By Nicholas Car

This document is a short overview of the Australian Biodiversity Information Standard (ABIS). It is only one of many parts of the ABIS and all the parts are defined in the ABIS Standard Definition.

1. What is ABIS?

ABIS is a data standard that specifies how information about biodiversity is to be represented for exchange and use in Australia.

It is a technical data standard and mandates a specific form of machine-readable information representation: RDF (Resource Description Framework). RDF is "a standard model for data interchange on the Web"[1], so ABIS data is machine-readable and able to be sent between users over the web.

Use of the ABIS results in biodiversity information being formulated into data that can be validated against ABIS requirements in an automated way and the standard provides validators (see How do I use it?).

ABIS models domain-specific concepts itself but mostly re-uses existing models. ABIS Parts describes them.

1.1. ABIS Parts

ABIS draws on multiple, existing, domain standards for many of its parts. For example, ABIS requires use of the TERN Ontology for the representation of Sampling, Samples, Sites and most aspects of filed sampling. Another example: the Open Geospatial Consortium's GeoSPARQL Standard must be used to represent spatial information.

The figure below shows the parts of ABIS and the list following it describes what they are all for.

ABIS Parts
Figure 1. The main part models within ABIS

Darwin Core Terms, GeoSPARQL and SOSA are international standards for biological, spatial and observations data respectively. The TERN Ontology, which uses all three of them, is a domain model about sampling and surveying created by the Terrestrial Ecosystems Research Network and the ABIS Data Management Ontology provides additional properties for system management of TERN data.

2. How do I use it?

The main things you can do with ABIS are:

  • Create

    • you can create data that conforms to ABIS

  • Validate

    • check that the data you’ve created is actually valid by applying a validator to it

  • Exchange

    • exchange ABIS data with organisations/systems that are designed to accept it, such as the Biodiversity Data Repository (BDR).

2.1. Create

ABIS data must be in an RDF fomat. RDF is a data model for expressing graphs - nodes of information related by defined types of edges - and there are several different formats that can be used for RDF. All are technically equivalent but different forms suite different people.

Perhaps the best way to start is to consider this small example data about an observation.

2.1.1. Example - tree width observation

This observation is a tree in at Site X.

Observation ID Long Lat Time Site Parameter Result Observer

4321

115.01

-33.86

21/09/23, 2:02:03pm

Site X

Trunk diameter at chest height

142±5cm

J. Bloggs

We have an Observation - an ABIS class of thing - with ID 4321, taken at a location, (115.01, -33.86), and at a particular time. Site is also something known to ABIS - see the TERN Ontology’s Site class definition.

We need to do a couple of things before turning this data into ABIS data:

  1. Conceptual split

    • we need to place information about the observation, the values obtained, the site and so on into the conceptual model of ABIS

    • the TERN Ontology separates an observation into the act of observing and resulting data from the act: - an Observation and a Result - and also splits the type of thing observed - the parameter, an Observable Property - from the method used - a Procedure

    • ABIS also knows about a "Site", so for this data we have:

      • an Observation - the thing identified with 4321

      • a Result - the value 42±5cm

      • an Observable Property - the parameter observed - here tree trunk diameter

      • a Procedure - the method used to obtain the result, see Reference Object ID below

      • a Site - the named location the Observation took place at

      • and a Person - the observer

  2. New Object IDs

    • we need to use IRIs to identify all new information defined in this data

    • this is the Observation and many of the things listed above

    • these need to be universally unique web addresses, like https://linked.data.gov.au/dataset/bdr/eg/sample/4324, not just simple IDs like 4321

  3. Reference Object IDs

    • we need to ensure that any objects referenced used are identified not in text but also using IRIS

    • reference objects like Procedure should be listed in published vocabularies

    • some reference objects like Person are IDed with IRIs via other initiatives, such as ORCID

    • some objects could be new in this data or reference objects created previously, such as a Site

For the first point, we need to either get a namespace for IRIs assigned to us for use for new objects - this is what the BDR team will do if you are registered to send ABIS data to the BDR, but you can use other IRI systems if you are using ABIS data for other purposes. Here we will just use http://example.org/ for demonstrating.

