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. 2016 Mar 29;3:160017. doi: 10.1038/sdata.2016.17

The Coral Trait Database, a curated database of trait information for coral species from the global oceans

Joshua S Madin 1,a, Kristen D Anderson 2, Magnus Heide Andreasen 3, Tom CL Bridge 2,4, Stephen D Cairns 5, Sean R Connolly 2,6, Emily S Darling 7, Marcela Diaz 1, Daniel S Falster 1, Erik C Franklin 8, Ruth D Gates 8, Mia O Hoogenboom 2,6, Danwei Huang 9, Sally A Keith 3, Matthew A Kosnik 1, Chao-Yang Kuo 2, Janice M Lough 2,4, Catherine E Lovelock 10, Osmar Luiz 1, Julieta Martinelli 1, Toni Mizerek 1, John M Pandolfi 11, Xavier Pochon 12,13, Morgan S Pratchett 2, Hollie M Putnam 8, T Edward Roberts 2, Michael Stat 14, Carden C Wallace 15, Elizabeth Widman 16, Andrew H Baird 2,b
PMCID: PMC4810887  PMID: 27023900

Abstract

Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism’s function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.

Subject terms: Community ecology, Marine biology, Biodiversity, Biogeography, Coral reefs

Background & Summary

Most ecosystems are rich in species that display a wide diversity of characteristics1 (i.e., traits). One way to make meaningful generalizations from this diversity has been to identify physiological, ecological or functional traits of organisms to infer (e.g., using traits as explanatory variables) patterns of demography, distribution and abundance, and more broadly, ecosystem function and evolution2. Moreover, species traits can be used as explanatory variables for the responses of ecosystems to environmental change, as functionally significant traits mediate species’ responses to disturbances3. Recently, research has demonstrated the utility of trait-based approaches for understanding the effects of anthropogenic disturbances4, the provisioning of ecosystem services5, species distributions6–8, species composition9,10, and energetic and ecological trade-offs11,12. In seminal papers, compilations of species trait data with broad taxonomic coverage have revealed, for example, a general axis of variation in plants that describes costs and benefits of key chemical, structural and physiological traits11; and factors influencing the metabolic rates of organisms13. However, such broad-scale insights have been restricted to relatively few taxonomic groups, often due to lack of data, particularly information about the ecological context in which data were collected, when such data do exist.

Trait data for stony corals (Cnidaria: Scleractinia) have been collected for more than 100 years and published in many languages. Sufficient data might well exist already for addressing broad-scale hypotheses regarding the ecology and evolution of corals. Although trait compilations are accumulating4,14–16, and new statistical approaches for analysing such data are emerging7,12, these datasets are typically gathered for specific traits in isolation to address specific questions which can result in duplication of effort by separate research groups (e.g., Darling et al.12 and Pratchett et al.17 both independently compiled growth rate data). Trait data also tend to be gathered rapidly, for instance with means extracted from tables that present a mixture of original data and data collected previously by others (i.e., meta-analyses). Such a rapid assembly of data can result in omission of important contextual information (e.g., local environmental conditions and levels of variation and replication), confusion about the origin of the data, preventing appropriate provenance and credit18, and the accidental duplication of data points in large datasets.

In this data descriptor, we introduce the Coral Trait Database: a curated database of trait information for coral species from the global oceans. The goals of the Coral Trait Database are: (i) to assemble disparate information on coral traits, (ii) to provide unrestricted, open-source access to coral trait data, (iii) to facilitate and encourage the appropriate crediting of original data sources, and (iv) to engage the reef coral research community in the collection and quality control of trait data. We release 56 error-checked, validated and referenced traits, and also provide their context of measurement, together with an online system for transparently and accurately archiving and presenting coral trait data in future research. Our vision is an inclusive and accessible data resource to more rapidly advance the science and management of a sensitive ecosystem at a time of unprecedented environmental change.

