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Biodiversity of the Gulf of Mexico Database (BioGoMx)
The Biodiversity of the Gulf of Mexico (BioGoMx) is a database on the biodiversity of living species found in the Gulf of Mexico. It is based on a comprehensive biotic inventory, conducted by the Harte Research Institute for Gulf of Mexico Studies between January 2004 to July 2009. A team of 140 taxonomists from 80 institutions in 15 countries, experts in their respective taxa, compiled the biodiversity data. Sources used included scientific collections in museums, research institutions, private collections, scientific literature, and personal observations. The taxonomy was updated based on the most recent studies accepted by the experts. The results of the inventory were published in a book, edited by Darryl L. Felder and David K. Camp, and published by Texas A&M University Press in 2009. The goals of BioGoMx are to make the information on Gulf of Mexico (GoMx) biodiversity readily available to researchers and students, to allow for cross-taxa and complex queries. Although an attempt was made to ensure as close representation in the book as possible, some assumptions were made, and some errors may have inadvertently been introduced in the database during the conversion from the book to the database. Wherever information in the database and book differ, the latter should be considered the most accurate, unless there is a statement to the contrary in the species pages, written by experts. Please report any errors found in BioGoMx in the space provided at the bottom of each species page. The information in BioGoMx is provided without any warranties.
Reference: Felder, D. L., and Camp, D. K. (eds.) 2009. Gulf of Mexico-Origins, Waters, and Biota. Volume 1. Biodiversity. Texas A&M University Press, College Station, Texas. 1393 pp. (and chapters herein). The book can be ordered as a hardcover directly from the publisher (TAMU Press), most bookstores (e.g. Amazon.com), or in electronic format at Google Books (note it is compatible with most e-readers, except Amazon’s Kindle).
How to use the database
Below are short instructions on how to use the database.
Figure 1. BioGoMx search form.
The BioGoMx homepage (http://gulfbase.org/biogomx) has a search form as shown at right (Figure 1). At the top there is a free-form search box that can be used to query all fields in the database. If the “Also search references and endnotes” check box is checked, the search terms will also include the references and endnotes for all records. Search terms can include any information, such as taxonomic names at any level, authors, habitat and biology descriptors, depths (in meters), distribution in the GoMx (as eight octants as shown in Figure 3 below), or even the words in references and endnotes. Note that incomplete words work as wildcards, e.g. searching for “ichth” will produce results such as Chondrichthyes, Thaumatichthyidae, Hirundichthys, etc; in contrast, a more complete word will result in fewer results.
Below the free-form search box is a series of drop-down menus for some of the more commonly used taxonomic categories, such as phylum, class and genus, as well as habitat and biology descriptors, the eight GoMx octants, and depth range. The drop-down menu displays ALL of the terms found in the database in the field searched. Although the lists are long, when you type the first one or a few letters, the list jumps to the point corresponding to the letters typed. For example, typing “mo” in the field Phylum will jump to the phylum Mollusca. You can continue to type further letters or scroll down the list until you find the search term you want to query. After filling out all of the search terms, click the button “Display results” below the search form. The system will query the database and produce a list of the species that correspond to the query. If you get too many results, try adding new search terms. To conduct a new search, use the “clear search form” at the bottom left of the search form.
The search results are displayed on the BioGoMx homepage, with a count of the number of records. By default, only the first 1,000 records will be displayed, but by clicking “View all” will display all records. The list of results can be downloaded as a CSV (comma-separated values) file by clicking on the button “Download results as CSV” on the top right of the results list. CSV files store data in plain, unformatted text, and can be read and edited by many spreadsheet software, including MS Excel, Google Docs and others, as well as text editors such as MS Word.
Figure 2. Search results for "pavoninus".
The list of results has four columns: Species name, Phylum, Habitat-biology, and "octants and depths" (described below). By default, the list is displayed in alphabetical order by species names. The list can be also sorted by phylum and habitat-biology by clicking on the column name. Clicking on any species in the results list opens a separate browser tab (or window, depending on browser).
Octants and depths
Figure 3. Gulf of Mexico showing biota distribution octants.
The eight boxes to the right of each species entry provide a shortcut reference to the geographic and depth distribution of the species as recorded in the database. The database subdivides the Gulf of Mexico into eight sectors (octants) as shown in the map at right (Figure 3). The top four boxes in the results list for each species correspond to the WNW, NNW, NNE, and ENE octants and the bottom four boxes correspond to the WSW, SSW, SSE, and ESE octants. The presence of colored depth bars within one of these boxes indicates the presence of the species in the corresponding octant of the Gulf of Mexico.
