Bio2RDF converts over 40 life science databases with over 30 billion triples into semantic web technologies to support biological discovery. It provides interlinked data through SPARQL endpoints in various locations. The presentation discusses Bio2RDF's methodology for converting, providing, and enabling reuse of data based on linked open data principles in order to encourage original data providers to directly publish RDF and link to other data sources.
Slides from my Metadata Workshop at Content Strategy Applied 2012. The session included several hands on exercises, which is where a lot of the interesting conversation took place.
by Sotiris Batsakis & Grigoris Antoniou, presented at the 3rd PRELIDA Consolidation and Dissemination Workshop, Riva, Italy, October, 17, 2014. More information about the workshop at: prelida.eu
The W3C Linked Data Platform (LDP) candidate recommendation defines a standard HTTP-based protocol for read/write Linked
Data. The W3C R2RML recommendation defines a language to map relational databases (RDBs) and RDF. This paper presents morph-LDP, a novel system that combines these two W3C standardization initiatives to expose relational data as read/write Linked Data for LDP-aware applications, whilst allowing legacy applications to continue using their relational databases.
EZID: Easy dataset identification & management
Joan Starr, Manager, Strategic and Project Planning and EZID Service Manager, California Digital Library
Data and data curation are assuming a growing role today’s research library. New approaches are needed both to address the resulting challenges and take advantage of the emerging opportunities. Long-term identifiers represent one such tool. In this presentation, Joan Starr will introduce identifiers and an application designed to make them easy to create and manage: EZID. She will provide a closer look at two identifier types: DOIs and ARKs, and discuss what bringing an identifier service to your institution might mean.
Using Dublin Core for DISCOVER: a New Zealand visual art and music resource f...Karen R
Poster presented at DC2002, Metadata for e-Communities: Supporting Diversity and Convergence, Florence, October 13-17, 2002
DC-2002-Florence Proceedings
http://dcpapers.dublincore.org/pubs/article/view/725
Slides from my Metadata Workshop at Content Strategy Applied 2012. The session included several hands on exercises, which is where a lot of the interesting conversation took place.
by Sotiris Batsakis & Grigoris Antoniou, presented at the 3rd PRELIDA Consolidation and Dissemination Workshop, Riva, Italy, October, 17, 2014. More information about the workshop at: prelida.eu
The W3C Linked Data Platform (LDP) candidate recommendation defines a standard HTTP-based protocol for read/write Linked
Data. The W3C R2RML recommendation defines a language to map relational databases (RDBs) and RDF. This paper presents morph-LDP, a novel system that combines these two W3C standardization initiatives to expose relational data as read/write Linked Data for LDP-aware applications, whilst allowing legacy applications to continue using their relational databases.
EZID: Easy dataset identification & management
Joan Starr, Manager, Strategic and Project Planning and EZID Service Manager, California Digital Library
Data and data curation are assuming a growing role today’s research library. New approaches are needed both to address the resulting challenges and take advantage of the emerging opportunities. Long-term identifiers represent one such tool. In this presentation, Joan Starr will introduce identifiers and an application designed to make them easy to create and manage: EZID. She will provide a closer look at two identifier types: DOIs and ARKs, and discuss what bringing an identifier service to your institution might mean.
Using Dublin Core for DISCOVER: a New Zealand visual art and music resource f...Karen R
Poster presented at DC2002, Metadata for e-Communities: Supporting Diversity and Convergence, Florence, October 13-17, 2002
DC-2002-Florence Proceedings
http://dcpapers.dublincore.org/pubs/article/view/725
Using Architectures for Semantic Interoperability to Create Journal Clubs for...James Powell
In certain types of _slow burn_ emergencies, careful accumulation and evaluation of information can offer a crucial advantage. The SARS outbreak in the first decade of the 21st century was such an event, and ad hoc
journal clubs played a critical role in assisting scientific and technical responders in identifying and developing various strategies for halting what could have become a dangerous pandemic. This paper describes a process for leveraging emerging semantic web and digital library architectures and standards to (1) create a focused collection of bibliographic metadata, (2) extract semantic information, (3) convert it to the Resource Description Framework /Extensible Markup Language (RDF/XML),
and (4) integrate it so that scientific and technical responders can share and explore critical information in the collections.
systems.
