What is GeoSymbio?

GeoSymbio is a hybrid web application of global geospatial bioinformatics and ecoinformatics for Symbiodinium-host symbioses. Genetic sequences of Symbiodinium are used to organize the individual organisms into clades. The primary repository for Symbiodinium sequence information, GenBank, possesses a multitude of redundant entries, often incomplete descriptions of associated attributes such as location or host, and little quality control on the submitted data. Given the fundamentally important role that these symbionts play in coral biology, this project compiles Symbiodinium ITS2 sequence information, identifies redundant entries, summarizes the attribute information for all sequences, identifies the geospatial location and temporal information of the specimen collection and disseminates the data through a web-enabled database and mapping website.

What is Symbiodinium?

Symbiodinium is the name of a dinoflagellate genus containing a diversity of uni-cellular photosynthetic strains that can be found free-living or symbiotic with a wide range of marine invertebrates.

Is the database comprehensive for all Symbiodinium studies?

Not yet. We focused our initial efforts on published studies that utilized the ITS2 region. Future efforts will include additional genes.

Can I add my work to the database?

Not yet but if you are interested in collaborating on the project, go to the Contact page and send us an email that includes your contact information, an idea of how you'd like to be involved, and the citation(s) of your work with PDF(s).

Does the database include the number of samples by site or host for each record?

No. There was a lack of consistent reporting of sample number in the studies that were included in the database. Thus, we choose not to include that information so that the structure of the database focuses on reported Symbiodinium ITS2 sequences and the bioinformatic and ecoinformatic attributes associated with those records.

Why do some of the Symbiodinium locations plot on land in the maps and KML file?

This could be for two reasons. First, the quality of the collection location description for records varied considerably. For example, records that only provided a "Country" or "SubRegion" as the finest level of detail for location often were plotted on land with a correspondingly large coordinate precision. Second, there are a set of records from aquariums that were plotted as the location of the aquarium, not the collection location. 

Who created this project?

GeoSymbio was created by a team of researchers at the Hawaii Institute of Marine Biology within the School of Ocean and Earth Science and Technology at the University of Hawaii at Manoa. The team is Erik Franklin, Michael Stat, Xavier Pochon, Hollie Putnam, and Ruth Gates. The contributions from the members are project concept: EF, MS, RG; web application development: EF; graphic design and layout: EF, MS; database design: EF, MS, XP; and bibliographic search and data entry: EF, MS, XP, HP.

I found an error, can it be fixed?

Yes. Please go to the Contact page and send us an email that includes your contact information, a description of the error and how it should be fixed, and we'll work on the request as soon as possible.

I'm having trouble with the csv files. Are they broken?

No, we have successfully tested them within text editors, spreadsheets, and database programs on PC and Mac/Linux platforms. Please note that the csv files use double quotations to identify text strings. Also, be  some text in cells exceed 255 characters.Please go to the Contact page and send us an email that includes your contact information, a description of the error and how it should be fixed, and we'll work on the request as soon as possible.

Who supported this project?

The National Marine Sanctuary Program (memorandum of agreement 2005-008/66882), the US Environmental Protection Agency Science To Achieve Results (STAR) PhD Fellowship (FP917096), the US National Science Foundation (NSF) for grants through Biological Oceanography (OCE-0752604, OCE-1041673) and the Long Term Ecological Research (LTER) program (NSF 04-17412) provided financial support for this research. This work was conducted as part of the "Tropical coral reefs of the future: Modeling ecological outcomes from the analyses of current and historical trends" Working Group supported by the National Center for Ecological Analysis and Synthesis, a Center funded by NSF (Grant #EF-0553768), the University of California, Santa Barbara, and the State of California.

How do I cite this website?

If you download any of the following files or use any information from GeoSymbio, please cite:

Franklin EC, Stat M, Pochon X, Putnam HM, Gates, RD (2012) GeoSymbio: a hybrid, cloud-based web application of global geospatial bioinformatics and ecoinformatics forSymbiodinium–host symbioses. Molecular Ecology Resources 12:369-373. doi: 10.1111/j.1755-0998.2011.03081.x

Can I trust this information?

We have subjected the GeoSymbio database to a rigorous QA/QC procedure amongst members of the research team and external auditors. With that said, the GeoSymbio research team, HIMB, SOEST, and UH make no warranty regarding these data, expressed or implied, nor does the fact of distribution constitute such a warranty. The GeoSymbio research team, HIMB, SOEST, and UH cannot assume liability for any damages caused by any errors or omissions in these data, nor as a result of the failure of these data to function on a particular system.