Say we use the IRI http://example.com/obs/4321 for the observation, http://example.com/site/x for Site X and https://orcid.org/0000-0000-1234-5678 for the person who made the observation - perhaps the person is a scientist using an ORCID to identify themselves in their publications - then we can make the following RDF, in the Turtle format:

PREFIX geo: <http://www.opengis.net/ont/geosparql#>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX sdo: <https://schema.org/>
PREFIX sosa: <http://www.w3.org/ns/sosa/>
PREFIX tern: <https://w3id.org/tern/ontologies/tern/>
PREFIX void: <http://rdfs.org/ns/void#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

<http://example.com/obs/4321>
    a tern:Observation ;
    prov:wasAssociatedWith <https://orcid.org/0000-0000-1234-5678> ;
    sosa:hasFeatureOfInterest <http://example.com/site/x> ;
    sosa:observedProperty <http://linked.data.gov.au/def/tern-cv/a3ad8f31-6896-416e-8ac6-bc61b93aaab5> ;
    sosa:usedProcedure <http://linked.data.gov.au/def/tern-cv/a3a41c41-f74e-48ec-b11c-78de3c99ce35> ;
    sosa:hasResult [
        a tern:Float ;
        rdf:value 142.0 ;
        tern:unit <https://qudt.org/vocab/unit/CentiM> ;
        tern:uncertainty 5 ;
    ] ;
    sosa:resultTime "2020-09-21T14:02:03"^^xsd:dateTime ;

    void:inDataset <http://example.com/dataset/123> ;
    geo:hasGeometry [
        geo:asWKT "POINT(115.01, -33.86)"^^geo:wktLiteral
    ] ;
.

<http://example.com/site/x>
    a tern:Site ;
    geo:hasGeometry [
        geo:asWKT "POLYGON(115 -33, 115 -34, 116 -34, 116 -33, 115 -33)"^^geo:wktLiteral
    ] ;
.

<https://orcid.org/0000-0000-1234-5678>
    a sdo:Person ;
    sdo:name "Joe Bloggs" ;
    sdo:email "joebloggs@hotmail.com"^^xsd:anyURI ;
.

In the data above, the Observation is:

<http://example.com/obs/4321>
    a tern:Observation ;
    # a series of other properties ..
.

There are many other examples of ABIS data in the Specification and also in tools that 'talk' ABIS, for example the BDR Gateway: https://gateway.bdr.gov.au.

To test, you may want to create RDF data files by hand, however, for automated production of ABIS data, you should use any one of very many RDF generation tools - just search for them!

Note also that systems to convert non-RDF data to ABIS RDF have been established as part of the Biodiveristy Data Repository project, see https://submission.bdr.gov.au.

2.2. Validate

You can validate RDF data files against any or all of the validators for its part models using a SHACL validation tool. SHACL is a graph validation language and SHACL tools apply validators to data and report pass/fail and, if fail, error messages.

A free, online, SHACL validation tool that allows you to select from stored validators or add your own validator is:

All the ABIS validators are pre-loaded into the BDR Gateway and you may submit data to the Gateway’s validation endpoint which is set up for testing. There are many pre-loaded valid and invalid examples of data there too to play with.

2.3. Exchange

If you have ABIS data that you want to submit to an ABIS system, you can do so by sending it in to the system in an automated way. For the BDR, you will need to have been issued with a BDR account and then you can send data to the BDR Gateway. The BDR is not the only system that undertstands ABIS data and other may accept submissions in other ways.

3. Who owns it?

ABIS is owned by AusBIGG, the Australian Biodiversity Information Governance Group. That group is supported by the Department of Agriculture, Water and the Environment.

4. How do I improve it?

Either contact AusBIGG or make direct contributions agains the ABIS repository that contains all of its source files:

Submissions agains ABIS will be reviewed in regular AusBIGG meetings and AusBIGG members will vote on their acceptance.

5. More help

Please be in contact with AusBIGG or read the ABIS Specification.

1. https://www.w3.org/RDF/