Download Bd Mapping Project Break

Bd Mapping Project Break-Out Group Notes
7 November 2007
Bd Mapping “Advisory Committee”
Dede Olson
Kathryn Ronnenberg
Mat Fisher
David Aanensen
Matthew Becker
Allison Buchanan
Caren Golberg
Alex Hyatt
Jenn Kerry
Jos Kielgast
Tiffany Kosch
Jenny Loda
Peter Murphy
Gabriela Parra
Oliver Ryder
Stephanie Shaw
Lee Skerratt
Beth Timpe
John Wood
Interests of Break-Out Group Members
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Distribution of Bd in SA (Peru)
Mapping in SA
Mapping Bd distribution (NZ)
How invasives spread worldwide
New Gis applications
Bioinformatics and tools for genome mapping for endangered species
conservation
Multilocus Sequence Typing (MLST) mapping
Immune response
Strain identification
Phylogenetics
Identification of new emerging agents
What interface will be used for
What variables should be collected
Coordinate accuracy
Some indications of what additional data are available
Encourage community data submission by providing a standard form
Information sharing/idea development (Bd central?)
Use Bd central as a model for other amphibian diseases.
Prelude
During the oral presentations on Day 2 of the Bd Conference in Tempe, AZ, it was
announced that the maps and data generated by the global Bd Mapping Project presented
by Dede Olson and Kathryn Ronnenberg, US Forest Service, Oregon, would migrate to
the spatialepidemiology website presented by Mat Fisher and David Aanensen, Imperial
College, UK. This website has longevity, more sophisticated mapping capabilities, and
would be an efficient way to take this effort into the future. Our break-out session was
intended to pursue these two talks and the proposed merger of datasets. Below are our
summary points and the brainstorming topics discussed during the session.
Summary Presented to Larger Group
Major Points
Consolidated points presented to larger group –
 “Bd Central” website – The spatialepidemiology.net/bd site can be expanded
minimally to include information specific to each country (centres of expertise,
diagnostic labs, lead researchers etc. to develop into Bd central.)
 Map(s)
 Data Standards.
 Consensus of loci for multilocus sequence typing.
Discussion in break-out group  Bd Central: Knowledge bases for countries available through central site
(accredited labs to send samples to)
 List of expertise or links to references
 Links to fact sheets
 Links to protocols for data survey (AU: need to be modified for global
applicability)
 Must accommodate private data, public data, sensitive locations
 Scales of mapping
 Minimum data set we will collect
 Feeds into Excel spreadsheet template and field data sheets
 Develop a consensus about loci for determining Bd multilocus sequence typing
 Refining and broadening diagnostic tests (accuracy, cost, efficiency)
 Field validation on different populations, parts of the world
Products/Lead/Timeline
Consolidated points presented to larger group  Bd Central (Mat/David, Dec/Jan – official release to coincide with publication.)
 Transfer of data to Bd Central (Dede/Kathryn, Dec/Jan?)
 Datasheet for standardization
 Factsheet: what to collect
 Maps
 PARC website (Dede, November-Dec.)
 Journal publication (Dede/Mat/David et al, Jan draft)
 National Geographic (Dede/Mat/David, late ‘08/early ‘09)
 Google Showcase (David/Mat, to coincide with publication)
Discussion in break-out group  Spreadsheet for data collection (Excel and field data sheet)
 Facilitate standardization/ease of entry
 Georeferenced comprehensive comparative Bd genomics database
 Bd Central knowledge base idea
 List of conference attendees for networking
 The map!
 Website, first cut
 Journal pub on mapping capability with combined data/Dede, Mat, David,
Kathryn/ early 2008
 Joint map in National Geographic 2008/2009
 Visualizing Patterns of Spread
 Google showcase (if it doesn’t compromise journal publication – to coincide with
initial publication.)
 Fact sheet with data collection standards.
 Bd-free Map
How you can help/Needs
Consolidated points presented to larger group  Get standardized data (accurate georeferences)
 Funding for person in London to further develop and maintain Bd Central
 Send information to us! – centres of excellence within countries, qPCR and other
diagnostic facilities.
 People to help collect data per countrry.
 Outreach Program
 List of database users for Bd Central
 Send information to Bd Central
 Support for work on what type of samples for Bd genetics.
 Utilise the associated publicity that will accompany The Year of the Frog to push
the facility and gain wider exposure.