Opening Keynote: The Many and the One: BCE themes in 21st century data curation
Allen Renear, Professor and Interim Dean, Graduate School of Library and Information Science, University of Illinois at Urbana-Champaign
Two scientists can be using "the same data" even though the computer files involved appear to be quite different. This is familiar enough, and for the most part, in small communities with shared practices and familiar datasets, raises few problems. But these informal understandings do not scale to 21st century data curation. To get full value from cyberinfrastructure we must support huge quantities of heterogeneous data developed by diverse communities and used by diverse communities -- often with widely varying methods, tools, and purposes. To accomplish this our informal practices and understandings much be replaced, or at least supplemented, by a shared framework of standard terminology for describing complex cascades of representational levels and relationships. Fundamental problems in data curation -- and in particular problems involving provenance, identifiers, and data citation — cannot be fully resolved without such a framework. Although the deepest problems here have ancient origins, useful practical measures are now within reach. Some recent work toward this end that is being carried out at the Center for Informatics Research in Science and Scholarship (CIRSS) at the Graduate School of Library and Information Science, University of Illinois at Urbana-Champaign will be described.
Dublin Core Registry to Support Multilinguality : Te Reo Māori Dublin Core Me...Karen R
11th Annual Open Forum for Metadata Registries
Metadata DownUnder - Metadata, Semantics and Interoperability in Practice. Sydney, NSW Australia 19 - 22 May 2008
Karen Coyle Keynote - R&D: Can Resource Description become Rigorous Data?eby
Work is beginning to transform the eloquent yet arcane texts called "library cataloging records" into data elements that will play well in the Web. Beginning with the upcoming revised cataloging rules, called
Resource Description and Access, a team of researchers is exploring the abstract model behind bibliographic description. Coyle will cover the
philosophy behind the project and will discuss current progress and goals, as well as fears, risks, and even some confusion.
RDAP13 Jian Qin: Functional and Architectural Requirements for MetadataASIS&T
Jian Qin, Syracuse University
Jian Qin, Syracuse University; Alex Ball, UKLON; Jane Greenberg, University of North Carolina at Chapel Hill: “Functional and Architectural Requirements for Metadata: Supporting Discovery and Management of Scientific Data”
Panel: Linked data and metadata (co-sponsored by the ASIS&T Digital Libraries SIG)
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
EURISCO and GBIF, at the European genbank network meeting (Bonn, April 2004)Dag Endresen
Potential relationship and collaboration between EURISCO and GBIF - a distributed network of databases for the ECP/GR D&I network meeting at ZADI Bonn Germany 11th April 2005. Dag Endresen (Nordic Gene Bank). GBIF is a Global Biodiversity Information Facility for free and open access to biodiversity data.
When we look at the rapid growth of scientific databases on the Internet in the past decade, we tend to take the accessibility and provenance of the data for granted. As we see a future of increased database integration, the licensing of the data may be a hurdle that hampers progress and usability. We have formulated four rules for licensing data for open drug discovery, which we propose as a starting point for consideration by databases and for their ultimate adoption. This work could also be extended to the computational models derived from such data. We suggest that scientists in the future will need to consider data licensing before they embark upon re-using such content in databases they construct themselves.
Acorn-Redecom 2010 Conference, at the University of Brasilia (Brasilia, D.F., Brazil), on May 14-15th, 2010 - Center for Communication Policy, Law, Economics and Technology - Session 1 - Room 2
Acorn-Redecom 2010 Conference, at the University of Brasilia (Brasilia, D.F., Brazil), on May 14-15th, 2010 - Center for Communication Policy, Law, Economics and Technology - Session 5 - Room 2
Using Architectures for Semantic Interoperability to Create Journal Clubs for...James Powell
In certain types of _slow burn_ emergencies, careful accumulation and evaluation of information can offer a crucial advantage. The SARS outbreak in the first decade of the 21st century was such an event, and ad hoc
journal clubs played a critical role in assisting scientific and technical responders in identifying and developing various strategies for halting what could have become a dangerous pandemic. This paper describes a process for leveraging emerging semantic web and digital library architectures and standards to (1) create a focused collection of bibliographic metadata, (2) extract semantic information, (3) convert it to the Resource Description Framework /Extensible Markup Language (RDF/XML),
and (4) integrate it so that scientific and technical responders can share and explore critical information in the collections.
systems.