The colored bars within each box indicate the depths at which the species is recorded in the database for that octant (Figure 4):
Figure 4. Color bars (left) corresponding to depth ranges (right).
Thus for Calocalanus pavoninus shown above, the database reports its presence at depths of 0 to 200m in the NNE, ENE, ESE, and SSE octants of the Gulf.
Hovering the mouse over a box with the mouse pointer will also report the octant and depth details from the database.
Each species in the BioGoMx database has its own page. At the top of the page, below the database name, are two links: 1) About the database, which links to this document, and 2) Another search, which links to the database homepage to conduct a new search.
Next, the species name is shown in a large font size, followed by the taxonomy, with some of the most commonly used taxonomic levels (Phylum, Class, Subclass, Order, Family, Genus, Species), as well as the Author(s) of the species.
Next is information about distribution, habitat, and biology. The distribution within the Gulf of Mexico has been broken down into eight octants (see Figure 3) and six depth classes (Figure 4). The GoMx range lists the octants where the species potentially occur or has been reported from. The minimum and maximum depths (in meters) are those reported for the species throughout its overall geographic range, and not necessarily its bathymetric range in the GoMx (refer to Felder and Camp, eds. 2009, for details on specific taxa). The Habitat-Biology lists some descriptors of the habitat or biology of the species.
On the right hand side there is a map of the GoMx with a representation of the distribution of the species within the GoMx, with the regions of the GoMx corresponding to octants and depth classes highlighted. The depth classes are color coded, with the shallow coastal waters represented in dark green, changing to light green, yellow, orange and red with increasing depth.
Next is a list of references used to document the species in the GoMx or other pertinent reference, as listed in Felder and Camp (eds. 2009), followed by endnotes (when available). Endnotes were used by the authors in the book to explain taxonomic decisions, comments on new GoMx records, listing of some specimens in museum collections, or other details. Following endnotes is a citation to the book chapter from where the information on the page was obtained, and a citation of the BioGoMx database.
Links to external resources provide direct searches for the species in question on Google, Google Images (note that Google Images is not curated by taxonomists, and many images may not represent the correct species, but may still be useful), Encyclopedia of Life, the World Register of Marine Species (WoRMS), and the Ocean Biogeographic Information System (OBIS), which may have additional distributional data on the species.
At the bottom of the page is a complete listing of the taxonomy as listed in Felder and Camp (eds., 2009). Note that fields without a value are not displayed.
Finally, at the very bottom, there is a comments window to provide feedback about the species. To submit a comment about the species, type the information in the box and provide your valid email; without an email, the comment cannot be submitted. The number in parenthesis following the species name is a unique species number (e.g. Spp-75-0141) used in BioGoMx. The first two digits following “Spp” represent the book chapter, followed the by species number. Each species page can be accessed directly if the species number is known.
Background and information about the database
The Biodiversity of the Gulf of Mexico Database (BioGoMx) was based on a comprehensive biotic inventory of the Gulf of Mexico sponsored by the Harte Research Institute for Gulf of Mexico Studies (HRI), Texas A&M University-Corpus Christi, which resulted in the book: Felder, D. L. and D. K. Camp (eds). 2009. Gulf of Mexico-Origins, Waters, and Biota. Volume 1. Biodiversity. Texas A&M Press, College Station, Texas. 1393 pp.
The biotic inventory was conducted by 140 taxonomic experts from 80 institutions in 15 countries, who were charged with documenting all living biodiversity in the Gulf of Mexico (GoMx), as of 2004. The resulting inventory listed 15,419 species in 40 phyla and divisions, arranged in 77 chapters, each encompassing a phylum, class or other taxonomic group. Each chapter has an introduction to the taxon, a short review of the state of the knowledge on the taxon in general, and in particular in the GoMx, a checklist of the living species, and a list of references used to document the species in the GoMx, its biology, or taxonomic questions. For purposes of this project, biodiversity of the Gulf of Mexico was defined as that documented to occur in marine habitats, coastal waters and tidal wetlands west of Cabo Catoche, Quintana Roo, Mexico (21°33'N, 87°00'W), that in waters north of a line from Cabo Catoche, Mexico, to Cabo de San Antonio, Cuba (21°51'N, 84°57'W), that from coastal waters and tidal wetlands between Cabo de San Antonio and Punta Hicacos, Cuba (23°12'N, 81°08'W), and that from waters and tidal wetlands of the Florida Straits and Florida Keys on or west of a line from Punta Hicacos, Cuba, to the vicinity of Key Largo, Florida (25°06'N, 80°26'W). This delineation thus included all marine waters and tidal wetlands extending to the eastern extreme of Florida Bay. It excluded Cay Sal Bank as well as the extensive system of islands and estuaries east of Punta Hicacos, Cuba.
