From WormBaseWiki
Revision as of 20:59, 12 October 2016 by Kyook (talk | contribs) (→‎Minutes)
Jump to navigationJump to search

September 27 2016


1) Type of submissions

  • For gene expression micropublications, the submission includes:

- reagents used to perform the experiment (transgene, construct, antibody, etc..)

- the read out of the experiment, i.e. image with pattern description and curated metadata

  • for phenotype micropublications, Nemametrix has 2 kind of tech notes:



the first one falls into the micropublication scope, the second is more like a Worm Breeder's Gazette article. Discuss.

2) Workflow

  • from Submission through the form till acceptance by a reviewer we need to track the submission and store metadata in a proper way. Are we going to:

- outsource to e-journal press or similar?

- develop in house? Need developer time, Who is going to do it


3) Editorial Board

  • if we start a journal we need an EIC (Paul?) and an editorial board.Who will select and contact the potential editorial board, when.

4) Need alternative title than 'Micropublication: biology' as colons can give problems for downstream XREF (from G3 experience)


1) Micro vs milli

  • Tim suggests to have narrative-containing Micropubs more similar to a short journal article
  • Those could be millipublications as opposed to just data-driven micropublications
  • Karen and Daniela will work on different types of Tech notes from Nemametrix and on Worm Breeder's Gazette articles to model that
  • multiple micropubs can be put together to have the narrative-containing (hypothesis driven) millipub
  • micropubs in the future could be a plug in we give to journal to collect metadata.

2) Workflow. Outsourcing vs in-house

  • Todd: outsourcing gives us more expertise but we loose control
  • Would be good to have more than one developer involved. Not much resources at the moment
  • We will touch base with the Collaborative Knowledge Foundation (CoKo, and see what a collaboration would entail.
  • We will continue to develop forms in-house to move on with the project
  • we will generate a database with Juancarlos that will store all data but is separate from Postgres used for WB data

3) Editorial board

  • PWS can be EIC, need to define scope and build editorial board

4) Title

  • We can call it 'Micropublication biology'
  • Daniela will check with XREF if calling it 'Micropublication-biology' with a dash -as per Tim's suggestion- will also be an possibility

5) Random

  • Tim suggesting to capture crispr reagents -> having them published as micros

6) We will have another call in 2 weeks -October 11 approx- unless we have more news from Nemametrix or there is something compelling to discuss.

October 12 2016


1) Reviewers suggestions and policy (1 vs 2 reviewers) for Nemametrix submissions.

  • We want to upload 4 nemametrix micropubs by the October 26th deadline
  • Need to send out to reviewers ASAP
  • To whom and how many?

2) Collaboration with the Coko foundation. [1]

  • They are happy to support us and are developing tools that perfectly fit with our project
  • They can write LoS or write grant together with us (Software is under MIT license) -> what do we want to do

3) Format of the micropub journal pages [2]

  • does the proposed format look ok?
  • this is the page we will send out for review and that will be converted in PDF if the micro is accepted


1) Reviewers:

  • we will have 1 reviewer and we will leave the option to be anonymous
  • we will send the first 2 micropubs to people that are aware of the project
  • will also ask authors if they have reviewer's suggestions
  • General comment from Tim: we need to put up an advertising show at the IWM

2) Coko

  • ok to explore partnering with them
  • K and D will set up the whiteboard session in SF to learn more and see what the collaboration will be
  • split tasks: we do curation, they do the software -> co-grant?

3) Format of the micro pub

  • ok as is now, will try to have a flexible format (one that allows various amounts of narrative)