Methods

The data are held in the Coral Traits Database (https://coraltraits.org). The database was designed to contain individual-level traits and species-level characteristics and is currently focused on shallow water zooxanthellate (‘reef building’) scleractinian corals. Individual-level traits include any potentially heritable quality of an organism19,20. In the database, individual-level traits are accompanied by contextual characteristics, which give information about the environment or situation in which an individual-level trait was measured (e.g., characteristics of the habitat, seawater or an experiment). These contextual variables are important for understanding variation in individual-level traits (e.g., as predictor variables in analyses). For example, if measurement of colony growth rate was measured at a given depth, the latter datum is included to provide important information for the focal measurement. Some individual-level traits have no or little variation (e.g., mode of larval development), and therefore contextual information is not required. Species-level characteristics do not have contextual information because they are characteristics of species as entities (such as geographical range size and maximum depth observed).

For simplicity, we use the single term ‘trait’ to refer to individual-level (variant and invariant), species-level (emergent) and contextual (environmental or situational) measurements. Moreover, these traits are grouped into ten use-classes based on various sub-disciplines of reef coral research: biomechanical, conservation, ecological, geographical, morphological, phylogenetic, physiological, reproductive, stoichiometric, and contextual.

Observation and measurements

The database contains two core data tables—Observations and Measurements—each of which has a series of associated tables (Fig. 1). We follow the high-level structure of the Observation and Measurement Ontology21 in that observations bind related measurements and potentially provide context for other observations.

Figure 1. Overview of the design of the Coral Trait Database.

Figure 1

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(a) The general schema consists of an Observation of a coral colony that is a collection of one or more Measurements associated with the colony. Solid borders represent table associations and dotted borders represent values. Observations have four table associations (contributor, coral species, resource and location) and one value for access (i.e., public or private). Measurements have four table associations (observation, trait, methodology and standard) and five values. (b) An example of an observation where coral growth rate was measured along with two contextual measurements (represented in the database by an eye). All observation-level attributes are required. Required measurement-level attributes are trait, standard, value and value type. Precision details are entered when a value type is not a raw value. Photograph: Emily Darling.

The observation table contains information about the observation of a coral or coral species. Observation-level data must include the Enterer, Species, Location and Resource. Access is an optional variable, and can be controlled by database users entering data for a project that has not yet been published (see https://coraltraits.org/procedures for more information). Observation-level data are the same for all measurements corresponding to the observation. Measurement-level data include the Trait, Value, Standard (measurement unit), Methodology, and estimates of precision (if applicable). The hypothetical example given in Fig. 1b is for growth rate that was measured within the context of a water depth and habitat that were given in the published resource.

The Species table provides taxonomy that is regularly updated by the Taxonomy Advisory Board (https://coraltraits.org/procedures) to keep pace with the rapid rate of revision22–24. The table contains the valid name for each coral species based largely on the World Register of Marine Species (http://www.marinespecies.org), the major clade (Basal, Robust or Complex25), family based on molecular work26, family based on morphology (following Cairns27 or Veron28), and other names and synonyms.

Data acquisition

All public data in the Coral Trait Database and included in this data descriptor release are linked with published resources, which include peer-reviewed papers, taxonomic monographs and books. The original source of entered data must be included (called the primary resource), even when extracted from secondary compilations (e.g., for the purpose of meta-analyses). Secondary sources can be included optionally, and so the database captures both the original data collector and subsequent data compilers, which allows both to be credited when re-using data. Measurement value types, which can be flexibly added to, currently include: raw, mean, median, maximum, minimum, expert opinion (the view of a single expert), group opinion (the consensus of a group of experts), and model derived. Continuous data are typically means extracted from tables or figures unless raw data are available. When available, aggregate values such as means and medians should be accompanied by the number of replicates and a measure of dispersion (e.g., standard deviation). Means and estimates of dispersion from figures in resources were captured using ImageJ29. The data released in this data descriptor have broad taxonomic (Fig. 2), global (Fig. 3) and phylogenetic (Fig. 4) coverage. However, some large data gaps exist, because few species have been comprehensively measured in many locations.

Figure 2. Trait by species matrix, illustrating coverage of trait data are currently available in the Coral Trait Database across the worlds 1547 coral species.