Opening Keynote: The Many and the One: BCE themes in 21st century data curation
Allen Renear, Professor and Interim Dean, Graduate School of Library and Information Science, University of Illinois at Urbana-Champaign
Two scientists can be using "the same data" even though the computer files involved appear to be quite different. This is familiar enough, and for the most part, in small communities with shared practices and familiar datasets, raises few problems. But these informal understandings do not scale to 21st century data curation. To get full value from cyberinfrastructure we must support huge quantities of heterogeneous data developed by diverse communities and used by diverse communities -- often with widely varying methods, tools, and purposes. To accomplish this our informal practices and understandings much be replaced, or at least supplemented, by a shared framework of standard terminology for describing complex cascades of representational levels and relationships. Fundamental problems in data curation -- and in particular problems involving provenance, identifiers, and data citation — cannot be fully resolved without such a framework. Although the deepest problems here have ancient origins, useful practical measures are now within reach. Some recent work toward this end that is being carried out at the Center for Informatics Research in Science and Scholarship (CIRSS) at the Graduate School of Library and Information Science, University of Illinois at Urbana-Champaign will be described.
Dublin Core Registry to Support Multilinguality : Te Reo Māori Dublin Core Me...Karen R
11th Annual Open Forum for Metadata Registries
Metadata DownUnder - Metadata, Semantics and Interoperability in Practice. Sydney, NSW Australia 19 - 22 May 2008
Karen Coyle Keynote - R&D: Can Resource Description become Rigorous Data?eby
Work is beginning to transform the eloquent yet arcane texts called "library cataloging records" into data elements that will play well in the Web. Beginning with the upcoming revised cataloging rules, called
Resource Description and Access, a team of researchers is exploring the abstract model behind bibliographic description. Coyle will cover the
philosophy behind the project and will discuss current progress and goals, as well as fears, risks, and even some confusion.
RDAP13 Jian Qin: Functional and Architectural Requirements for MetadataASIS&T
Jian Qin, Syracuse University
Jian Qin, Syracuse University; Alex Ball, UKLON; Jane Greenberg, University of North Carolina at Chapel Hill: “Functional and Architectural Requirements for Metadata: Supporting Discovery and Management of Scientific Data”
Panel: Linked data and metadata (co-sponsored by the ASIS&T Digital Libraries SIG)
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
EURISCO and GBIF, at the European genbank network meeting (Bonn, April 2004)Dag Endresen
Potential relationship and collaboration between EURISCO and GBIF - a distributed network of databases for the ECP/GR D&I network meeting at ZADI Bonn Germany 11th April 2005. Dag Endresen (Nordic Gene Bank). GBIF is a Global Biodiversity Information Facility for free and open access to biodiversity data.
When we look at the rapid growth of scientific databases on the Internet in the past decade, we tend to take the accessibility and provenance of the data for granted. As we see a future of increased database integration, the licensing of the data may be a hurdle that hampers progress and usability. We have formulated four rules for licensing data for open drug discovery, which we propose as a starting point for consideration by databases and for their ultimate adoption. This work could also be extended to the computational models derived from such data. We suggest that scientists in the future will need to consider data licensing before they embark upon re-using such content in databases they construct themselves.
Acorn-Redecom 2010 Conference, at the University of Brasilia (Brasilia, D.F., Brazil), on May 14-15th, 2010 - Center for Communication Policy, Law, Economics and Technology - Session 1 - Room 2
Acorn-Redecom 2010 Conference, at the University of Brasilia (Brasilia, D.F., Brazil), on May 14-15th, 2010 - Center for Communication Policy, Law, Economics and Technology - Session 5 - Room 2
Acorn-Redecom 2010 Photo Archive Keynote Speaker Mario RipperMarcioAranha
Acorn-Redecom 2010 Conference, at the University of Brasilia (Brasilia, D.F., Brazil), on May 14-15th, 2010 - Center for Communication Policy, Law, Economics and Technology - Keynote Speaker Mario Ripper
Acorn-Redecom 2010 Conference, at the University of Brasilia (Brasilia, D.F., Brazil), on May 14-15th, 2010 - Center for Communication Policy, Law, Economics and Technology - Session 2 - Auditorium
Acorn-Redecom 2010 Conference, at the University of Brasilia (Brasilia, D.F., Brazil), on May 14-15th, 2010 - Center for Communication Policy, Law, Economics and Technology - Session 6 - Room 1
Acorn-Redecom 2010 Conference, at the University of Brasilia (Brasilia, D.F., Brazil), on May 14-15th, 2010 - Center for Communication Policy, Law, Economics and Technology - Coffee-break 1
Acorn-Redecom 2010 Conference, at the University of Brasilia (Brasilia, D.F., Brazil), on May 14-15th, 2010 - Center for Communication Policy, Law, Economics and Technology - Session 5 - Room 1
I was hired to reinvent this presentation. As a result, here's what the client said:
Your work on our ILS webinar has helped our clients stay focused and really understand our product when explaining it via our webinars and presentations. Our close rates have increased 50% since you designed our webinar to streamline exactly what it is we sell."
