Semantically Aggregating Marine Science Data

Developing data aggregation applications from a community

standard semantic resource

Adam Leadbetter & Roy LowryBritish Oceanographic Data Centre

alead@bodc.ac.uk & rkl@bodc.ac.uk

Outline• A little history• The EMODnet use case• The NERC Vocabulary Server solution• Conclusions

A Little History

A Little History

A Little History

The EMODnet Use Case• Semantic aggregation:

1. Deciding what the aggregated parameter is (and what it is to be called)

2. Deciding which “Parameter Usage Vocabulary” codes are to be included in the aggregated parameter

3. Providing this information to the aggregation software

4. Aggregating the data

The NERC Vocabulary Server solution

• Two fold:

•Develop semantic aggregation work from other projects

•Expose the underlying semantic model beneath the “BODC Parameter Usage Vocabulary (P01)”

The NERC Vocabulary Server solution

• RDF/XML driver file always accessible from the URL of the aggregation parameter

• Application software could either call the URL in real time or cache the knowledge base

• Governance simply(!) supplies agreed aggregation names and their mappings to P01

• BODC keeps governance informed of additions to P01 so mappings can be kept up to date.

http://vocab.nerc.ac.uk/collection/P25/current/

NETMAR Aggregation / Validation

Latitude

Depth

Temperature

Salinity

Sea Water Density

Calculation

http://netmar.nersc.no

NETMAR Aggregation / Validation

Latitude

Depth

Temperature

Wave period

Sea Water Density

Calculation

http://netmar.nersc.no

The NERC Vocabulary Server solution

Concentration of tributyltin cation {tributylstannyl TBT+ CAS 36643-28-4} per unit dry weight of biota {Mytilus

galloprovincialis (ITIS: 79456: WoRMS 140481) [Subcomponent: flesh]}

http://vocab.nerc.ac.uk/collection/P01/current/MMUSDTBT/

The NERC Vocabulary Server solution

Concentration of tributyltin cation {tributylstannyl TBT+ CAS 36643-28-4} per unit dry weight of biota {Mytilus

galloprovincialis (ITIS: 79456: WoRMS 140481) [Subcomponent: flesh]}

The NERC Vocabulary Server solution{"measurement":"Concentration", "substance": {

"primaryName":"tributyltin cation","synonym":["tributylstannyl","TBT+"],"CAS":"36643-28-4"},

"measurementMatrixRelationship":"per unit dry weight of the", "matrix":"biota", "organism": {

"taxon":"Mytilus galloprovincialis","aphiaID":"140481","name":"unspecified ","gender":"unspecified","stage":"unspecified","part":"flesh","specifics":"unspecified"},

"technique":"unspecified", "definition":"Unavailable"}

The NERC Vocabulary Server solution

P01 URI

MarineSpecies

S25 URI

The NERC Vocabulary Server solution

Substance Or Taxon

Property Kind

MarineSpecies

P01 URI

S25 URI

The NERC Vocabulary Server solution

Substance Or Taxon

Property Kind

P01 URI#organism

#substance

ChEBIMarineSpecies

The NERC Vocabulary Server solution

Substance Or Taxon

Property Kind Matrix Technique

P01 URI#organism

#substance#matrix #technique

ChEBIMarineSpecies

https://github.com/adamml/semantic_model

Benefits• Easily integrated into software

• Ocean Data View • SISSVoc • Drupal

• Fits the Linked Data model• Which we’ve been exploring with:• Biological & Chemical Data Management Office• Chandler et al. IN52B-05• Rolling Deck to Repository• Arko et al. IN53C-1574• and others http://odv.awi.de/

https://www.seegrid.csiro.au/wiki/Siss/SISSVochttp://linked.bco-dmo.org/

http://linked.rvdata.us/

Benefits

Benefits

Journal of Ocean Technology 8(3):7-12https://github.com/adamml/LinkedOceanDataCloud

Summary• NERC Vocabulary Server• Existing NVS uses allow for semantic

aggregation of data• But lacking ability to discover which concepts

can be marked up• This will be achieved by exposing the

underlying semantic model• Collaboration through Ocean Data Interoperability

Platform (ODIP)• Glaves and Schaap IN53D-1598• Compatible with CSIRO work (Cox et al., IN52B-08)

alead@bodc.ac.uk & rkl@bodc.ac.uk