Bongaerts P, Perez-Rosales G, Radice VZ, Eyal G, Gori A, Gress E, Hammerman NM, Hernandez-Agreda A, Laverick J, Muir P, Pinheiro H, Pyle RL, Rocha L, Turner JA, Booker R (2019) Mesophotic.org: a repository for scientific information on mesophotic ecosystems. Database 2019:baz140. doi.org/10.1093/database/baz140
The primary entities in the database are scientific publications, for which standard citation data and the full-text contents are indexed. In addition, the following metadata are manually curated (and validated by at least 3 editorial members):
true
/ false
.
Indicates whether the publications presents data from, or presents a discussion on, the mesophotic depth range (true
), or whether it is focused on another depth range (e.g. shallow or deep-sea) but relevant to mesophotic studies (false
), and therefore included in the database. The mesophotic depth range is defined to be from 30-150 m.
true
/ false
.
Indicates whether the publications presents data from, or presents a discussion on, a “mesophotic coral reef ecosystem (MCE)” as characterized by the following definition (altered from the Hinderstein et al. 2010 definition): “characterized by the presence of photosynthetically active corals, algae and associated communities at depths ranging from 30 to 150 m in tropical and subtropical regions” (true
), or whether it is focused on an ecosystem that does not fall under this definition (false
). The altered definition is to reflect the fact despite the “presence of light-dependent corals”, they are often a very small component of the overall ecosystem (particularly at lower mesophotic depths); additionally, while photosynthetically-active, the “dependence” on light may be debatable at lower mesophotic depths. Ecosystems that do not fall under this definition are those in Mediterranean and temperate systems (not subtropical/tropical), or azooxanthellate systems such as subtropical Oculina reefs (not a photosynthetically-active community).
true
/ false
.
Indicates whether the publications presents data from, or presents a discussion on, a “temperate mesophotic ecosystem (TME)” (true
), or whether it is focused on an ecosystem that does not fall under this definition (false
).
true
/ false
.
Indicates whether the publication presents novel data (true
) or instead represents a review or meta-analysis (false
).
true
/ false
.
Indicates whether the publication includes the establishment of one or more new scientific names of species (true
). Publications reporting on new species without establishing new scientific names for them are not included (e.g. undescribed, cryptic lineages discovered in a phylogenetic study) (false
).
integer
(in meters).
“The lesser depth of a range of depth below the local surface, in meters” (sensu DarwinCore). More specifically, this indicates the depth (in meters) of the shallowest data record (e.g. specimen or transect) in the presented dataset or meta-analysis (using normal rounding to obtain integer). Only given for publications that present "Original data". Personal observations mentioned in the publication are not included.
integer
(in meters).
“The greater depth of a range of depth below the local surface, in meters” (sensu DarwinCore). More specifically, this indicates the depth (in meters) of the deepest data record (e.g. specimen or transect) in the presented dataset or meta-analysis (using normal rounding to obtain integer). Only given for publications that present "Original data". Personal observations mentioned in the publication are not included.
integer
(in meters).
“The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive” (sensu DarwinCore).
integer
(in meters).
“The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive.” (sensu DarwinCore).
Scientific
/ Technical
/ Popular
.
Indicates whether the publication is scientific (peer-reviewed), technical (which can be either peer-reviewed or non-peer-reviewed) and popular.
Article
/ Review
/ Chapter
/
Book
/ Report
/ Thesis
.
Indicates the format of the publication.
categorical
.
Indicates the platform(s) used to collect the presented data. Only
given for publications that present `Original data`.
show categories
Acoustic Telemetry
15
,
Aquarium-based
19
,
Autonomous Underwater Vehicle (AUV)
47
,
Baited Remote Underwater Video (BRUV)
33
,
Coring / drilling
12
,
Dredging / trawling
53
,
Drop / Towed Video
35
,
Fishing
43
,
In-situ instrumentation
25
,
Land-based
39
,
Manned Submersible
168
,
Rebreather
165
,
Remotely Operated Vehicle (ROV)
189
,
SCUBA (open-circuit or unspecified)
441
,
Snorkeling
11
,
Sonar / Multibeam
62
,
Surface-deployed sensors and samplers
40
.
categorical
.
Indicates the research field(s) the publication can be categorized
under.
show categories
Acoustics
7
,
Behavior
34
,
Biodiversity
373
,
Biomedicine
4
,
Climate Change
38
,
Community structure
347
,
Connectivity
107
,
Disturbances
104
,
Ecology
367
,
Evolution
29
,
Fisheries
68
,
Geomorphology
102
,
Long-term monitoring
79
,
Management and Conservation
113
,
Methods and Technology
26
,
Molecular ecology
105
,
Oceanography
46
,
Paleoecology
24
,
Physiology
126
,
Reproduction
55
,
Taxonomy
163
,
Vision
1
.
categorical
.
Indicates the focal taxon/taxa of the publication.
show categories
Actiniaria and Ceriantharia (Sea anemones)
9
,
Algae (Macro, Turf and Crustose Coralline)
126
,
Antipatharia (Black Corals)
62
,
Bacteria and Archaea
17
,
Cetacea (Dolphins, Whales)
1
,
Crustacea
30
,
Fishes
296
,
Hydrozoa
15
,
Octocorallia (Soft Corals)
126
,
Other endosymbionts (non-Symbiodinium)
5
,
Other invertebrates
61
,
Overall benthic (groups)
182
,
Plankton
8
,
Porifera (Sponges)
106
,
Scleractinia (Hard Corals)
330
,
Seagrass
7
,
Symbiodinium (zooxanthellae)
76
,
Viruses
3
,
Zoantharia (Zoanthids)
9
.
categorical
.
