DataONE:Notebook/Summer 2010/2010/07/01 chat

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In the chat room: Heather Piwowar (, Nicholas Weber (

9:00 AM Heather: You've been invited to this chat room!
 Valerie has joined
 Heather: Good morning all!
 Nicholas: Hi
9:01 AM Sarah: hello
 Valerie has left
9:02 AM Heather: Whoops we lost Valerie
9:03 AM Valerie has joined
 Valerie: hello
 Heather: Hi Valerie
  Hope you've all had a good week?
  The Evolution meeting was very interesting. Lots of learning and new contacts.
 Valerie: yes, it finally cooled down here/I finally fixed the reboot error on my computer
9:04 AM Nicholas: Heather how big was the conference ?
  in terms of attendees I suppose
 Heather: 1800 attendees for the main one
 Nicholas: whoa
 Valerie: wow
 Heather: a hundred or two for the smaller iEvoBio, informatics-related
9:05 AM yeah. lots of parallel sessions. lots of diversity, it was great.
  any quesitons or thoughts before we dive in talking about knoxville?
9:06 AM (feel free to say no, otherwise not clear how long is a long enough pause via chat...)
 Nicholas: I don't think so
 Heather: valerie? sarah?
 Valerie: do we need to have an article draft written by then or just the presentation?
9:07 AM Heather: Valerie I think in your case an article draft would be helpful
  Or at least an article outline
 Valerie: ok, cool
 Heather: In part to direct where your analysis goes for the last few weeks.
9:08 AM Sarah: sorry for the slow response. I'm good. I'm treating my powerpoint outline as my manuscript outline.
 Valerie: I'm sort of doing that as well
 Heather: ok, good.
9:09 AM Sarah: the knoxville data analysis will be my preliminary/test analysis for the final data
 Heather: well then two overall things before we dig into details on presentations....
 Nicholas: me as well... I looked at the presentation as poster material that will get developed into an article
 Heather: yup, sounds good guys. your presentations reflect that.
  more on that in a minute....
9:10 AM I just want to get your thoughts on a few other things first to make sure I don't forget.
  first: the proposed structure of the day has mentor presentations, then a break, then intern presentations back to back
9:11 AM I was thinking of suggesting that instead we have a fairly lengthy opportunity for discussion after each intern presentation
  something like 30mins
  what do you think?
9:12 AM opinions on discussion length, structure?
 Valerie: sure (although I will admit that a 30 minute discussion about my project sounds a bit intimidating/daunting)
 Heather: I appreciate that, Valerie :)
9:13 AM in part I think it is worth making sure we frame this as a working session
 Sarah: i think 30 min total would be good....15-20 presentation, 10-15 questions
 Heather: so the 30mins aren't critiques... they are truely discussion.
 Valerie: oh, I thought you had meant 30 minutes for discussion
  30 minutes all together sounds fine
 Nicholas: maybe we ramp it up, so that initially we spend some time talking about each presentation, but spend more time when they are finished looking for overlaps?
  just a suggestion
 Heather: I did actually think 30 mins for discussion, you interpreted me correctly
9:14 AM yup, nic.
 Valerie: that makes sense
 Heather: ok, thanks guys. so maybe 15-20mins after each, then more later.
 Sarah: yeah, maybe a group "think-tank" after we observed all the presentations would be good
 Valerie: agreed
 Sarah: with shorter q and a time after each presentation
9:15 AM Nicholas: yes
 Heather: btw I don't know if you ever get a chance to be in a doctoral consortium where there is 30mins of group discussino on your project after your talk.... if so, go for it.
  daunting, but very helpful.
  sarah, gotcha.
  I think we'll suggest a bit of both then.
 Nicholas: are those consortium's fellow doctoral candidates ?
9:16 AM Heather: yes, from different universities.
  conferences often offer them
 Nicholas: I often see them, but I wasn't sure the structure
 Heather: you get feedback from a variety of faculty from other unis + the other students. structure is of course different in different conferences.
9:17 AM anyway, worth applying, very useful.
 Valerie: good to know
 Heather: ok. another thought.
  what do you think of a 30 minute segment during the 2 days in which we talk about OWW
9:18 AM perhaps each of the three of you + me + maybe someone else present three slides:
  1. How I used OWW, 2. what I liked, 3. what I didn't like
 Valerie: sure
 Sarah: sure. is the other group using it? have the mentors really embraced it (I'm feeling like not so much)
9:19 AM Heather: nope
  but at the NESCent session in the Evolution meeting,
  Todd touted your use of it as one of the "open science" initiatives going on
 Nicholas: ha
 Heather: associated with NESCent.
