References

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Introduction

  1. Geographic distribution of marine species
    • Focus on zooplankton (majorly copepods) and larval fish species. Query their distribution in Asia and the western Pacific (10-40ﾟN, 105-135ﾟE) by scientific names.
    • ODB bio-database is the major data source. ODB data was collected from MOST bio-projects, related dissertations and journals, as well as contributions from marine ecology scientists. The data also incorporated open data in this region (10-40ﾟN, 105-135ﾟE) which collected by COPEPOD (Coastal and Oceanic Plankton Ecology, Production and Observation Database).
    • Automatically import OBIS (Ocean Biogeographic Information Syste, iobis.org) API to fetch their open data for querying species distribution. Please refer to OBIS websites, policies and API discriptions.
    • Get the distribution of querying species on the gradients of SST and salinity. It helps to figure out the correspondence between geographic distribution and range of adaptability to SST/Salinity.
  2. Regional species richness and composition
    • Using ODB bio-data with abundance records to evaluate species composition in each sampling site or grid.
    • Newly Update Open-data download for regional species composition, data source citation, and polygonal query mode by left-side draw-toolbar.
    • Get the correlations between community abundance of taxonomic groups and the environmental factors. Besides latitude, longitude, and sea depth, the environmental factors includes SST, salinity, and chlorophyll, which are gridded in 0.5°. Salinity data comes from NOAA NCEP GODAS, whereas SST and chlorophyll come from NASA Earth Observations.
  3. Download data (taxonomic list, and data source citation) or figures (PNG) of analyses. Apply for raw data by emailing your query criteria
  4. Open API: Extension functions of BioQuery map query for statistical computing. Note: some of these functions are time-consuming. API usage is integrated in BioQuery GUI, and the document can also be found in bio.odb.ntu.edu.tw/openapi

Usage

  1. Query geographic distribution of marine species
    • Input scientific name in the searh field, and some species for candidates may drop-down. You can also select species from Tree list, which is a tree-like selector structured by taxonomic levels and groups. Open lower levels (down-to family, and species level) by clicking triangular labeler on the tree nodes. Hold ‘Ctrl’ key for multiple selections, then ‘Apply’, and ‘Query’ them.
    • Search results are shown in table list and their geographic distribution in the basemap. Citations and related information about a specific distribution site would pop-up if you click that site. The left-side table also provides anchor points to jump to the sites in the map, and more searching options to filter the results.
    • Newly Update Download the taxonomy list for each queryed species and data-cited source by clicking ‘Download’ button. The geographic distribution is shown in a bounding box (BBOX: xmin, ymin, xmax, ymax), or a point with coordinate if only one record found.
    • Distribution on gradients of SST and salinity：click to span Advanced analyses interface, and show the distribution of querying species on the gradients of SST and salinity (note: if not shown, click 【Submit and analyze】). Further remove/select the blue grids on map to remove/add those sites within grids in this distribution analysis. The grid size can be controlled by the radio buttons, and then just click 【Submit and analyze】again. Choose SST-Salinity or Geography to 【Download Figs】for the distribution maps. (Need 【Submit and analyze】when choosing the radio buttons)


* Note: This query only support a maximum 3 species at one time, and display the results in different colors. The scientific names in query should be under 'family' level (i.e., family, genus and species). The query performs exact searching, and does not match all species under queried family and genus. It means that if you search family and genus, the results show the records in database which only identified to that level (spp.).
# Remarks: The query for the distribution of one species does not mean the whole geographic distribution range of that
# species, but only the records that ODB and external data source (such as OBIS) have.  Note that the data record from
# OBIS have no attributes about life-history stage that might cause confusion when searching larval fish species. The
# 'Site_OBIS' layer can be turn-off from right-top corner layer-control.
  1. Query regional species richness and composition
    • Enter ‘Setting’ menu for the following options. The options mean filtering and query criteria in analyzing species composition of each site. Just leave it blank if not needed, and ‘Apply’ to close the ‘Setting’ menu.
      • Taxonomic groups: Constrain the species to be under some taxonomic groups (can be blank, or multi-selected).
      • Sample date range: Filter the data by sampling date range.
      • Depth: Filter sampling depth (in unit of meter).
      • Mesh size: Filter mesh size used in trawling (in unit of mm).
      • Sample season：Filter sampling season (can be multi-selected).
      • Grid: Analyze species composition by original sampling coordinates (Raw), or 0.25-, 0.5-, 1-, 2-degree gridded coordinates. Gridded coordinates are shown in table list of results. Note, in basemap, the distribution is still plotted in raw coordinates. Species composition (shown in pie chart) in each site within the same grid would be consistent。
      • Taxon level: Constrain the taxonomic level in the analysis. For example, by choosing ‘genus’, congeneric species would be regarded as the same taxonomic groups and their abundance within the same grid would be summed. The results in pie chart only demonstrate the composition of that specific level.
      • Abundance unit: Most of the ODB data with abundance is in unit of individuals per cubic meter (per/m3), and some in per square meter (per/m2). Note, if you constrain ‘Taxonomic groups’ as ‘demersal fish’, the abundance unit would be limited as ‘per/m2’ in the analysis.
      • Abundance/Occurrence: Choose ‘Abundance’ to use logarithmic mean species abundance (within one grid) to evaluate species composition. Choose ‘Occurrence’ to count the presence of each species sampled in all the casts within one grid.

    • ‘Analyze species composition’ to get the final results.
    • Icon: ‘List taxa in sites/polygons’ to get taxonomic list and then can be downloaded by ‘Download’ icon.
    • Icon: ‘List citation in sites/polygons’ to get data source citation and then can be downloaded by ‘Download’ icon.

  1. Query polygonal regions
    • Left-side Draw Toolbar：add some polygons or square-box on map, after analyzing the species composion by your setting, click Query drawn polygons at top-corner to turn on/off regional query mode. By turning-on, the species composition and relative abundance (RA) in each polygon shown in table, and pie-chart shown by clicking the polygon on map.
    • Switch to taxonomic list by clicking ‘List taxa in sites/polygons’ and download.
    • Click agan ‘Query drawn polygons’ and turn-off this polygonal query mode.

  1. Advanced analysis with ocean environment
    • Correlations between environmental factors：click to span Advanced analyses interface, and show the correlations between community abundance of taxonomic groups and the environmental factors.
    • The environmental factors can be multi-selected from drop-down menu (if none selected, show the correlations with latitude, longitude, and sea depth). The grid size can be controlled by the radio buttons, and then just click 【Submit and analyze】again.
    • Click【Download Figs】to download the result of correlation analysis.


* The results are shown in both table and map. Further click one site will show the species composition, ordered by top 50 (in site) or 200 (in polygon) species in that specific site, in a pie chart. Use mouse over the color bar to display related information.   
# Remarks: The species richness and composition in any site exist systematic bias due to the uneven number of casts in
# sites of our available data. To evaluate species diversity, we will demonstrate some statistic results in future update
# to take the sampling bias into consideration.
  1. Apply for raw data by query criteria
    • ‘ Email technician’ can automaticaly append your criteria in querying species composition in the email to ODB technician. The technician then can fetch the raw data by the same query criteria after receiving the email of application. User can download the file and reload it to re-analyze。
    • According to the data release policies of MOST, the applicants should additionally fill out the application form (as the link in the ‘Email technician’ menu) and email the specimen signature to the ODB technician.





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