Indicates the geographic location the publication focuses on.
show categories
American Samoa
9
,
Aruba
2
,
Australia - Coral Sea
19
,
Australia - Great Barrier Reef
46
,
Australia - Northern Australia
13
,
Australia - Scott Reef
4
,
Australia - Southeastern Australia
20
,
Australia - Western Australia
18
,
Bahamas
51
,
Barbados
6
,
Belize
15
,
Bermuda
30
,
Bonaire
16
,
Brazil - Eastern Brazil
39
,
Brazil - Fernando Noronha
6
,
Brazil - St Peter and St Paul Archipelago
9
,
Brazil - Trindade and Martin Vaz
10
,
British Virgin Islands
2
,
Brunei
2
,
Cayman Islands
19
,
Chagos Archipelago
2
,
Christmas Island
1
,
Colombia - Caribbean Sea
7
,
Colombia - Pacific Ocean
0
,
Cook Islands
7
,
Costa Rica - Pacific Ocean
5
,
Croatia
3
,
Cuba
11
,
Curaçao
51
,
Denmark
1
,
Djibouti
1
,
Dominica
3
,
Dominican Republic
2
,
Easter Island
7
,
Ecuador - Galápagos Islands
1
,
Egypt - Red Sea
5
,
El Salvador
1
,
Fiji
10
,
France - Mediterranean Sea
3
,
French Polynesia
9
,
Greece
3
,
Grenada
1
,
Guadeloupe
2
,
Honduras - Bay Islands
15
,
India - Western Continental Shelf
2
,
Indonesia
11
,
Israel - Mediterranean Sea
2
,
Israel - Red Sea
76
,
Italy - Adriatic Sea
5
,
Italy - Ionian Sea
4
,
Italy - Ligurian Sea
23
,
Italy - Mediterranean
15
,
Italy - Tyrrhenian Sea
36
,
Jamaica
27
,
Japan - Ogasawara
1
,
Japan - Ryukyu Islands (Okinawa)
30
,
Kiribati
1
,
Madagascar
1
,
Malaysia
2
,
Malta
0
,
Martinique
1
,
Mauritius
2
,
Mayotte
1
,
Mexico - Baja California
4
,
Mexico - Caribbean
7
,
Mexico - Gulf of Mexico
3
,
Micronesia - Caroline Islands (Pohnpei)
13
,
Micronesia - Chuuk atoll
2
,
Micronesia - Guam
8
,
Micronesia - Mariana Islands
8
,
Micronesia - Marshall Islands
9
,
Montserrat
0
,
Navassa Island
1
,
Netherlands Antilles - Saba Bank
1
,
New Caledonia
4
,
New Zealand
3
,
Norway
0
,
Oman
1
,
Panama - Caribbean Sea
3
,
Panama - Pacific Ocean
3
,
Papua New Guinea
13
,
Peru
1
,
Philippines
18
,
Pitcairn Islands
2
,
Poland
2
,
Portugal
5
,
Portugal - Azores
3
,
Puerto Rico
75
,
Republic of Maldives
5
,
Republic of Palau
16
,
Saint Kitts and Nevis
1
,
Saint Lucia
2
,
Saudi Arabia - Red Sea
3
,
Seychelles
1
,
Singapore
2
,
Solomon Islands
3
,
South Africa
6
,
Spain - Atlantic
1
,
Spain - Mediterranean Sea
23
,
St Vincent
2
,
Sudan - Red Sea
5
,
Sweden
2
,
São Tomé and Príncipe
2
,
Taiwan
8
,
Tanzania
1
,
Tonga
3
,
Trinidad and Tobago
2
,
Turkey - Mediterranean Sea
3
,
Turkey - Sea of Marmara
2
,
Turks and Caicos
1
,
US Virgin Islands
64
,
USA - Continental Atlantic
28
,
USA - Continental Pacific
9
,
USA - Gulf of Mexico
57
,
USA - Hawaii
93
,
USA - Johnston Atoll
10
,
USA - Pulley Ridge
33
,
Vanuatu
3
,
Venezuela - Caribbean
3
.
2016-now: The second (latest) release: A beta version of the new mesophotic.org went on-line in June 2016, coinciding with the 13th International Coral Reef Symposium in Hawai'i (USA). This new version is backed by a relational database that contains extensive metadata on all of the listed publications, and offers searching across the full contents of the indexed publications.
2012-2016: Wordpress & social media: Over the past several years, a simplified semi-static (Wordpress) version with just news items and a list of publications/abstracts replaced the original (databases-backed) website. Admittedly only as a temporary solution, however due to a lack of time a new back-end was not developed until 2016. Instead, there was an increased focus on using social media (Facebook and Twitter) to communicate news around mesophotic coral ecosystems.
2008-2011: The original release: The mesophotic.org website officially went on-line in 2008 when it was first announced at the 11th International Coral Reef Symposium in Ft. Lauderdale (Florida / USA) and the International Collaborative Workshop to Prioritize Research and Management Needs for Mesophotic Coral Ecosystems in Jupiter (Florida / USA). The original website was started by Pim Bongaerts (The University of Queensland), with support from Felix Martinez and Lara Hinderstein (National Oceanic Atmospheric Administration - Center for Sponsored Coastal Ocean Research). Over these initial years, the website received small grants from the Center for Sponsored Coastal Ocean Research (CSCOR/NOAA), the Perry Institute for Marine Science (PIMS), the University of Puerto Rico at Mayagüez (UPR) and the Pacific Blue Foundation. The website eventually went down due to being hacked (and admittedly not the most secure PHP coding practises).
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