This is a lecture note #10 for my class of Graduate School of Yonsei University, Korea.
It describes SPARQL to retrieve and manipulate data stored in Resource Description Framework format
Re-using Media on the Web: Media fragment re-mixing and playoutMediaMixerCommunity
A number of novel application ideas will be introduced based on the media fragment creation, specification and rights management technologies. Semantic search and retrieval allows us to organize sets of fragments by topical or conceptual relevance. These fragment sets can then be played out in a non-linear fashion to create a new media re-mix. We look at a server-client implementation supporting Media Fragments, before allowing the participants to take the sets of media they have selected and create their own re-mix.
Towards semantic systems chemical biology Bin Chen
introduce a semantic framework for studying systems chemical biology / systems pharmacology, in which three major projects (Chem2Bio2RDF, Chem2Bio2OWL, SLAP (semantic link association prediction) are covered.
Create Linked Open Data (LOD) Microthesauri using Art & Architecture Thesaurus (AAT) LOD. View and manage options by a non-techy person. Everyone can use, create,
derive from, & map to AAT microthesauri and make the digital collection become LOD-ready dataset.
This is a lecture note #10 for my class of Graduate School of Yonsei University, Korea.
It describes SPARQL to retrieve and manipulate data stored in Resource Description Framework format
Re-using Media on the Web: Media fragment re-mixing and playoutMediaMixerCommunity
A number of novel application ideas will be introduced based on the media fragment creation, specification and rights management technologies. Semantic search and retrieval allows us to organize sets of fragments by topical or conceptual relevance. These fragment sets can then be played out in a non-linear fashion to create a new media re-mix. We look at a server-client implementation supporting Media Fragments, before allowing the participants to take the sets of media they have selected and create their own re-mix.
Towards semantic systems chemical biology Bin Chen
introduce a semantic framework for studying systems chemical biology / systems pharmacology, in which three major projects (Chem2Bio2RDF, Chem2Bio2OWL, SLAP (semantic link association prediction) are covered.
Create Linked Open Data (LOD) Microthesauri using Art & Architecture Thesaurus (AAT) LOD. View and manage options by a non-techy person. Everyone can use, create,
derive from, & map to AAT microthesauri and make the digital collection become LOD-ready dataset.
The Role of Metadata in Reproducible Computational ResearchJeremy Leipzig
Reproducible computational research (RCR) provides the keystone to the scientific method, packaging the transformation of raw data to published results in a manner than can be communicated to others. Developing RCR standards has been a growing concern of statisticians, data scientists, and informatics professionals. Metadata provides context and provenance to raw data, and is essential to both discovery and validation RCR. This presentation will give an overview for emerging metadata standards in data, analysis, pipelines tools, and publications.
This presentation looks in detail at SPARQL (SPARQL Protocol and RDF Query Language) and introduces approaches for querying and updating semantic data. It covers the SPARQL algebra, the SPARQL protocol, and provides examples for reasoning over Linked Data. We use examples from the music domain, which can be directly tried out and ran over the MusicBrainz dataset. This includes gaining some familiarity with the RDFS and OWL languages, which allow developers to formulate generic and conceptual knowledge that can be exploited by automatic reasoning services in order to enhance the power of querying.
Lecture Notes by Mustafa Jarrar at Birzeit University, Palestine.
See the course webpage at: http://jarrar-courses.blogspot.com/2014/01/sparql-rdf-query-language.html
and http://www.jarrar.info
The lecture covers:
- SPARQL Basics
- SPARQL Practical Session
Part 4 of tutorials at DC2008, Berlin. (International Conference on Dublin Core and Metadata Applications). See also part 1-3 by Jane Greenberg, Pete Johnston, and Mikael Nilsson on DC history, concepts, and other schemas. This part focuses on practical issues.