The editors of the book (Felder and Camp) attempted to maintain a standard format across the taxonomic groups. The nature of a few taxa, however, required a deviation from the norm, for example the birds lack information on depth range, and parasitic species had the host(s) listed. Because of limited space (on paper), the tabular checklist only allowed a limited space for information. The checklist consisted of six columns listing the updated taxonomy, including all higher taxonomic levels; a few of the more pertinent abbreviations on the habitat and biology; the depth range; the overall geographic range; the distribution within the Gulf of Mexico; and finally some of the pertinent references and endnotes explaining taxonomic issues or details on the record of that species. The species included in each checklist were based on the literature, museum and institutional collections, and observations by professional observers (e.g. in the case of marine mammals). Because of time and space constraints, a listing of the compilation of all records of all species was not possible. Instead, distribution of each species within the GoMx was ultimately reported as the expert’s knowledge of the occurrence of the species in four quadrants or eight octants of the GoMx.
The BioGoMx database was developed by converting the information in the Felder and Camp book into a database. The original chapter authors were invited to perform the conversion, but only a few (four) authors had the time and/or technical expertise to do so. All of the crustacean chapters (16) were converted by a team of researchers (Gema Armendáriz and Fernando Álvarez) at the Universidad Nacional Autónoma de México (UNAM) in México City. The remaining 57 chapters were converted by Fabio Moretzsohn at HRI in Corpus Christi, Texas. Proofing of the database against the book was performed and errors introduced in the database were corrected. However, despite our best efforts to correct errors, some may still be in the database. Whenever the database differs from data in Felder and Camp (eds., 2009), the book is to be considered more accurate, unless a statement to the contrary by an expert appears in the corrections field in the species page. Please report any corrections in the comments box at the bottom of each species page.
It should be pointed out that the distribution reported in the database DOES NOT correspond to individual specimens or observations, but rather represents the probable distribution of the species in the GoMx as judged by the expert. In an attempt to refine the resolution of distribution, the GoMx distribution was divided in eight octants and six depth classes. Jorge Brenner, formerly at HRI and now at The Nature Conservancy, developed a set of 48 polygons (8 octants x 6 depth classes) in a GIS, based on the bathymetry of the GoMx, and an arbitrary point, approximately the centroid of each polygon, was assigned to represent each polygon. Potential caveats of this approach include an overestimation of the species true distribution when the GoMx distribution was reported (in the book) as occurring in all four quadrants, and in all depth classes spanned by the depth range. Expert advice is here requested to correct and minimize species distribution overestimation; corrections should be submitted via the comments window at the bottom of each species page.
Patrick Michaud, at GulfBase.org, developed the web services, queries and web interface of the database at GulfBase. Philip Goldstein and Melissa Reed-Eckert, at OBIS-USA, and Edward Vanden Berghe, at IOBIS, assisted in the development of the database for OBIS. The distributional data can be accessed at the Ocean Biogeographic Information System (OBIS), OBIS-USA, and at the Global Change Master Directory, at NASA‘s Goddard Space Flight Center. Note that the BioGoMx data in OBIS, OBIS-USA and NASA show species distributions as points; those points represent the approximate centroid of each polygon where the species is recorded in the database.
A mapping application tool using selected taxa from this dataset was developed by Stephanie Glenn, Zach Vernon and researchers at Houston Advanced Research Center (HARC), in collaboration with Fabio Moretzsohn, Wes Tunnell, Jorge Brenner and Tom Shirley at HRI. The mapping application can be accessed through a portal in the Central Southwest Gulf Coast Information Node (CSWGCIN). CSWGCIN is part of the National Biological Information Infrastructure (NBII), a collaborative program between government agencies, academic institutions, non-government organizations and industry to increase access to biodiversity resources in the U.S.A.
Listed in phylogenetic order, with phyla or divisions in bold:
Protista: Prokaryotes, Archaea, Bacteria, Cyanobacteria, Ciliophora, Fungi, Foraminifera, Dinoflagellata, and Diatoms (Bacillariophyta).
