16:04:16 RRSAgent has joined #HCLS 16:04:16 logging to http://www.w3.org/2012/02/21-HCLS-irc 16:04:25 +Bosse 16:05:09 meeting: HCLS IG weekly: HCLS Pharmceutical in Clinical Research 16:05:32 +mscottm2 16:05:37 chair: Vijay Bulusu 16:05:40 mscottm2 has joined #hcls 16:06:50 scribenick: ericP 16:07:35 topic: Vijay introduction 16:07:43 vbulusu: work in pharma 16:07:53 ... invited by ericP to chair HCLS 16:08:18 ... the cochairs and ericP discussed domain-specific calls for: 16:08:20 ... .. interest to industry 16:08:33 ... .. task force coodination 16:08:40 ... there are two TFs in this focus: 16:08:53 ... .. Systems Bio, chair: Helena Deus 16:09:19 ... .. Pharmacogenomics, chair: Michel Dumontier 16:09:32 ... looking for new ideas and use cases for these task forces 16:09:47 ... will discuss a new task force for which I'm recruiting members 16:10:06 topic: Systems Biology for Drug Discovery 16:10:19 Helena: in Bio, many things go wrong at the pathway level 16:10:31 ... e.g. signally pathway failures result in cancer 16:10:50 ... so we'll look at data made available by TCGA 16:11:05 ... RDF-izing the 8.3TB of TCGA is unreallistic 16:11:24 ... instead we'll take data from 8 or 9 interesting proteins 16:11:44 ... annotate the proteins with results [from TCGA] 16:12:29 ... we need to look for TCGA resources and extract the 8 or 9 target proteins 16:12:36 ... first telco this week 16:12:54 ... at the beginning, we'll be recruiting participants 16:13:11 ... i've heard lots of interest 16:13:24 vbulusu: who do you have alread? 16:13:50 Helena: Jun Zao, ericP, Michael Miller (Institute for Systems Bio) 16:14:20 ... hoping to recruit more bioinformatisists (as opposed to computer geeks) 16:14:33 vbulusu: overlap with Sylventa's BEL Framework? 16:14:51 Helena: there's a lot of overlap. expect to use their vocabs 16:15:04 ... they're not annotating experimental data as far as i know 16:16:00 ... michel demo'd SBML last week. should be relevent 16:16:54 ericP: Ted Slater described thinking of BEL in terms of a surface syntax for RDF 16:17:44 ACTION: ericP to connect Ted Slater to Helena 16:18:30 ACTION: ericP to connect Dave Hau to Helena 16:20:34 -[IPcaller] 16:21:21 mscottm2: Sylventa said they wanted to put BEL forward as a standard. have they come to W3C? 16:22:14 http://selventa.com/technology/bel-framework 16:22:47 ericP: they spoke about the openness in a presentation at the Cambridge Semantic Web Gathering 16:23:04 Helena: my current wiki page is about recruitment 16:23:43 ... people in this group expect to work bottom-up 16:23:54 ... people say what they expect to achieve 16:24:12 http://www.w3.org/wiki/HCLSIG/SysBio 16:24:17 michel: would like to see some structure, expected outcomes 16:24:29 Helena: i can add vision and goals to the wiki 16:25:01 vbulusu: adding the members will help 16:25:07 achille_z has joined #hcls 16:25:21 vbulusu: do you need pharma folks? 16:25:27 Helena: desparately 16:25:39 vbulusu: bioinformatics and systems bio focus? 16:25:50 Helena: the bioinformatics is just how to glue stuff together 16:26:10 ... exploring our models to see if we can learn stuff about the biology 16:26:44 ACTION: vbulusu to recruit in pharma for Systems Biology for Drug Discovery 16:27:05 +[IPcaller] 16:27:16 matthias_samwald1 has joined #hcls 16:27:24 michel: IO-Informatics might be interested 16:27:56 Helena: will reach out to Eric Gombocz 16:28:23 topic: Pharmacogenomics 16:28:46 michel: we'll be looking at data related to pharmacogenomics 16:28:50 ... e.g. 16:28:56 ... .. patient stratification 16:29:00 ... .. risk assessment 16:29:08 ... .. dosing 16:29:26 ... gathering related data, e.g.: 16:29:34 ... .. clinical trial outcome 16:29:43 ... .. efficacy 16:30:01 ... we can marshal data from e.g. PharmGKB, or clinical trial 16:30:11 ... wherever we can map genotype to phenotype 16:30:27 ... idea is that we have a pharmacogenomics KB 16:30:42 ... i got clinical annotation from PharmGKB 16:30:57 ... PGKB license issue: 16:31:03 ... .. you need to apply for access 16:31:10 ... .. you can't redistribute 16:31:33 ... maybe we can negotiate, but barring that, we can make available the [triplifying] scripts 16:31:55 ... we want to ask questions of the KB, with inference 16:32:07 ... will support Clinical Decision Support 16:32:26 ... we have folks from: 16:32:30 -[IPcaller] 16:32:30 ... .. mayo clinic 16:32:39 ... .. variety of academic institutions 16:33:02 +[IPcaller] 16:33:11 ... missing industry, e.g. those interested in clinical trials or FDA [,EMA] submissions, adverse event reporting 16:33:57 vbulusu: looking at use cases, have you looked at how to select a smaller set of use cases? 