Understanding RDF: the Resource Description Framework in Context (1999)Dan Brickley
Dan Brickley, 3rd European Commission Metadata Workshop, Luxemburg, April 12th 1999
Understanding RDF: the Resource Description Framework in Context
http://ilrt.org/discovery/2001/01/understanding-rdf/
Jarrar: RDF Stores -Challenges and SolutionsMustafa Jarrar
Lecture Notes by Mustafa Jarrar at Birzeit University, Palestine.
See the course webpage at: http://jarrar-courses.blogspot.com/2014/01/web-data-management.html , and http://www.jarrar.info
you may also watch this lecture at: http://www.youtube.com/watch?v=chYftg1bJCg
The lecture covers:
Part I: Querying RDF(S P O) tables using SQL
Part 2: Practical Session (RDF graphs )
Part 3: SQL-based RDF Stores
RDF is a general method to decompose knowledge into small pieces, with some rules about the semantics or meaning of those pieces. The point is to have a method so simple that it can express any fact, and yet so structured that computer applications can do useful things with knowledge expressed in RDF.
As described in the April NISO/DCMI webinar by Dan Brickley, schema.org is a search-engine initiative aimed at helping webmasters use structured data markup to improve the discovery and display of search results. Drupal 7 makes it easy to markup HTML pages with schema.org terms, allowing users to quickly build websites with structured data that can be understood by Google and displayed as Rich Snippets.
Improved search results are only part of the story, however. Data-bearing documents become machine-processable once you find them. The subject matter, important facts, calendar events, authorship, licensing, and whatever else you might like to share become there for the taking. Sales reports, RSS feeds, industry analysis, maps, diagrams and process artifacts can now connect back to other data sets to provide linkage to context and related content. The key to this is the adoption standards for both the data model (RDF) and the means of weaving it into documents (RDFa). Drupal 7 has become the leading content platform to adopt these standards.
This webinar will describe how RDFa and Drupal 7 can improve how organizations publish information and data on the Web for both internal and external consumption. It will discuss what is required to use these features and how they impact publication workflow. The talk will focus on high-level and accessible demonstrations of what is possible. Technical people should learn how to proceed while non-technical people will learn what is possible.
Talk delivered at YOW! Developer Conferences in Melbourne, Brisbane and Sydney Australia on 1-9 December 2016.
Abstract: Governments collect a lot of data. Data on air quality, toxic chemicals, laws and regulations, public health, and the census are intended to be widely distributed. Some data is not for public consumption. This talk focuses on open government data — the information that is meant to be made available for benefit of policy makers, researchers, scientists, industry, community organisers, journalists and members of civil society.
We’ll cover the evolution of Linked Data, which is now being used by Google, Apple, IBM Watson, federal governments worldwide, non-profits including CSIRO and OpenPHACTS, and thousands of others worldwide.
Next we’ll delve into the evolution of the U.S. Environmental Protection Agency’s Open Data service that we implemented using Linked Data and an Open Source Data Platform. Highlights include how we connected to hundreds of billions of open data facts in the world’s largest, open chemical molecules database PubChem and DBpedia.
WHO SHOULD ATTEND
Data scientists, software engineers, data analysts, DBAs, technical leaders and anyone interested in utilising linked data and open government data.
The Role of Metadata in Reproducible Computational ResearchJeremy Leipzig
Reproducible computational research (RCR) provides the keystone to the scientific method, packaging the transformation of raw data to published results in a manner than can be communicated to others. Developing RCR standards has been a growing concern of statisticians, data scientists, and informatics professionals. Metadata provides context and provenance to raw data, and is essential to both discovery and validation RCR. This presentation will give an overview for emerging metadata standards in data, analysis, pipelines tools, and publications.
This presentation looks in detail at SPARQL (SPARQL Protocol and RDF Query Language) and introduces approaches for querying and updating semantic data. It covers the SPARQL algebra, the SPARQL protocol, and provides examples for reasoning over Linked Data. We use examples from the music domain, which can be directly tried out and ran over the MusicBrainz dataset. This includes gaining some familiarity with the RDFS and OWL languages, which allow developers to formulate generic and conceptual knowledge that can be exploited by automatic reasoning services in order to enhance the power of querying.
