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 25Aquarium-based 38Autonomous Underwater Vehicle (AUV) 62Baited Remote Underwater Video (BRUV) 55Coring / drilling 32Dredging / trawling 90Drop / Towed Video 88Fishing 63In-situ instrumentation 58Land-based 66Manned Submersible 219Rebreather 221Remotely Operated Vehicle (ROV) 333SCUBA (open-circuit or unspecified) 659Snorkeling 18Sonar / Multibeam 135Surface-deployed sensors and samplers 76 .
  • Research field: categorical. Indicates the research field(s) the publication can be categorized under. show categories

    Acoustics 13Behavior 57Biodiversity 648Biomedicine 18Climate Change 78Community structure 519Connectivity 138Disturbances 168Ecology 595Evolution 41Fisheries 107Geomorphology 179Long-term monitoring 93Management and Conservation 203Methods and Technology 57Molecular ecology 175Oceanography 80Paleoecology 49Physiology 186Reproduction 79Taxonomy 214Vision 3 .
  • Focus taxon/taxa: categorical. Indicates the focal taxon/taxa of the publication. show categories

    Actiniaria and Ceriantharia (Sea anemones) 18Algae (Macro, Turf and Crustose Coralline) 206Antipatharia (Black Corals) 89Bacteria and Archaea 29Crustacea 49Fishes 407Fungi 12Hydrozoa 36Marine mammals 5Octocorallia (Soft Corals) 205Other endosymbionts (non-Symbiodinium) 10Other invertebrates 131Overall benthic (groups) 369Plankton 11Porifera (Sponges) 191Protists (non-Symbiodiniaceae) 25Scleractinia (Hard Corals) 462Seagrass 10Symbiodinium (zooxanthellae) 99Viruses 6Zoantharia (Zoanthids) 20 .
  • Geographic location: categorical. Indicates the geographic location the publication focuses on. show categories

    Albania 1American Samoa 12Aruba 2Australia - Coral Sea 26Australia - Great Barrier Reef 64Australia - Northern Australia 18Australia - Scott Reef 4Australia - Southeastern Australia 41Australia - Western Australia 40Bahamas 55Barbados 6Belgium 3Belize 16Bermuda 40Bonaire 19Brazil - Eastern Brazil 65Brazil - Fernando Noronha 14Brazil - St Peter and St Paul Archipelago 12Brazil - Trindade and Martin Vaz 10British Virgin Islands 3Brunei 2Canada - Atlantic Ocean 3Canada - British Columbia 12Cape Verde 1Cayman Islands 25Chagos Archipelago 3Chile 9Chile - Easter Island 14China - South China Sea 7Christmas Island 1Clipperton Island 1Colombia - Caribbean Sea 15Colombia - Pacific Ocean 1Comoros 2Cook Islands 8Costa Rica - Caribbean Sea 1Costa Rica - Pacific Ocean 15Croatia 9Cuba 11Curaçao 60Cyprus 2Denmark 2Djibouti 2Dominica 3Dominican Republic 2Ecuador - Galápagos Islands 4Egypt - Red Sea 6El Salvador 2England 3Fiji 11France - Atlantic Ocean 2France - Mediterranean Sea 18French Guiana 1French Polynesia 23Germany 2Greece 10Grenada 1Guadeloupe 3Honduras - Bay Islands 19India - Andaman and Nicobar Islands 4India - Arabian Sea 2India - Bay of Bengal 1Indonesia 14Iran 1Ireland 1Israel - Mediterranean Sea 12Israel - Red Sea 107Italy - Adriatic-Ionian 28Italy - Ligurian-Tyrrhenian 107Italy - Mediterranean 33Jamaica 27Japan 7Japan - Ogasawara 1Japan - Ryukyu Islands (Okinawa) 44Kiribati 1La Perouse 1Lebanon 1Madagascar 4Malaysia 2Malta 1Martinique 1Mauritius 2Mayotte 6Mexico - Baja California 6Mexico - Caribbean Sea 7Mexico - Gulf of Mexico 10Mexico - Pacific Ocean 2Micronesia - Caroline Islands (Pohnpei) 18Micronesia - Chuuk atoll 2Micronesia - Guam 11Micronesia - Mariana Islands 8Micronesia - Marshall Islands 13Montenegro 1Morocco 6Mozambique 1Myanmar - Andaman Sea 6Navassa Island 1Netherlands 1New Caledonia 8New Zealand 12Norway 6Oman 1Panama - Caribbean Sea 4Panama - Pacific Ocean 4Papua New Guinea 18Peru 3Philippines 27Pitcairn Islands 2Poland 4Portugal 10Portugal - Azores 5Puerto Rico 82Republic of Maldives 8Republic of Palau 20Reunion Island 3Romania 1Saba Bank 2Saint Kitts and Nevis 1Saint Lucia 2Salas y Gomez Nazca Ridge 2Saudi Arabia - Red Sea 9Saya de Malha Bank 2Scotland 5Seychelles 8Singapore 3Solomon Islands 6South Africa 12South Korea - Jejudo Island 2Spain - Atlantic Ocean 6Spain - Canary Islands 4Spain - Mediterranean Sea 54St Vincent 2Sudan - Red Sea 5Sweden 2São Tomé and Príncipe 2Taiwan 16Tanzania 3Tonga 3Trinidad and Tobago 2Tunisia 1Turkey - Mediterranean Sea 9Turkey - Sea of Marmara 10Turks and Caicos 1US Virgin Islands 69USA - Continental Atlantic Ocean 41USA - Continental Pacific Ocean 27USA - Gulf of Mexico 68USA - Hawaii 126USA - Johnston Atoll 11USA - Pulley Ridge 35Vanuatu 4Venezuela - Caribbean Sea 3Vietnam 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).

 
Current contributors
Pim Bongaerts
California Academy of Sciences
Editor & Website development

Ryan Booker

Editor & Website development

Veronica Radice
Old Dominion University
Editor & Coordinator - Behind the Science

Gonzalo Pérez-Rosales
Hong Kong University of Science and Technology
Editor

Alejandra Hernandez-Agreda
California Academy of Sciences
Editor

Angela Stevenson

Database contributor

Clara Diaz

Database contributor

Erika Gress
James Cook University
Database contributor

Gaby Carpenter

Database contributor

Erika Gress
James Cook University
Database contributor

Héloïse Rouzé

Database contributor

Jack Laverick

Database contributor

Alexis Sturm
Harbor Branch Oceanographic Institute
Database contributor

Nicola Foster

Database contributor

Ryan Eckert
Harbor Branch Oceanographic Institute
Database contributor

Tal Idan
Tel Aviv University
Database contributor

  Are you interested in helping out? Let us know!

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

Gal Eyal

Data curation - Publications

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

Andrea Gori

Data curation - Publications

Nicholas Hammerman
University of Queensland
Data curation - Book chapters

Felix Martinez
National Oceanic and Atmospheric Administration


Hudson Pinheiro
California Academy of Sciences
Data curation - Publications

Richard Pyle
Bishop Museum


Luiz Rocha
California Academy of Sciences
Contributor - Social Media

Michael Studivan
University of Miami
Coordinator - Social Media

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