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deepcarbon.net
Xiaogang Ma, Patrick West, John Erickson, Stephan Zednik,
Yu Chen, Han Wang, Hao Zhong, Peter Fox
Tetherles...
Outline
• Deep Carbon Observatory
• Deep Carbon Virtual Observatory (DCvO)
– Architecture of DCvO
– DCO Ontologies
– Bound...
A 10-year (2009-2019) initiative to intensify
global attention and scientific effort in the
burgeoning field of deep carbo...
• Faculty, staff and students from the Tetherless
World Constellation (TWC) at Rensselaer
Polytechnic Institute (RPI)
• Re...
Deep Carbon Virtual Observatory
Scientists – actually ANYONE - should be able to access a
global, distributed knowledge ba...
Deep Carbon Virtual Observatory
• A vision of the DCvO:
– A conceptual model of the interplay between data, people,
public...
DCvO “Architecture”
7
vivo.cornell.edu
VIVO - represents
academic research
communities
DCO ontology:
a model for concept types and relationships...
Ontologies and schemas
used in the DCO web portal
9
Name Prefix
Dublin Core Metadata Element Set dc
DCMI Metadata Terms dc...
Ontologies and schemas
used in the DCO web portal
10
DCO Boundary Activities are driving the extensions
within the DCO Ont...
DCO Extension for Project Updates
11
12
Dynamically generated list of Grants
that are part of the Deep Carbon
Observatory. Users can click through to
learn mor...
13
Grant page lists all projects and
reporting updates for each of the
projects and field studies
DCO Extension for Data Types
14
15
A Few Boundary Activities
• Given a DOI pull publication information from CrossRef
and/or Web of Science
• DCO IGSN All...
Modern informatics enables a new scale-free
framework approach
• Use cases
• Stakeholders
• Modeling
• Ontologies
• Evalua...
What does a DCO data
publication look like?
17
18
Identification and annotation
Information on the landing
page of a dataset
19
Linking to enable forward and backward tracking
Landing page of Helium Concept
20
Landing page of a
person
Linking to build Collaborations
21
Landing page of a
research area
Linking to build Collaborations
22
DCO Knowledge Graph Analytics
Thus… progress…
• Integrative – semantics
• Transparent – semantics
• Collaborative – semantics
• Application integration
...
Thank you!
24
Patrick West, westp@rpi.edu, https://deepcarbon.net, http://tw.rpi.edu
25
An integrated portal: deepcarbon.net
26
Faceted
publication
browser
Repository for archiving datasets
Archived datasets of ‘Noble
gas isotope abundances in
terrestrial fluids’
27
Collaboration tools
Group Based CollaborationGroup data
deposit and
reporting
Listings of
group content
Group
management
a...
29
RDA DTR and PIT adoption
The DTR
primitives are
comparable
to a list of
BASIC DATA
TYPE CLASSES
in the DCO
ontology, e....
Results of data type specification
• Updates to the DCO Ontology:
– A new class dco:DataType. Each specific data type is a...
31
• New datasets available via dataset browser
• Includes citations to the originating publication
• Data files accessibl...
32
DCO Knowledge Store Analytics
33
DCO Knowledge Store Visualizations
All information is linked and traceable!
34
Mediation
From: C. Borgman, 2008, NSF Cyberlearning Report, Illustration by Roy Pea and Jillian C. Wallis
6th
Generation
A...
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From data portal to knowledge portal: Leveraging semantic technologies to support interdisciplinary studies

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Scientific research practices regularly adopt new technologies and platforms in an effort to increase information timeliness, sharing and discoverability. There are many initiatives related to open data, open code, open access, open collections, composing the topic of Open Science in academia. Being open has two levels of meanings. The first is to make the data, code, sample collections and publications, etc. freely accessible online. The other is the annotation and connection between those resources to establish the provenance information for reproducible scientific research. In this paper we present our work on a web portal for the Deep Carbon Observatory (DCO) community. The DCO is a 10-year (2009-2019) initiative to intensify global attention and scientific effort in the burgeoning field of deep carbon science. Inspired by guiding questions such as “how much carbon does Earth contain?”, “where is it?” and “what can deep carbon tell us about origins?” more than 1000 scientists across the world are actively participating in the DCO community. The DCO web portal is a research collaboration website developed to keep track of all researchers, organizations, instruments, field sites, and research outputs related to the DCO community. We intend for the DCO web portal to be a knowledge portal - adopting state-of-the-art semantic technologies to support various stages of the scientific process within and beyond the DCO community.

