Peter H. Wiebe and Nancy Copley

Woods Hole Oceanographic Institution

How does CMarZ Work?

CMarZ Information SystemDatabase /OBIS/ Species Pages

-handouts-

Data accuracy issues and comments (from 2005)

• Obsolete records are being widely disseminated by NODC, OBIS, and potentially by CMarZ.

• Mapping improvements and the addition of new precise data, will be a major task of CMarZ.

• Any historical taxa data should be used extremely carefully. The species are only as good as the individuals that originally identified them, and even then the various species classifications have changed repeatedly over the last 50 years and will continue to do so.

• Utilize only validated records of known provenance, validated by taxonomic experts. 

• Start by showing all the data even if wrong or mistaken and making this very plain in the introduction. Refine these data through review, which could then add quality notes to the datasets; open this process to all, not just current CMarZ folk.

• Include additional notes or flags to warn and/or provide correct identifications.

• Identify Species Page "editors" - likely Steering Group and/or Network members - who agree to review the information submitted to create and update Species Pages for particular taxonomic groups within their expertise.

Data accuracy (Nishida ‘05)

• At least three classes of data sources of different taxonomic precision/accuracy for CMarZ species pages:

– (1) currently accepted taxonomic revisions (papers), of particular taxa with distributional information

– (2) data sets from projects, cruises, etc., many of which have been incorporated into OBIS but with different levels of taxonomic precision depending on the project and species

– (3) original information from submitters.

• The class-1 source above may be most reliable in terms of taxonomic precision, and will be provided by asking relevant taxonomic specialists (i.e. the authors) for their cooperation with CMarZ. The data input, particularly in cases where distributional data are not in an electric file, may be a problem; a data input system within the CMarZ office would be appreciated.

• The class-2 source will be most problematic, while its potential is large with respect to fine aerial and temporal coverage and quantitative information. Screening of the original data-sets by specialists cooperating with CMarZ will be necessary in all these cases. Such screening will require information on

– the literature on which the identification was based– the characters used to distinguish the respective species from its close relatives– the persons who identified the species, and, as the last resort– examination of original specimens may be necessary

• The class-3 source may be what is meant by the "information entry form". Evaluation may be rather simple, and will be accomplished through direct communication between submitters and cooperating specialists.

• The distributional map of the species pages, therefore, should show only data points that survived such screenings, rather than showing OBIS records directly.

• 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• Event log• Net tow CTD data (MOCNESS -1/4, -1, -10)• Along track depth, gyro, meteorological, wind data• Winch data for net tows

• Data sets almost ready to be served:– Oithonidae (Nishida)– Ostracoda (Angel)

Data Management

Progress

Objectives

• Add more data sets.

• Provide data visualization and mapping service.

• Species page creation software is now ready for 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.

Species PagesProgess to Date

Objectives• Involve more Taxonomists in Species Page 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.

Challenges• We must solicit involvement in the creation of these pages.

• Contact colleagues directly.• Send out invitations via other zooplankton outlets.

• Make sure the pages are attracting Contributors by being easy to use.• Improve feedback mechanisms and error messages for Contributors.• Accept pages written in non-English languages.

• Gain the attention of the public (scientists, students, educators, policy makers) who will benefit from the pages.• Provide searches using fuzzy matches.• Work with other groups who are also making Species Pages.

• Quality control is an issue if we import their data into our pages.• Determine which datasets should be imported to CMarZ and which should remain on creator’s site – is data static or dynamic?

• Who should be able to edit a species page besides the original contributor and the Editor? – what about other contributors?

CMarZ Network

CMarZ Taxonomist

Network

Species Page Contributors

Networks

•  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.

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.

Genus-Species-Subsp.ID#

AuthorityAuthority Date

Valid / not Valid

SynonomyID #

SynonymAuthority

Authority Date

HierarchyID #URL

Hierarchy authority

Features (Species Descrip)

ID #Text: long, including URLs

& html formatted text.

EcologyID #

Type: text or linktext

SizeID #

Size type: prosome / total lengthStage / sex

Minimum / maximumAuthority for lengths

Authority datesUnits

GeneticsID #

Accession numberAccession # URL

Bottle #Gene:MtCOI, 18SrRNA

SequenceCollection RegionCollection Date

Latitude, LongitudeDepth Min/Max

CollectorCollection Station URL

ImagesID #

Image TypeCaption

URL

Data URLsID #

Data URLData URL description

CitationsID #

Reference type: citation / URLReference text

DistributionID #

GeolocationDepth distribution

Reside on WHOI server; placed there by editor.

