About:


When extracting data from this portal for publication, please cite:

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

Mission

  • Collate available research focusing on the mesophotic depth zone, and make it accessible through a single webportal.
  • Allow for the identification of knowledge gaps around particular taxa and geographic areas at mesophotic depths
  • Provide a central place on the web for the exchange of scientific information and ongoing research efforts
  • Act as an independent platform and shared resource for and by the mesophotic research community.

Metadata

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):

  • Mesophotic: 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.
  • Mesophotic Coral Ecosystem (tropical & subtropical) : 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).
  • Temperate Mesophotic Ecosystem: 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).
  • Original data: true / false. Indicates whether the publication presents novel data (true) or instead represents a review or meta-analysis (false).
  • Reports new species: 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).
  • Minimum depth: 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.
  • Maximum depth: 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.
  • Latitude: 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).
  • Longitude: 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).
  • Publication type: Scientific / Technical / Popular. Indicates whether the publication is scientific (peer-reviewed), technical (which can be either peer-reviewed or non-peer-reviewed) and popular.
  • Publication format: Article / Review / Chapter / Book / Report / Thesis. Indicates the format of the publication.
  • Platform: categorical. Indicates the platform(s) used to collect the presented data. Only given for publications that present `Original data`. show categories

    Acoustic Telemetry 13Aquarium-based 18Autonomous Underwater Vehicle (AUV) 42Baited Remote Underwater Video (BRUV) 31Coring / drilling 11Dredging / trawling 49Drop / Towed Video 33Fishing 35In-situ instrumentation 24Land-based 34Manned Submersible 163Rebreather 151Remotely Operated Vehicle (ROV) 179SCUBA (open-circuit or unspecified) 419Snorkeling 11Sonar / Multibeam 62Surface-deployed sensors and samplers 40 .
  • Research field: categorical. Indicates the research field(s) the publication can be categorized under. show categories

    Acoustics 5Behavior 32Biodiversity 354Biomedicine 3Climate Change 29Community structure 330Connectivity 97Disturbances 92Ecology 342Evolution 22Fisheries 61Geomorphology 97Long-term monitoring 74Management and Conservation 103Methods and Technology 26Molecular ecology 100Oceanography 44Paleoecology 24Physiology 116Reproduction 45Taxonomy 155Vision 1 .
  • Focus taxon/taxa: categorical. Indicates the focal taxon/taxa of the publication. show categories

    Actiniaria and Ceriantharia (Sea anemones) 9Algae (Macro, Turf and Crustose Coralline) 118Antipatharia (Black Corals) 59Bacteria and Archaea 16Crustacea 28Fishes 282Hydrozoa 13Octocorallia (Soft Corals) 118Other endosymbionts (non-Symbiodinium) 5Other invertebrates 54Overall benthic (groups) 175Plankton 4Porifera (Sponges) 97Scleractinia (Hard Corals) 307Seagrass 4Symbiodinium (zooxanthellae) 74Viruses 1Zoantharia (Zoanthids) 9 .
  • Geographic location: categorical. Indicates the geographic location the publication focuses on. show categories