Figure 2

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Blue cells correspond with the traits released in this data descriptor. Grey cells correspond with other available data for which thorough error checking is still being conducted.

Figure 3.

Figure 3

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Figure 4. The phylogenetic coverage of traits in the Coral Trait Database, for the subset of species in the current molecular phylogeny.

Figure 4

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As for Fig. 2, blue cells indicate traits for species released in this data descriptor and grey cells indicate other available information in the database, still being federated.

Data Records

A static release of the 56 traits contained in this descriptor is available from the Coral Trait Database (Data Citation 1) and Figshare (Data Citation 2). Details and references for the trait data are summarised in Table 1 (available online only). Up-to-date data can be downloaded directly from the database. However, as validation (see Technical Validation, below) and data entry is ongoing, users are recommended to pull data from the static releases, to ensure results remain consistent as the database is updated. Both static releases and datasets downloaded from the database are accompanied by the primary (and, if applicable, secondary) resource lists for the data, which should be credited wherever feasible.

Table 1. Overview of traits in release 1.1.1, including descriptions, measurement standards, the number of measurements and the references.

Class Name Description Standard Default unit Categories Category descriptions Measurements References
N/A denotes not applicable.                
Biomechanical Colony shape factor A dimensionless measure of mechanical vulnerability to hydrodynamic disturbance (see Madin and Connolly 2006). Colony shape factor is a function of colony size, and therefore each observation should also include a colony size measurement. Currently published data is only available for three species. Dimensionless N/A N/A N/A 1158 30
Larval swimming speed The swimming speed, typically the maximum, of coral larvae. Speed mm s−1 N/A N/A 394 31–40
Skeletal density The material density of coral skeleton. Porosity measurements can be converted to density by multiplying the reciprocal of porosity by the maximum density of aragonite (2.94 g cm^−3). Density g cm−3 N/A N/A 378 16,17,41–74
Skeletal micro-density The fine-scale specific gravity of the material from which coral skeleton is constructed (Bucher et al. 1998, following terminology from Barnes & Devereux 1988). Micro-density should be closer to the density of solid aragonite (~2.96 g cm^−3) than to typical bulk densities, because it does not capture corallite voids (i.e., porosity). Density g cm−3 N/A N/A 9 45
Substrate attachment Whether or not individuals attach to substrates, including reef, rock and wood. Category N/A attachedunattachedboth Attached to the substratumNot attached to the substratumFound both attached and unattached to the substratum 1464 28,75–77
Conservation IUCN Red List category Red list categories are from Delbeek et al. (2009) as compiled by Carpenter et al. (2009). Category N/A VULCNTDDCREN VulnerableLeast concernNear threatenedData deficientCritically endangeredEndangered 818 4,78
Ecological Abundance GBR The typical local abundance of species when found on the Great Barrier Reef, Australia. Data were extracted from textual descriptions in Veron (1996) by Diaz and Madin (2011). Category N/A rareuncommoncommon Typically rare where foundTypically uncommon where foundTypically common where found 400 79,80
Abundance world The typical local abundance of species from Veron (2000). It is suspected that many species listed as rare are abundant at some localities. Furthermore, as Bridge et al. (2013) point out, some are abundant at depth. Category N/A rareuncommoncommon Typically rare where foundTypically uncommon where foundTypically common where found 823 4,28,78,81–84
Depth lower The maximum (deepest) observed depth of a species. Data are a mix of individual-level local observations and species-level global estimates based on expert opinion. Length m N/A N/A 1214 4,78,85–105
Depth upper The minimum (shallowest) observed depth of a species. Data are a mix of individual-level local observations and species-level global estimates based on expert opinion. Length m N/A N/A 1147 4,78,87,89,95,97–99,102–105
Generation time The average age of mothers in populations. This characteristic has only been empirically estimated for three species as far as we know ([Babcock 1991](/resources/273)). Values in Carpenter et al. (2008) are unreliable and we advise against using them. Duration years N/A N/A 3 106
