About BISMaL data

What kind of data does BISMaL have?

The data of BISMaL can be roughly divided into two components, "occurrence records" and "taxon metadata".

Occurrence records of organisms

Occurrence records include information of "when" and "where" the organism was collected or was observed, and is the most important component of data on BISMaL. Occurrence records are stored on BISMaL in a "DarwinCore" format. DarwinCore is a data standard to exchange information of biological specimens and enables us to handle a wide variety of data elements: scientific name of organisms, date and locality that collection/observation occurred, name of person who identified the specimen, data source, citation etc. BISMaL can handle data elements involved in the OBIS extension of DarwinCore, and some additional elements involved in DarwinCore1.4 draft standards. In using BISMaL, you may browse detailed occurrence records in DarwinCore format, browse a distribution map based on occurrence records of each taxon. You may also download the occurrence records themselves. Please follow the instructions in "How to use BISMaL" and learn how to use BISMaL.

Taxon metadata

Taxonomic information
BISMaL holds information about scientific names of taxonomic groups of organisms. Valid names as well as invalid names are registered to BISMaL and hierarchically arranged following the Linnean classification system. The name information is essential for BISMaL to bind and display occurrence records, including different names (synonyms) of a taxon, in each taxon page. Recognition of a valid or invalid name and a taxonomic status of an organism are based on scientific publications in taxonomy (details of quality control may be found here). However, the taxonomic status and the validity of a scientific name of a taxon are sometimes unstable and may differ from researcher to researcher. On BISMaL, valid and invalid names of taxa have an aspect of operational units to handle data in the system. Please note that absolute taxonomical/biological accuracy on the taxonomic information in BISMaL is not assured. To treat a taxonomically uncertain group, BISMaL uses "(unranked)" or "(uncertain)" instead of a taxonomic rank such as Phylum, Class or Order. "(Unranked)" is used for a taxonomic group when its taxonomic rank/position is not specified in the classification system. In many case, "(unranked)" is used with the term of "incertae sedis" in BISMaL. When validity of a taxonomic group cannot be determined based on scientific publications, BISMaL assign "(uncertain)" to the group. A type of synonym is indicated after the synonymized name. The following table shows types of synonyms used in BISMaL.
Junior Synonym Of two synonyms (synonym: different scientific names which denote the same taxon), the later established name
Junior Homonym Of two homonyms (homonym: a name spelled exactly like another name published for a taxon), the later established name
Alternate Representation Different representation which is taxonomically acceptable (e.g.; names with and without subgenus)
Spelling Variation Orthographic variant including incorrect spelling or variation caused from agree/disagreement in Latin grammatical gender
A combination of the above types is also used.
Selected photographs and descriptions of organisms
Using BISMaL, you can browse selected photographs and descriptions including morphological characters, ecological trait of each taxon or other kinds of information. Although selected images and descriptions are currently restricted to a small amount of total taxa, we are planning to intend them. If a taxa is listed on the Red List of the Ministry of the Environment Government of Japan, its red list category is indicated at the item of the Red List status.
Red lists:
Ministry of the Environment Government of Japan (2015)【哺乳類】環境省レッドリスト2015. Accessed through: Ministry of the Environment website, 環境省レッドリスト2015の公表について, Attachment 4 at http://www.env.go.jp/press/files/jp/28083.pdf on 2017-09-29 (in Japanese).
Ministry of the Environment Government of Japan (2012) [Birds] The 4th Version of the Japanese Red List (2012). Accessed through: Ministry of the Environment website, 第4次レッドリストの公表について (お知らせ), Attachment 7-2 at http://www.env.go.jp/press/files/jp/20551.pdf on 2017-9-29 (in Japanese).
Ministry of the Environment Government of Japan (2012) [Reptiles] The 4th Version of the Japanese Red List (2012). Accessed through: Ministry of the Environment website, 第4次レッドリストの公表について (お知らせ), Attachment 7-3 at http://www.env.go.jp/press/files/jp/20552.pdf on 2017-09-29 (in Japanese).
Ministry of the Environment Government of Japan (2013) [Brackish-water / Freshwater Fishes] The 4th Version of the Japanese Red List (2013). Accessed through: Ministry of the Environment website, 第4次レッドリストの公表について (汽水・淡水魚類) (お知らせ), Attachment 7 at http://www.env.go.jp/press/files/jp/21437.pdf on 2017-09-29 (in Japanese).
Ministry of the Environment Government of Japan (2012) [Insects] The 4th Version of the Japanese Red List (2012). Accessed through: Ministry of the Environment website, 第4次レッドリストの公表について (お知らせ), Attachment 7-5 at http://www.env.go.jp/press/files/jp/21555.pdf on 2017-09-29 (in Japanese).
Ministry of the Environment Government of Japan (2012) [Shellfish] The 4th Version of the Japanese Red List (2012). Accessed through: Ministry of the Environment website, 第4次レッドリストの公表について (お知らせ), Attachment 7-6 at http://www.env.go.jp/press/files/jp/20555.pdf on 2017-09-29 (in Japanese).
Ministry of the Environment Government of Japan (2012) [Invertebrates] The 4th Version of the Japanese Red List (2012). Accessed through: Ministry of the Environment website, 第4次レッドリストの公表について (お知らせ), Attachment 7-7 at http://www.env.go.jp/press/files/jp/20556.pdf on 2017-09-29 (in Japanese).
Ministry of the Environment Government of Japan (2012) [Plants I] The 4th Version of the Japanese Red List (2012). Accessed through: Ministry of the Environment website, 第4次レッドリストの公表について (お知らせ), Attachment 7-8 at http://www.env.go.jp/press/files/jp/20557.pdf on 2017-09-29 (in Japanese).
Ministry of the Environment Government of Japan (2012) [Plants II] The 4th Version of the Japanese Red List (2012). Accessed through: Ministry of the Environment website, 第4次レッドリストの公表について (お知らせ), Attachment 7-9 at http://www.env.go.jp/press/files/jp/20558.pdf on 2017-09-29 (in Japanese).
Playing movies & viewing images
JAMSTEC holds video and image records captured by manned/unmanned submersibles during their investigations, and those movies and images of deep-sea organisms are opened to public through the JAMSTEC E-library of Deep-sea Images. There will be a video/image list attached to each taxon if it was taken by cameras during JAMSTEC's deep sea researches, so you may find and play the movies and view images through BISMaL. Please read "How to use BISMaL" for details about playing movies and viewing images on BISMaL.
Literature
Useful publications and references of names and descriptions of each taxon are registered to BISMaL to specify the source of information. Users may check those publications and references in each taxon page on BISMaL.

