NeMys: an evolving biological information

system, a state of art

Deprez, Tim (UGent)Vincx, Magda (UGent)

Vanden Berghe, Edward (VLIZ)Mees, Jan (VLIZ)

Introduction ...

FIELDGUIDE

Mysid Shrimp:

More then 1000 species ...

PicturesKeysMaps...

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

• 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

Data in NeMys ...

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

The structure of NeMys

TAXONOMY

LiteratureCollectionsGeographyMorphology

MorphometryGeneticsPictures

Comments...

TAXONOMY

LiteratureCollectionsGeographyMorphology

MorphometryGeneticsPictures

Comments...

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 theWAN-environment

• Users do not need to know how

to work with databases• Distributed data-input and data-maintenance

DIGIR

VLIZ GBIF OBIS

ERMS ...

The Mysida dataset as an exampleThis 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

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

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 ...

Conclusions ... 1200 species digital information system 3 taxonomists-man-yearNumber of taxonomist is going down

URGENT need to startdigitising 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/