  ! :)
9:20 AM so clearly it has value, and I think it is worth taking the opportunity to figure out what worked what didn't
 Nicholas: is it being used in the wider dataOne project at all?
 Heather: how we/future interns/future scientists of this type might beable to use it better, etc.
  Not yet, outside of my own research, which I'm slowly starting to put up and do openly there.
9:21 AM sound reasonable? or does anyone have a different suggestion on how to structure an OWW take-away session?
 Valerie: maybe a panel discussion as opposed to three separate presentations?
9:22 AM Sarah: my only idea is that maybe we could walk through the online system, rather than having slides
 Valerie: yeah
 Heather: cool
 Sarah: a panel would be a good addition to that
 Nicholas: I'd like to hear how other are experiencing it so I think this sounds good
 Heather: so each of the three of you could perhaps click through a bit of your notebooks/pages
  while explaining how you did things, what you liked, what you didn't
9:23 AM Sarah: yeah, and more casual so people can pipe up when they have a question
 Heather: then at the end we have an open discussion about ways to do it better, suggeestions we might have for OWW, etc.
 Valerie: that sounds great
 Heather: I like the panel idea, though it makes me think given the nature of this meeting
  maybe we take it one level less organized that that and have it be a circle discussion or something.
9:24 AM ok. what do you think, 5-10 mins each for an OWW recap
 Valerie: sure
 Nicholas: that sounds good
 Heather: with room for discussion at the end, so maybe 45 mins total?
9:25 AM Valerie: sounds fine
 Sarah: good by me
 Heather: sarah, sounds right to you?
  ok, good.
  Anything else before we dig into presentations?
  I think the main structure of the meeting is just mentor presentations
9:26 AM then intern presentations, then group discussion, then breakout sessions
  so let me know if there is any other structured discusison you'd like to have
9:27 AM Presentations.
  Nice work on the content of what you've been doing.
9:28 AM One thing that struck me about all three is that you've really focused on the methods and interm results
  This makes sense, it is what presentations usually consist of
  In this case, though, we really are looking for more emphasis on motivation and background, as well as lessons learned and areas for discussion
9:29 AM as well as middle content
  so really 1/3, 1/3, 1/3
  let me tell you why:
  not everyone in the room will have been thinking about these projects, so they'll appreciate the motivation.
9:30 AM even more, we want to hear what You think the motivation is. As you write it up, you'll need to describe the background, rationale, etc
  and so this is a great idea to get feedback on your understanding of it
  then, at the end, we want lots of emphasis on how the project went, what questions you have
9:31 AM since this is as much a learning experience as a research-output experience
9:33 AM Nicholas: when you say questions we have... you mean questions for the mentors with respect to what we've gathered? or questions in a larger sense about what our gathered data means related to each other?
 Heather: oops, I'm disconnected, do you get this?
9:34 AM you there?
 Nicholas: yes
 Valerie: yes
 Heather: sorry about that
 Nicholas: I don't think I received your reply
 Heather: I'm in a hotel lobby....
 Sarah: yeah, i'm good
 Heather: here was the last bit
  this may mean that you need to streamline the methods and results slides you have right now....
keep the details in the back of your slidedeck in case we get there in questions or break-out sessions....
oops, I'm disconnected, do you get this?
  we want to hear how it went, what you've learned
  so, what do you think, does that make sense?
 Valerie: that does make sense
9:35 AM Nicholas: makes sense
 Sarah: i was planning on discussing my rationale as I went through the that part of what we're getting at?
  not just, "I did this", but " i decided to do this b/c"
9:36 AM Heather: some. but we're also looking for the motivation for doing the project.
  Now I know you guys didn't pick the projects
  so in some ways it isn't your motivation
  but it will be helpful to hear you say why you think doing this project is important
9:37 AM your view of how it relates to other work
  how you envision your results being used
  In no way intended to be a test of your understnding of the related literature
  that's not what it is about
  but tell us what you think, and then the mentors can help you fill in the gaps
9:38 AM with what they think :)
 Valerie: ah, yeah. I had been wondering if I had to do a prior review of data citation literature prior to writing the article/presentation
  this makes more sense now
9:39 AM Heather: And feel free to say "so I don't know why this bit matters" or whatever. It is intended to be that sort of presentation, rather than a polished finished product
  sarah, nic, can you see that working for you?
