- Kbase-microcomm - mailman3.cels.anl.gov

Re: [Kbase-MicroComm] new time?
by Folker Meyer 18 Apr '13

18 Apr '13

I can do 2pm thursday's (CST). Since I am traveling as well, we need to cancel this week. Unless anyone objects lets use 2pm CST. Best, Folker On Apr 18, 2013, at 12:23 AM, Andreas Wilke <wilke(a)mcs.anl.gov> wrote: > Hi Dylan, > > a) we can pick a new time, perhaps in our afternoon , is Thursdays still ok for you? > b) I have to cancel tomorrow since I am traveling. > > Andreas > > Sent en route > > On Apr 17, 2013, at 11:15 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > >> Hi all, >> >> is there another time that might work for you guys, either thursday or another day? Frankly, anything before 10:30am PDT for me often conflicts with my son's preschool drop-off and subsequent transit to work. I really shouldn't be talking on the phone and driving (in fact, I was pulled over for doing that today!). >> >> Thanks, >> - Dylan >> >> _______________________________________________ >> Kbase-microcomm mailing list >> Kbase-microcomm(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-microcomm > _______________________________________________ > Kbase-microcomm mailing list > Kbase-microcomm(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-microcomm

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Re: [Kbase-MicroComm] new time?
by Dylan Chivian 17 Apr '13

17 Apr '13

OK. Thursday afternoon is great. Pick a time. Thanks, - Dylan On Wed, Apr 17, 2013 at 3:23 PM, Andreas Wilke <wilke(a)mcs.anl.gov> wrote: > Hi Dylan, > > a) we can pick a new time, perhaps in our afternoon , is Thursdays still > ok for you? > b) I have to cancel tomorrow since I am traveling. > > Andreas > > Sent en route > > On Apr 17, 2013, at 11:15 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > > > Hi all, > > > > is there another time that might work for you guys, either thursday or > another day? Frankly, anything before 10:30am PDT for me often conflicts > with my son's preschool drop-off and subsequent transit to work. I really > shouldn't be talking on the phone and driving (in fact, I was pulled over > for doing that today!). > > > > Thanks, > > - Dylan > > > > _______________________________________________ > > Kbase-microcomm mailing list > > Kbase-microcomm(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/kbase-microcomm >

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Re: [Kbase-MicroComm] new time?
by Andreas Wilke 17 Apr '13

17 Apr '13

Hi Dylan, a) we can pick a new time, perhaps in our afternoon , is Thursdays still ok for you? b) I have to cancel tomorrow since I am traveling. Andreas Sent en route On Apr 17, 2013, at 11:15 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > Hi all, > > is there another time that might work for you guys, either thursday or another day? Frankly, anything before 10:30am PDT for me often conflicts with my son's preschool drop-off and subsequent transit to work. I really shouldn't be talking on the phone and driving (in fact, I was pulled over for doing that today!). > > Thanks, > - Dylan > > _______________________________________________ > Kbase-microcomm mailing list > Kbase-microcomm(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-microcomm

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new time?
by Dylan Chivian 17 Apr '13

17 Apr '13

Hi all, is there another time that might work for you guys, either thursday or another day? Frankly, anything before 10:30am PDT for me often conflicts with my son's preschool drop-off and subsequent transit to work. I really shouldn't be talking on the phone and driving (in fact, I was pulled over for doing that today!). Thanks, - Dylan

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Re: [Kbase-MicroComm] call today
by Dylan Chivian 11 Apr '13

11 Apr '13

Hi Folker, Sorry about earlier. I was dropping my kid off at preschool. We might want to find a later time in the day so this doesn't happen again. As for your stuff, no quibbles on my end. I'm putting together something some stuff for Berkeley to do and then the executive team can reconcile and prioritize across science domains. Thanks, - Dylan On Thu, Apr 11, 2013 at 9:40 AM, Folker Meyer <folker(a)anl.gov> wrote: > hi all. > > after waiting for 10 minutes ANdi and I have decided to go to grab lunch. > I will need to submit the list later today. Any last minute feedback is > welcome of course. > > best, > Folker > > On Apr 11, 2013, at 11:21 AM, Folker Meyer <folker.meyer(a)gmail.com> wrote: > > > Hi all, > > > > I do not know which number we are planning on using by I think we need > to discuss the 3 months and 18months plans today. > > > > I don't have any other agenda items. > > > > What number are we using? the standard KBase one? (866 740 1260)? I > have another one ready to use. > > > > best, > > Folker > > > > _______________________________________________ > > Kbase-microcomm mailing list > > Kbase-microcomm(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/kbase-microcomm > >

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Re: [Kbase-MicroComm] call today
by Folker Meyer 11 Apr '13

