May 16th, 2015 Additions: Evangelos Pafilis
Group from Crete
Neil met these folks at JGI.
- Georgos - Marine population genetics, looking into microbial genomics
- Evangelos - Bioinformatician, text mining for species names & descriptors, global collaboration for marine microbial sampling.
- Eleni Hatziyanni - Government of Crete, resource management and planning
- Karthik - Terrestrial Ecology, rOpenSci
- Neil Davies - Moorea IDEA, Gump Field Station
- Charlotte Cabasse - Ethnography
- Dav Clark - D-Lab, Data Science Collaborative
- Falk Schuetzenmeister - GIF, CNR, ecoengine
Other Moorea/biocode folks
Berkeley Lab - Lewis Lab
- http://berkeleybop.org/: Berkeley Bioinformatics Open-source Projects
- Suzi Lewis - LBL (firstname.lastname@example.org)
- Chris Mungall - LBL
The story so far…
Started with genetic sequencing (biocode), expanding to bio-social understanding throughout time:
- How do we best represent that system today?
- How did that system come to be in the past?
- Socially / human?
- Simulate future states of the system.
Theoretical physicist from Switzerland (Matthias Troyer (ETH) et al. ?), Rich Williams, set up computational ecology group at MS Research, Cambridge.
- See: http://ogdoad.ethz.ch/idea/Home.html (1st Island Digital Ecosystem Avatars Workshop ETH Zürich, November 18 – 20, 2013) on “Grand Challenge Questions”
- See: Nature News: “Tropical paradise inspires virtual ecology lab” http://www.nature.com/polopoly_fs/1.16710!/menu/main/topColumns/topLeftColumn/pdf/517255a.pdf
- See: http://mooreaidea.org/data for the different types of data being integrated: BIOCODE, CRIOBE, MCR LTER, MIRADA, Landscape model, Bathymetry, Social, Archeological
Pilot project on water models.
20 “nodes” - organizational clusters of people.
Realizing the value of good data encoding standards, data exchange and openness.
Setting up platform for data management, incorporating historical collections, building capacity that could be applied to Moorea IDEA. Already working with multiple communities.
Georgos has government research institute intended to be a hub for Greece on bioinformatics, has a slide deck he uses to inspire traditional researchers to join with the larger project. This center is the largest in Greece, even larger than biomedical research centers.
Crete is ~600,000 people in “23 Mooreas” in area. Also much less isolated system than Moorea. E.g., economic crisis impacts the ecology of villages as young people come back from cities. More specifically, there is a shift to organic farming. In the north of Greece, it gets quite cold - folks cut down forests illegally.
Charlotte is interested in the political transformation of Crete. What kinds of political experiments can we observe (or perhaps support).
A hub for single-point-access to the Greek Biodiversity Data, Information and Knowledge is being setup. The relevant project is “https://www.lifewatchgreece.eu/”, the Greek node of the EU LifeWatch infrastructure (http://lifewatch.eu).
What is the data science side?
Open science project. Are there ways Crete would like to contribute to Moorea (or the IDEA infrastructure more generally)? Is there a community of “early adopters?” What is central organization? Is there a technical framework (or a social one)?
A core is available on biocoding, but Neil suggests this can be improved. Foodwebs are similarly developed, still lots of data science challenges.
Stay focused on local, but want tools to be generally useful. Synthesis of data from different projects is an ideal. This already happens in food web research (genetic data, occurrence data, interaction occurrence, spatio-temporal, lots of siloed research).
Jorrit suggests that we should start with making things useful, then proceed to standards. Find 2, 3 use cases, list data scripts to be used (e.g. rOpenSci).
Karthik points out that things like this happen at LTER and pisco (sp?), but very siloed. Data ONE has lots of funding, but it’s all behind the scenes. Lean approach could provide tools as they come to allow immediate leverage.
(Cross-referencing, this is somewhat different than what’s currently happening with ODK. It would be good to see what Matt, Waylon and crew think about the dangers here - folks expect support once things are delivered.)
Concerns - BIDS can’t do much beyond space and connections. We need funds to pay a fraction of a person’s time.
Talking about what BIDS can do - we should fly Tony Fountain up for a talk!
Pilot projects - folks have started building a 4D avatar presented on wall in Zurich, ability to layer data (done by folks in Zurich, also working on Singapore).
A central concern from Neil, keep physical model (for example) interacting with social and biological models to avoid re-creation of scientific silos.
What is an avatar? Best representation of the thing (but there are many). Avatar itself is not visible (it’s too complex, humans can’t see all of it).
