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 26 ,  Aquarium-based 38 ,  Autonomous Underwater Vehicle (AUV) 65 ,  Baited Remote Underwater Video (BRUV) 57 ,  Coring / drilling 32 ,  Dredging / trawling 92 ,  Drop / Towed Video 88 ,  Fishing 63 ,  In-situ instrumentation 62 ,  Land-based 68 ,  Manned Submersible 219 ,  Rebreather 225 ,  Remotely Operated Vehicle (ROV) 342 ,  SCUBA (open-circuit or unspecified) 668 ,  Snorkeling 19 ,  Sonar / Multibeam 138 ,  Surface-deployed sensors and samplers 82 .
• Research field: categorical. Indicates the research field(s) the publication can be categorized under. show categories
  
  Acoustics 14 ,  Behavior 57 ,  Biodiversity 664 ,  Biomedicine 18 ,  Climate Change 81 ,  Community structure 531 ,  Connectivity 141 ,  Disturbances 174 ,  Ecology 603 ,  Evolution 41 ,  Fisheries 107 ,  Geomorphology 184 ,  Long-term monitoring 94 ,  Management and Conservation 209 ,  Methods and Technology 59 ,  Molecular ecology 181 ,  Oceanography 88 ,  Paleoecology 50 ,  Physiology 191 ,  Reproduction 80 ,  Taxonomy 217 ,  Vision 3 .
• Focus taxon/taxa: categorical. Indicates the focal taxon/taxa of the publication. show categories
  
  Actiniaria and Ceriantharia (Sea anemones) 18 ,  Algae (Macro, Turf and Crustose Coralline) 208 ,  Antipatharia (Black Corals) 93 ,  Bacteria and Archaea 31 ,  Crustacea 51 ,  Fishes 413 ,  Fungi 12 ,  Hydrozoa 38 ,  Marine mammals 5 ,  Octocorallia (Soft Corals) 212 ,  Other endosymbionts (non-Symbiodinium) 10 ,  Other invertebrates 134 ,  Overall benthic (groups) 378 ,  Plankton 11 ,  Porifera (Sponges) 195 ,  Protists (non-Symbiodiniaceae) 26 ,  Scleractinia (Hard Corals) 471 ,  Seagrass 10 ,  Symbiodinium (zooxanthellae) 101 ,  Viruses 6 ,  Zoantharia (Zoanthids) 20 .
• Geographic location: categorical. Indicates the geographic location the publication focuses on. show categories
  