Life history strategy Life history strategies broadly capture the various investments in growth, reproduction, and survivorship that differentiate species. Category cat competitiveweedystress-tolerantgeneralist Efficient at using resources and can dominate communities in productive environmentsOpportunistically colonize recently disturbed habitatsAdvantageous traits in chronically harsh environmentsDo well in habitats where competition is limited by low levels of stress and disturbance 143 12
Water clarity preference Preferred water clarity environment. Derived from preferred habitat textual descriptions, mostly from Veron and Stafford-Smith (2002), and published in Diaz and Madin (2011). Category N/A bothclearturbid Found in both clear and turbid water environmentsFound predominantly in clear water environmentsFound predominantly in turbid water environments 933 28,79,81,83
Wave exposure preference Preferred hydrodynamic exposure environment. Derived from preferred habitat textual descriptions, mostly from Veron and Stafford-Smith (2002), and published in Diaz and Madin (2011). Category N/A protectedbroadexposed Found predominantly in sheltered environmentsFound in both sheltered and exposed wave environmentsFound predominantly in exposed wave environments 933 28,79,83
Geographical Eastern-most range edge Eastern-most edge of a species range given as longitude, typically calculated from shapefiles. May also include one-off published observations. Not to be confused with eastern-most longitude relative to Greenwich. The value that results in the greatest range extent is used when species are synonymized. Longitude deg N/A N/A 709 107
Geographical region Presence in broad ocean and geographical regions. Binomial N/A Indian OceanWestern and Central PacificWestern AtlanticEastern PacificEastern AtlanticSubantarctic and Antarctic N/A 2316 14,27
Indo-Pacific faunal province Presence in the eleven Indo-Pacific faunal provinces established in Keith et al. (2013). Category N/A Africa-IndiaAndaman-Nicobar IslandsAustralianFiji-Caroline IslandsHawaii-Line IslandsIndonesianJapan-VietnamPersian GulfPolynesiaRed SeaTonga-Samoa N/A 3814 7
Northern-most range edge Northern-most edge of a species range given as latitude, typically calculated from shapefiles. May also include one-off published observations. The value that results in the greatest range extent is used when species have been synonymized. Latitude decimal degree N/A N/A 709 107
Ocean basin The ocean basin in which a species is found. Indian and Pacific Oceans are grouped as ‘pacific.’ Category N/A pacificatlantic Present in the Indo-PacificPresent in the Atlantic 1494 14,27
Range size Geographic range size of species calculated from shapefiles. Be aware that there are different definitions of range size. For example, Veron (2000) range sizes are the sum of ecoregion sizes in which a species occurs; whereas, Hughes et al. (2013) range sizes capture the full extent of a species and so will be larger than Veron (2000) range sizes. Largest range size is used when species are synonymized. Area km2 N/A N/A 1477 28,107
Southern-most range edge Southern-most edge of a species range given as latitude, typically calculated from shapefiles. May also include one-off published observations. The value that results in the greatest range extent is used when species have been synonymized. Latitude decimal degree N/A N/A 709 107
Western-most range edge Western-most edge of a species range given as longitude, typically calculated from shapefiles. May also include one-off published observations. Not to be confused with western-most longitude relative to Greenwich. The value that results in the greatest range extent is used when species have been synonymized. Longitude decimal degree N/A N/A 709 107
Morphological Coloniality Whether mature individuals of a species are colonial, solitary or either colonial or solitary (both). Category N/A colonialsolitaryboth Mature individuals are colonialMature individuals are solitaryMature individuals can be either colonial or solitary 1613 28,77
Colony maximum diameter The maximum diameter of a colony. At this stage, most maximum diameters have been extracted from monographs. However, new published records of large colonies should also be entered. Length cm N/A N/A 537 28,75,80,83,84,108–128
Corallite width maximum The maximum typical corallite width, axial corallite width or valley size. Length mm N/A N/A 733 28,77,81,121,129–133
Corallite width minimum The minimum typical corallite width, axial corallite width or valley size. Length mm N/A N/A 688 28,77,81,121,129–133
