For Biodiversity Informatics workshop in Stockholm, Friday September 13. Describing some of the tools in the mx system for mx; a collaborative web-based content management system for evolutionary systematists, particularly those working on descriptive taxonomy. Yoder, M.J., Dole, K., Seltmann, K., and Deans, A. 2006-Present. Mx, a collaborative web based content management for biological systematists.

1. mx & dbs Katja Seltmann (katja_seltmann@ncsu.edu) mx (http://hymenoptera.tamu.edu/wiki)

3. Morphbank (NSF DBI-0446224)

4. National Evolutionary Synthesis Center (NESCent) (NSF EF-0423641)

5. PEET: Monographic research on parasitic Hymenoptera (NSF DEB-0328922)

6. Nescent DB Hackathon Workshop (Matt Yoder & K. Seltmann participants

7. NSF TOL grant (Heraty via Sharkey et al.)

8. NSF TOL grant (MartínRamírez and Jonathon Coddington)

9. NSF PEET grant (Anthony Cognato)

10. NSF PEET grant DEB-0328922 (Dr. Bob Wharton)

12. Fredrik Ronquist & Greg Riccardi

13. All the contributors

16. Design for audience :: is the most important factor *Greater the diversity of user-groups the less specific the data requirements. *Suggest that lack of specificity in primary data collection may reduce quality of data. extension curators taxonomists

17. specific expert system

18. mx history and players: (http://hymenoptera.tamu.edu/wiki/) mx is coded by Matt Yoder, Krishna Dole (retired), Katja Seltmann and with help from Andy Deans. Johan Lijleblad has provided documentation and much useful feedback. Many others, in particular the Wharton (TAMU), Cognato (MSU), and Heraty (UCR) labs have provided feedback. We are very open to having others join us. There is no formal means of citing mx, you might use something like this: Yoder, M.J., Dole, K., Seltmann, K., and Deans, A. 2006-Present. Mx, a collaborative web based content management for biological systematists. Various previous projects influenced the development of mx, in particular: The table structure for specimens and collecting event related data is loosely based on the TAMUIC insect collection's database programmed by Yoder and Oswald. That database was in turn loosely based on a very early draft (pre 1998) of the Specify table structure. Some of the tables containing matrix related data are based on Yoder's early MS Access database mtrx, which was greatly simplified from GregorHagedorn's software Delta Access (apparently no longer available on-line). .

20. workbench for revisionary taxonomy and systematics

21. looking for creative solutions based on experience

22. power in relational dbs

23. specific expert system

24. rapid development

25. agile

27. Restful CRUD (create, read, update, delete)

28. Easy upload transactions in rake tasks

29. test driven development

30. creator & updater on and id

31. encryption & security

32. UTF8

33. Model View Controller (MVC)

35. Databases in general: Definition: “A database is an integrated collection of logically related records or files which consolidates records into a common pool of data records that provides data for many applications. A database is a collection of information that is organized so that it can easily be accessed, managed, and updated.” - www. wikipedia.org Three models: relational, hierarchical and network Relational: The purpose of the relational model is to provide a declarative method for specifying data and queries Hierarchical: tree like structure (one to one; one to many relationships) Network: each record can have multiple relationships object-relational mapping (ORM) Relational database, text file, xml potentially all databases or data sources Experience with MySQL Diacritic marks (ontology?) Versioning

36. Object-Relational Mapping (ORM) libraries map database tables to classes. If a database has a table called orders, our program will have a class named Order. Rows in this table correspond to objects of the class—a particular order is represented as an object of class Order. Within that object, attributes are used to get and set the individual columns. Our Order object has methods to get and set the amount, the sales tax, and so on. -Thomas & Hannson. Agile Web Development with Rails

39. security model: private until made public groups trust in groups

40. OTU is the key

41. wiki help:

42. image management:

43. figuring:

44. There are a various open source plugins and widgets used in mx: Input draw Phylowidget RelationBrowser The GoogleMaps API Attachment fu BetterNestedSet

45. Versioning solution in MySQL/RoR (John Will Fail : fail@cenotaph.org)

46. Species Table Starts as a perfect mirror of the species table Adds version number when version is released Version released at anytime: export as pdf, html, XML Ghost of Species Table accepted Columns not seen publically id date_created date_modified

47. matrices vssubmatrices: clone and share display of large matrices one click coding export (nexml) import

48. annotations: tags and confidences

49. public pages::Electronic key publication standards: Data publication and dissemination of interactive keys under the open access model -ZooKeys (in prep) Stand alone publication Data files necessary to recreate the key DOI and kept with publisher

50. public pages:

51. public pages:

52. public pages:

53. public pages:

55. http://www.opendatacommons.org

58. Morphbank (NSF DBI-0446224)

59. National Evolutionary Synthesis Center (NESCent) (NSF EF-0423641)

60. PEET: Monographic research on parasitic Hymenoptera (NSF DEB-0328922)

61. Nescent DB Hackathon Workshop (Matt Yoder & K. Seltmann participants

62. NSF TOL grant (Heraty via Sharkey et al.)

63. NSF TOL grant (MartínRamírez and Jonathon Coddington)

64. NSF PEET grant (Anthony Cognato)

65. NSF PEET grant DEB-0328922 (Dr. Bob Wharton)

67. Fredrik Ronquist & Greg Riccardi

68. All the contributors

69. SCAMIT: Southern California Marine Invertebrate Taxonomists