9:40 AM Nicholas: yes... I think I've got some retooling to do but I think this makes sense
 Valerie: same here
9:41 AM Sarah: yeah, I'm adding some placeholder slides as we speak
 Heather: great. so aim for 1/3, 1/3, 1/3.
  For the last third, one of the things that didn't make it into the early slide decks was a discusison of limitations
9:42 AM Also, I think one or two of you mentioned future work, but not all....
  that is useful too
 Sarah: meaning problems we've encounterd?
  i've added that and future work last night
 Heather: yeah, so problems you encountered, for sure
 Valerie: I put in a bit about stumbling and figured I'd elaborate in the actual presentation
 Heather: we definitely want that
 Sarah: since this is less formal, I think i'll also add a slide about questions this has drummed up but that i won't be able to address in the scope of this project
 Heather: yes, valerie, your stumbling stuff was great
9:43 AM yes sarah super
  I also mean limitations in the traditional paper sense
  so any method of doing research has limitations
  in generalizability, if you on;y looked a t a few journals
9:44 AM Nicholas: what we didn't look at why we disregarded it...right?
 Valerie: ah
 Heather: or in formal assessment, in valerie's case, since she didn't actually have a "gold standard" set of ideal results that she was comparing her search results to
  or nic, in your case, it could be
9:45 AM that you are only looking at the journal's written policies
  but you don't know how actively they enforce them
  or or you weren't looking at their instructions to reviewers
  or ???
  basically, if you were to critique your own study design, what would you say are its limitations?
9:46 AM (doesn't mean it is a bad study, all studies have limitations)
  a classic limitation is that association does not implly causation, for example.
  does that help?
 Nicholas: yes
 Valerie: yes
 Sarah: yep
9:47 AM Heather: good.
  ok, have you guys had a chance to look at each other's slides?
 Valerie: a bit
 Sarah: briefly
9:48 AM Nicholas: yes
 Heather: how about this then
  rather than making this chat take hours
 Valerie: I like the Prezi layout, neat use of an infographic
 Nicholas: its really easy to learn and fun... I hope its ok Im using this format heather?
 Heather: (no kidding. Nic, that is neat! I hadn't seen tha tbefore)
9:49 AM Nicholas: ok cool
 Heather: go nuts.
  ok, so why don' tyou have a look at each other's and actively make some comments on OWW etc
9:50 AM Sarah: will do
 Heather: I'll do that too
 Valerie: ok
 Heather: I did make a few specific notes I think that I'll add here right now
  but otherwise I'll add other comments on OWW talk pages too.
9:51 AM Here's what I had, in addition to comments already made:
  for all three:
  - Need the why
- why this project
- who is the audience
- what will it help them do
- what is previous work in this area
(might not know some of this. that is ok. advisors will help)
  for the last third:
  - what format are you thinking for final output? where to submit?
- anticipated shedule: what to do in the next few weeks?
- limitations
- things that didn't work well, were difficult
- things you are worried about
9:52 AM especially worth highlighting the "anticipated schedule" part
  we only have really two weeks after Knoxville, right?
 Valerie: right
 Heather: Expectation isn't that you'll have finished papers done by then
  but expectation is that the data collection is done
  and analysis is ideally done too
9:53 AM so that places some tight restrictions on what the future-work can be, within the scope of the project
  so, using these presentations as working and communication documents,
  I think it would be in your best interests to make it really clear what you plan to try to accomoplish in those two weeks
9:54 AM so that others can give you feedback on that
  ok, other notes:
 Nicholas: just an fyi for Valerie and Sarah , July 23rd is final due date for IDCC I'm trying to use that for my "due date"
 Heather: great.
9:55 AM Valerie: good to know
 Heather: There is also an ASIS&T poster deadline on July 16th (I think)
  that could be a deadline for people who were planning to attend that. In Pittsburgh in Oct this year
  I'd explcitly include your publication thoughts in your presentations
  so that you can get feedback on those
9:56 AM Nicholas: great
 Heather: Don't be afraid to be wrong or naive or ambitious or whatever.
  You are supposed to be learning, so put it all out there.
 Valerie: ok
 Heather: nic, a few points on your presentation content:
9:57 AM "better assess their influence"
but why would we want to do that?
