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 15Aquarium-based 19Autonomous Underwater Vehicle (AUV) 47Baited Remote Underwater Video (BRUV) 33Coring / drilling 12Dredging / trawling 53Drop / Towed Video 35Fishing 43In-situ instrumentation 25Land-based 39Manned Submersible 168Rebreather 165Remotely Operated Vehicle (ROV) 189SCUBA (open-circuit or unspecified) 441Snorkeling 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 7Behavior 34Biodiversity 373Biomedicine 4Climate Change 38Community structure 347Connectivity 107Disturbances 104Ecology 367Evolution 29Fisheries 68Geomorphology 102Long-term monitoring 79Management and Conservation 113Methods and Technology 26Molecular ecology 105Oceanography 46Paleoecology 24Physiology 126Reproduction 55Taxonomy 163Vision 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) 126Antipatharia (Black Corals) 62Bacteria and Archaea 17Cetacea (Dolphins, Whales) 1Crustacea 30Fishes 296Hydrozoa 15Octocorallia (Soft Corals) 126Other endosymbionts (non-Symbiodinium) 5Other invertebrates 61Overall benthic (groups) 182Plankton 8Porifera (Sponges) 106Scleractinia (Hard Corals) 330Seagrass 7Symbiodinium (zooxanthellae) 76Viruses 3Zoantharia (Zoanthids) 9 .
  • Geographic location: categorical. Indicates the geographic location the publication focuses on. show categories

    American Samoa 9Aruba 2Australia - Coral Sea 19Australia - Great Barrier Reef 46Australia - Northern Australia 13Australia - Scott Reef 4Australia - Southeastern Australia 20Australia - Western Australia 18Bahamas 51Barbados 6Belize 15Bermuda 30Bonaire 16Brazil - Eastern Brazil 39Brazil - Fernando Noronha 6Brazil - St Peter and St Paul Archipelago 9Brazil - Trindade and Martin Vaz 10British Virgin Islands 2Brunei 2Cayman Islands 19Chagos Archipelago 2Christmas Island 1Colombia - Caribbean Sea 7Colombia - Pacific Ocean 0Cook Islands 7Costa Rica - Pacific Ocean 5Croatia 3Cuba 11Curaçao 51Denmark 1Djibouti 1Dominica 3Dominican Republic 2Easter Island 7Ecuador - Galápagos Islands 1Egypt - Red Sea 5El Salvador 1Fiji 10France - Mediterranean Sea 3French Polynesia 9Greece 3Grenada 1Guadeloupe 2Honduras - Bay Islands 15India - Western Continental Shelf 2Indonesia 11Israel - Mediterranean Sea 2Israel - Red Sea 76Italy - Adriatic Sea 5Italy - Ionian Sea 4Italy - Ligurian Sea 23Italy - Mediterranean 15Italy - Tyrrhenian Sea 36Jamaica 27Japan - Ogasawara 1Japan - Ryukyu Islands (Okinawa) 30Kiribati 1Madagascar 1Malaysia 2Malta 0Martinique 1Mauritius 2Mayotte 1Mexico - Baja California 4Mexico - Caribbean 7Mexico - Gulf of Mexico 3Micronesia - Caroline Islands (Pohnpei) 13Micronesia - Chuuk atoll 2Micronesia - Guam 8Micronesia - Mariana Islands 8Micronesia - Marshall Islands 9Montserrat 0Navassa Island 1Netherlands Antilles - Saba Bank 1New Caledonia 4New Zealand 3Norway 0Oman 1Panama - Caribbean Sea 3Panama - Pacific Ocean 3Papua New Guinea 13Peru 1Philippines 18Pitcairn Islands 2Poland 2Portugal 5Portugal - Azores 3Puerto Rico 75Republic of Maldives 5Republic of Palau 16Saint Kitts and Nevis 1Saint Lucia 2Saudi Arabia - Red Sea 3Seychelles 1Singapore 2Solomon Islands 3South Africa 6Spain - Atlantic 1Spain - Mediterranean Sea 23St Vincent 2Sudan - Red Sea 5Sweden 2São Tomé and Príncipe 2Taiwan 8Tanzania 1Tonga 3Trinidad and Tobago 2Turkey - Mediterranean Sea 3Turkey - Sea of Marmara 2Turks and Caicos 1US Virgin Islands 64USA - Continental Atlantic 28USA - Continental Pacific 9USA - Gulf of Mexico 57USA - Hawaii 93USA - Johnston Atoll 10USA - Pulley Ridge 33Vanuatu 3Venezuela - 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).

 
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

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
California Academy of Sciences
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