Difference between revisions of "Calls"

From WormBaseWiki
Jump to navigationJump to search
Line 15: Line 15:
===Publisher issue===
===Publisher issue===
*Shall we start contacting EZID and ask about using ‘micropublication: biology’ as publisher?
*Shall we start contacting EZID and ask about using ‘micropublication: biology’ as publisher?
===Website stats===
===Website stats===
Line 34: Line 33:
* if it’s a major change: tim’s suggestion:
* if it’s a major change: tim’s suggestion:
“there should be some note on the article indicating that it it a corrected version, with the data of the new version, below the published online date.”
“there should be some note on the article indicating that it it a corrected version, with the data of the new version, below the published online date.”
=May 23 2017=
=May 23 2017=

Revision as of 15:49, 30 May 2017

May 30 2017


ZFIN participation

After the meeting Doug started working on a phenotype submission form draft:

‘I already have an early draft of what a phenotype submission might look like for us. I'm currently soliciting curator feedback here on that.’

Copyright issues

  • Doug asking:

‘Have you guys thought about copyright issues at all WRT micropublication? For example the disclaimer I see on some of your submission forms could say something like "I understand that this submission will go through a peer review process and upon passing peer review will be added to the ZFIN database in an open acceess format. Copyright remains with the data submitter. Where DOES copyright remain, and are micropublications open access?’

  • Contacted Jane Mendel to see if WormBook had to get formal licensing from Creative Commons

Publisher issue

  • Shall we start contacting EZID and ask about using ‘micropublication: biology’ as publisher?

Website stats

  • Number of visitors still increased- 169 unique/week, 634 page views

Knudra submission

  • Any news from the reviewer? Shall we send out to another one?


  • News?


  • Micropublication: biology button on the WB homepage -> should be up? on which release? WS259?
  • Todd -> Twitter account? need changes in DNS records?

Corrections post publications

  • how shall we deal with them? If it’s a simple typo shall we just manually edit it?
  • if it’s a major change: tim’s suggestion:

“there should be some note on the article indicating that it it a corrected version, with the data of the new version, below the published online date.”

May 23 2017


  • U01 results -> when is the advisory council meeting?
  • update on submissions
    • Wang accepted
    • prahlad submission rejected by 1 reviewer, contacted another reviewer for second opinion.
    • Knudra submission sent out for review
  • booklet -> will send to nemametrix once all submissions are in for final design
    • deadline for sending for printing June 7th
  • E-life
  • IWM: poster, sign up form, glossy print outs of the micros, banner
  • Twitter account, atmicropublication.org -> todd any update?
  • Submission options:
    • The current Submit Data should be changed into Curate data (to discuss at WB group meeting)
    • Submit data should be just micropublication
  • put out new blog post once pending submissions are accepted
    • #1: e.g.: 'join the Prahlad lab, Sieburth lab, knudra and micropublish on micropublication:biology...'
    • #2: when allele-sequence form is ready: 'publish your sequencing data..'
    • #3: when allele-phenotype form is ready: 'publish your phenotype data..'



  • council has been completed.
  • Paul wrote to NIH. The NIH person in charge is on vacation.


  • Ask Prahlad to do what the reviewer suggested. we give it a chance to fix it


  • might be a little while before they get back to us, Matt B is swamped with other stuff. Karen will find out.

eLife discussion

Patterson: arnold like to put people in touch with each other. Stebbins was saying to have something big and use an existing brand and use other infrastructures.
Patterson was at plos and started currents, minipub style with no database connections.
it was also interfering with their business model (Plosone) 
Patterson: Paul would like to ask what they can do to help.
Tim: part of it is the main bread and butter is going to be the micropublication or the minipublication
Having the publisher infrastructure will help out. If micros are the main route he’s not sure we need to deal with a publisher.
Paul: I want to see everything built from the ground up. Micros first and minis built up on that. Links to database is important. bottom line is where do we get fundings. If we have no funding we need to partner with someone- some .org publisher, university libraries, commercializing it? (not ideal). 
If you build it up in pieces what parts do we build ourselves and what we give out to people.
Todd’s argument is to have a platform that everyone uses. what is todd envisioning as platform?
Todd: technical thing, how do we approach the engineering, if we build it in a such a way that other people could easily plug in into their system it would be like an API that they can integrate. We develop a development platform that other people can incorporate. 

Paul: like high wire 
todd: if the grant comes through we do it like this. if we want or need to commercialize we could go that route as well. 
Tim: in terms of clients: micropub is now just for worm, 
Paul: we want to develop the infrastructure flexible enough to plug in whatever species or data. 
todd: Elsevier would want to have our platform because it creates more engagement with the community. Encourage the collegial sharing
Tim: who would elsevier use our model 
Todd: if we are funded we make us available as a service
Tim: e-life is more compatible than Plos
Paul will talk to patterson and Kristen in 2 weeks. 
the way we go about building this out -if we have open ended design it will be beneficial
Paul: colleagues in geology and astrophysics that have the same issues and are interested
Tim: part of the design is to go out of our usual stakeholders and see that we don’t automatical exclude them 
Karen: in terms of funding: our funding is specific to the biological field
Todd: if it’s designed in an open ended fashion we could apply to other societies
Karen wants to expand the mark-up but where are the authoritative databases?
Todd: providing avenues to publish scientific observations that would never see the light of day and cross-referencing to databases.
Paul: he talked to fly persons and they are interested.
Tim: at some point we’ll face the issue of making it a sustainable operation.

