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 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 .
• Research field: 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 .
• Focus taxon/taxa: 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 .
• Geographic location: 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 .

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).