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Developing data aggregation applications from a community standard semantic resource Adam Leadbetter & Roy Lowry British Oceanographic Data Centre [email protected] & [email protected]

Semantically Aggregating Marine Science Data

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Presented at the American Geophysical Union Fall Meeting 2014 (8th - 13th December) in San Francisco.

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Page 1: Semantically Aggregating Marine Science Data

Developing data aggregation applications from a community

standard semantic resource

Adam Leadbetter & Roy LowryBritish Oceanographic Data Centre

[email protected] & [email protected]

Page 2: Semantically Aggregating Marine Science Data

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

Page 3: Semantically Aggregating Marine Science Data

A Little History

Page 4: Semantically Aggregating Marine Science Data

A Little History

Page 5: Semantically Aggregating Marine Science Data

A Little History

Page 6: Semantically Aggregating Marine Science Data

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

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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)”

Page 8: Semantically Aggregating Marine Science Data

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/

Page 9: Semantically Aggregating Marine Science Data

NETMAR Aggregation / Validation

Latitude

Depth

Temperature

Salinity

Sea Water Density

Calculation

http://netmar.nersc.no

Page 10: Semantically Aggregating Marine Science Data

NETMAR Aggregation / Validation

Latitude

Depth

Temperature

Wave period

Sea Water Density

Calculation

http://netmar.nersc.no

Page 11: Semantically Aggregating Marine Science Data

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/

Page 12: Semantically Aggregating Marine Science Data

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]}

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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"}

Page 14: Semantically Aggregating Marine Science Data

The NERC Vocabulary Server solution

P01 URI

MarineSpecies

S25 URI

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The NERC Vocabulary Server solution

Substance Or Taxon

Property Kind

MarineSpecies

P01 URI

S25 URI

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The NERC Vocabulary Server solution

Substance Or Taxon

Property Kind

P01 URI#organism

#substance

ChEBIMarineSpecies

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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

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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/

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Benefits

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Benefits

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

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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)

[email protected] & [email protected]