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 12 ,  Aquarium-based 14 ,  Autonomous Underwater Vehicle (AUV) 32 ,  Baited Remote Underwater Video (BRUV) 22 ,  Coring / drilling 9 ,  Dredging / trawling 42 ,  Drop / Towed Video 24 ,  Fishing 29 ,  In-situ instrumentation 17 ,  Land-based 29 ,  Manned Submersible 152 ,  Rebreather 135 ,  Remotely Operated Vehicle (ROV) 164 ,  SCUBA (open-circuit or unspecified) 390 ,  Snorkeling 10 ,  Sonar / Multibeam 54 ,  Surface-deployed sensors and samplers 36 .
• Research field: categorical. Indicates the research field(s) the publication can be categorized under. show categories
  
  Acoustics 4 ,  Behavior 28 ,  Biodiversity 323 ,  Biomedicine 3 ,  Climate Change 16 ,  Community structure 312 ,  Connectivity 87 ,  Disturbances 81 ,  Ecology 307 ,  Evolution 19 ,  Fisheries 53 ,  Geomorphology 82 ,  Long-term monitoring 64 ,  Management and Conservation 90 ,  Methods and Technology 25 ,  Molecular ecology 96 ,  Oceanography 41 ,  Paleoecology 21 ,  Physiology 108 ,  Reproduction 43 ,  Taxonomy 140 ,  Vision 1 .
• Focus taxon/taxa: categorical. Indicates the focal taxon/taxa of the publication. show categories
  
  Actiniaria and Ceriantharia (Sea anemones) 6 ,  Algae (Macro, Turf and Crustose Coralline) 101 ,  Antipatharia (Black Corals) 46 ,  Bacteria and Archaea 15 ,  Crustacea 26 ,  Fishes 258 ,  Hydrozoa 10 ,  Octocorallia (Soft Corals) 107 ,  Other endosymbionts (non-Symbiodinium) 4 ,  Other invertebrates 43 ,  Overall benthic (groups) 165 ,  Plankton 3 ,  Porifera (Sponges) 76 ,  Scleractinia (Hard Corals) 278 ,  Seagrass 3 ,  Symbiodinium (zooxanthellae) 71 ,  Viruses 1 ,  Zoantharia (Zoanthids) 9 .
• Geographic location: categorical. Indicates the geographic location the publication focuses on. show categories
  
  American Samoa 5 ,  Aruba 2 ,  Australia - Coral Sea 16 ,  Australia - Great Barrier Reef 36 ,  Australia - Northern Australia 9 ,  Australia - Scott Reef 4 ,  Australia - Southeastern Australia 17 ,  Australia - Western Australia 15 ,  Bahamas 42 ,  Barbados 5 ,  Belize 13 ,  Bermuda 23 ,  Bonaire 13 ,  Brazil - Eastern Brazil 31 ,  Brazil - Fernando Noronha 2 ,  Brazil - St Peter and St Paul Archipelago 6 ,  Brazil - Trindade and Martin Vaz 8 ,  British Virgin Islands 2 ,  Brunei 1 ,  Cayman Islands 14 ,  Chagos Archipelago 1 ,  Christmas Island 1 ,  Colombia - Caribbean Sea 6 ,  Colombia - Pacific Ocean 0 ,  Cook Islands 5 ,  Costa Rica - Pacific Ocean 4 ,  Croatia 3 ,  Cuba 8 ,  Curaçao 44 ,  Denmark 1 ,  Djibouti 1 ,  Dominica 3 ,  Dominican Republic 2 ,  Easter Island 6 ,  Ecuador - Galápagos Islands 1 ,  Egypt - Red Sea 3 ,  El Salvador 1 ,  Fiji 8 ,  France - Mediterranean Sea 3 ,  French Polynesia 5 ,  Greece 3 ,  Grenada 1 ,  Guadeloupe 1 ,  Honduras - Bay Islands 13 ,  India - Western Continental Shelf 2 ,  Indonesia 7 ,  Israel - Mediterranean Sea 1 ,  Israel - Red Sea 61 ,  Italy - Adratic Sea 5 ,  Italy - Ionian Sea 4 ,  Italy - Ligurian Sea 22 ,  Italy - Mediterranean 15 ,  Italy - Tyrrhenian Sea 36 ,  Jamaica 20 ,  Japan - Ogasawara 1 ,  Japan - Ryukyu Islands (Okinawa) 24 ,  Kiribati 1 ,  Malaysia 2 ,  Malta 0 ,  Martinique 1 ,  Mauritius 2 ,  Mexico - Baja California 3 ,  Mexico - Caribbean 6 ,  Mexico - Gulf of Mexico 1 ,  Micronesia - Caroline Islands (Pohnpei) 9 ,  Micronesia - Chuuk atoll 2 ,  Micronesia - Guam 7 ,  Micronesia - Mariana Islands 7 ,  Micronesia - Marshall Islands 6 ,  Montserrat 0 ,  Navassa Island 1 ,  Netherlands Antilles - Saba Bank 1 ,  New Caledonia 3 ,  New Zealand 2 ,  Norway 0 ,  Oman 1 ,  Panama - Caribbean Sea 3 ,  Panama - Pacific Ocean 3 ,  Papua New Guinea 6 ,  Peru 1 ,  Philippines 12 ,  Pitcairn Islands 2 ,  Poland 2 ,  Portugal 5 ,  Portugal - Azores 1 ,  Puerto Rico 66 ,  Republic of Maldives 3 ,  Republic of Palau 8 ,  Saint Kitts and Nevis 1 ,  Saint Lucia 2 ,  Saudi Arabia - Red Sea 1 ,  Seychelles 1 ,  Solomon Islands 1 ,  South Africa 5 ,  Spain - Atlantic 1 ,  Spain - Mediterranean Sea 20 ,  St Vincent 2 ,  Sudan - Red Sea 4 ,  Sweden 2 ,  São Tomé and Príncipe 2 ,  Taiwan 4 ,  Tonga 3 ,  Trinidad and Tobago 2 ,  Turkey - Mediterranean Sea 3 ,  Turkey - Sea of Marmara 2 ,  Turks and Caicos 1 ,  US Virgin Islands 57 ,  USA - Continental Atlantic 24 ,  USA - Continental Pacific 8 ,  USA - Gulf of Mexico 46 ,  USA - Hawaii 77 ,  USA - Johnston Atoll 9 ,  USA - Pulley Ridge 31 ,  Vanuatu 3 ,  Venezuela - 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).