Jeopardy with questions about different aspects of American culture: geography, history, pop culture, sport and miscellaneous.
You can use it for intermediate ESL
Linked Data Basics Slot in WWW2012 Tutorial: Practical Cross-Dataset Queries on the Web of Data
http://latc-project.eu/events/www2012-tutorial-cross-dataset-queries
This is part 2 of the ISWC 2009 tutorial on the GoodRelations ontology and RDFa for e-commerce on the Web of Linked Data.
See also
http://www.ebusiness-unibw.org/wiki/Web_of_Data_for_E-Commerce_Tutorial_ISWC2009
This is part 2 of the ISWC 2009 tutorial on the GoodRelations ontology and RDFa for e-commerce on the Web of Linked Data.
See also
http://www.ebusiness-unibw.org/wiki/Web_of_Data_for_E-Commerce_Tutorial_ISWC2009
Open data is a crucial prerequisite for inventing and disseminating the innovative practices needed for agricultural development. To be usable, data must not just be open in principle—i.e., covered by licenses that allow re-use. Data must also be published in a technical form that allows it to be integrated into a wide range of applications. The webinar will be of interest to any institution seeking ways to publish and curate data in the Linked Data cloud.
This webinar describes the technical solutions adopted by a widely diverse global network of agricultural research institutes for publishing research results. The talk focuses on AGRIS, a central and widely-used resource linking agricultural datasets for easy consumption, and AgriDrupal, an adaptation of the popular, open-source content management system Drupal optimized for producing and consuming linked datasets.
Agricultural research institutes in developing countries share many of the constraints faced by libraries and other documentation centers, and not just in developing countries: institutions are expected to expose their information on the Web in a re-usable form with shoestring budgets and with technical staff working in local languages and continually lured by higher-paying work in the private sector. Technical solutions must be easy to adopt and freely available.
Creating a sustainable business model for a digital repository: the Dryad exp...ASIS&T
Creating a sustainable business model for a digital repository: the Dryad experience
Peggy Schaeffer
Datadryad.org
Presentation at Research Data Access & Preservation Summit
22 March 2012
Presentation for the OCLC Linked Data Roundtable event for IFLA Helsinki 2012. Covers the reasoning behind the BL's linked open data version of the British National Bibliography, the processes needed to create the service and challenges to be addressed.
Slides of the presentation by Robert Isele of Free University of Berlin, Germany in the course of the LOD2 webinar: SILK on 21.02.2012 - for more information please see: http://lod2.eu/BlogPost/webinar-series
This presentation was provided by Abigail Sparling and Adam Cohen of The University of Alberta Library, during the NISO webinar "Implementing Linked Library Data," held on November 13, 2019.
Usage of Linked Data: Introduction and Application ScenariosEUCLID project
This presentation introduces the main principles of Linked Data, the underlying technologies and background standards. It provides basic knowledge for how data can be published over the Web, how it can be queried, and what are the possible use cases and benefits. As an example, we use the development of a music portal (based on the MusicBrainz dataset), which facilitates access to a wide range of information and multimedia resources relating to music.
This webinar in the course of the LOD2 webinar series will present use cases and live demos of D2R (Free University Berlin) and Sparqlify (University of Leipzig).
D2R Server is a tool for publishing relational databases on the Semantic Web. It enables RDF and HTML browsers to navigate the content of the database, and allows applications to query the database using the SPARQL query language.