Discussion in break-out group  Identify people who want to start using the Bd Central system as private database
users
 Decide on markers to use for Bd genome
 Support for work on deciding what types of samples will be appropriate for Bd
genetics
 Outreach program
 Personnel
 London-bioinformatician/web developer
 Curators per country or region
Questions
 What is the priority of the Map?
Multiple Choice: 5 choices – Urgent to Not-a-Priority
Group Vote: Important, 2nd highest choice
 What are the funding sources?
Not determined/discussed.
Minutes of Discussion
Brainstorming Session
Genetic Topics – related to mapping Bd strains on spatialepidemiology
 MLST sequence typing (relationships between strains both genetically and
geographically, through mapping and diagrams)
 Do lineages differ in virulence, and if so how?
 Need to choose common set of markers to map (in the genomic sense)
 Problems: too many loci, too expensive
 Need to identify most useful markers, and possibly resequence current isolates at
these markers rather than the current ones--need to decide asap which set to use so
tests can be standardized (current batch of 17 are Tim James’s)
 7-10 of current lot may be on the same chromosome
 Don’t currently know which markers are connected with virulence--how to
choose?
 Ask genomics community to do a more comprehensive Bd genome analysis to
help us choose? May be in the works already (Erica Rosenblum; isolates from
Joyce)
 Need community decision and grant to develop further--time delay
 Need cultures to do sequencing (try to do with swabs--John Wood)
Mapping Topics – related to next round of data collection for mapping
 Encourage collection of more accurate and more consistent geographic
coordinates; protocols for data entry
 Present in a way that people will want to participate
 Identification of country-specific curators to take responsibility for data checking.
In some places (AU), this is regulated; may be true for other agencies or
institutions as well
 Public data release is not allowed until given the OK by the provider.
 Minimal data for each isolate choose from: lat/long, diagnostic technique, species,
life stage, location identifier, accuracy, test result, time/date (format issues), type
of test, contact, reference, captive/wild/introduced/native?, sex, health status,
elevation
 Notes on available data: might be better to allow users to add columns for
experiment-specific data for their own access
 Standardization of data: should fields be the same or compatible with other
similar datasets (i.e., avian influenza website)
 Less than minimum doesn’t go live automatically; public/private flags only work
if minimum data are entered
 Quality control? Is it down to the person who submits data? Should we identify
curators as a priority?
 Published status of data is recorded and unpublished data remains the property of
the private database owner until publication when the data can be made public.
 Diagnostics: Was it done in an accredited laboratory? What’s the sensitivity of the
test?
 Levels of access: can be available to public, or only to collector
 Is country-level only data worth collecting?
Or is at least the minimum data set needed to say anything with any confidence?
 How do we deal with prevalence vs. sample size for negative data?
 How confident are we in this data?
 How many samples were run?
 Quantify uncertainty levels, so we may “flag” data that is of low quality, or
suspect quality.
 Mortality data: was there mortality associated with Bd detection? How well
linked was this mortality with the Bd infection? (strong or weak association…)
 Cause of death (Lee Skerratt): to attribute a cause of death you usually need to
have an expert.
 Data already collected by Kathryn & Deanna:
 Fields: continent, country, region, state/province, site number, latitude,
longitude, coordinate source, information source (excel file by email,
within email, within journal, grey literature, newspaper report), date of
occurrence, date of publication, contact (name + email), taxa group (anura,
salamandra, other), family, species (binomial latin), number of animals
(positive, negative, sampled), analysis method, locality description, notes,
reference.
 Every datapoint is on the level of an individual.
 How much of a detective do we need to be in terms of proofing the data people
put into the database? Ideally the system will be robust enough to capture errors
and flag inconsistencies in data prior to entry.
 We don’t need to “reinvent the wheel” in terms of what data fields we collect.
We can use other disease databases as a model that can guide us in terms of what
variables we need to minimally collect.
 Can or should we ask that some specialist journals require submission of points to
database for publication?
 How do we deal with private land issues for privacy of locations? Human
databases use lowest level of jurisdiction, but will that work for Bd?
 Centroids, approximate designation, or protected location designation? Would
need a code for a site record
 Danish environmental information system randomizes the location within a grid
field (isn’t centroid, size is controllable by species)
 We can make a map pin ‘fuzzy’ for approx. coords. or color them differently
 Different views of map: one with exact locations only, one with larger regions
plotted rather than points (e.g., London postcodes for medical research)
 Various levels of display can be provided through the website (country level,
diagnostic technique, etc.)