11 Apr '13

hi all. after waiting for 10 minutes ANdi and I have decided to go to grab lunch. I will need to submit the list later today. Any last minute feedback is welcome of course. best, Folker On Apr 11, 2013, at 11:21 AM, Folker Meyer <folker.meyer(a)gmail.com> wrote: > Hi all, > > I do not know which number we are planning on using by I think we need to discuss the 3 months and 18months plans today. > > I don't have any other agenda items. > > What number are we using? the standard KBase one? (866 740 1260)? I have another one ready to use. > > best, > Folker > > _______________________________________________ > Kbase-microcomm mailing list > Kbase-microcomm(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-microcomm

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call today
by Folker Meyer 11 Apr '13

11 Apr '13

Hi all, I do not know which number we are planning on using by I think we need to discuss the 3 months and 18months plans today. I don't have any other agenda items. What number are we using? the standard KBase one? (866 740 1260)? I have another one ready to use. best, Folker

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call cancelled
by Dylan Chivian 21 Mar '13

21 Mar '13

no point. thanks, - dylan

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Re: [Kbase-MicroComm] [Kbase-devel] Starting a discussion of metadata in KBase
by Stephen Chan 14 Mar '13

14 Mar '13

Folker, Thanks for the reply - I am focused on a particular deliverable, so my comments are framed in that context as a use case: On Thu, Mar 14, 2013 at 11:01 AM, Folker Meyer <folker(a)anl.gov> wrote: > - MetaZen is indeed a frontend to create spreadsheets (and prefill some fields) > - The "schema" we devised is indeed implemented in a database allowing the queries. I use "schema" because it is a very lightweight solution more an overlay really. A closer reading of the doc answered this for me, thanks for indulging my short attention span. Since the metadata solution is a lightweight overlay, and the metadata requirements seem to be driven by "meta-metadata" templates, it sounds like we could (relatively) easily use this as a metadata layer for other services. Is it being used for anything else currently, for example, to store the metadata for the Shock service? > - regarding Stephen's question about a single integrated query capability: the "schema" we use links IDs to metadata. I believe we need the ability to link all KBase objects (from narrative to metagenome reads etc.) to metadata. With many different lightweight "schemas" used along the way. If you look at the way the "schemata" are implemented, you will see they are suited for this. I'd say a single KBase ID needs to link to the only one object irrespective of location in KBase. I think that a scheme for kbase wide object ids, and common metadata layer would be a vital first step to federating the data store silos. > I think one key question we have to ask ourselves is: Do we want to work with the international standards community (e.g. GSC) and expand on their "templates" or go our own way? > > With MG-RAST we have chosen to work with the community (and are now part of this community), evolving standards and CVs where needed (sometimes too slow). For us that has produced the situation where users are happy to provide minimal data and many are asking for more metadata. We basically get the same number of complaints about too little and too much metadata --> must mean we did the right thing. ;-) > Metadata is comes out of how the data is used - and we are breaking some new ground in how the data is used (do the current communities have metadata that captures what the narrative interface use cases?) Steve

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Re: [Kbase-MicroComm] [Kbase-devel] Starting a discussion of metadata in KBase
by Shiran Pasternak 14 Mar '13

14 Mar '13

On Mar 14, 2013, at 2:01 PM, Folker Meyer <folker(a)anl.gov> wrote: > - Many users find metadata annoying and don't like to provide it. Our approach has been to tell them they get better service if they provide the metadata and also provide tools that make minimal metadata easy --> Metazen. > - Marcin is right that richer metadata is important (this is solved via the "environmental packages") and the notion of different levels of metadata. Richness and ease of use are somewhat opposite goals, Doreen points out that we will have to coerce our users to do the right thing. One way might be to have tools in KBase that require certain sets of metadata to work e.g. the use of certain CVs for experimental conditions. > - We probably should go for multiple levels of metadata completeness, encouraging the users to add as much as they can, while requiring a minimal subset. At least that is what we did in MG-RAST. Hope I'm not going too off-topic here. Sunita and I have been brainstorming just a few days ago about building functionality for rudimentary annotation of ontology terms from cited literature, which is very often (always?) associated with GEO data sets. This service would essentially use natural language processing[1] to mine papers for these mappings. This would be in the very common case that GEO data is not already associated with metadata. An NLP approach, as far as current pipelines go, have very high false-positive rates. But we can model it in such way that captures a measure of confidence about the mapping, so unreliable mappings aren't taken as Truth. Maybe these annotations can serve as a very liberal baseline for categorizing entities, when users don't care about providing the mappings themselves. Shiran [1] Disclaimer: I'm NOT an NLP expert! :)

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