Tuesday 17 July
Book in at recept
Overview of Post
genomics and Proteomics Programme status.
Update on NEBC core
Linux, including update on National Grid Service access (Stewart)
Update on Envbase status
Review of contact with PGP researchers for design, analysis, etc. (Bela)
Course plans (Bela)
Barcoding and Genquery update (Tim)
MIBBI update (Chris)
Ontology and standards (Norman)
NEBC PGP September r
NERC PGP Science meeting 24
mber, Milton Keynes.
Time may vary depending on above schedule
TAB and the Bio
Investigation model (format as a common way to
omics investigation to ArrayExpress, Pride, Meda
Update on the O'Mixed project
Investigation Index (using Investigation, Study, Assay)
General discussion on topics raised d
uring the day.
Notes from NEBC
EBI workshop 19
20 Feb 2007.
Dawn introduces workshop.
Round table introductions from all attendees.
Dawn briefly reviewed the minutes from the previous workshop. Slides still need to b
e supplied from those
that presented them at the Dec 06 meeting in Cambridge.
The agenda for this two day meeting was discussed and agreed as appropriate.
Logistics. Dawn stated that CEH had not yet arranged the transfer of money to the EBI for Chris Tay
position as MIBBI programmer. Dawn is waiting for Will Thomas, NERC EG Science Programme
Administrator, to confirm the transfer.
Dawn and Bela gave a brief overview of the NERC Omic Data Strategy Meeting that took place on 2
the MRC, London
. The meeting attendees are forwarding a plan to NERC ISG that outlines what they
Dawn mentioned that NEBC has a new website since July 2006 and has a Wiki that will be used to post the
minutes and presentations from this workshop.
that there is no change in the status of the MSI paper.
The OBI meeting in San Diego was then discussed. Many of the workshop attendees went to this OBI
meeting, and the talks revolved around the OBI milestones set in San Diego and that a Google calenda
available that displayed the key dates.
Chris Taylor presented the MIBBI website and explained what MIBBI is. It has superseded the MICheck
name as that URL was already taken. It has several participant projects. It uses XML forms. Lots of MIAME
Tim gave an update on MIBBI, MIGS and EnvBase websites using GCat. He reviewed the use of Orbeon (did
not like it as a programming tool). Action to check website for terms
Dawn search on google?
Tanya reviewed the GCat
GSC background and l
Dawn suggested a meeting between Tim, Chris, Tanya and Dawn to discuss GCat
Lunch at 12.45
After lunch, David Shotton gave a brief talk on his project at the Zoology Department, Oxford University.
They are building a web
e database for biology. The plan is to have researchers enter their
metadata about images on a web based form as soon as the images are created, and to use this data and
database as part of any paper submission. This will hopefully make the database useful
to those inputting
the data as an aid to publishing papers, and to those requesting the data at a later date.
They will have RDF support.
Graham Klyne followed David’s talk with details about the methods they will use for the database and how it
a distributed database accessible from the web. It will use public repositories and individual servers.
able sources but not providing mash
ups. They will test the system with several of their in
researchers in the Zoology department. Any system
has to have a positive gain for researchers or they will
not use it.
Norman gave a brief overview of the Habitat Ontology that he is working on. He said that “flicker”, the
website service for displaying photographs, may be useful for distributing data?
Allyson Lister then gave a presentation on the CISBAN project, and how they are implementing the FuGE
milestone 3 object model. It is Java based. Uses POJO’s
Giles Velarde gave a talk about the Streptobase project that his group at Manchester University
on. It uses maxdbrowse code, has web access.
Dave and Giles updated the group on the omixed.org website and project. Dave’s Generic Experiment Model
is almost done. It has no documentation and is rough round the edges. This is for the generi
c version of
Omixed has a website, and has a Flash version of a possible user based web access form. The Flash version
is a test/play version for Giles.
A follow up action is to see what was in the Sabre proposal that can be used for omixed.
A general discussion followed regarding MAGE
The Monday session closed at 5pm.
Bela began with an overview of the Excel spreadsheets that NEBC have created for annotating data for
Philippe presented his dat
a on the Excel spreadsheet based IDF file system (MGED Format), for multi omic
Tab. Check the PRIDE harvester website at EBI. MAGE
TAB does not produce XML.
Can we use Google spreadsheets?
Action on Ashley to see if NEBC spreadsheets ca
n be made available on Google spreadsheets so that they
are available on
line. (Even though they already on a website).
Tim gave a demo of EnvBase and Handlebar. Reviewed data entries and showed the options available to
users of Handlebar. EnvBase has no
unique persistent ID. Can we get EnvBase entry by webpage?
Tim discussed the meeting he and Dawn had with Renzo and Wolfgang from the Max Planck Institute,
Bremen regarding their request to use Handlebar. Security of system was an issue. Spreadsheet
data and validation on upload to database was also an issue. Check out MEGX.
Andy Jones gave a FuGE presentation on the project history, background. The FuGE model, UML to XML.
AndromeDA. More complex than Maxd. FuGE v1 due by April 2007.
Accepted by MSI and PSI.
Action on Dawn to email andy re GSC input to FuGE.