Growth form typical The growth form (morphology) of a species as derived from text descriptions in Veron (2000). The ‘typical’ growth form is given for each species, rather than all forms that might be observed in the field. Category N/A encrustinglaminarsubmassivemassivecolumnarbranching_closedbranching_opentables_or_platesdigitatecorymbosehispidoseencrusting_long_uprights Overlaying the substratumThin sheets often forming whorlsNot quite massiveSolid with similar shape in all directionForming columnsBranches in clusters or tuftsBranches of similar length given off at similar anglesColony outline in the shape of a table i.e., a top with one central leg or side-attached tableEncrusting with regular short upright branchesFlat topped clumpsOpen-branched except with a second type of branch given off at regular intervalsOverlaying the substratum with long branches 773 28
Growth form Veron The growth form (morphology) of a species as derived from text descriptions in Veron (2000). Species can have more than one growth form, and therefore captures some degree of morphological plasticity. Category N/A encrustinglaminarsubmassivemassivecolumnarbranching_closedbranching_opentables_or_platesdigitatecorymbosehispidoseencrusting_long_uprights Overlaying the substratumThin sheets often forming whorlsNot quite massiveSolid with similar shape in all directionForming columnsBranches in clusters or tuftsBranches of similar length given off at similar anglesColony outline in the shape of a table i.e., a top with one central leg or side-attached tableEncrusting with regular short upright branchesFlat topped clumpsOpen-branched except with a second type of branch given off at regular intervalsOverlaying the substratum with long branches 1168 28
Growth form Wallace The growth form (morphology) of a species as derived from text descriptions in Wallace (2012). Species may, but tend not to, have more than one growth form. Category N/A arborescentarborescent_tablescorymbosecaespitosecaespitose_corymbosehispidoseencrustingelkhorncuneiformtables_or_plates Branches of similar length given off at a similar angles. Open branchingOpen branched tablesFlat topped clumpsBranches in clusters or tufts. Closed branchingFlat topped closed branching clumpsArborescent except with a second type of branch given off at regular intervals around the primary branchAdhering to or overlaying the substratumBranches in the shape of the horns of an ElkBranches shaped like a wedgeColony outline in the shape of a table, i.e., a top with one central leg or pedicle, may be side-attached table 122 77
Growth outline type Whether or not a colony tends to approach a predictable outline. This trait was included in Wallace et al. (2012), and so has been measured mostly for Acropora. Category N/A Indeterminatedeterminate Colony grows apparently without any intrinsic restrictionColony grows to a more or less predictable outline 119 77
Polyps per area The number of polyps found in a given colony surface area. Density units cm−2 N/A N/A 55 16,70,72,106,121,129,131–147
Phylogenetic Genus fossil age Date of the first palaeontological occurrence of morphologically defined genera based on the published literature. Million years ago mya N/A N/A 3799 7,28,148–150
Genus fossil stage The geochronological unit of the first palaeontological occurrence of morphologically defined genera based on the published literature. Category N/A Recent, Eocene, Oligocene, Miocene, Ypresian, Miocene middle, Cretaceous Lower, Aptian, Jurassic Upper, Eocene middle, Cretaceous Upper, Turonian, Cretaceous, Cretaceous upper, Pleistocene, Priabonian, Cretaceous middle, Pliocene, Barremian, Neocomian, Chattian, Thanetian, Danian, Kimmeridgian, Miocene upper, Burdigalian, Oligocene middle, Rupelian upper, Tortonian, Cenomanian, Pleistocene-?Oligocene, Miocene Lower, Aquitanian, Eocene-Cretaceous, Pliocene-Pleistocene, Palaeocene, Rupelian, Bathonian N/A 2335 28,149,150
Species age phylogeny This is the phylogenetic tip length based on a phylogeny of 1547 species reconstructed using supertree and MCMC methods, incorporating molecular, morphological and taxonomic data. Million years ago mya N/A N/A 1461 151
Physiological Calcification rate The rate at which aragonite is laid down per unit of skeletal surface area. When using this data, be aware that this trait is measured in numerous ways. Percent per year % yr−1 N/A N/A 320 16,17,41,43,46,48,50,53,54,63,67,70–72,74,152–170
Dark respiration The rate of oxygen consumption measured in the darkness per unit of skeletal surface area. Values may include both light enhanced dark respiration and dark acclimated dark respiration. Rate μmol O2 cm−2 h−1 N/A N/A 46 16,138,139,144,152,157,171–179
Gross photosynthesis The rate of oxygen production measured in the light per unit of skeletal surface area. This includes oxygen consumption due to light respiration. Rate μmol O2 cm−2 h−1 N/A N/A 37 16,138,139,144,152,157,171–173,175–179