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From data portal to knowledge portal: Leveraging semantic technologies to support interdisciplinary studies

  1. 1. deepcarbon.net Xiaogang Ma, Patrick West, John Erickson, Stephan Zednik, Yu Chen, Han Wang, Hao Zhong, Peter Fox Tetherless World Constellation Rensselaer Polytechnic Institute From data portal to knowledge portal: Leveraging semantic technologies to support interdisciplinary studies
  2. 2. Outline • Deep Carbon Observatory • Deep Carbon Virtual Observatory (DCvO) – Architecture of DCvO – DCO Ontologies – Boundary activities – Discovering information by clicking through • Summary 2
  3. 3. A 10-year (2009-2019) initiative to intensify global attention and scientific effort in the burgeoning field of deep carbon science 3
  4. 4. • Faculty, staff and students from the Tetherless World Constellation (TWC) at Rensselaer Polytechnic Institute (RPI) • Responsible for – DCO Architecture and technology infrastructure – DCO Computer Cluster – The Deep Carbon Virtual Observatory DCvO Deep Carbon Observatory – Data Science 4
  5. 5. Deep Carbon Virtual Observatory Scientists – actually ANYONE - should be able to access a global, distributed knowledge base of scientific data and information that: • appears to be integrated • appears to be locally available • is in a language (written, programming, or science) that is understandable and can be shared Data intensive – volume, complexity, mode, scale, heterogeneity, … in an OPEN WORLD 5
  6. 6. Deep Carbon Virtual Observatory • A vision of the DCvO: – A conceptual model of the interplay between data, people, publication, instruments, models, organizations, etc. – Identify, annotate and link all key entities, agents and activities – A repository for datasets and associated metadata – Unique and powerful data and metadata visualization for dissemination of information – Facilitates the discovery of potential collaborations – An integrated portal for diverse content and applications (Fox et al., 2014) 6
  7. 7. DCvO “Architecture” 7
  8. 8. vivo.cornell.edu VIVO - represents academic research communities DCO ontology: a model for concept types and relationships DCO ontologies extend each other and the VIVO ontology 8
  9. 9. Ontologies and schemas used in the DCO web portal 9 Name Prefix Dublin Core Metadata Element Set dc DCMI Metadata Terms dct VIVO Core vivo VIVO Scientific Research Ontology scires Data Catalog Vocabulary dcat Bibliographic Ontology bibo Citation Counting and Context Characterization Ontology c4o Citation Typing Ontology cito FRBR-Aligned Bibliographic Ontology fabio Event Ontology event Friend of a Friend foaf vCard Ontology vcard Geopolitical Ontology geo Simple Knowledge Organization System skos DCO Ontology dco PROV Ontology prov
  10. 10. Ontologies and schemas used in the DCO web portal 10 DCO Boundary Activities are driving the extensions within the DCO Ontologies
  11. 11. DCO Extension for Project Updates 11
  12. 12. 12 Dynamically generated list of Grants that are part of the Deep Carbon Observatory. Users can click through to learn more, and members can create reports to be sent to funding orgs
  13. 13. 13 Grant page lists all projects and reporting updates for each of the projects and field studies
  14. 14. DCO Extension for Data Types 14
  15. 15. 15 A Few Boundary Activities • Given a DOI pull publication information from CrossRef and/or Web of Science • DCO IGSN Allocation Agent to work with the IGSN Registry • Integration with existing data portals and repositories • Data Rescue activities
  16. 16. Modern informatics enables a new scale-free framework approach • Use cases • Stakeholders • Modeling • Ontologies • Evaluation 16
  17. 17. What does a DCO data publication look like? 17
  18. 18. 18 Identification and annotation Information on the landing page of a dataset
  19. 19. 19 Linking to enable forward and backward tracking Landing page of Helium Concept
  20. 20. 20 Landing page of a person Linking to build Collaborations
  21. 21. 21 Landing page of a research area Linking to build Collaborations
  22. 22. 22 DCO Knowledge Graph Analytics
  23. 23. Thus… progress… • Integrative – semantics • Transparent – semantics • Collaborative – semantics • Application integration – Yep – semantics 23
  24. 24. Thank you! 24 Patrick West, westp@rpi.edu, https://deepcarbon.net, http://tw.rpi.edu
  25. 25. 25 An integrated portal: deepcarbon.net
  26. 26. 26 Faceted publication browser
  27. 27. Repository for archiving datasets Archived datasets of ‘Noble gas isotope abundances in terrestrial fluids’ 27
  28. 28. Collaboration tools Group Based CollaborationGroup data deposit and reporting Listings of group content Group management and messaging 28
  29. 29. 29 RDA DTR and PIT adoption The DTR primitives are comparable to a list of BASIC DATA TYPE CLASSES in the DCO ontology, e.g. Dataset, Image, Video, Audio, etc. A registered DCO dataset is asserted as an instance of one of those basic data type classes. It is possible to further annotate the dataset with the SPECIFIC DATA TYPES defined within a DTR, and each data type has a unique PID. A Few Boundary Activities
  30. 30. Results of data type specification • Updates to the DCO Ontology: – A new class dco:DataType. Each specific data type is an instance of it – An object property dco:hasDataType linking a dataset and a data type – A collection of other classes and properties associated with dco:DataType 30
  31. 31. 31 • New datasets available via dataset browser • Includes citations to the originating publication • Data files accessible through dataset repository Thermodynamic Data Rescue
  32. 32. 32 DCO Knowledge Store Analytics
  33. 33. 33 DCO Knowledge Store Visualizations
  34. 34. All information is linked and traceable! 34
  35. 35. Mediation From: C. Borgman, 2008, NSF Cyberlearning Report, Illustration by Roy Pea and Jillian C. Wallis 6th Generation All these generations of mediation are in effect as we collaborate 35

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