Lecture Notes by Mustafa Jarrar at Birzeit University, Palestine.
See the course webpage at: http://jarrar-courses.blogspot.com/2014/01/sparql-rdf-query-language.html
and http://www.jarrar.info
The lecture covers:
- SPARQL Basics
- SPARQL Practical Session
Part 4 of tutorials at DC2008, Berlin. (International Conference on Dublin Core and Metadata Applications). See also part 1-3 by Jane Greenberg, Pete Johnston, and Mikael Nilsson on DC history, concepts, and other schemas. This part focuses on practical issues.
Understanding RDF: the Resource Description Framework in Context (1999)Dan Brickley
Dan Brickley, 3rd European Commission Metadata Workshop, Luxemburg, April 12th 1999
Understanding RDF: the Resource Description Framework in Context
http://ilrt.org/discovery/2001/01/understanding-rdf/
Jarrar: RDF Stores -Challenges and SolutionsMustafa Jarrar
Lecture Notes by Mustafa Jarrar at Birzeit University, Palestine.
See the course webpage at: http://jarrar-courses.blogspot.com/2014/01/web-data-management.html , and http://www.jarrar.info
you may also watch this lecture at: http://www.youtube.com/watch?v=chYftg1bJCg
The lecture covers:
Part I: Querying RDF(S P O) tables using SQL
Part 2: Practical Session (RDF graphs )
Part 3: SQL-based RDF Stores
RDF is a general method to decompose knowledge into small pieces, with some rules about the semantics or meaning of those pieces. The point is to have a method so simple that it can express any fact, and yet so structured that computer applications can do useful things with knowledge expressed in RDF.
As described in the April NISO/DCMI webinar by Dan Brickley, schema.org is a search-engine initiative aimed at helping webmasters use structured data markup to improve the discovery and display of search results. Drupal 7 makes it easy to markup HTML pages with schema.org terms, allowing users to quickly build websites with structured data that can be understood by Google and displayed as Rich Snippets.
Improved search results are only part of the story, however. Data-bearing documents become machine-processable once you find them. The subject matter, important facts, calendar events, authorship, licensing, and whatever else you might like to share become there for the taking. Sales reports, RSS feeds, industry analysis, maps, diagrams and process artifacts can now connect back to other data sets to provide linkage to context and related content. The key to this is the adoption standards for both the data model (RDF) and the means of weaving it into documents (RDFa). Drupal 7 has become the leading content platform to adopt these standards.
This webinar will describe how RDFa and Drupal 7 can improve how organizations publish information and data on the Web for both internal and external consumption. It will discuss what is required to use these features and how they impact publication workflow. The talk will focus on high-level and accessible demonstrations of what is possible. Technical people should learn how to proceed while non-technical people will learn what is possible.
Talk delivered at YOW! Developer Conferences in Melbourne, Brisbane and Sydney Australia on 1-9 December 2016.
Abstract: Governments collect a lot of data. Data on air quality, toxic chemicals, laws and regulations, public health, and the census are intended to be widely distributed. Some data is not for public consumption. This talk focuses on open government data — the information that is meant to be made available for benefit of policy makers, researchers, scientists, industry, community organisers, journalists and members of civil society.
We’ll cover the evolution of Linked Data, which is now being used by Google, Apple, IBM Watson, federal governments worldwide, non-profits including CSIRO and OpenPHACTS, and thousands of others worldwide.
Next we’ll delve into the evolution of the U.S. Environmental Protection Agency’s Open Data service that we implemented using Linked Data and an Open Source Data Platform. Highlights include how we connected to hundreds of billions of open data facts in the world’s largest, open chemical molecules database PubChem and DBpedia.
