How to find information about biodiversity in OpenBiodiv?

There are four approaches for exploration of data stored in the graph:

General search

The general search is available on the homepage of OpenBiodiv and allows exploration of the knowledge graph based on key terms like taxonomic names, persons, articles. The user only needs to type the name of an entity of interest belonging to one of the above-mentioned types and the system finds information about it. Misspelling the name is not a problem because the Elasticsearch index supports fuzziness for maximum edit distance allowed for matching. It can also automatically determine the semantic type of the searched entity.

User applications

Literature exploration

This application is designed to answer the following general question: Find me information about an entity mentioned within a certain article section in OpenBiodiv. The results will show the number of mentions of this entity (e.g. taxonomic name) in each section of interest (e.g. Titles (X), Abstracts (Y), Treatments (Z), etc.) and aggregated by articles.

By clicking on the hyperlinked number, the user is redirected to the article section where that entity is mentioned.

A simple graphic representation of the information, for example, about Element X mentioned in Y titles and Z abstracts (plot comparison) illustrates the distributions of the element in the searched sections.

In addition to being visualised in the web page, the results can be exported to a CSV file for further use.

Co-occurrences

This application extends the functionality of the Literature exploration app by adding two or more data elements (named entities), e.g. taxon names, sequences, specimens, specific terms, etc. to be searched together within a given context. For example, some possible questions are:

Give me article sections or taxon treatment sections where Data element 1 and Data element 2 are mentioned together, e.g.:

Taxon name A & Taxon name B
Sequence C & Taxon name Y
Taxon name X & Treatment Y

External links

The basic aim of this data discovery application is to search, discover and display data available from trusted external resources, for example specimens, collections, sequences, taxon names, literature, persons and others. The element of interest may be present also in OpenBiodiv.

This service is available also as a an additional step to other apps. For example, when one is making a bibliographic exploration about a certain named entity, it could have the option to ask for additional information about that entity available from external resources.

The data records and their identifiers obtained as a result of the search across various resources can be stored as CSV file or RDF using the SCOR ontology.

Alerts

OpenBiodiv performs a number of queries at regular intervals to generate reports and send these to the users subscribed to the RSS & E-mail Alert service. The queries can deliver for example:

• All mentions of specimens from a collection or institution based on either citations of a particular collection/Institution code or use of specimen identifiers in the examined materials (material citations).
• All taxon treatments (new taxa, re-descriptions, nomenclatural changes and others) published within a particular taxon.
• All newly published literature that mentions a certain taxon or other named entity of interest (e.g. sequence).