Re: HCLS chartering/next steps Thur 26 May

Hi, long thread... I'm answering to this post, but I have read through it down (at least to some point, I'm offline now). two things: - as for marketing and engagement of outside community, I'm not sure having technological-oriented task forces is that bad. Sure BioRDF and LODD are confusing, be

Re: HCLS chartering/next steps Thur 26 May

Hi, long thread... I'm answering to this post, but I have read through it down (at least to some point, I'm offline now). two things: - as for marketing and engagement of outside community, I'm not sure having technological-oriented task forces is that bad. Sure BioRDF and LODD are confusing, be

Re: HCLS chartering/next steps Thur 26 May

I see it this way: translational / \ / \ life clinical sci* (aka health care) (aka bio) and life sci includes all the life sciences - metatenomics, environmental, etc. carbon based = organic = life science On May 26, 2011, at 5:29 PM, Michel_Dumontier wrote

RE: HCLS chartering/next steps Thur 26 May

Hi all, The way I see it we have 3 primary application areas: 1 - clinical 2 - translational 3 - life sciences* Each of these present concrete problems that need to be worked on, and I don't think we want to overspecify what those are as they will change with time and with the members that ac

Post doctoral scholar position in Semantic Web and Biomedical Informatics at Case Western Reserve University

Apologies for cross-posting ** Post-doctoral Scholar Position in Semantic Web and Biomedical Informatics   Division for Medical Informatics, Case Western Reserve University, Cleveland, OH   We are seeking candidates at the intersection of computer science, medicine and clinical tra

RE: HCLS chartering/next steps Thur 26 May

hi david and matthais, "(for example, the original idea of BioRDF was mainly to convert biomedical data to RDF, but over the years this also became a major focus of other task forces such as LODD)" along david's point, i would argue that because the problem the two groups are trying to solve, Bio

Re: HCLS chartering/next steps Thur 26 May

On Thu, 2011-05-26 at 16:43 +0200, Matthias Samwald wrote: > I agree with Tim's ideas. The different task forces should be > problem-focused. This would also help to reduce the redundancy between > task forces (for example, the original idea of BioRDF was mainly to > convert biomedical data to RDF,

RE: Minimum information about a mutation

hi joanne, +1! cheers, michael > -Original Message- > From: Joanne Luciano (gmail) [mailto:jluci...@gmail.com] > Sent: Thursday, May 26, 2011 9:31 AM > To: Michael Miller > Cc: Jim McCusker; Chris Baker; w3c semweb HCLS > Subject: Re: Minimum information about a mutation > > sounds like

Emerging Linked Life Data Best Practices W3C Note

Hi; On the Wiki I see that there is a task entitled "Emerging Linked Life Data Best Practices W3C Note" (http://www.w3.org/wiki/HCLSIG#tasks), is anyone working on such note? Cheers -- Mikel Egaña Aranguren, PhD http://mikeleganaaranguren.com Marie Curie post-doc at Ontology Engineering Gro

Re: Minimum information about a mutation

sounds like provenance to me. joanne On May 26, 2011, at 12:15 PM, Michael Miller wrote: > hi jim, > > you're not giving us much to go on, the actual step by step use case would > be great. > >> What is needed for people to trust these observations? > > a description of how the observation wa

RE: HCLS chartering/next steps Thur 26 May

hi tim, my feeling is that we have a problem 'Bio' (specifically gene expression at this point but that focus can change) and we are actively using a semantic web technology 'RDF' as the solution. that is why we are a subgroup and not the entire effort. i believe our problem space gives us a

RE: Minimum information about a mutation

hi jim, you're not giving us much to go on, the actual step by step use case would be great. > What is needed for people to trust these observations? a description of how the observation was made, whatever technology was behind it (looking through a microscope, performing a qPCR assay, mass spec

Re: HCLS chartering/next steps Thur 26 May

Agree - again, same as I said in remarks to Michael Miller. On May 26, 2011, at 11:51 AM, M. Scott Marshall wrote: > Hi Tim, > > I agree with the principle. Just want to point out that the > Terminology task force has been looking at a very specific problem - > detecting discrepancies between

Re: HCLS chartering/next steps Thur 26 May

HI Michael, As I said, problem focused activities hiding in solution-focused groups. The BioRDF group's very name is solution-focused. Granted, over its recent history there has been a strong problem focus in the actual activities, I am thinking of the gene list work here. But someone lookin

Re: Minimum information about a mutation

On May 26, 2011, at 11:44 AM, Jim McCusker wrote: > I'm looking for an agreed upon way to describe observation of > particular functional (AA change) mutations in specific specimens. > What is needed for people to trust these observations? provenance? > > Jim > > On Thu, May 26, 2011 at 11:37

Re: HCLS chartering/next steps Thur 26 May

Hi Tim, I agree with the principle. Just want to point out that the Terminology task force has been looking at a very specific problem - detecting discrepancies between clinical reports from radiology and pathology: http://www.w3.org/wiki/HCLSIG/Terminology/PathRadCorrelation The main problem pro

Re: Minimum information about a mutation

I'm looking for an agreed upon way to describe observation of particular functional (AA change) mutations in specific specimens. What is needed for people to trust these observations? Jim On Thu, May 26, 2011 at 11:37 AM, Michael Miller wrote: > hi jim, > > i don't think this is what MIAMI-like

