How to use BISMaL

BISMaL Manual [PDF File]

BISMaL aims to accumulate and provide biological information of all marine species around Japan. Using BISMaL, you may browse/download occurrence records of organisms after searching and filtering them by geographic regions, taxa, etc. or may browse the detailed information of each taxon. BISMaL supports English and Japanese and you may change language by clicking "Engilish" or "日本語" in the menu on the top of each page.

Searching occurrence records of organisms

Search page of occurrence records

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Click "Occurrence records" in the menu on the top of each page, you will jump to the search page of occurrence records. In the search page, a map is shown under the menu, and the localities of records are shown as colored grids following the number of records in each grid (no grid is shown if no record exists at the locality). Under the map, a taxonomic tree and dataset list in BISMaL are shown, and the list of occurrence records is displayed below them.
You may search and filter records by setting geospatial areas in the map, selecting taxa in the tree and/or specifying datasets. Records are also filtered and sorted in the list of occurrence records.

Setting geospatial areas

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Click the "area-setting" icon under the "zooming" icon on the upper left in the map. By clicking and dragging on the map, a rectangle is drawn on the map, and grids inside the rectangle are highlighted. You may set more than 2 rectangles. In the case, current rectangle is highlighted by yellow frame.

In the "Rectangles" window, displayed by clicking "+" button on the right of the "Rectangles" in the window on the right of the map, minimum and maximum values of latitude and longitude covered by the current rectangle are shown in text boxes. You may directly edit those values to modify the area covered by the rectangle. In the lower part of "Rectangles" window, icons indicating rectangles on the map are shown. The color of each icon corresponds to that of a rectangle on the map. You may set a rectangle inactive by checking off the checkbox on the left corner of the corresponding icon or delete a rectangle by clicking "x" on the right corner of the corresponding icon.

You may find a polygon list including typical marine areas around Japan in the "Regions" window (click "+" button on the right of the "Regions" in the window on the right of the map, then the “Regions” window will be expanded). You may set an area on the map by clicking the checkbox of your favorable area listed in the polygon list. Then, grids involved in the polygon will be highlighted on the map.

Each color of grids indicates the number of records involved in the grid. It is shown in the "Legends" window displayed by clicking "+" button on the right of the "Legends" in the window on the right of the map.

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By clicking a grid on the map, a balloon will appear. Coordinates (latitudes and longitudes) of the grid and information of records involved in the grid (numbers of records and taxon) are shown in the upper and lower parts, respectively, in the balloon. If you click the blue text string "Add to Rectangles", a rectangle covering the grid will be drawn on the map and added to the "Rectangles" window.

Selecting taxa

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A hierarchical taxonomic tree is shown under the map described above, and you may filter records by selecting taxa in the tree. You may explore the tree by expanding or collapsing lower taxa. Click the triangles on the left of any taxon name to see its lower taxa. Check/uncheck checkboxes on the left of taxon names to select/unselect occurrence records of your favorable taxa. Your operation will be reflected on the map above the tree. Please note that all taxa are selected by default and that lower taxa are selected/unselected if its higher taxon is checked/unchecked.

Specifying datasets

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A dataset on BISMaL is a group of occurrence records sharing a same institution code and collection code. You may specify one or more datasets to filter records before your browsing and downloading records.
On the right side of the taxonomic tree, you may find a list of datasets registered to BISMaL. In the dataset list, dataset names as well as the numbers of taxa and records involved in each dataset are shown. Check or uncheck checkboxes on the left of dataset names to select or unselect datasets. Each name of a dataset works as a link to move to the portal page of that dataset.

Occurrence records

Details of occurrence records of organismsImage Description
Occurrence records filtered by rectangles/regions on the map, taxon and datasets are listed on the bottom of the page. You may browse each record information, sorting and filtering records.
In the list of occurrence records, basic information of each record such as its identification (e.g. Institution code + collection code + catalog number), scientific name (*1), basis of record (*2), coordinates (latitude and longitude), locality, depth, etc. will be shown. Click each ID (the linked blue texts) to view each record’s detailed information.
*1: synonyms may be included. The "scientific name" field of BISMaL follows the scientific name attached to each occurrence record which came from different data sources/data providers.
*2: "Basis of record" are abbreviations which stand for, observation (O), a specimen in a collection (S), a collected living organism (L), a collected germplasm/seed (G), a photograph (P), a record derived from literature where original basis unknown (D).
Sorting and filtering in the list of occurrence recordsImage Description
You may sort and filter records to find particular records in the list of occurrence records. To sort records, click a column title in the list. To filter records, input a string or select an option in each box under column title and then click the "Apply filter" button above the list. Click the "Clear" button on the right of the "Apply filter" button to cancel the filtering.