Growth rate Typically, the yearly extension for branching and massive corals, or simple linear extension. Growth rate is sometimes measured using different dimensions (e.g., diameter and radius) or over shorter periods of time (e.g., month), which are indicated by measurement standards and methodologies, and so values may need to be standardised before comparisons among measurements can be made. Extension rate (linear) mm yr−1 N/A N/A 1297 12,16,17,41,43,46,48,50,51,53,54,56,57,59,61–63,65–68,70–74,106,113,138,169,170,180–316
Mitotic index The percentage of cells in the paired stage of cell division. Percent % N/A N/A 31 16,317–322
Protein biomass The amount or biomass of protein per unit of skeletal surface area. Density mg cm−2 N/A N/A 32 16,138,139,171,179,323–329
Symbiodinium clade The genetic identity of Symbiodinium found in coral tissue at the clade level (broad level of major symbiont taxa). This is typically identified using regions of the nuclear ribosomal DNA, but other regions are also used. Category N/A A, B, C, D, F, G, H, I N/A 3147 15,330–379
Symbiodinium density The number of symbiont cells per unit of skeletal surface area. Density units cm−2 N/A N/A 4062 16,164,171,320,380–393
Symbiodinium subclade The genetic identity of Symbiodinium found in coral tissue at the level below clade, but usually above species. This is typically identified using the nuclear ribosomal DNA Internal Transcribed Spacer region (ITS2), but other markers are also used. Category N/A N/A N/A 3068 15,76,330–338,340–345,347–365,367–379
Tissue thickness The distance from the external surface to the internal surface of the coral tissue. Length mm N/A N/A 59 16,72,273,306,388,394
Zooxanthellate Is the species zooxanthellate? Category N/A zooxanthellateazooxanthellateboth Contain zooxanthellae within their tissuesDon't contain zooxanthellae within their tissuesSometimes contain zooxanthellae within their tissues 1548 27,28,75,76,78,91,395–420
Reproductive Mode of larval development The mode of larval development classified as either a brooder, where fertilization is internal and colonies release planulae larvae, or a broadcast spawner, where gametes are release for external fertilization and the planulae develops in the plankton. Category N/A bothbrooderspawner individual colonies both brood and spawnFertilization internalFertilization external 814 14,32,35,84,120,141,146,234,235,421–523
Oocyte size at maturity The diameter of mature oocytes in a population. Determined by histology or dissection or measuring the size of eggs once released from the colony in broadcast spawners. Length μm N/A N/A 133 234,423,425,428,436,441,448,460,478–480,483,484,493,494,498,500,510,519,521,524–530
Propagule size on release The size of eggs or planula larvae on release. Length μm N/A N/A 67 423,425,428,478,480,483,484,493,510,512,525,528–531
Sexual system Each polyp of the population having gametes of only one sex (either male or female) at maturity (gonochore); one or more polyps of the population having both male and female gametes at maturity (hermaphrodite). Category N/A gonochorehermaphrodite Only one sex in all polypsBoth sexes in at least one polyp 1153 14,35,84,141,146,234,235,422–429,432,436,438–443,445–449,451–454,456–458,460,461,463–469,471,472,476–481,483–489,492–513,515–523,525,532–550
Symbiodinium sp. in propagules Whether or not mature eggs or larvae contain Symbiodinium sp. at the time of release from the parent. Typically determined by eye, rarely by histology or fluorescent microscopy, which are required for confirmation. Binomial N/A yesno Symbiodinium sp. in propagulesNo Symbiodinium sp. in propagules 818 14,120,146,234,235,424–427,429,436,438,440,441,444,447,451,453,455,456,458,460,466,468,473,474,476,479,483,484,488,489,493–501,505,511,512,517,522,525,535,538,541,549,551–555
Stoichiometric Chlorophyll a The amount of chlorophyll a in coral tissue, typically given per unit surface area. Density μg cm−2 N/A N/A 110 16,144,171,179,215,222,323,328,329,383,388,389,556–571
Lipid content The amount of lipid is tissue. Density mg cm−2 N/A N/A 13 16,325–328,385,572
Nitrogen concentration The amount of nitrogen in tissue. Percent % N/A N/A 131 573
Phosphorus concentration The amount of phosphorus in tissue. Percent % N/A N/A 142 573
RNA:DNA ratio The relative quantities of RNA and DNA. Ratio x:y N/A N/A 80 573
Total biomass The dry weight of holobiont tissue, typically reported as mass per unit of skeletal surface area of a colony. Density mg cm−2 N/A N/A 3867 16,138,139,157,325,327,328,389,392,560,564,574,575
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Technical Validation

