- Database of Phylogenetic Knowledge
- Bill Piel
TreeBaseII has the kind of granular schema that would be a good challenge to try to accommodate using cdao. What is missing from cdao (and nexml) is the notion of a "study" with various types of metadata, including publication/reference metadata (which is somewhat dc-like).
Its not clear what reference to site. The TreeBase "Intro" page cites about 7 different references up to 2000, including posters and papers. Some of the papers apparently are scientific studies and not implementation papers. Some of the most likely candidates for a TreeBase citation are as follows (perhaps we should include all of these):
- Sanderson, et al., 1994 (Am. Jour. Bot.), cited 59 times, can't track citing papers
- Sanderson, et al., 1993 (Syst. Biol.) cited 29 times, most citing papers are meta-analyses ! (that's good)
- Morel, 1996, cited 21 times
Information gathered on TreeBASE for the Related Artefacts page.
TreeBase is a database developed with the stated purposes of archiving published data sets and supporting meta-analyses.
We are mainly interested in a current effort to develop a new schema for TreeBase II (these are images of the schema; Arlin has UML and XMI versions from the developers that he can share within the evoinfo group).
- The specification language is SQL
- The scope covers character data, trees, and some analysis information; essentially it is a large subset of what is covered in a NEXUS file
- Within this scope, the schema has similar limitations to NEXUS (poor support for specifying models and complex data sets)
- Development is controlled by the administrators
- We are not aware of a versioning policy.
- We are not aware of a conformance policy. The administrators are loose about the NEXUS format for uploading data to TreeBase. In the past they have corrected invalid files received from users.
- TreeBase is actively used and we expect that the TreeBase II update will take place eventually
- TreeBase is widely used for archiving in some areas of the systematics community. It has not been widely used for meta-analyses, to our knowledge. Currently the interface is very limited.