Sparqlify is a tool enabling one to define expressive RDF views on relational databases and query them with a subset of the SPARQL query language. By featuring a novel RDF view definition syntax, it aims at simplifying the RDB-RDF mapping process.
more to be found at:
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
Francesca Gottschalk - How can education support child empowerment.pptxEduSkills OECD
Francesca Gottschalk from the OECD’s Centre for Educational Research and Innovation presents at the Ask an Expert Webinar: How can education support child empowerment?
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
How libraries can support authors with open access requirements for UKRI fund...
W4 4 marc-alexandre-nolin-v2
1. Bio2RDF: Convert, Provide And
Reuse.
Marc-Alexandre Nolin1, Jacques Corbeil1,
Luc Lamontagne1, Michel Dumontier1,2
1
Laval University, Canada
2
Carleton University, Canada
manolin@gmail.com
2. Presentation Plan
• Bio2RDF
– Methodology
• Data conversion
• Data provision
• Reuse
• Future work
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 2
3. Bio2RDF
• Bio2RDF uses open-source Semantic Web
technologies to provide interlinked life science
data to support biological knowledge discovery.
• Over 40 databases converted
• Over 30 billion triples
• Global mirroring
– Quebec City, Quebec, Canada
– Ottawa, Ontario, Canada
– Guelph, Ontario, Canada
– Brisbane, Australia
– part of LOD mashup at http://lod.openlinksw.com
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 3
4. 2010 Linked Open Data Cloud
“Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/”
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 4
5. Bio2RDF is the major contributor
to the Life Sciences LOD
“Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/”
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 5
6. What is Linked Open Data?
• Linked open data is
• data that is free to use
• machine understandable (uses RDF/OWL)
• can be looked up using web protocols
• has meaningful relations between data items
(generated from supplied cross-references, or
text-based mappings)
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 6
7. LOD Methodology
Applying Tim Berners-Lee 4 rules
1. Use URIs as names for things
2. Use HTTP URIs so that people can look up those
names
3. When someone looks up a URI, provide useful
information, using the standards (RDF*, SPARQL)
4. Include links to other URIs, so that they can
discover more things
– http://www.w3.org/DesignIssues/LinkedData
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 7
8. Bio2RDF Methodology
We extend LOD rules by:
1. Consistently naming all resources
http://bio2rdf.org/namespace:identifier
2. Resolving Bio2RDF URIs to a set of statements
about the requested resource
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 8
9. Data providers have been
linking data for years
• Links are done from
one HTML page to
another
• This works for human
consumption, but
doesn’t scale with huge
amounts of data
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 9
10. However, most linked open data is
created and provided without the
help of the original data provider
11. Why be part of the linked data
cloud?
• Enable queries that span over more than 1
database.
– Example: filtering a PubMed search by a
microarray level of expression filter
• Reduce the size of a database by only
referencing data instead of including it in
a database record (e.g. citations)
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 11
12. But something is missing !
derived from Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-
cloud.net/”
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 12
13. Presentation Plan
• Bio2RDF
• Data conversion
• Data provision
• Reuse
• Future work
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 13
14. Convert
• Take a step back and think about what your data
represents.
• Forget about the way it is currently represented in
your relational database
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 14
15. What is RDFizing?
• RDFizing converts legacy data into one or
more RDF statements or triples:
<Subject> <Predicate> <Object>
• Triples have correspondence for a standard
database
– Subject row identifier
– Predicate column name
– Object value
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 15
16. Convert
• Converting to RDF just for the sake of providing
another format will not add much to your offering
if the result is your old relational database format
… in RDF
• Get rid of relational database artifacts while
rdfizing
1. Uses simple and stable identifiers to name
resources
2. Create types for the entities that your data refers to
with in your data and specify the nature of the
relations that hold between them
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 16
17. Presentation Plan
• Bio2RDF
• Data conversion
• Data provision
• Reuse
• Future work
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 17
18. Provide – RDF Documents
• URIs can be created with a REST-like look
• Example of stable URIs
http://purl.uniprot.org/uniprot/P19367
http://bio2rdf.org/uniprot:P19367
• Documents containing statements should be
accessible using web technology (HTTP protocol)
• Provide data dumps
• But in the LOD world, we want to query online
databases!
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 18
19. Provide - SPARQL
• SPARQL is the query language for RDF/OWL
that uses web technology (HTTP)
• SPARQL endpoints make it possible to query
databases using SPARQL
• Distributed SPARQL will carve up the query and
determine which endpoints need to be queried
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 19
20. Provide
• Publish the scheme you will use for your URIs so
that other providers may use it
• Provide access to documents with resolvable URIs
(can be looked up using a web browser)
http://geneprovider.com/gene:identifier
• Now other data providers can use this identifer
instead of copying the data into their own!