The database is curated on a voluntary basis, which includes a Managerial Board, Editorial Board, Taxonomy Advisory Board and Database Administrator (https://coraltraits.org/procedures). Database Contributors who add data for a new trait are typically asked to be that trait’s editor. Quality control of data and editorial procedures include:

  1. Contributor approval: Database users must request permission to become a database contributor, and any observations entered by the contributor are associated with their user account.

  2. Editorial approval: Once a contributor enters an observation of a coral trait, an email is sent automatically to the editor of that trait. The editor must approve the observation to remove the ‘pending’ flag from the observation record.

  3. User feedback: Data issues can be reported for any observation using a simple form. Editors are automatically emailed if an issue with one of their traits is reported.

  4. Duplicate detection: Measurements with the same value, resource, location and species are flagged for confirmation.

  5. Outlier detection: Frequency histograms are generated in real time when loading trait pages. Outliers can be detected visually (e.g., a very large value for continuous data or a category that has one or few associated measurements for categorical data).

Usage Notes

The data release is a compressed folder containing two files:

  1. A csv-formatted data file containing all publicly available observation and measurement data, which includes contextual data.

  2. A csv-formatted resource file containing all the resources (primary and secondary) that correspond with the data. Users are expected to cite the data correctly using these resources.

An example for extracting and reshaping release data for analysis can found online (https://coraltraits.org/procedures).

Additional Information

Table 1 is only available in the online version of this paper.

How to cite this article: Madin, J. S. et al. The Coral Trait Database, a curated database of trait information for coral species from the global oceans. Sci. Data 3:160017 doi: 10.1038/sdata.2016.17 (2016).

Supplementary Material

sdata201617-isa1.zip (4.2KB, zip)

Acknowledgments

The authors would like to thank Macquarie University’s Genes to Geoscience Research Centre for supporting the Coral Trait Working group. In particular, we would like to thank Mark Westoby, Mariella Herberstein and Sam Newton. J.S.M. was supported by an Australian Research Council Future Fellowship. S.A.K. and M.H.A. were supported by the Danish National Research Foundation. C.E.L. and J.M.P. were supported by an Australian Research Council Discovery Project (DP0986179). T.B., S.R.C., M.O.H., C.-Y.K., J.M.P., M.S.P., T.E.R. and A.H.B. were supported by the ARC Centre of Excellence for Coral Reef Studies.

Footnotes

The authors declare no competing financial interest.

Data Citations

  1. Madin J. S. 2016. The Coral Trait Database. https://coraltraits.org/releases/ctdb_1.1.1.zip
  2. Madin J. S. 2016. Figshare. http://dx.doi.org/10.6084/m9.figshare.2067414

References

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Citations

  1. Madin J. S. 2016. The Coral Trait Database. https://coraltraits.org/releases/ctdb_1.1.1.zip
  2. Madin J. S. 2016. Figshare. http://dx.doi.org/10.6084/m9.figshare.2067414

Supplementary Materials

sdata201617-isa1.zip (4.2KB, zip)

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