Lessons from reviewing and synthesising evidence on crime reduction
Synthesising disparate data resources to obtain composite estimates of geophylogeny
-
Upload
rutger-vos -
Category
Technology
-
view
488 -
download
1
description
Transcript of Synthesising disparate data resources to obtain composite estimates of geophylogeny
![Page 1: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/1.jpg)
SYNTHESISING DISPARATE DATA RESOURCES TO OBTAIN COMPOSITE ESTIMATES OF GEOPHYLOGENY
Rutger Vos
![Page 2: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/2.jpg)
A simple assignment?
Refine a tree for the Primates with taxonomic and systematic data
Add divergence dates
Add occurrence data Visualize the result Use public web
services
![Page 3: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/3.jpg)
Actually not so easy…
![Page 4: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/4.jpg)
The Tree of Life Web Service
Using PhyloWS we traversed the Tree of Life and built a local, semantically annotated copy of the Primate clade
![Page 5: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/5.jpg)
Adding taxonomic metadata
Using the uBio PhyloWS service we enhanced our tree with further taxonomic annotations and links, and expanded some genera
![Page 6: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/6.jpg)
Fetching additional tree data
Using the TreeBASE PhyloWS service we fetched additional data to resolve the tree further using a “supertree” approach
![Page 7: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/7.jpg)
Computing node ages
The TimeTree PhyloWS service allowed us to anchor molecular (i.e. relative) node ages on absolute dates
![Page 8: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/8.jpg)
Adding occurrence data
Using the GBIF XML API, we then fetched occurrence records for the species in our tree
![Page 9: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/9.jpg)
Visualizing the result
![Page 10: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/10.jpg)
Implementation
Except for GBIF, all services: return NeXML implement PhyloWS
Semantic annotations using RDFa
Glued together with Perl
![Page 11: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/11.jpg)
Challenges
Although some services have the same API, no GUI exists to chain them together
No web services for computationally intensive steps
Data and metadata are messy and sparse
![Page 12: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/12.jpg)
Conclusions
The tree of life can be covered with all sorts of metadata (taxonomic, molecular, biogeographic, paleontological), viewable in different ways
Standards still incompletely defined and adhered to, though
![Page 13: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/13.jpg)
Shameless plug: PhyloTastic
A web service to extract subsets of taxa from megatrees and annotate them
Deliverable of the first HIP hackathon, at NESCent, in June 2012
![Page 14: Synthesising disparate data resources to obtain composite estimates of geophylogeny](https://reader038.fdocuments.us/reader038/viewer/2022110115/54929588ac7959292e8b464f/html5/thumbnails/14.jpg)
Acknowledgements