Quality control of data

Occurrence records

To maintain reliability and quality of data registerd in BISMaL, we continuously check occurrence records of organisms and correct misspelling, discrepancy in georeferences, incorrect dates, etc. However, discrepancies and data errors potentially take place on BISMaL as they do in any publication. Thus, the quality control guideline mentioned above does not assure the absolute correctness of data on BISMaL. User peer-review and any feedback on data quality will be beneficial to BISMaL. Please contact the BISMaL operating team if you find any problems or errors. Your cooperation would be greatly appreciated.

Taxonomic information and description of each organism

After checking and compilation based on scientific data sources (literature and authorized databases such as WoRMS) and advices by authorities in related fields, taxonomic information will be registered to BISMaL. Invalid names of organisms will be registered if it is necessary for BISMaL to handle its data. Data sources of each taxon are registered to BISMaL, and users are able to check them on the Literature tab on the bottom part in each taxon page.
Researchers sometimes have different opinions on classifications and names of organisms. Those issues should be solved through discussions on taxonomy and systematics. Therefore, absolute correctness of taxonomic information on BISMaL is not assured. Please note that recognition of valid names and appropriate classification of organisms may sometimes differ from researcher to researcher, and are also changeable due to following advances in related fields.

Use of data

BISMaL does not control or limit any non-commercial use of any kind of data accessible through its website. As a matter of common courtesy, we recommend our users to contact and inform each data provider as possible in use or translation of BISMaL data for presentations or publications. Please email the BISMaL operating team if the data provider of any data is uncertain. Users who wish to use BISMaL data for commercial purposes must ask the BISMaL operating team for permission.
Users should be aware of possible errors, including in the use of species names, geo-referencing, data handling etc. JAMSTEC, who manages BISMaL, and the data providers of BISMaL are not responsible for such potential errors or for the results of use or translation of those data. Additionally, please read the descriptions in J-OBIS website for data published through BISMaL.
Appropriate caution and background knowledge about marine biodiversity is required to use, translate or analyze the data provided through BISMaL.

Copyright and ownership of data

Copyright and ownership of data/dataset, including photographs, movies, collection/observational records or etc., provided through BISMaL is attributed to the original data provider. Data providers may be displayed under photographs and/or in the "Source" elements in occurrence records. Please contact the BISMaL operating team if any data provider of a data is uncertain.

Citing data and BISMaL

We recommend users to cite and to acknowledge the data provider in using any data or dataset published through BISMaL. Users may find a form to cite the data provider in the "Citation" field of each data. Please check this field at first when citing a data/dataset that you have used.
BISMaL asks you to use the following prescribed form to refer BISMaL itself:

Japan Agency for Marine-Earth Science and Technology (2009 onwards).
Biological Information System for Marine Life at
http://www.godac.jamstec.go.jp/bismal/. Accessed on yyyy-mm-dd.