WBConfCall 2013.08.15-Agenda and Minutes

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Discuss WormMine

Release Milestones for WS240

As we want to do "themed" releases, are there any plans for WS240? Especially since any "themed" activity needs to happen until the upload date (as in: a few weeks).

Thomson-Reuters Data Citation Index

Kevin sent Caltech an email about attributions for gene records on 8/9. Do we need to discuss this further?

Juancarlos: Outstanding Help Desk issues

Help Desk issues

No response to user


- Difference between files in ftp folders

- ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/annotation/geneIDs/

- ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/annotation/gene_ids/

Help desk issues untouched for a long time

https://github.com/WormBase/website/issues/1471 Karen, Paul Davis, Mary Ann lin-15, comments wanted, consider helped ?

https://github.com/WormBase/website/issues/1403 Karen, Lincoln, Raymond gbrowse visualization, lots of comments, consider helped ?

when Abby is back from vacation :

https://github.com/WormBase/website/issues/1462 Kevin, Abby Was fixed on staging by Joejimbo months ago, can it be closed ?

https://github.com/WormBase/website/issues/997 Karen, Abby Track authentication, Karen asks Abby if we can close this. Consider helped ?

when Mary Ann is back from vacation :

https://github.com/WormBase/website/issues/1393 Mary Ann forwarded to Mark Edgley, we will write back, did we hear back ?

29-Aug-13 - We did and I am still working on this. (Mary Ann)

https://github.com/WormBase/website/issues/1318 Mary Ann Contaced Jonathan Hodgkin, we will write back, did we hear back ?

29-Aug-13 - We didn't. Have forwarded to Tim. (Mary Ann)



Raymond, JD, Kevin, Todd, Paul S, Michael P

Glad that people are interested and want to add more things, but not ready to yet. Will make a table about future data classes. Currently expanding existing classes. Upgraded data loader, can add data that is a tag, instead of just data in a tag.

Does it handle acedb hashes? If it can be reached through xpath, it can be handled.

Will next release allow download of Sequence parts? From the GFF. Not resolved yet, it's a deep Intermine issue, talking to InterMine to diagnose. Need this before turning off WormMart.

WormMart data being so old, should we discourage people from using it? It's better to encourage other ways of getting the data.

WormMart still needed for at least another 6 months, be more transparent about what data is still needed there. Compare this to JD's list of data to be added. Some data in Ensembl. Need Batch Genes.

WormMart has 1/100th of 1% of this year's usage. We could turn it off without anyone noticing for 2 weeks.

JD's WormMine table here http://wiki.wormbase.org/index.php/WormMine#New_data_wishlist

Release Milestones for WS240

Michael P, Raymond

Themed releases, what news-worthy data is there? Needs to be done in the next 3 weeks for WS240.

Nothing from Caltech. Still in internal discussion.

Coordinate data mining and display.

Sequence Feature is still ongoing.

Got 1 hour to get in notes for WS239 release

Thomson-Reuters Data Citation Index

Kimberly, Kevin, Raymond, Paul S, Paul D

Caltech hasn't commented to Kevin.

Encourage us to do the best we can, even though attribution is very complicated. Just "WormBase" is not enough. They don't want genes lacking a CGC name. Only want Concise description and author list. Authors of concise description, or papers? Not sure. More names, more people get credit. Kevin will try to get clearer definition of "attribution". No limit on authors included. Will try to match "spirit" of it. All concise descriptions should have a curator. Should be automated. Attribution is an optional field, but they'd rather we didn't. Title is CGC name with 1-line description. Abstract is the concise description.

FTP geneID files

Todd, Michael P, Kevin


Generated by build, at OICR. OICR had a different file, we were planning to consolidate into one file. Legacy files on ftp site.

We're keeping this one


This directory has been removed