Plantae: Rhodophyta (red algae), Chlorophyta (green algae), Phaeophyta (brown algae), and Embryophyta (plants).
Animalia: Porifera (sponges); Cnidaria: Octocorallia (sea fans), Scleractinia (hard corals), Antipatharia (black corals), Ceriantharia (tube anemones), Medusozoa (medusas), Cubozoa (box jellyfish), Scyphozoa (true jellyfish), Hydrozoa (hydroids), and Siphonophora (siphonophores); Ctenophora (comb jellies); Platyhelminthes: “Turbellaria” (Acoelomorpha and Platyhelminthes), Trematoda (trematodes and flukes), and Cestoda (tapeworms); Dicyemida (Rhombozoa); Gnathostomulida (gnathostomulids); Rotifera (rotifers or wheel animals); Acantocephala (acanthocephalans); Nemertea (ribbon worms); Mollusca (mollusks): Aplacophora, Polyplacophora (chitons), Gastropoda (snails, gastropods), Cephalopoda (squids and octopods), Bivalvia (clams), and Scaphopoda (tusk shells); Annelida (ringed worms): Polychaeta (polychate worms), Hirudinida (leeches), and Siboglinidae (“Pogonophora” and Vestimentifera) (bearded worms); Echiura (spoon worms); Sipuncula (peanut worms); Tardigrada (water bears); Arthropoda (arthropods): Xyphosura (horseshoe crab), Pycnogonida (sea spiders), Crustacea (crustaceans): Cephalocarida (horseshoe shrimps), Mystacocarida (mystacocarids), Cirripedia (barnacles), Branchiura (fish lice), Copepoda (copepods), Ostracoda (Myodocopa, Podocopa) (ostracods), Leptostraca (leptostracans), Stomatopoda (mantis shrimp), Lophogastrida (lophogastrids), Mysida (opossum shrimps), Amphipoda (amphipods), Isopoda (isopods), Tanaidacea (tanaids), Cumacea (hooded shrimp), Euphausiacea (krill), and Decapoda (crabs, shrimps and lobsters); Gastrotricha (hairy backs); Nematoda (nematodes or roundworms); Priapulida (penis worms); Loricifera (loriciferans); Kinorhyncha (mud dragons); Phoronida (horseshoe worms); Brachiopoda (brachiopods or lamp shells); Entoprocta (entoprocts); Ectoprocta (Bryozoa or moss animals); Chaetognatha (arrow worms); Hemichordata (hemichordates); Echinodermata (starfish, crinoids and sea cucumbers); Chordata (chordates): Cephalochordata, Urochodata (sea squirts), and Vertebrata (vertebrates): Pisces (fishes), Reptilia (reptiles), Aves (birds), Mammalia (mammals).
Name: Dr. Fabio Moretzsohn
If any of the records from the Biodiversity of the Gulf of Mexico Database (BioGoMx) are used in an analysis or report, the provenance of the original data must be acknowledged and the BioGoMx notified (see Contact Us). The BioGoMx and the Harte Research Institute for Gulf of Mexico Studies (HRI) and its staff are not responsible for damages, injury or loss due to the use of these data. Acknowledge the use of specific records from contributing databases in the form appearing in the ‘Citation’ field thereof (if any); and acknowledge the use of the BioGoMx facility. For information purposes, email the full citation of any publication made (printed or electronic) that cites BioGoMx or any constituent part. Recognize the limitations of data in BioGoMx.
Funding provided by
Moretzsohn, F., J. Brenner, P. Michaud, J.W. Tunnell, and T. Shirley. 2013. Biodiversity of the Gulf of Mexico Database (BioGoMx). Version 1.0. Harte Research Institute for Gulf of Mexico Studies (HRI), Texas A&M University-Corpus Christi (TAMUCC), Corpus Christi, Texas. 25 May 2013.
Database description and disclaimer at: http://gulfbase.org/biogomx/about.php (this page)
GulfBase is a project of the
Research Institute for Gulf of Mexico Studies at Texas A&M University-Corpus Christi.
To give proper credit to the original authors, please cite information taken from GulfBase by the original source as displayed.
To cite GulfBase, use: F. Moretzsohn, J.A. Sánchez Chávez, and J.W. Tunnell, Jr., Editors. 2013. GulfBase: Resource Database for Gulf of Mexico Research. World Wide Web electronic publication. http://www.gulfbase.org, 25 May 2013.
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