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April 25 2017

Agenda and Minutes

Data not shown

4 major publishers responded that is ok to publish data not shown or unpublished results:

  • GSA
  • The Company of Biologists (Publisher of Development, Disease Models and Mech, Journal of Cell Science, J Exp Biol)
  • American Society of Cell Biology (Publisher of Mol Biol Cell)
  • American Society of Microbiology (Publisher of Mol Cell Biol)

Waiting for Elsevier's final reply. They did not see anything wrong with it but they will double check with other colleagues.

IWM Booklet

Summary of Karen's discussion with Knudra/Nemametrix

  • NemaMetrix would love to sponsor the printing of the micropub book up to $1K
  • NemaMetrix and Knudra would love to have a "double "full page" ad in the booklet
  • To maximize the impact of the micropub book distribution we would love to support you in following a standard 3,2,1 marketing launch (3 emails go out letting people know to be expecting the micropub book at the conference). These would be the strongest if they all came from WormBase but we can also support that with NemaMetrix and Knudra email lists
  • We would be happy to add the 'micropub book' onto our daily giveaway raffle helping to drive traffic to your booth
  • We would also be happy to participate in any follow-on activity such as surveys, etc.
  • shall we also have a raffle and give prizes to people that try to use the form? e.g. 2x 20$ amazon vouchers


  • Han Wang (Paul's lab) will submit 2 micropubs, 1) novel good alleles for known genes that were recovered from forward genetic screens (allele phenotype info) 2) Gal4 drivers mapping information
  • Karen and Daniela will have a meeting with Knudra this coming Thursday

April 11 2017

Agenda and Minutes

  • Knudra interested in micropubs. From Chris: " null alleles for unc-18 that we are characterizing and would love to understand what phenotypic and genotypic observation would be worthy of micro-publication?"
    • Karen will set up a meeting with Knudra to evaluate what kind of metadata they want to provide. Daniela reached out to Mary Ann to get an .ace example for engineered allele curation.
  • IWM booklet -mock-up here: [[1]]
    • We need to add a slide on what micropubs are, maybe also a couple of blank pages (notepad style to allow people to take notes during the meeting). think of having an extra swag that we will give away if people come to the booth to give their e-mail address. Add an example of how to submit.
    • some ideas on swag here:
    • Before the IWM we need to add a 'Micropublish' box on the WormBase homepage (linking out to the Micropublication:biology site), so it will be easy for users to get there.
  • Will talk Friday April 14th with Ruth, Tracey about Data not shown

April 4 2017

Agenda and Minutes

Tim's minipub

    • Tim will send a couple of corrections for the micropub text
    • Tim will send a reviewer suggestion
    • We will not request images mandatory for each micropub

GAL4 driver lines

  • ready to submit?
    • will give Paul a deadline for submission

Data not shown

  • ok to start contacting publishers to ask their policies?
    • Yes, we should start asking Elsevier and ping again GSA

March 27 2017

Agenda and Minutes

Minipubs Discussion

  • need to revise the workflow for minipubs before proceeding with Tim's pcn-1 submission


  • We propose to charge companies an Article Processing Charges (APC) but we will waive the fee for academics.
  • Sustainability will be an issue around year 4. If the system will be adopted by the community and we will get enough submissions, wouldn't a 50$ charge/submission be acceptable- also for academia? ~100 submissions/month = 1FTE?

Minipublication name

  • If we are not limiting the number of micros in a mini, shall we consider to use a different name for the longer narratives?
  • The word 'Mini' alludes to something small or of short length

March 21 2017


Data not shown original Article

  • Tim: Shall we not emphasize in the micropub that the "data not shown" was mentioned in another paper? Will journals think that "data not shown" belongs to that journal?
  • The reviewer to which we sent out the cyb-3 micropub last week suggested the opposite: make sure that in the micropub is emphasized that it was data mentioned but not shown in a previous publication. Cite the publication.
  • Ask Ruth Isaacson's advice?

Micropubs embedded in Minipubs

  • send out for review just the mini pub or each individual micropub first? We touched on the topic last friday (Tim, Karen, Daniela). Tim was suggesting to send out just the mini pub.
  • Pros:
    • We use less reviewers
  • Cons:
    • we normally assign DOIs to the micropubs AFTER the reviewer approves the micropub
    • we think of building up MINIpubs from existing micropubs. In the case we are dealing with, we are defragmenting a longer piece into smaller pieces
    • to mirror the process on how we would deal it in the future, we should send individual findings to reviewers first, we could send a couple of micros to each reviewer: e.g. one will evaluate the 2 expression results, the other will evaluate the phenotype ones.

Biocuration poster


  • Received one submission out of 8 requests.


Data not shown original Article

  • Forget about Data not shown for now and focus on unpublished results (journals may think data not shown belongs to them)

Micropubs embedded in Minipubs

  • Send minipubs data just to one reviewer, assign DOIs to each individual finding and to the mini


  • at the booth have an example on how micro and minipubs will look on CVs

March 8 2017

Agenda and minutes

  • Celebrate the score
    • Paul e-mailed the program director and see what the percentage is
    • critique was good, few minor points to address, e.g.:
      • high throughput data
      • collaboration with publishers -we could contact e-life, collaboration with the Coko foundation deals with the publishing cycle already
      • charging for submissions? yes for companies, not for academia, will say we will waive submission charges for academia
  • Booth at the IWM
    • Shall we have one?
      • yes, we will have one, pay through WB
  • Booklet at the IWM (see github #52)
    • Gather micros to generate the booklet
      • booklet: have one of two each flavor submissions
data not shown: 1 or more
reagent: e.g. gal-4 drivers
new interesting unpublished data 
negative data
ask people what would you like to see published-what you know as common knowledge and has never been published
    • Distribute booklet at posters that feature the micros and at booth (WB, Nemametrix, TransgeneOme(?) etc)
  • Tim's micropub -how to deal with longer narratives
    • Daniela/Karen will work with Tim to get the atomized data from his submission and will work to generate the MINI-Publication (composed of 2+ micros)
    • Confidence rating discussion (shall we allow authors to put in the confidence level of a result)
  • Mitani alleles (see github #51)
    • Can Paul reach out to Shohei and initiate the collaboration?
      • yes he will. We might set up a conf call with Mitani to discuss it in greater detail
      • we can think of having robot generated descriptions for the mitani alleles
      • if a mitani allele is tested by someone else and gets different results it will be a new micro that will cite the original submission from Mitani
  • Alternatives for the current Micropublication: biology site (see github #25)
    • very time consuming right now loading articles into our current site, we need to figure out how to make this more efficient- can we get something better for the 20-50 articles in time for the IWM?
      • Daniel W could dedicate some time on the project at the beginning (manual entry), we will continue to look into alternatives and, if the grant goes in, we will implement this in phase 1
  • Other points
    • microreviews

2106 meetings