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mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
mx & dbs
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mx & dbs

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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 …

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.

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  • Add diagram suggesting how if generalized then must remove restrictions and the expertise in the system decreases. Design for the intended audience is most important factor. ‘Expert systems’ will never be completely simple, thus they must be carefully tailored to the particular expert. One system for all may not be the solution.Suggesting that a bottom up approach, many small individualized initiatives are beneficial. Mx moving away from show pages => workbench => import and export data
  • General MX introduction:93 tablesRequire identifiers on specimens. Specimen information makes data repeatable, thus pushing for images, keys, characters to be attached to specimen information. More specific.Local host here::127
  • Mostly matt responsible, although gaining ground as SF project with others involved. Francois, Fail, Myself, (2 others?)
  • General MX introduction:93 tablesRequire identifiers on specimens. Specimen information makes data repeatable, thus pushing for images, keys, characters to be attached to specimen information. More specific.Local host here::127
  • Come common database activities rails makes easier. Show detail of mx database and explain how it is a product of rails as a programming philosophy
  • Really I only have experience with relational databases, with a bit of experience using xml as a text db. Searching solutions? Problems with Treehopper. Versioning and the scamit solution. Emphasis on experimentation and creativity to solve problems. Not suggesting that these are the ‘right’ answer.
  • Simple newick trees
  • The problem: Need a way to propose changes, track changes from version to version and to roll back if necessaryEach table has a ghost table these start as a perfect mirror of the species table and add rows for any edit proposed to the species table. If an edit is accepted than it moves to the species table.When a version of the species list is made ‘official’ it is exported in html version, pdf and soon XML (soon as we can figure out what format to follow). Easy to do this using Rails.
  • Transcript

    • 1. mx & dbs
      Katja Seltmann (katja_seltmann@ncsu.edu)
      mx (http://hymenoptera.tamu.edu/wiki)
    • 2. Wiki:
      (http://hymenoptera.tamu.edu/wiki/)
      Acknowledgments
      Funding:
      The following sources of funding have directly or indirectly supported the development of mx, or have used mx to manage data:
      • NSF Advances in Biological Informatics (DBI-0850223)
      • 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)
      • 11. A Texas A&M Ecology and Evolutionary Biology Graduate Student Travel Grant to Matt Yoder
      Intellect, enthusiasm & hard work:
      • Matthew J. Yoder (diapriid@gmail.com), Krishna Dole, Andrew Deans (andy_deans@ncsu.edu), John W. Fail (fail@cenotaph.org) and others
      • 12. Fredrik Ronquist & Greg Riccardi
      • 13. All the contributors
      • 14. SCAMIT: Southern California Marine Invertebrate Taxonomists
    • 15.
    • 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).
      .
    • 19.
      • focus moving to data import => export
      • 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
      • 26. open source
    • Rails solutions that help make development more agile (web 2.0):
      • Many small tables, object database model in the sense introduces the ideas of
      polymorphism and encapsulation into the database. Tables in rails correspond to a model
      and are strictly named.
      • MySQL but its hidden (can use other dbs)
      • 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)
      • 34. migrations (easy to update a db and propagate those updates from development to
      production environment
      • little tough to deploy in comparison, but Passenger gem works; Dreamhost for US non-profits
      Browser
      Controller View
      Model Database
    • 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
    • 37.
    • 38.
    • 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:
    • 54.
    • 55. http://www.opendatacommons.org
    • 56.
    • 57. Katja Seltmann
      katja_seltmann@ncsu.edu
      Wiki:
      (http://hymenoptera.tamu.edu/wiki/)
      Acknowledgments
      Funding:
      The following sources of funding have directly or indirectly supported the development of mx, or have used mx to manage data:
      • NSF Advances in Biological Informatics (DBI-0850223)
      • 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)
      • 66. A Texas A&M Ecology and Evolutionary Biology Graduate Student Travel Grant to Matt Yoder
      Intellect, enthusiasm & hard work:
      • Matthew J. Yoder (diapriid@gmail.com), Krishna Dole, Andrew Deans (andy_deans@ncsu.edu), John W. Fail (fail@cenotaph.org) and other mx hackers
      • 67. Fredrik Ronquist & Greg Riccardi
      • 68. All the contributors
      • 69. SCAMIT: Southern California Marine Invertebrate Taxonomists

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