WHO SHOULD ATTEND
Data scientists, software engineers, data analysts, DBAs, technical leaders and anyone interested in utilising linked data and open government data.
balloon Fusion: SPARQL Rewriting Based on Unified Co-Reference InformationKai Schlegel
Presentation for 5th International Workshop on
Data Engineering meets the Semantic Web (DESWeb)
In conjunction with ICDE 2014, Chicago IL, USA, March 31, 2014 held by Kai Schlegel
Sesam4 project presentation sparql - april 2011Robert Engels
This slide set is a provided by the SESAM4 consortium as one out of three Technology Primers on Semantic Web technology. This Primer is on SPARQL and gives you a short introduction to its constructs followed by some examples. You can find the belonging slideset at youtube,
Sesam4 project presentation sparql - april 2011sesam4able
This slide set is a provided by the SESAM4 consortium as one out of three Technology Primers on Semantic Web technology. This Primer is on SPARQL and gives you a short introduction to its constructs followed by some examples. You can find the belonging slideset at youtube under SESAM4.
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
As AI technology is pushing into IT I was wondering myself, as an “infrastructure container kubernetes guy”, how get this fancy AI technology get managed from an infrastructure operational view? Is it possible to apply our lovely cloud native principals as well? What benefit’s both technologies could bring to each other?
Let me take this questions and provide you a short journey through existing deployment models and use cases for AI software. On practical examples, we discuss what cloud/on-premise strategy we may need for applying it to our own infrastructure to get it to work from an enterprise perspective. I want to give an overview about infrastructure requirements and technologies, what could be beneficial or limiting your AI use cases in an enterprise environment. An interactive Demo will give you some insides, what approaches I got already working for real.
Generating a custom Ruby SDK for your web service or Rails API using Smithyg2nightmarescribd
Have you ever wanted a Ruby client API to communicate with your web service? Smithy is a protocol-agnostic language for defining services and SDKs. Smithy Ruby is an implementation of Smithy that generates a Ruby SDK using a Smithy model. In this talk, we will explore Smithy and Smithy Ruby to learn how to generate custom feature-rich SDKs that can communicate with any web service, such as a Rails JSON API.
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
Essentials of Automations: Optimizing FME Workflows with ParametersSafe Software
Are you looking to streamline your workflows and boost your projects’ efficiency? Do you find yourself searching for ways to add flexibility and control over your FME workflows? If so, you’re in the right place.
Join us for an insightful dive into the world of FME parameters, a critical element in optimizing workflow efficiency. This webinar marks the beginning of our three-part “Essentials of Automation” series. This first webinar is designed to equip you with the knowledge and skills to utilize parameters effectively: enhancing the flexibility, maintainability, and user control of your FME projects.
Here’s what you’ll gain:
- Essentials of FME Parameters: Understand the pivotal role of parameters, including Reader/Writer, Transformer, User, and FME Flow categories. Discover how they are the key to unlocking automation and optimization within your workflows.
- Practical Applications in FME Form: Delve into key user parameter types including choice, connections, and file URLs. Allow users to control how a workflow runs, making your workflows more reusable. Learn to import values and deliver the best user experience for your workflows while enhancing accuracy.
- Optimization Strategies in FME Flow: Explore the creation and strategic deployment of parameters in FME Flow, including the use of deployment and geometry parameters, to maximize workflow efficiency.
- Pro Tips for Success: Gain insights on parameterizing connections and leveraging new features like Conditional Visibility for clarity and simplicity.
We’ll wrap up with a glimpse into future webinars, followed by a Q&A session to address your specific questions surrounding this topic.
Don’t miss this opportunity to elevate your FME expertise and drive your projects to new heights of efficiency.
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
The Art of the Pitch: WordPress Relationships and SalesLaura Byrne
Clients don’t know what they don’t know. What web solutions are right for them? How does WordPress come into the picture? How do you make sure you understand scope and timeline? What do you do if sometime changes?