Jorrit raises idea of two kinds of outputs - rough educational / public-facing materials are easy, but still force debugging and integration of information. Scientific applications can build on this effort to do more rigorous work.
Charlotte’s question about how to use this for climate change education / policy. Dav’s response is that this is too hard, just make something interesting that helps people explore according to their interest. Neil confirms this idea.
Evangelos has example of conveying messages with materials from human anatomy textbooks?
- Show top (marine) predators in Moorea ecosystem & what they rely on
(including abiotic structures, water temperature…). Do the humans.
- Coastal SEES - looking at coral reefs & fisheries
- Coupled natural-human systems (has food webs)
- Crete has many raptors, vultures, etc.
- Commercial fish species (similar to above)
- Mosquitos & infectious disease (for terrestrial)
- Different mosquitos have different infectiousness (could perhaps even simulate with trait data)
- Could tie into Crete with other vector studies?
- Model and predict: if you reduce water how will it affect mosquito population?
- Water? From different perspectives (i.e., species, geology)?
- Simulate removal of marine protected areas / increase fisheries (reef turns to algae due to loss of herbivorous fish).
Relatedly - what makes its way to textbooks, and what remains only with experts? There are very few complete food webs (most complete appear to be lake systems, or marine).
We’d like an “ecologically aware” Google search. This is an extension of what Tony Dell and colleagues did with their “One Cubic Foot” project. Example of unjustified conflation between two types of hawkfish. Perhaps could have been prevented with trait bank (e.g., mouth morphology) - work by Chris Meyer (has data on what was in guts, biocoded these contents, then screened against reference database).
- Get interactions between software projects (e.g., EOL, GBIF, GLoBI, ENVIRONMENTS-EOL). This would be available, e.g., in the references tab in GLoBI. Show interactions across tools, databases, primary literature, etc. Also show where things are, as a reference tool.
- ENVIRONMENTS and related projects:
- ENVIRONMENTS: Identification of Environment Descriptive Terms in Text http://environments.hcmr.gr/
- SPECIES and ORGANISMS: Identification of Taxonomic Mentions in Text http://species.hcmr.gr
- EXTRACT: Interactive Extraction of Environment Metadata http://environments.hcmr.gr/biocreative.html
- Cretan Bird - Environment distribution: visualization This is merely a visual summary of the environments (ENVO terms mined from the EOL - “global scale”) for birds associated with Crete (according to GBIF occurrence data – “local scale”). Landscape ecology, citizen science and other projects could be supported from such integrative analysis. Data from the “global scale” could be used to make predictions at the “local scale”, e.g. “in which type of environment according to the global literature might a bird be found in unexplored region?”
- “Polytraits: A database on biological traits of polychaetes”
http://polytraits.lifewatchgreece.eu/ , a manually curated database on
biological traits of polychaetes (bristle worms, Polychaeta: Annelida).
- The list of the full trait definitions is available at: http://polytraits.lifewatchgreece.eu/terms
- “supporting evidence” is being tracked e.g. http://polychaetes.lifewatchgreece.eu/taxonomy/term/5126/traits
- please contact Dr. Faulwetter (email@example.com) for more information
Can we get text mining data from Evangelos into GLoBI? Extend EOL? But his system works better with sequences due to use of NCBI taxonomy. If want species name without knowing exact DNA / ID, that could be a draft approach. This would be a data source in the GLoBI ecosystem. Note that all species from Moorea will have a sequence in the gene bank!
Hackathon in ID Bio (in Gainesville, FL) in June or so, looking at doing the above.
Process of annotation of papers might be quite similar to Nick Anderson / Hypothes.is / Text Threshr approach to news articles. Note funding from Sloan. Hybrid approaches may help streamline this approach. Talk to Spencer about using this tool?
Chris Mungall knows of literature on text mining protein-protein interactions.
BiodiversityHeritageL library (http://www.biodiversitylibrary.org/) may be a good source. BHL in collaboration with Prof. Ananiadou, Dr Navarro (NACTEM, UK) and other colleagues are already working on http://miningbiodiversity.org/
“Guts of the Avatar”
- Paragraph for Phenotype RCN funding - working meeting modeling species interactions: ontologies and other data science approaches.
List from a few select data sources (papers, experts) from a few key (island) systems (Moorea/Crete/Hawaii) on terms they use:
- Relationship types (slide from Chris Meyer; and from Evangelos)
- Body part terms
- Life history stages/states terms
- Basis of observation (evidence type) for interactions
Map those terms to ontologies
- Conference (might include biology, and social science funding - Perhaps Matrix for both funding and / or space?)