Will come from ubio / ITIS / Species 2000 and edited by Contributor as needed.

Species Page Database

ID # is a unique numberfor each species in the database.

Nav Species Info Images

Some 2005 comments from CMarZ Steering Committee members on Species Page design and implementation

• Who is the target audience? The public, policy makers, students, scientists, all?

– Mostly scientists, but all the others to a lesser degree.

• Will the taxonomic hierarchy be "clickable" to get to other groups or species? One of the big impediments to using a database of this type is the amount of navigation required to find or compare species. A tree-type arrangement might be nice for that, and although frames can cause problems, they are also useful for accelerating navigation.

– There are several options for searching the database: by name/synonym, keyword, contents

• Have a model figure of a copepod, each part of the figure can be "clickable", when it is clicked, it will show the taxonomic characters (drawn in detail) so we can distinguish it with other similar species.

– This is possible and is (low) in the queue.

• The picture should be much larger and more prominent at the top center, then "technical" information in a panel below.

– Picture gallery and maps are on right side.

• Identify Species Page "editors" - likely Steering Group and/or Network members - who agree to review the information submitted to create and update Species Pages for particular taxonomic groups within their expertise.

– This is being done with on-line form

Some 2005 comments from CMarZ Steering Committee members on Species Page design and implementation

• Some kind of pages/figures that allow navigating for the non-expert are really needed. Higher level pages with thumbnails and names only would be very helpful.

– See phyla page with thumbnails and brief descriptions.

• Concentrate solely on the distinguishing features between it and closely related species. Replace the box "Description" with "Distinguishing features"

– This is done for Calanus; information provided is up to the contributor but we can encourage this.

• Coastal species are going to present a lot of problems where several species have been confused. It will take some careful editing out of records before certain dates in order to present the most up-to-date thinking on the issue.

• Acknowledgement of submitter– Done. This is part of information submitter by contributor.

• Provide a way for users to provide feedback, corrections, etc.– This is available.

• How do we integrate copyrighted material into Species Pages without requiring copyright waivers from publishers for every item.

• A key aspect of our approach to data management is the sharing of all data collected by the many funded projects and their scientist participants via a web-based data and information distribution system (http://www.cmarz.org/jg/dir/CMarZ/).

• This sharing fosters the cooperative research approach, strengthens existing partnerships, and leads to higher data quality, which is essential if the data are to be effectively used in resource assessment and management. In addition, more and better kinds of analyses are possible when related data sets can be considered and analyzed together.

• To accomplish the data sharing and outreach activities, CMarZ uses the JGOFS/GLOBEC data management system [1,2] developed to handle multi-disciplinary data sets in a unique way.

• The software is open source and is available to everyone. Data can be viewed via any standard browser, such as Internet Explorer, Mozilla, Safari, and Netscape and includes such features as data downloads, basic X-Y data plotting, data selection (e.g., show all the data where the water depth is less than 150 meters), and data projection (e.g., only show the latitude, longitude, depth, and sea surface temperature values.)

• Data contributors are encouraged to serve their data from their own computers (with software that enables them to become an integral part of the distributed data management system) so that the most up-to-date version is always available. If the data contributor is not able to do this, the data are served by CMarZ’s data server located at Woods Hole Oceanographic Institution.

Data Management

• The data acknowledgment policy insures that data are used for scholarly purposes by the academic, management, industry, and scientific communities, with the understanding that any such use will properly advise and acknowledge the originating investigators.

• Use of these data for commercial purposes is prohibited without prior written permission from CMarZ Data Management Office.

• Data are the intellectual property of the collecting investigator(s). The intellectual investment and time committed to the collection of a data set entitles the investigator to the fundamental benefits of the data set.

• Publication of descriptive or interpretive results derived immediately and directly from the data is the privilege and responsibility of the investigators who collect the data.

• Researchers are strongly encouraged to submit all data as soon as possible after the completion of their project.

• We respect the desires of researchers who would like to publish data prior to making the data publicly available.

• We will work with researchers on a case-by-case basis to allow a grace period, typically three years from the date of data collection, for publication purposes. Data will be appended to the database, but will not be accessible to third parties until the grace period has expired.