- inform new policy
- know what changes to lobby for in current policy
- evidence to help convince people 
- know patterns so can look at other patterns
  - other reasons ???
9:58 AM In general, I think your audience will find it easier to quickly absorb your metadata fields and extracted variables if they are in lists rather than paragraph form
  even though that means it may not all fit on one slide as nicely
  remember your audience is new to this stuff, so make it easily absorbable for them
 Nicholas: ok
 Heather: For repositories, are dois accession numbers?
9:59 AM curious to know how many offer dois...
  Also, I think on the funders page
  you list some numbers without having the denominator on the same page
  so for exampel if you are saying 3 is like this and 8 is like that, make sure the total number is also on the page
10:00 AM or maybe provide a percentage for some of the larger categories
 Nicholas: is it more effective to use % ?
 Heather: yeah it depends, but maybe yes.
 Nicholas: I wasn't sure, because the sample size is relatively small
 Heather: change them to %, and make sure that the total number is also on the same page
  ideally you'd have confidence intervals, but not clear you want to go there for this presetnation
10:01 AM also, if you have questions about your planned analysis, then metntion that.
  talk about your planned final output. is it just descriptive? is there a hypothesis (maybe not?) ?
10:02 AM include some "stumbles" to the extent that you had some
  it may be effective to extract a few of the policy sentences as examples
  though I know you'll be pushing it with time.
  that's what I had.
 Nicholas: time is 25min or 20 min?
10:03 AM Heather: 20 mins I think
 Nicholas: ok
 Heather: though if you've got other slides, keep them in the back and we can go through them in breakout sessions if it is helpful
  any questions on that feedback, or thoughts about why it wouldn't work, or ?
10:04 AM Nicholas: no no thats great
 Heather: ok!
 Nicholas: I've just been feeling a bit in the last few days, like I've analyzed a lot of policies
  and not found a lot of explicit direction
 Heather: explict direction in what way?
 Nicholas: so it's a bit hard to say... well I didn't find much
 Heather: ok.
10:05 AM so in general not a lot of relevant policies, is that right?
 Nicholas: I mean direction to authors, grantees depositors
 Heather: gotcha.
  and this bothers you?
  does it bother you because you think you've missed something? or ?
10:06 AM Nicholas: well, I'm just wondering if I took the best approach, in hindsight
 Heather: ok.
 Nicholas: maybe this is something that comes out of our discussion
  and we can assess it then
 Heather: great, well rather than trying to solve that for you right now, yes, exactly, bring it up.
10:07 AM that would work?
 Nicholas: yup
 Heather: ok. good.
 Nicholas: (sorry for the delay Valerie)
 Valerie: it's cool
10:08 AM Heather: Valerie, I love your stumbles section
  definitely pull it into the slides
  I think it conveys the results even more than the tables you have in there right now
 Valerie: ok, there are definitely more things I could add now that I think about it
 Heather: In some ways, for me, the comparisons between repositories are where the interesting stuff comes out
10:09 AM and some of that is lost when the repositories are on different slides as it is now
 Valerie: yeah, I tried at first to put all three on one slide
 Heather: so you could consider reformatting to make the point clear,
  yeah, I bet it could be hard
 Valerie: which resulted in 12 pt font. I remember someone telling me to use no smaller than 20 or 18 for ppt
 Heather: yeah.
  you could try to lose a bit of detail then.
10:10 AM or just have + ++ +++ for very good, not so good, etc
  or even better, flush out a bit what you mean by good
  it isn't clear
  is it that the results didn't return any hits
 Valerie: ok, that was something I meant to go into more detail about
 Heather: or they returned hits that were swamped with unrelated hits
 Valerie: ok
10:11 AM Heather: maybe you could imagine a key to make sort of a summary chart to explain
  what returned a lot of things, but useless, versus hardly any things but useful, etc.
  there are ways to plot that on a precision/recall curve, but wont' go into that right now plus you don't have a formal gold standard to compare against....
  so just do what makes sense for now
10:12 AM Valerie: ok, that's good to know
 Heather: then I think I wrote this down before I read your stumbles section, but fyi....
  what were some of the themes of the difficulties?
how do these compare with what you expected?
synonyms? lack of unique identifiers?
what did you think they might be? what were they?
  and in general, as someone who is trying to find data reuses,
  what has been difficult?
what tools would have made this easier?
what policies or pratices by authors etc would have made it easier?