    American Samoa 7Aruba 2Australia - Coral Sea 17Australia - Great Barrier Reef 40Australia - Northern Australia 11Australia - Scott Reef 4Australia - Southeastern Australia 19Australia - Western Australia 17Bahamas 46Barbados 6Belize 15Bermuda 26Bonaire 16Brazil - Eastern Brazil 36Brazil - Fernando Noronha 4Brazil - St Peter and St Paul Archipelago 8Brazil - Trindade and Martin Vaz 9British Virgin Islands 2Brunei 1Cayman Islands 17Chagos Archipelago 2Christmas Island 1Colombia - Caribbean Sea 6Colombia - Pacific Ocean 0Cook Islands 5Costa Rica - Pacific Ocean 4Croatia 3Cuba 11Curaçao 49Denmark 1Djibouti 1Dominica 3Dominican Republic 2Easter Island 6Ecuador - Galápagos Islands 1Egypt - Red Sea 4El Salvador 1Fiji 9France - Mediterranean Sea 3French Polynesia 6Greece 3Grenada 1Guadeloupe 2Honduras - Bay Islands 15India - Western Continental Shelf 2Indonesia 9Israel - Mediterranean Sea 2Israel - Red Sea 70Italy - Adriatic Sea 5Italy - Ionian Sea 4Italy - Ligurian Sea 22Italy - Mediterranean 15Italy - Tyrrhenian Sea 36Jamaica 25Japan - Ogasawara 1Japan - Ryukyu Islands (Okinawa) 27Kiribati 1Malaysia 2Malta 0Martinique 1Mauritius 2Mexico - Baja California 3Mexico - Caribbean 6Mexico - Gulf of Mexico 1Micronesia - Caroline Islands (Pohnpei) 11Micronesia - Chuuk atoll 2Micronesia - Guam 7Micronesia - Mariana Islands 8Micronesia - Marshall Islands 8Montserrat 0Navassa Island 1Netherlands Antilles - Saba Bank 1New Caledonia 4New Zealand 2Norway 0Oman 1Panama - Caribbean Sea 3Panama - Pacific Ocean 3Papua New Guinea 10Peru 1Philippines 14Pitcairn Islands 2Poland 2Portugal 5Portugal - Azores 3Puerto Rico 70Republic of Maldives 5Republic of Palau 11Saint Kitts and Nevis 1Saint Lucia 2Saudi Arabia - Red Sea 2Seychelles 1Solomon Islands 1South Africa 5Spain - Atlantic 1Spain - Mediterranean Sea 23St Vincent 2Sudan - Red Sea 5Sweden 2São Tomé and Príncipe 2Taiwan 6Tonga 3Trinidad and Tobago 2Turkey - Mediterranean Sea 3Turkey - Sea of Marmara 2Turks and Caicos 1US Virgin Islands 60USA - Continental Atlantic 25USA - Continental Pacific 8USA - Gulf of Mexico 51USA - Hawaii 85USA - Johnston Atoll 9USA - Pulley Ridge 32Vanuatu 3Venezuela - Caribbean 2 .

Release history

  • 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).

 
Current contributors
Pim Bongaerts
California Academy of Sciences
Website development

Ryan Booker
Global Underwater Explorers
Website development

Veronica Radice
Old Dominion University
Coordinator - Behind the Science

Gonzalo Perez-Rosales
CRIOBE - Centre de Recherches Insulaires et Observatoire de l’Environnement
Coordinator - Publications

Ryan Eckert
Harbor Branch Oceanographic Institute
Data curation - Publications

Gal Eyal
The University of Queensland
Data curation - Publications

Erika Gress
James Cook University
Data curation - Publications

Alejandra Hernandez-Agreda
James Cook University
Coordinator - Book chapters

Jaaziel García-Hernández
University of Puerto Rico-Mayagüez
Data curation - Book chapters

Nicholas Hammerman
University of Queensland
Data curation - Book chapters

Jack Laverick

Data curation - Book chapters

Michael Studivan
University of Miami
Coordinator - Social Media

Luiz Rocha
California Academy of Sciences
Contributor - Social Media

  Are you interested in helping out? Let us know!

Past contributors
Norbert Englebert
The University of Queensland
Data curation - Publications

Andrea Gori

Data curation - Publications

Felix Martinez
National Oceanic and Atmospheric Administration


Hudson Pinheiro
California Academy of Sciences
Data curation - Publications

Richard Pyle
Bishop Museum


Joe Turner

Data curation - Publications

Source code
This web application was written in Ruby (2.5.0) on Rails (5.1.4), with the code publicly available on GitHub.
Contact
For any questions, please contact us at: info[at]mesophotic.org