Carbonate Organisms

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Carbonate Organisms dataset information page

Short Description

Carbo OKB.png
Placeholder image for Carbo* OKB

Statement: Organism Knowledge Base supporting Carbonate Models

Abstract: Page in construction 20 Aug 2013 ---------

Carbonate sediments and rocks are mostly formed through biological activities: reproduction, growth, calcification, mortality and reworking. The features, scales and rates of these processes are mostly biologically mediated, though they are also controlled by physical-chemical factors such as geography, oceanography, substrates.

The biological factors are at first sight, horrendously complicated. The Organism Knowledge Base (OKB) here is a way of suppressing the scope of biological diversity but achieving the carbonate processes. We call this simplification "Numerical Aquarium" - a few of the most important, most representative, best documented species are put into the OKB and then used by the models. Their details include reproduction, growth, dimensions and shapes live and post-mortem, environment and event sensitivities, dependencies.

The OKB is used by the carbo* model suite (see ''). Carbo* combines the biological and physical-chemical factors to simulate the initiation, growth and fate of carbonate buildups of many types - coral reef, deep-water coral, bryozoan, Halimeda, algal pavement.

The carbo* group - based in the Carbonate FRG of the CDSMS - is posting the OKB to foster community science advancement. We hope to attract comment including critical review, but also to make the work available for other modeling efforts. Lastly, where the OKB becomes useful we hope that others will add more organisms and more data so it can model carbonate environments and buildups more comprehensively.

The OKB consists of: (i) an EXCEL sheet which suits manual data entry and documentation by humans; (ii) a text export of that sheet; (iii) Python 2.7 software to perform QAQC checking and to transfer the data to a format more suited for machines, (iii) data in that machine-suitable format.

For further information contact: "Burgess, Peter" <>,

"Donald Potts: <>, "Chris Jenkins" <>.

Page in construction 20 Aug 2013 ---------

Data format

Data type: Life Forms"Life Forms" is not in the list (Climate, Cryosphere, Human dimensions, Hydrography, Land Cover, Oceanography, River discharge, Surface properties, Sea level, Substrates, ...) of allowed values for the "Data type" property.
Data origin: Measured
Data format:
Other format: pdf
Data resolution: NA
Datum: NA

Data Coverage

Spatial data coverage: NA
Temporal data coverage: Time series
Time period covered: NA


Download data: poster ChrisJenkins.pdf
Data source: poster ChrisJenkins.pdf