Why we need a semantic web frameworkfor marine ecos stem indicatorsfor marine ecosystem indicators

Stace E. Beaulieu (stace@whoi.edu) and Andrew R. MaffeiWoods Hole Oceanographic Institution

P t A F M i Di St f P t i k W t d X M h ll MPeter A. Fox, Massimo Di Stefano, Patrick West, and X. Marshall MaTetherless World Constellation, Rensselaer Polytechnic Institute

Jonathan A Hare Michael FogartyJonathan A. Hare, Michael Fogarty, Kim Hyde, and Sean LuceyNOAA Northeast Fisheries Science Center

ECO-OP is supported byECO OP is supported by NSF Interop #0955649

Ocean Sciences Meeting 2014 1

What is an ecosystem indicator?“based on

IdentifyDevelop 

monitoring &

based on verifiable data [and] conveys

i f tiDevelop conceptual model

Identify management objectives & 

targets

monitoring & reporting systems

information about more than itself”

Communicate and interpret Calculate 

indicators

Gather & review 

Identify possible 

Test & refine indicators with 

Determine key questions & 

indicatorsindicatorsdataindicators stakeholdersindicator use

Diagram and quote modified from:Identify & consult stakeholders/ 

Biodiversity Indicators Partnership (2011)http://www.bipindicators.net

audience

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 2

An ecosystem indicator is BigData

IdentifyDevelop 

monitoring &

‐Dataheterogeneity

data

Develop conceptual model

Identify management objectives & 

targets

monitoring & reporting systems

‐ Data integration‐ Provenance

Communicate and interpret Calculate 

indicators

data

Identify possible 

Test & refine indicators with 

Determine key questions &  data

data

indicatorsindicatorsindicators stakeholdersindicator use

data

Identify & consult stakeholders/  Indicator may not have same meaning asaudience

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future

‐Indicator may not have same meaning assource data

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Why we need a semantic web frameworkfor marine ecos stem indicatorsfor marine ecosystem indicators

“Web of data”Web of data

‐ Uses Linked Data standards

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future

‐ Uses Linked Data standards‐ Knowledge base currently describes 3.22 million things in an ontology

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Large Marine Ecosystems (LMEs) of the World

U.S. Northeast ShelfNortheast ShelfLME

http://www.lme.noaa.gov/LMEWeb/downloads/lme_biomass.pdf

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 5

Use Case: Ecosystem Status Report for the LME

Goal: “traceability, repeatability, explanation, verification, and validation” for ecosystem data and information products in the NEFSC Ecosystem Status Reportin the NEFSC Ecosystem Status Report Indicators

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 6

Example Indicator #1: Primary Production

Similar data product from another groupthat also provides indicators for the LME

Figure in Report

http://www.seaaroundus.org/lme/7.aspx 

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future

Why different? I manually determined the provenance …

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Diagram of source datasets “funneling”into deri ed data prod ctinto derived data product

Person who generated 

the indicator

Source data from different

Derived Dataset used in different 

providers Figure in Report

Process Steps at eachSteps at each 

arrow

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 8

Provenance: the history, or lineage,to trace deri ed data prod cts back to so rce datato trace derived data products back to source data

Person who generated 

the indicator

Source data from different

? ? ?

Derived Dataset used in?

different providers

used in Figure in Report

Chl‐a Primary SST

yproduction

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 9

“Semantic provenance”domain-specific ontologies considered

Linked Ocean Data

GCMD

https://github.com/adamml/LinkedOceanDataCloud/blob/master/linkedOceanDataCloud.jpg

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 10

Adopt PROV-O: Linked Data provenance ontology pro ides domain

E tit

- provides domain-independent classes and properties

EntitySubclass: Dataset

- can be extended to create domain-specific classes and properties

Person who generated 

the indicator

http://www.w3.org/TR/prov‐o/ W3C Recommendation 30 April 2013

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 11

PROV-O adopted for Global Change Information System(GCIS)

GCIS ontology

(GCIS)

Key Message linked to Dataset

PROV ontology

Key Message linked to domain concept

http://cmapspublic3.ihmc.us/rid=1L2W4LDNM‐D80T3Z‐10N0/GCIS%20report‐specific%20key%20messages.cmap

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 12

Extension of GCIS ontology for ECO-OP use case

But what was missing from GCIS ontology?

ActivityDataset generation: “crux” of the

ActivitySubclass:DatasetGeneration

ECO‐OP use caseGeneration

PROV‐ES:Earth Science Provenance Ontology working group

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future

Earth Science Provenance Ontology working groupis testing subclasses of this activity

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Prototype using IPython Notebook

Can we automate the capture of machine‐readable, provenance metadata, while

Source Dataset

provenance metadata, while the scientist is generating the indicator?

EntitySubclass: Dataset

ActivityActivitySubclass: IPythonNotebookRun

Dataset generation

Manual:Dataset matched (dc:subject) to a concept in Linked Oceanto a concept in Linked Ocean Data vocabulary (skos:Concept)

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 14

Example Indicator #2: North Atlantic Oscillation

We used IPython Notebook to reproduce the Chapterto reproduce the Chapter on Climate Forcing in the Ecosystem Status Report

http://tw.rpi.edu/web/doc/AGUFM/2013/ReproducibilityInOceanSciences

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 15

Bring provenance tracking to the scientist

Source Dataset

DataData processing

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 16

Screenshot of IPython Notebook used to track provenance

http://ipython.org/

‐ Notebooks are formatted as JSON files

‐We are currently coding theWe are currently coding the provenance triples to JSON‐LD (lightweight Linked Data format)

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 17

Specific outcomes of ECO-OP use case

1) Implement PROV provenance capture for derived dataset in IPythonNotebookNotebook

2) Extend GCIS ontology to include the activity of dataset generation, and provide testbed for PROV ES granularity of this activityprovide testbed for PROV‐ES granularity of this activity

3) Establish best practices for semantic annotation of derived dataset in Integrated Ecosystem Assessment

DiscoveryUnderstandinggRe‐usabilityData Integration

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 18

Why we need a semantic web frameworkfor marine ecos stem indicatorsfor marine ecosystem indicators

Future work

ECO‐OPuse case

http://linkeddatadeveloper.com/Projects/Linked‐Data/media/fig11.2.png• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 19

Ecosystem‐based management involves the sharing of data and information products among diverse stakeholders

Can an intelligent agent find the overlap infind the overlap in datasets used in marine ecosystem assessments?

http://www.iucnredlistofecosystems.org/http://www.oceanhealthindex.org/

• Motivation • Use Case • Adopt ontologies • Evaluate prototype • Future 20

http://tw.rpi.edu/web/project/ECOOP

Peter FoxPatrick West,Massimo Di Stefano,M h ll M

Jon Hare,Mike Fogarty,Kim Hyde,S L

Andy MaffeiJoe FutrelleCyndy Chandler

Marshall MaLinyun Fu,Jin Zheng

Sean Lucey,Geret DePiper

ECO-OP is supported by

Thanks!

ECO OP is supported by NSF Interop #0955649

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