An introduction to data-intensive palaeobiological research through the PaleoDB

1. An introduction to data-intensive palaeobiological research through the PaleoDB General introduction to the Palaeobiological Database Project http://www.nceas.ucsb.edu/~alroy/

2. PaleoDBServing the community since 2000

3. Structure of PaleoDB record Record ID number links everything

4. Basis of PaleoDB: Published literature • All entries relate back to a publication (including field notes) • Main elements of a record • Publication • Taxonomic information • Collection(s) from publication • Taxonomic lists and abundance data from • publication

5. Locality versus collection Collection 2 Collection 1 • A locality is a place (x, y co-ordinates) that can be distinguished from another place • A collection is a collection of fossils, which can be from EXACTLY the same locality but with differences in: • Collecting team • Collecting time • Collecting level

6. PaleoDBCurrent admin team

7. Browsers and hardware PaleoDB was built by Mac users in Perl Runs best on Safari and Firefox Explorer is not a good choice (standards problems) Mirror Servers [Macquarrie, NCEAS, Madison, MfN] Experimental read-only Grid server (Glasgow) hosted by ScotGrid Many R projects have sprung from PaleoDB

8. PaleoDBJoining the PaleoDB: the two routes • Enterer • - Anyone • Your AUTHORIZER emails • John Alroyto get you added • RESPONSIBLE for your • errors to YOUR authorizer • - Can become Authorizer • Authorizer • Usually a Ph. D. holder • Email John Alroyto be • added: alroy@nceas.ucsb.edu • or john.alroy@mq.edu • RESPONSIBLE for your • errors and those of your • enterers

9. PaleoDB subsets Sepkoski’s Compendium Evolution of Terrestrial Ecosystems database Neptune (deep-sea microfossils) Various datasets related to published papers

10. PaleoDB working groupshttp://www.paleodb.org/cgi-bin/bridge.pl?user=Guest&action=displayPage&page=working_groups Marine invertebrate Micropaleontology Paleobotany Taphonomy Vertebrate paleontology

11. Exercise time Use sheets to identify bare minimum

12. PaleoDBThe ground rules • Enter ALL the data you can! • Watch your typos, especially with taxon names • DO NOT alter taxonomy tables if you don’t know • what you’re doing • DO NOT generate a duplicate locality just because • someone else owns the locality already. Email the • Authorizer • If you use the PaleoDB, please acknowledge it. • If you publish a paper using our data, get a publication • number

13. Adding new reference

14. Adding new reference

15. Completed reference

16. Taxonomic data

17. Go to RichButler’s taxonomytip sheet and PaleoDB taxonomy tips

18. Taxonomic data: what’s already in the OSA

19. Problem: Anyone can alter taxonomy tables Alterations in the taxonomic area can Cascade through large Sections of the database. Mistakes can lead to serious problems and are very time consuming to fix - If you don’t know what you’re doing consult the FAQs - If you typo a taxon name, let John Alroy know - Subspecies can be problematic - Don’t enter a taxonomic hierarchy without good evidence it is widely accepted

20. Taxonomic data

21. Taxonomic data: next step

22. Taxonomic data: opinion

23. Collection data: make sure this is a new collection 1 degree square

24. Collection data: Basic info

25. Collection data:Geography

26. Where in the world is that?

27. Where in the world is that?

28. Where in the world is that?

29. Collection data: Stratigraphy

30. Stratigraphy help: GeoWhen and National Geological Surveys

31. Collection data: Geology

32. Collection data: Preservation

33. Collection data: Components

34. Collection data: Collecting info

35. Taxonomic occurrences:

36. Summary of occurrences