Welcome to TitanPad!
==General Meeting Information==
* [http://twc.titanpad.com/273 This Titan Pad]
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* Call-in information
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==Agenda==
*
==Attendance==
*Deborah
* Ping
* Han
* Sky
* Josh
*==Past Action Items==
*
==Action Items==
*
==Notes==
Josh - wll introduce himself
-started as a biologist and a veterinarian.
previously worked in natural history museums. and comes from a taxonomy background
look at broad range of characteristics to figure out where to put animal in a hierarchical arrangement of x.
josh has a masters in entemology (sp?)
also worked at national zoo. later fish and wildlife service - took care of exotic animals .
about 7 domestic animals..... about 30,000 beyond that
often presented with animal never seen before or have litle knowledge of. really need to address this
through a taxonomic approach.... e.g., a zebra is more like a horse than other.
relationships, related non domestic animals back to domestic animals
make comparisions,
what are the characterists that the species need to exist
identify the features from clinical, behaveral aspects
wildlife enginerring
population and dieases in the wild, different to dealing with individual
how do you provide info in that format that they can reuse,
info in a easily understood format
training is mainly about domestic animals
biologists know a lot about species, but not much about dieseases
some other researchers know a lot about diesease, but no about species,
how to connect the scientiests from the 2 domains
think about different features, factors (history, disease, patterns, symptoms), take literature, go throught
papers, extract valuable info about foundings, and link them more easily (this is interesting since it could
link to our connections with elsevier)
descriptors that can be used in many different ways, wouldn't create duplicated ontologies
Deborah: have you started with the descriptors?
Josh: we have an ontology that's an attempt.
Link to Josh's HTML output of his work in Protoge http://dl.dropbox.com/u/32676148/wildpro%20class%20structure.html
Josh will also be emailing out his original Protoge file to Deborah, Ping, and Han (ans Sky).
interesting use case - make a resource that works for both people who know about animal disease
symptoms and patterns (e.g. veterinarians) and others who know about wildlife environments. motivation for wild pro
interesing review of the ontology Josh worked on.
There may be connections between this and ICF - http://www.who.int/classifications/icf/en/
intl classification of functioning, disability, and health, and disability (which was made to complement
ICDx (like ICD9 and 10) which is just diseases (for humans)
Snomed, 20 different ways to describe bacterial diseases, no way to find out their relationships
Canadians start another project, but not use Snomed
We didn't have to depend that everyone uses the same systems,
but to define what the important characteristics were
josh's system is the "bucket" approach
take 5-6 things that are important and define those well
species, sex, age, location, disease
take all of the data sets that exist and do not try to merge things with different terminologies, then try to
sort on only the 5-6 things used above
e.g., how many birds of species x were found dead in region y in time period z
this seems where a facet browser like s2s
Overlap between Josh's work and TWC work:
What are the effects of the contaminants on population?
Global biodiversity forum - mostly taxonomists.
gbif.org is another resource
BISON - USGS replica of GBIF in terms of observational observations - expanding to include additional
info
also taxonomic data working group - is that tadwig?
make sure to make a note that there will be other sources of information. Many other sources could be
mappedto the same concepts.
Sky might be able to give us a list to link to for this
todo - make sure to link to this wildlife health reporter
todo - have Josh send his health effect ontology
gary lasky (sp?) wisconsin - can do things similar to this.
josh - might be able to send link
queston - how do we handle distinction between acute and chronic? josh mentions that muchof this was
motivated by work done largely on mallards
petuxin (sp?) does most of the pesticide testing
he mentions that pesticides have a different effect on some birds for example
some birds much more susceptible for example to botchalism
might look at range - species known to most sensitive to most resistant
look for data on most sensitive animal
josh - do you have health effects for fish?
Josh: yes, I can refer you to some domain experts.
****Todo - josh and sky - no but he has a connection- frank panic? katherine densmore (sp?)
seattle lab - does contaminant stuff.
or columbia - contaminants in fish.
might check with american bird conservancy
they worked on birds and pesticides
Is waterfowl aquatic life?
working to bring together university partnerships
sky is setting up a new organization
research grade science
sky is testing the waters with the ACER group
fiscal year 2013 should have money.
possibly some before that
trying to make sure we have a direct connection to usgs
Sky's notes from an earlier email.
Josh and I chatted for a bit yesterday, and we're looking forward to our discussion today. Josh will have
some good insights for the developing ontology based on his work. We talked yesterday about the
concept of case definition used mostly in public health where diagnoses are based on a group of
sometimes interrelated key factors that are observed and/or measured in a case of a particular disease or
outbreak of some kind. There is some interesting work on applying ontology to case definitions in the
bioinformatics world that I haven't gotten very deep into yet. This paper is pretty interesting http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf. I've also started looking at some work on a
"BioCaster disease surveillance system" (http://born.nii.ac.jp/_dev/static/about) that looks quite
interesting and is very much grounded in what appears to be a fairly robust ontology.
On the flip side of surveilling for health problems and disease outbreaks, I can also envision having a
number of key factors that trend more toward healthy environmental conditions, providing a way that the
ontology could be used to highlight environmental conditions more favorable to healthy outcomes. In the
field of wildlife management, we are often looking at tradeoffs across some large ecosystem that provides
different types of services and habitat. There are many competing interests at work across the landscape,
and resource managers and regulators often have to weigh many factors in their decisions. The more
broadly they can look at various issues across ecosystems, asking the right kinds of questions about why
some phenomenon is occurring or how best they might bring about a particular outcome, the better their
chances of finding a more optimal solution amongst all the competing factors. Just increasing the pool of
observation and measurement information on key factors doesn't help unless there is some reasonable
way to wade through it all. An ontology that enables reasoning through many thousands or millions of
observations and distinct data points to understand whether an ecosystem, at various scales, is trending
health or not so healthy at various levels of granularity, would be immensely useful.
An interesting area that Josh will also be able to speak to today is the role of citizen science in reporting
on some of the key factors that might go into case definition. He and colleagues at the University of
Wisconsin and some other USGS folks were responsible for the WHER application that I've pointed you
all to in the past, and Josh has a real interest in bringing together data from across many different sources
to examine potential disease and other wildlife health processes.