TreeBASE

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TreeBASE

  • 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

TreeBASE Information

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).

  1. The specification language is SQL
  2. The scope covers character data, trees, and some analysis information; essentially it is a large subset of what is covered in a NEXUS file
  3. Within this scope, the schema has similar limitations to NEXUS (poor support for specifying models and complex data sets)
  4. Development is controlled by the administrators
  5. We are not aware of a versioning policy.
  6. 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.
  7. TreeBase is actively used and we expect that the TreeBase II update will take place eventually
  8. 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.