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The Fossil Calibrations database is a product of the NESCent working group Synthesizing and databasing fossil calibrations: divergence dating and beyond.
Fossils play a key role in estimating the divergence times between groups of species. Researchers combine fossil data with molecular (sequence) data to infer dates on internal nodes in the tree of life. Few scientists have expertise with both the methods for data analysis and with the paleontological data, and fossils are therefore often used incorrectly (placed in the wrong place on the tree or assigned dates that are inaccurate or overly precise).
The working group, with scientists who have expertise in both molecular phylogenetics and paleontology, have published a set of best practices for publishing fossil calibrations, created a new publication stream for fossil calibration papers at Palaeontologia Electronica (PE). The fossil calibration database supports the entry of structured data associated with PE calibration papers.
Data entry supports the structured data associated with PE fossil calibration papers. At this point, authors will not be entering the data. PE editors will be doing the data entry and therefore data entry requires a login.
The data model includes information about the publication, node name, minimum and maximum age of the node, fossils used to date the node and a definition of the node.
The phylogenetic placement page describes the design and implementation of this node definition feature.
The database supports multiple types of search:
- full-text search via a google-type text box on the main page
- browsing via a (modified) NCBI taxonomy: Browse
- advanced search by taxa, age, time, etc: Search
The database does not currently support programmatic access, but this is planned for 2104.
- Working group members: Dan Ksepka and Jim Parham, David Polly
- NESCent Informatics: Karen Cranston (NESCent) and Jim Allman
The Fossil Calibrations database is being readied for public release at http://fossilcalibrations.org/. PE is in the process of taking over hosting of the database and web-application, and release of the site is planned for early 2015.