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NeMys: an evolving biological information system, a state of art

NeMys: an evolving biological information system, a state of art. Deprez, Tim (UGent) Vincx, Magda (UGent) Vanden Berghe, Edward (VLIZ) Mees, Jan (VLIZ). Introduction. ?. FIELD GUIDE. ?. Mysid Shrimp: More then 1000 species. Pictures Keys Maps. What is NeMys.

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NeMys: an evolving biological information system, a state of art

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  1. NeMys: an evolving biological information system, a state of art Deprez, Tim (UGent) Vincx, Magda (UGent) Vanden Berghe, Edward (VLIZ) Mees, Jan (VLIZ)

  2. Introduction ... ? FIELD GUIDE ? Mysid Shrimp: More then 1000 species ... Pictures Keys Maps ...

  3. What is NeMys .. • Taxonomical research tool – web application • A system in which any type of data about taxa can be brought together in a fully digital way ... • Literature • Morphology • Morphometry • Collections • Pictures • Molecular data • Observations • Links • Notes • ... • Easy in use ... Do not expect all taxonomist (biologists) to become informaticians

  4. Data in NeMys ... • 21000 taxa • Several datasets (5 under development) • World mysids (1200 sp) • Marine Free Living Nematodes (5600 sp) • Peperomia (3700 sp) • ... • 14700 pictures • 11000 literature references • 12000 geographical records • 7500 morphological records • 5600 morphometrical records • 4000 locations (georeferenced) • 700 collection specimens

  5. The history of NeMys ... • 1997: first steps taken in creation of a biological database for Nematoda biodiversity • 1999: NemasLan (first official version), access-based LAN application • 2000: MysidLan (same as Nemaslan but for Mysida) • 2000: Taxonlan (Generic Lan version of Nemaslan – Mysidlan) • 2002: First steps taken in putting the data online (as shown on COD) • 2003: First version of NeMys with mirror site on VLIZ • 2004: NeMys was connected to biodiversity data portals through a DIGIR provider

  6. The structure of NeMys TAXONOMY • Webapplication: • http://intramar.ugent.be/nemys/ • all data consultation online • all data input online • all dataset maintenance online •  • Database with datasets fully • Consultable and managable in the • WAN-environment •  • Users do not need to know how • to work with databases • Distributed data-input • and data-maintenance Collections Geography Morphology Morphometry Genetics Pictures Comments ... Literature DIGIR VLIZ GBIF OBIS ERMS ...

  7. The Mysida dataset as an example • This dataset is the largest and most documented dataset running on NeMys now. • Taxonomy: 1108 species with 217 synonyms. • Literature: 3935 references of • which 1265 are in PDF format • accessible through the VLIZ • library. • Media: 2845 pictures • 400 collection items • Records: all european species • have morphological and • geographical data

  8. Some technical aspects ... • Technology used: SQL-server + ASP Gradually moving into PHP • Online entry-modules, management modules, ... offer a more user-friendly environment BUT are hard to program and controll on data-input must be implemented in the program code. • The system now uses a taxonomic hierarchy as its base although in many cases it may be usefull to add more taxonomic views! HOW TO HANDLE THIS - INTEROPERABILITY • e.g. Complete phylogenetic based taxonomy (morph, mol) • Partial phylogenetic systems (e.g. For a genus, family) • Generic structure: creating a new dataset takes 10 minutes

  9. Some technical aspects ... • Identification module (Characters, States, Measurements) Webbased identification based on the data entered in the database ... • For small datasets online modules work reasonable (100 species) • Bigger datasets this becomes to slow (e.g. Nematoda dataset) • Key-generator: create keys for regions, selected taxa, ... • Online phylogenetic analysis • (New Hampshire – NemATOL project) • Observation – modules  enter observations on specimens, field observations (not based on literature source) • Lat-long coordinates – country: how to define in which country a certain location is located (Suggestions???) • Creation of regional checklists ...

  10. Conclusions ... 1200 species  digital information system  3 taxonomists-man-year Number of taxonomist is going down URGENT need to start digitising data/knowledge into taxonomical information systems Not only for: handsome groups (fishes, birds, whales) But more urgently also for: Nematodes, Amphipodes, Tardigrades, Sipunculids, Cumaceans, ... People should start to see the scientific value of this kind of research http://intramar.ugent.be/nemys/

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