16:34:18 michel: this [wiki] list is from the relevent TMO use cases 16:34:36 ... some from IO-Informatics, and mscottm2 had breast cancer use cases 16:34:43 ... so yes, we need to identify a small set 16:34:58 matthias_samwald has joined #hcls 16:35:06 ... potentially, each individual can set up a use case which drives their personal interests 16:35:49 ... i expect significant overlap due to the paucity of data 16:36:36 ... gene expression, DBSNP, performance of (anti-rejection) drugs 16:37:44 ericP: feel free to be a tyrant 16:39:23 vbulusu: pharma focused on precision medicine 16:40:01 ... mostly these folks would be interested in joining the HCLS community where it can give them quick answers 16:41:10 topic: recruitment 16:41:42 michel: we can ask industry what they need done, and peridically get sanity checks 16:41:53 ... but in the end, we want assurances of adoption 16:42:25 mscottm2: great if you can find someone in a hospital or pharma setting who's not expecting a shrink-wrapped solution 16:42:33 ... get them to bring us interesting problems 16:43:12 ... most folks in those settings don't see the prob with working in monolithic applications 16:44:31 someone who can bring a problem for us to solve and become a sort of 'client' 16:45:26 Helena: have you looked at pharmacoglycomics? 16:45:39 mscottm2: looked at some sugars when i was an underground 16:46:12 michel: looked at some sugars when i was an underground 16:46:23 ... know folks at bioCanada who look at e.g. qualitiy of peptides ... 16:46:58 Helena: if you know the glycosimation patter, you can predict binding 16:47:06 s/was an underground/was an undergrad/ 16:47:41 glycosylation 16:48:11 s/glycosimation patter/glycosylation pattern/ 16:49:01 topic: task force for rendering experimental information in an open manner 16:49:54 vbulusu: in 2009, Pistoia started an Electronic Lab Notebook working group to exploit the info captured in (different) ELNs 16:50:06 ... also to share info in the pharma with other organizations 16:50:43 ... looking at what they've done, they worked for a year trying to create ELN standards so that e.g. CambridgeSoft data could work with Exceleris 16:50:55 http://www.pistoiaalliance.org/ 16:51:06 ... they stopped in early 2011 when some members didn't adopt and proposed standards 16:51:16 ... need is still out there. 16:51:52 ... pharmas need to exchange with Clinical Research Organizations 16:52:06 ... every pharma will say they need standards in this space 16:53:35 ... expect to start with formulation chemistry, not biology 16:55:05 eric, correction "expect to start with medicinal chemistry", not formulation chemistry 16:55:22 ericP: access control in ELN for example for CROs, capture somethings in BEL framework. 16:56:27 http://www.w3.org/2012/hcls-resources/pipeline.svg 16:57:10 http://www.sciencedirect.com/science/article/pii/S1359644609000737 16:57:30 michel: met Jeremy Fray (S'Hampton) has been working on chem lab notebooks 16:57:46 ... he's got a representation for synthetic chemistry 16:58:04 ... track whether you are doing stuff in the right order, and what are the values you're obtaining 16:58:54 Michel mentions Peter Murray-Rust / Cambridge (Open Knowledge Foundation) in the context of patents 16:59:05 ... Peter Murray Rust validates patents by seeing if the chemical processes follow a single transformation 16:59:27 vbulusu: looked at Rust, and Jeremy's work is definitely in line. good connections 17:00:04 michel: i don't think Jeremy focuses on inferencing; just capture for later SPARQL query 17:00:24 ... BEL may be more focused on inferencing 17:01:02 a(foo) upregulates b(c(bar)) . 17:03:34 RRSAgent, please draft minutes 17:03:34 I have made the request to generate http://www.w3.org/2012/02/21-HCLS-minutes.html ericP 17:03:46 -EricP 17:03:47 -Sean_Martin 17:03:48 -Bosse 17:03:50 -Helena 17:03:51 RRSAgent, please make log world-visible 17:03:53 -michel 17:03:55 Thaks everyone! 17:04:02 -mscottm2 17:04:47 -[IPcaller] 17:04:48 SW_HCLS()11:00AM has ended 17:04:48 Attendees were [IPcaller], Helena, Sean_Martin, michel, EricP, Bosse, mscottm2 17:09:11 vbulusu has joined #hcls 17:09:32 eric? 17:51:57 matthias_samwald has joined #hcls 17:54:25 matthias_samwald1 has joined #hcls 19:46:00 matthias_samwald has joined #hcls 20:37:44 mscottm2 has joined #hcls 21:38:59 matthias_samwald has joined #hcls