Outreach and social media

  • Todd signed up for a twitter account and he generated the username micropub7n
  • will see if he can ask to have micropubs
  • todd needs to make small changes to the DNS records of the domain so we can get the list done- will get in touch with Daniela

Submit data vs curate data

  • will ask juan carlos to have a pop-up when users submit that will ask:has this information been published before? if yes will redirect to the curation form, if no will go to micropubs

May 16 2017


Arnold foundation

  • Update from Paul on Arnold's call
  • Update Coko on the call's outcome?
  • Next steps


  • Update on submissions
    • Prahlad
    • Han
    • Knudra
    • Jorgensen?

Micropub button on WormBase homepage

  • Todd can we prioritize this?

TWU visit

  • people interested in the micropub idea
  • asked if micros are visible in Google and Google Scholar


Arnold foundation

  • Paul talked to Mike Stebbins and Kristen (Coko)
  • Arnold is really excited about it, and they were trying to figure out what to do in this area. They wanted to know if it was a worm specific endeavor or a general one -> general one
  • Stebbins thought that to do it right we have to partner with a publisher to really get it going -> e.g.: e-life? mark patterson
  • Todd contrasting the idea, maybe partner with a technology company (Google?)

Micropub button on WormBase homepage

  • Will be live in the next WB release (next week or so)


May 9 2017


Arnold foundation

  • LoS for Coko
  • Update from Paul (Mike Stebbins)
  • Action plan
    • depending on IF and WHEN we will need to submit a proposal for Arnold:
- submit same proposal if U01 is turned down? will need to expand
- talk openly with Mike Stebbins and disclose that we are waiting on the NIH response and will tailor the Arnold proposal accordingly?
- if Coko gets the Arnold grant and we don’t, would they still build our infrastructure

Micropublication form updates

  • Added suggested reviewer field
  • Added title field
  • Added ISH

Potential submissions

  • Veena Prahlad (reviewer of a previous micropub) wants to submit smFISH data

Website views post blog

  • Still increase of website views


  • will send examples as soon as we get data not shown/unpublished for their journals

Micropub button on WormBase homepage

  • Todd can we prioritize this?



  • Stebbins cancelled the meeting, we'll see if we hear back

May 2 2017



  • Gave us the OK to publish 'unpublished data' - do not specifically mention data not shown, which was in the original request
  • they'd like to link back to our Database and propose 2 options:
    • 1. Banner linking as already established with Wormbase. Nonetheless, this is general (only Wormbase banner appearing on ScienceDirect) and if not already linked to Wormbase, the article will have to be re-supplied on our end, which means a very manual and time costly process.
    • 2. Evolving article feature. This feature will allow to host on our platform a specific PDF containing the additional information and links to it, that will be visualized as an additional pdf that readers can download when downloading the original article. See an example here: http://www.sciencedirect.com/science/article/pii/S1755436514000607 . It is still a manual process at the moment, but it does not involve re-supplying of the article.
  • Shall we opt for the banner linking one?


  • We met with Chris and Trisha (Knudra) and they will prepare a micropub submission, they will also reach out to their customers and see if they can supply one, too.
  • they (and Matt Beaudet from Nemametrix) gave suggestions for the booklet, Matt strongly supports having PDFs versions of the articles in the booklet, even if hard to read. Chris from Knudra said they could provide magnifying glasses as swag
  • Booklet link: https://docs.google.com/presentation/d/1MpxxYIxZ6eBXxWDmm8UuoHS244DBA9EAJb0AexFM1oM/edit#slide=id.p6

Blog post

  • We posted a call for expression data on the blog on Friday
  • Since the post page views of micropublication biology have increased (from ~70-80 unique visitors per week to 115)

micropub e-mail

  • Todd please correct misspelling in the mailing list

Other updates?

  • Jorgensen?
  • Han will submit 2 micros by the end of next week



  • we will request to go with the banner linking option


  • Better to have the pdf in one page other than spread over 2 pages

micropub e-mail

  • Todd fixed it

Other updates?

  • Todd contacted Jorgensen, no response yet
  • Tim: plan for making the micropub easily found on the wormbase web homepage
    • Add a button on Wormbase called Micropublication: biology linking to website -between submit data and Parasite
  • Arnold's foundation VP want to chat with Paul about micropubs
  • Daniela will remove links to WBPapers that are not live in WormBase yet
  • will meet next week, if no major updates will schedule in 2 weeks

April meetings


March Meetings


2106 meetings