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 20
21. Presentation Plan
• Bio2RDF
• Data conversion
• Data provision
• Reuse
• Future work
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 21
22. Reuse
• RDF version of your documents without
resolvable external links is just another file
format
• One of the most problematic issues is that
the RDF generated by some providers are
only inward looking -> they don’t reuse
published URIs (Polite URI)
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 22
23. Reuse
• Example with Uniprot RDF
• Uniprot is one of the first data providers to offers
stable and resolvable URI for its documents.
However, we can’t use directly the RDF they
provide. Look at this extract of Human HK1 in RDF
<rdf:Description rdf:about="http://purl.uniprot.org/uniprot/P19367">
<rdf:type rdf:resource="http://purl.uniprot.org/core/Protein" />
<rdfs:seeAlso rdf:resource="http://purl.uniprot.org/refseq/NP_277035.2"/>
</rdf:Description>
• The problem is that http://purl.uniprot.org/refseq/NP_277035.2
resolves to the NCBI HTML page of NP_277035.2
• Since NCBI does not provide RDF, it’s a dead end
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 23
24. Reuse
• Uniprot did the same things we have done at
Bio2RDF. They create a URI in their namespace.
From that URI which they control, they decided to
redirect to the original HTML document of the
specified ID
• The difference with Bio2RDF is that we also
resolve the other URI to an RDF document
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 24
25. Reuse
• Relational database artifacts : copying of data
from one provider to another
• Uniprot Citation entry IN a protein document
<rdf:Description rdf:about="http://purl.uniprot.org/citations/10686099">
<rdf:type rdf:resource="http://purl.uniprot.org/core/Journal_Citation" />
<title>Crystal structures of mutant monomeric hexokinase I reveal multiple
...</title>
<author>Aleshin A.E.</author>
<author>Kirby C.</author>
<skos:exactMatch rdf:resource="http://purl.uniprot.org/medline/20223513" />
<skos:exactMatch rdf:resource="http://purl.uniprot.org/pubmed/10686099" />
</>
• In a Linked Data world, you only need to have a
link to the PubMed URI at NCBI. The up to date
information is there.
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 25
26. With all this, how is now the LOD for life
sciences by original data providers ?
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 26
27. What is still missing !
“Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/”
2010-10-13 Bio2RDF: Convert, Provide And Reuse. 27
29. The new version of LOD for
life sciences by original providers
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30. Something is missing !
“Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/”
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31. Bottom line
• That is not quite what we had at the beginning
• The original network made by third party provider still
exist. Use it like if it was another provider.
• What about documents without an RDF version?
– From NAR, there is 1230 databases. Too much for Bio2RDF or
any other to convert entirely.
– Use third party providers, like Bio2RDF, NeuroCommons,
LinkedLifeData, Shared Names, etc.
– Add these in addition to original data URIs
– Some databases, for various reason, might never create RDF
version of their data. So third party will continue to have their use
by providing their data in RDF
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32. By applying those conversion, publication and
reuse rules to your data, we will witness the
birth of a more stable network of linked data
… and the death (in the very long term) of
Bio2RDF.
Let's kill Bio2RDF together !!
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33. Presentation Plan
• Bio2RDF
• Data conversion
• Data provision
• Reuse
• Future work
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34. Future Work
• Data processing workflow
• New facet-based user interface to browse
and formulate sophisticated queries
• Full text indexing for autocompletion
support
• Exploring knowledge discovery
possibilities in the linked data network
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35. Thanks
• Bio2RDF community
– Centre de recherche du CHUL
– Dumontier Lab members
– QUT eResearch Center
• Triplestore provided by Openlink Virtuoso
• François Belleau
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36. Acknowledgment
• Marc-Alexandre Nolin funding provided by
CANARIE via the C-BRASS project
• Servers in Quebec City are provided by
Jacques Corbeil of Laval University
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37. Contact Information
• Mailing list : bio2rdf@googlegroups.com
• URL : http://bio2rdf.org
• Wiki : http://sourceforge.net/apps/mediawiki/bio2rdf
• Blog : http://bio2rdf.blogspot.com
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