  Albania 1 ,  American Samoa 12 ,  Aruba 2 ,  Australia - Coral Sea 26 ,  Australia - Great Barrier Reef 64 ,  Australia - Northern Australia 18 ,  Australia - Scott Reef 4 ,  Australia - Southeastern Australia 41 ,  Australia - Western Australia 40 ,  Bahamas 55 ,  Barbados 6 ,  Belgium 3 ,  Belize 17 ,  Bermuda 41 ,  Bonaire 19 ,  Brazil - Eastern Brazil 65 ,  Brazil - Fernando Noronha 14 ,  Brazil - St Peter and St Paul Archipelago 12 ,  Brazil - Trindade and Martin Vaz 10 ,  British Virgin Islands 3 ,  Brunei 2 ,  Canada - Atlantic Ocean 3 ,  Canada - British Columbia 12 ,  Cape Verde 1 ,  Cayman Islands 25 ,  Chagos Archipelago 5 ,  Chile 9 ,  Chile - Easter Island 14 ,  China - South China Sea 7 ,  Christmas Island 1 ,  Clipperton Island 1 ,  Colombia - Caribbean Sea 16 ,  Colombia - Pacific Ocean 1 ,  Comoros 3 ,  Cook Islands 8 ,  Costa Rica - Caribbean Sea 1 ,  Costa Rica - Pacific Ocean 15 ,  Croatia 9 ,  Cuba 14 ,  Curaçao 60 ,  Cyprus 2 ,  Denmark 2 ,  Djibouti 2 ,  Dominica 3 ,  Dominican Republic 2 ,  Ecuador - Galápagos Islands 4 ,  Egypt - Red Sea 6 ,  El Salvador 3 ,  England 3 ,  Fiji 11 ,  France - Atlantic Ocean 2 ,  France - Mediterranean Sea 20 ,  French Guiana 1 ,  French Polynesia 25 ,  Germany 2 ,  Greece 11 ,  Grenada 1 ,  Guadeloupe 4 ,  Honduras - Bay Islands 19 ,  India - Andaman and Nicobar Islands 4 ,  India - Arabian Sea 1 ,  India - Bay of Bengal 1 ,  Indonesia 17 ,  Iran 1 ,  Ireland 1 ,  Israel - Mediterranean Sea 13 ,  Israel - Red Sea 108 ,  Italy - Adriatic-Ionian 28 ,  Italy - Ligurian-Tyrrhenian 107 ,  Italy - Mediterranean 34 ,  Jamaica 27 ,  Japan 7 ,  Japan - Ogasawara 1 ,  Japan - Ryukyu Islands (Okinawa) 47 ,  Kenya 1 ,  Kiribati 1 ,  La Perouse 2 ,  Lebanon 1 ,  Madagascar 4 ,  Malaysia 2 ,  Malta 1 ,  Martinique 1 ,  Mauritius 2 ,  Mayotte 6 ,  Mexico - Baja California 7 ,  Mexico - Caribbean Sea 7 ,  Mexico - Gulf of Mexico 11 ,  Mexico - Pacific Ocean 2 ,  Micronesia - Caroline Islands (Pohnpei) 20 ,  Micronesia - Chuuk atoll 2 ,  Micronesia - Guam 12 ,  Micronesia - Mariana Islands 8 ,  Micronesia - Marshall Islands 13 ,  Montenegro 1 ,  Morocco 6 ,  Mozambique 2 ,  Myanmar - Andaman Sea 6 ,  Navassa Island 1 ,  Netherlands 1 ,  New Caledonia 9 ,  New Zealand 11 ,  Norway 6 ,  Oman 1 ,  Panama - Caribbean Sea 4 ,  Panama - Pacific Ocean 4 ,  Papua New Guinea 17 ,  Peru 3 ,  Philippines 28 ,  Pitcairn Islands 2 ,  Poland 4 ,  Portugal 10 ,  Portugal - Azores 5 ,  Puerto Rico 82 ,  Republic of Maldives 8 ,  Republic of Palau 21 ,  Reunion Island 3 ,  Romania 1 ,  Saba Bank 2 ,  Saint Kitts and Nevis 1 ,  Saint Lucia 2 ,  Salas y Gomez Nazca Ridge 2 ,  Saudi Arabia - Red Sea 9 ,  Saya de Malha Bank 2 ,  Scotland 5 ,  Seychelles 9 ,  Singapore 3 ,  Solomon Islands 6 ,  South Africa 14 ,  South Korea - Jejudo Island 3 ,  Spain - Atlantic Ocean 6 ,  Spain - Canary Islands 4 ,  Spain - Mediterranean Sea 56 ,  St Vincent 2 ,  Sudan - Red Sea 5 ,  Sweden 3 ,  São Tomé and Príncipe 2 ,  Taiwan 17 ,  Tanzania 4 ,  Tonga 3 ,  Trinidad and Tobago 2 ,  Tunisia 1 ,  Turkey - Mediterranean Sea 10 ,  Turkey - Sea of Marmara 10 ,  Turks and Caicos 1 ,  US Virgin Islands 69 ,  USA - Continental Atlantic Ocean 41 ,  USA - Continental Pacific Ocean 27 ,  USA - Gulf of Mexico 72 ,  USA - Hawaii 126 ,  USA - Johnston Atoll 11 ,  USA - Pulley Ridge 35 ,  Vanuatu 4 ,  Venezuela - Caribbean Sea 3 ,  Vietnam 1 .

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).