Transcript Wiebe/Copley -_How Does CMarZ work? Data and Species Pages

How does CMarZ Work?
CMarZ Information
System / Database
/OBIS/ Species Pages
Peter H. Wiebe and Nancy Copley
Woods Hole Oceanographic Institution
Accessed from the CMarZ Data Server
http://www. cmarz.org
CMarZ Data Serving System Has Two Components
1) Environmental and other information about
collections and cruises.
2) Species pages.
• The CMarZ Data Management System
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Background, architecture
Tour of the on-line database
Progress to Date
Future Objectives
• Species Pages
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The CMarZ Networks
What are Species Pages?
Overview of Species Pages architecture
Progress to Date
Future Objectives
Data Management System
• Uses JGOFS/GLOBEC software: an open source
(free) relational data information management
system.
• Design allows growth without significant changes
to architecture of the data management system.
The data directory organizes the data and
provides links to data objects
The Inventory Provides the List of the
Data types collected on the Cruise
The data inventory has several levels,
which provide access to the data themselves
and information about the data status.
The Event Log provides Essential Information
About the Deployment of Gear and Other
Events that occur during the cruise.
Data may reside on remote
servers
Information About Your
Data
• Metadata are crucial for others to be
able to use an investigator’s data.
• This information comes from the
contributing investigator(s).
METADATA GUIDELINES FOR
(ZOO) PLANKTON DATA
Plankton “metadata” refers to ancillary information about and related
to the plankton data themselves, such as the methods and processes
involved in measuring or observing these “data” and the conditions
under which the plankton were sampled. This additional information is
needed to examine and utilize the plankton data in a meaningful and
appropriate way.
1) Metadata-fields relating to the entire CRUISE
2) Metadata-fields relating to a specific STATION
3) Metadata-fields relating to the NET TOW or BOTTLE
CAST
4) Metadata-fields relating to the SAMPLING GEAR
5) Metadata-fields relating to SAMPLE PROCESSING
6) Metadata-fields relating to SAMPLE ITSELF
Information taken from Report of the Working Group on Zooplankton
Ecology Gijón, Spain 24–26 February 2003 [ICES CM 2003/C:01
Ref. ACME] ANNEX 3: WGZE METADATA GUIDELINES FOR (ZOO)
PLANKTON DATA DRAFT, 24 February 2003.
Documentation page
- gives background information on dataset
Data Management
Progress
• Infrastructure is setup; positioned to accept data.
• Data sets currently available:
– ZooGene Copepods & Euphausiids
• genetic sequences and station data
– Ronald H. Brown cruise, April 2006
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Event log
Net tow CTD data (MOCNESS -1/4, -1, -10)
Along track depth, gyro, meteorological, wind data
Winch data for net tows
– Oithonidae (Nishida)
• Data sets almost ready to be served:
– Ostracoda (Angel)
– Sea Education Association (SEA)
– NOAA/NMFS Ecological Monitoring Time Series
Data Management
Objectives
• Add more data sets.
• Provide data visualization and mapping service.
Species Pages
• The CMarZ Networks
• What are Species Pages?
• Overview of Species Pages architecture
• Progress to Date
• Objectives
CMarZ Network
CMarZ
Taxonomist
Network
Networks
Species Page
Contributors
Zooplankton taxonomists,
ecologists, oceanographers,
researchers, students, technical
staff, and others who are committed
to working toward the goal of
completing a global biodiversity of
holozooplankton by 2010.
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Confirm identification of species
Collaborate on global surveys
Prepare inventories of species
Prepare a bibliography
Request funding from CMarZ for
specific projects
• May be a Species Page Contributor
• Taxonomic experts provide
information for the creation of
species pages in area of expertise.
What are Species Pages?
Species Pages are a set of web
pages that are created using
information in our database.
Information is supplied by
taxonomic experts via the web.
Dynamic - only the most up-todate information supplied by the
Contributors is used to create the
pages.
Species Pages Database
• Uses MySQL: an open source (free) relational
database management system.
• Design allows growth without significant changes
to architecture of the database.
• Experts enter information via the web into tables.
These tables are used to create the species page ‘onthe-fly’ when requested by a user.
Species Page Database
ID#
Authority
Authority Date
Valid / not Valid
Citations
ID #
Reference type: citation / URL
Reference text
Nav
Will come
from ubio /
ITIS /
Species
2000 and
edited by
Contributor
as needed.
Genus-Species-Subsp.
Species Info
Synonomy
ID #
Synonym
Authority
Authority Date
Images
Genetics
Hierarchy
ID #
Accession number
Accession # URL
Bottle #
Gene:MtCOI, 18SrRNA
Sequence
Collection Region
Collection Date
Latitude, Longitude
Depth Min/Max
Collector
Collection Station URL
ID #
URL
Hierarchy authority
Images
ID #
Image Type
Caption
URL
Reside on
WHOI server;
placed there by
editor.
Size
Ecology
Distribution
ID #
Type: text or link
text
ID #
Geolocation
Depth distribution
Features (Species Descrip)
Data URLs
ID #
Text: long, including URLs
& html formatted text.
ID #
Data URL
Data URL description
ID #
Size type: prosome / total length
Stage / sex
Minimum / maximum
Authority for lengths
Authority dates
Units
ID # is a unique number
for each species in the database.
Species Page Creation & Access
Experts
Public
- Join Species Page
Contributors Network
- Search Species Pages by:
Get username & password
Editor - checks page
Name
-mainly formatting, figures, links
Keywords
- Makes page publicly accessible
- Log on
Current Listings
Hierarchy
-Add new species
Species name, authority, date
-Add new data
- synonyms
- ecology
- taxonomic hierarchy
- genetics
- distinguishing features
- references
- size
- figures
- distribution
- data links
- Update data
Add, edit or delete text, figures or
links
Search for Species
Search Results
Join Networks
Logging on to the Species Page Contributors Area
Main Page for Contributors
Species Tables
Species Pages
Progess to Date
• Species page creation software is now ready for
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taxonomist Contributors to begin building pages.
A search utility with several searching options is
functioning and available the public.
Two experts have created pages.
Other experts (9) have joined as Species Page
Contributors.
12 pages have been created.
Future Objectives
• Involve more Taxonomists in Species Page
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creation.
Train them to enter information into pages.
Ensure instructions are clear and program is as
simple to use as possible while requiring a
minimum of oversight.
Have hundreds of pages available by next year.
Acknowledgements
– Bob Groman, Data Management System,
WHOI
– Dicky Allison, Data Management System,
WHOI
Thank You