10:13 AM those sort of take-aways would have a lot of value I think
  not sure if my comments are clear, so ask if not. that's all I had
10:14 AM Valerie: ok, those are valid and reflect things I wasn't sure if I had detailed enough
  I'll revise the presentation based on your comments and add more on motivation/where to go from here in the coming weeks.
 Heather: yeah, your call, I'm not sure all of the things I raised can be covered within your time, so take it in the spirit intended.
10:15 AM Sarah, just had a few comments on yours
  more motivation, discussion of limitations, etc as above
10:16 AM Sarah: yeah, i've added space for that now
 Heather: Add a slide on "the unexpected" or something, articulating that it took longer than you might have guessed to standardize on fields, or coordinate data extraction, or sync with OWW, or whatever is true
  Also, esp important for your because it is so data collection heavy... add a forecast for the next few weeks
10:17 AM How long it it taking you to do the extraction?
  Are you getting faster?
  Do you think a bio background is necessary?
  (basically lessons-learned on doing this sort of extraction)
  then how does this translate into data collection that you have planned for the next few days or weeks
10:18 AM and what analysis you're aiming to have done
 Sarah: ok. for now i'm giving a conservative estimate of having one more journal done (total of three) and compariative/correlative analyses
 Heather: perfect
10:19 AM so flush out future work, too. if someone (you? someone else?) were to try to collect a bigger set in the future, what would you recommend?
  I know you've already given that thought
  And then the part we haven't figured out at all yet is how we are going to sync up data across projects
10:20 AM Not sure how that is going to work, given our time contraints
  So I think mostly we highlight that as a plan, with actual feasibility unknown, and then
10:21 AM talk about it in our discussion sections
  what do you guys think?
 Sarah: i'm using nic's stuff on a a regular basis and have some ideas for syncing it...but that's on a limited basis since I'm only looking at 3 journals that usually only utilize 3 depositories
 Heather: ok good to know
 Nicholas: right, and I've collected some data especially for Sarah's journals
 Heather: great
 Nicholas: w/r/t funding sources
10:22 AM so it would be nice to have time to think about how we can bring that together
 Heather: yes
  so maybe all three of you, highlight in your presentaitons where you have some overlap
 Valerie: ok
 Heather: in data use, data collection columns, etc
  (I think you are doing this already)
10:23 AM and then we'll purposefully talk about integration within our data citation breakout sessions.
  future integration, I mean...
  ok. that's all I had.
10:24 AM When do you guys get in, will you be there for dinner on the 6th?
 Nicholas: I think I get in at 8 on the 6th
 Valerie: my flight gets in around 8
10:25 AM a late dinner?
 Heather: ok. Not so much dinner then.
 Sarah: i'm about the same i think
 Heather: ok. In that case we'll probably just see each other in the morning
10:26 AM I think they other group is getting together to go over slides in the morning
  but that'll be pretty early for the west-coasters amongst us
10:27 AM so I think the schedule (to be circulated soon) has us meeting at about 8:30
  any other thoughts or feedback?
10:28 AM Nicholas: are we meeting at the hotel?
 Heather: good question, I'm not sure, but I'll get it cleared up
 Sarah: also, what's the schedule for the 8th?
  and are most people staying until the 9th?
 Valerie: I'm staying until the 9th
 Heather: I;ll be staying till the 9th
 Nicholas: I fly out the morning of the 9th
 Sarah: ok. good.
10:29 AM Heather: great. dinner on the 8th then!
 Sarah: sounds good
 Heather: (my bday, actually, so glad to have dinner companions ;) )
 Nicholas: nice
 Heather: should we schedule a chat for early next week?
 Valerie: neat
10:30 AM sure
 Heather: thinking not, given the holiday?
 Valerie: oh
 Heather: (though I'm in Canada, so for me the holiday is actually today, so doesn't matter)
 Valerie: ah, people were tweeting about Canada day
10:31 AM Heather: ok, so no scheduled chat?
  but ping me/each other if want to chat
 Valerie: ok, definitely
 Heather: otherwise we'll just comment on slides via OWW
10:32 AM Valerie: sounds like a plan
 Heather: ok! Sarah you'll put this chat up? thanks guys
 Nicholas: bye, thanks
 Nicholas has left
10:33 AM Sarah: will do. bye!
 Valerie: thanks for the feedback
  talk to you later