The BIEN update – why? because its muy bien
May, 2017 edition
Hello everyone, welcome to the somewhat regular BIEN update. A lot has happened with BIEN over the past six months. The winter months have been marked by many new BIEN developments, releases, and updates. The BIEN core team – Brad Boyle, Jeanine McGann, and Brian Maitner have made a significant number of new advances. Here is a summary of all of the various database and computational developments during 2017 so far . . . .
BIEN International Biogeography Society meetings and informatics workshop
We had an full capacity BIEN meeting at the start of the IBS meeting in Tucson Arizona where we kicked off the new efforts of 2017. The group outlined short and long term goals for the next 1-3 years and celebrated with many presentations of new science and new collaborations.
In addition, the BIEN group participated in a workshop organized by Cory Merrow et al. entitled "Integrating and cleaning biodiversity data: Workflows to model ranges and merge associated ecological, phylogenetic, and trait information." The schedule, talks, and code can be found here.
BIEN Database update and computation
- We are now up to database version BIEN3.4
- Integration of all database code from past two years into single automated pipeline.
- Private and public database schemas now fully synchronized (only difference is data embargoes in public database)
- Citable database versioning, with retrievable archives of past versions (going forward, starting from current version)
- Revised endangered species embargoes in public database (IUCN redlist species [CR & EN], CITES, & US federal and state threatened & endangered species).
- Extensive new metadata, including information on data access & ownership, data quality, methodology, locality, and high-level summaries of database content.
- Ground work completed on reporting data download and access statistics to data providers (herbaria)
- New optimizations & indexes provide 1-2 orders of magnitude performance increase for common queries.
- We have migrated all of our database and computation efforts over to a new BIEN server!, 2-3x faster than previous, with 5x more disk space. Here are some specs – The server has 20 cores, 256 GB of memory, and 12 TB of disk running Ubuntu 14.04.
BIEN R package developments:
We have now released a BIEN R package to access the BIEN public data and many deliverables. It is now available on CRAN and Github – just search for ‘bien’ . Here are several updates regarding the R package:
- Manuscript outlining R BIEN is now in review at Methods in Ecology and Evolution
- Working beta version of the package to access the private database, called "todoBIEN"
- New functions/functionality
- Automated citation and acknowledgement generation with the function "BIEN_metadata_citation"
- Added functions to access stem data
- By default, queries now exclude species flagged as introduced
- We are now serving approximately 1 million trait records including plant habit data (search for all data for trees! for lianas, or just epiphytes!)
- New updates to plant habit data and trait metadata
- Trait names have been standardized according to http://www.top-thesaurus.org/
- The original BIEN2 range maps will be available soon.
- Production version of the site was moved to new server at NCEAS. Much faster rendering and processing.
- Development version of site is currently on a server at UofA. Now we can test new features and make changes without disrupting the ‘live’ site. A local Github repository was added to this server as well.
- Login/registration requirement was removed. It is now optional as there are some functions (like the report issues form) that require it.
- Beta version of range issues report from is ready once all parties have approved
- Queries were updated to match RBIEN.
- Private version of site is currently being tested.
- Range maps are in the process of being moved from Cyverse to our NCEAS server.
- Much of the information displayed on this site from the database (such as bien summary data, data contributors, and herbaria) has been moved out the old MySQL DBs on nimoy and into PostgreSQL databases on vegbiendev. Queries have also been updated.
- There is now an RBIEN info page on this site with links to CRAN, Github, tutorials, and a data dictionary.
- There is also a link to the old Salvias.net site (which is now semi-retired). Salvias databases were recently backed up and stored as tar.gz files, but they are available to anyone who wants them.
- A bulk download of all BIEN3 range maps is available now. We are working on getting first generation BIEN2 maps as well.
- Currently working on a data providers page where providers can view stats about their data’s usage.
Meet our new BIEN server – based at NCEAS . . .