography study in the netherlands
15:39:04 <ericP> DanielD: expect NCI-backed standard for annotation medical images on the web
15:39:58 <ericP> ... controlled terminologies where possiblem for SNOMED, ... , something for regions
15:40:52 <ericP> [scribe distracted -- missed stuff]
15:41:19 <ericP> alanr: some work on annotations on Alan Brain Atlas
15:41:30 <ericP> ... there are existing region taxonomies
15:43:03 <ericP> ... another connection: Bijan Parsia said he'd be working on spacial reasoning
15:43:11 <ericP> ... (above, near...)
15:43:40 <alanr> s/spacial/spatial/
15:43:54 <ericP> Zakim, take up agendum 6
15:43:54 <Zakim> agendum 6. "text mining" taken up [from Scott_Marshall via ericP]
15:44:17 <mscottm> http://www.biosemantics.org/index.php?page=anni-2-0
15:44:28 <ericP> ScottM: looked at Annie
15:44:50 <ericP> ... nice handling of synonyms for say, protiens
15:45:20 <ericP> ... once you pick a URI system, you will have Biologists who use their own names for, say, protein or gene
15:45:27 <ericP> ... you need a tool to manage the mapping
15:46:17 <ericP> ... done internally in text mining systems
15:47:13 <ericP> ... perhaps we can re-use unique concept identifier techniques from text mining systems
15:48:08 <ericP> ... my group provides web services for text mining packages; does not try text mining packages itself
15:48:24 <ericP> ... albert shuman has a nice overview of different systems
15:48:38 <ericP> ... UIMA framework came up
15:48:49 <ericP> ... migrated from IBM to apache
15:48:59 <ericP> ... makes text mining sysems more inter-operable
15:49:11 <ericP> ... noticed a corpus for huntingtons
15:50:47 <ericP> alanr: working on extraction of named entities (diseases, phenotypes, ... whatever) and interactions
15:51:02 <ericP> ... some results from geneways (SP?)
15:51:07 <ericP> ... still pretty noisy
15:51:23 <ericP> ... all in PDF -- coding to convert to HTML
15:52:03 <ericP> ScottM: Lucine uses PDF format
15:52:33 <ericP> alanr: Lucine treats the document as a bag of words -- scrambling the order won't change the results
15:53:14 <ericP> ... believe HTML is the easiest to work with
15:55:41 <matthiassamwald> Dietrich Rebholz-Schuhmann
15:56:16 <ericP> Susie: can you share Rebholz's tutorial?
15:56:31 <ericP> ScottM: sure -- it's on-line
15:57:07 <ericP> alanr: matthiassamwald wrote some related code
15:57:49 <ericP> matthiassamwald: you can give it a pubmed identifier or query and you get back a list of annotated abstracts
15:57:59 <matthiassamwald> http://whatizit.neurocommons.org
15:58:07 <dlrubin> dlrubin has joined #BioRDF
15:59:33 <alanr> http://svn.neurocommons.org/svn/trunk/nlp/soc_textmining/
16:00:11 <ericP> ScottM: advantage of using web services is that you can point at a service as the provenance of a piece of extracted data
16:00:47 <Zakim> -DanielRuben
16:00:48 <Zakim> -Susie
16:00:49 <Zakim> -Alan
16:00:50 <Zakim> -Scott_Marshall
16:00:50 <Zakim> -Kei_Cheung
16:00:52 <ericP> RRSAgent, please draft minutes
16:00:52 <RRSAgent> I have made the request to generate http://www.w3.org/2007/08/27-BioRDF-minutes.html ericP
16:00:54 <Zakim> -matthiassamwald
16:00:55 <Zakim> -Don_Doherty
16:00:56 <Zakim> -EricP
16:00:57 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:00:59 <Zakim> Attendees were Don_Doherty, Susie, EricP, matthiassamwald, Alan, Kei_Cheung, Scott_Marshall, DanielRuben
16:01:10 <ericP> RRSAgent, please make log world-visible
16:02:30 <dlrubin> dlrubin has left #BioRDF