RE: Minimum information about a mutation

hi jim, i don't think this is what MIAMI-like standards are needed for--are you actually just looking for a nomenclature to describe this? or do you need a metric to evaluate the underlying papers? cheers, michael > -Original Message- > From: Jim McCusker [mailto:james.mccus...@yale.edu

RE: HCLS chartering/next steps Thur 26 May

hi all, tim, your remarks confused me. like lena, i have found BioRDF to be problem-centric. the fact that we are working on solutions to the problem is what brings me to the table. without that, BioRDF would be without me. i stayed in the shadows for many years because i saw a lot of disc

RE: HCLS chartering/next steps Thur 26 May

In addition to having the "problem" based task forces, I would suggest that we establish sub-groups based on interest/technical capability with responsibilities to develop and maintain our efforts. · Terminology (to coordinate and maintain a shared vocabulary) · Knowledge Bases

Re: HCLS chartering/next steps Thur 26 May

I agree with Tim's ideas. The different task forces should be problem-focused. This would also help to reduce the redundancy between task forces (for example, the original idea of BioRDF was mainly to convert biomedical data to RDF, but over the years this also became a major focus of other task

Re: HCLS chartering/next steps Thur 26 May

Hi all, I agree with a focus on creating "problem-centric" task forces - to be honest, I always felt bioRDF to be a problem-centered group (i.e. trying to solve a current problem in life sciences, not looking for a problem given a solution). I do believe, however, that we need to make sure that w

Re: HCLS chartering/next steps Thur 26 May

Beyond the target areas, do we have any guidelines on the skill sets that are for a project to proceed / succeed. How much clinical knowledge is required from the team to facilitate a meaningful contribution to clinical practice based on a robust semantic implementation. Likewise what amount of kno

Re: HCLS chartering/next steps Thur 26 May

Tim, Thanks for your thoughts. I agree with you and would like to add an evaluation criteria component - these efforts (imo) should be targeted at having an impact on clinical outcome. Joanne ~~ Joanne S. Luciano, PhD

Re: HCLS chartering/next steps Thur 26 May

On Thu, 26 May 2011 06:55:07 -0700, Tim Clark wrote: I would lose the solution-based Task Groups and reformulate them as problem-based. for example, BioRDF has been working on gene lists for transcriptomic experiments, we might recharter that Task Group to work on Genomic Experiments

Re: HCLS chartering/next steps Thur 26 May

Hi, I guess my comment would be, setting Translational Medicine as a major priority = ok, making it the only priority = not ok. +1 My personal recommendation would be to formulate the charter around accelerating biomedical research and promoting cross-discipline sharing, across the full

Re: HCLS chartering/next steps Thur 26 May

Tim, Thanks for your thoughts. I agree with you and would like to add an evaluation criteria component - these efforts (imo) should be targeted at having an impact on clinical outcome. Joanne On May 26, 2011, at 9:55 AM, Tim Clark wrote: > Dear HCLS colleagues > > I guess my comment would be

RE: HCLS chartering/next steps Thur 26 May

+1 By charting a course towards solving outstanding problems or an application area, we are well motivated to develop and evaluate the (SW) solutions. The resulting work can find a nice home in both technical and non-technical forums, which increases our outreach potential. M From: public-se

TM teleconference call

Hi TM'ers Just a friendly reminder of today's teleconference call : ''' Conference Details''' * Date of Call: Thursday May 26 2011 * Time of Call: 12:00pm - 1:00pm ET * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.26.46.79.03 (Paris, France) * Dial-In #: +44.203.318.0479 (Lon

Re: HCLS chartering/next steps Thur 26 May

Dear HCLS colleagues I guess my comment would be, setting Translational Medicine as a major priority = ok, making it the only priority = not ok. TM applications are important, and do potentially integrate many of the things we have all been working on. But they are far from covering all the b

Re: HCLS chartering/next steps Thur 26 May

I'm not sure we need a different IG. If the focus is integration of data... environment and health are far... but in theory not that far... ciao, Andrea Il giorno 26/mag/2011, alle ore 14.31, Helena Deus ha scritto: > Hi, > > That is a very good point, thanks Mikel and Andrea! > Do you have poin

Re: HCLS chartering/next steps Thur 26 May

Hi, That is a very good point, thanks Mikel and Andrea! Do you have pointers to such type of data? Shall we consider an IG for "basic" life sciences? The LS part of HCLS has indeed been gaining adepts rapidly and it may make sense to reflect that in the charter. Cheers, Lena 2011/5/26 Mikel Ega

Re: HCLS chartering/next steps Thur 26 May

Hi; I should attend the conference call but I just want to add that I concur with Andrea in that the HCLS IG should consider the environmental realm, since loads of new ecological/environment data, with new challenges to be addressed, are waiting to be represented semantically. That's precise

Re: HCLS chartering/next steps Thur 26 May

Hi, I see myself as more involved in the next incarnation of the charter ;) Unfortunately, today is a travel day and I cannot attend the conference call. I have two questions/ideas, which don't really map to the current sub-groups, but just in case they ring some bell: -) Is the HCLS exclusively

Re: Good news from the EBI Semantic Web Industry Workshop and LODD members

Hi, this looks pretty comprehensive. Below is the list of speakers: * *M. Scott Marshall* (The W3C consortium). Where is the W3C now and what should happen next? * *Phil Brooks* (Eli Lilly), Semantic Web for Health Care and Life Sciences