All these questions and more will be explored as we talk about matching clients’ needs with what your agency offers without pulling teeth or pulling your hair out. Practical tips, and strategies for successful relationship building that leads to closing the deal.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
Elevating Tactical DDD Patterns Through Object CalisthenicsDorra BARTAGUIZ
After immersing yourself in the blue book and its red counterpart, attending DDD-focused conferences, and applying tactical patterns, you're left with a crucial question: How do I ensure my design is effective? Tactical patterns within Domain-Driven Design (DDD) serve as guiding principles for creating clear and manageable domain models. However, achieving success with these patterns requires additional guidance. Interestingly, we've observed that a set of constraints initially designed for training purposes remarkably aligns with effective pattern implementation, offering a more ‘mechanical’ approach. Let's explore together how Object Calisthenics can elevate the design of your tactical DDD patterns, offering concrete help for those venturing into DDD for the first time!
Dev Dives: Train smarter, not harder – active learning and UiPath LLMs for do...UiPathCommunity
💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™:
See how to accelerate model training and optimize model performance with active learning
Learn about the latest enhancements to out-of-the-box document processing – with little to no training required
Get an exclusive demo of the new family of UiPath LLMs – GenAI models specialized for processing different types of documents and messages
This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath.
Speakers:
👨🏫 Andras Palfi, Senior Product Manager, UiPath
👩🏫 Lenka Dulovicova, Product Program Manager, UiPath
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
UiPath Test Automation using UiPath Test Suite series, part 3DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 3. In this session, we will cover desktop automation along with UI automation.
Topics covered:
UI automation Introduction,
UI automation Sample
Desktop automation flow
Pradeep Chinnala, Senior Consultant Automation Developer @WonderBotz and UiPath MVP
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
3. SPARQL: The query language of the
Semantic Web
● SPARQL: SPARQL Protocol And Query
Language
● SPARQL (“sparkle”) is a W3C
recommendation that is part of the semantic
web stack
● A SPARQL query allows you to search
linked data based on the structure of the
triples it contains
● SPARQL can be used to explore the
structure of RDF graphs and to transform
linked data
4. Anatomy of a SPARQL query
● SPARQL queries have a regular structure
composed of the following parts:
○ Prefix declarations: Shortcuts for URIs used in the
query (e.g. rdf, rdfs, bio2rdf)
○ Dataset definition: RDF graph to query (support for
this option is SPARQL endpoint engine dependent)
○ Result clause: Data returned by the query
○ Query pattern: Graph pattern used to search the
RDF data
○ Query modifiers: Limiting, ordering, other forms of
result rearrangements
5. Anatomy of a SPARQL query
#comments can be included
PREFIX prefixA: <http://example.org/prefixA#>
PREFIX prefixB: <http://example.org/prefixB:>
SELECT ...
FROM <http://example.org/myDataset>
WHERE {
...
} LIMIT 10
6. Federated SPARQL queries over >1 endpoint
use the SERVICE keyword
PREFIX prefixA: <http://example.org/prefixA#>
PREFIX prefixB: <http://example.org/prefixB:>
SELECT ...
FROM <http://example.org/myDataset>
WHERE {
SERVICE <http://somewhere.org/sparql> {
...
}
} LIMIT 10
7. Four SPARQL query variants
SELECT: SQL style result set retrieval. Lets you
specify the variables you wish to retrieve from the data.
CONSTRUCT: Create a custom RDF graph based on
a query criteria. Triples can be extracted verbatim as
they exist in the queried triple store or re-constructed
to create new RDF data.
ASK: Tests whether the triplestore or graph contains
the specified statement. Returns TRUE or FALSE.
DESCRIBE: Returns all of the triples that contain a
specified resource.
8. EXAMPLE: SELECT
Data from Bio2RDF Gene dataset:
<http://bio2rdf.org/geneid:19> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/geneid_vocabulary:Gene> .
<http://bio2rdf.org/geneid:19> <http://bio2rdf.org/geneid_vocabulary:has_symbol> "ABCA1" .
<http://bio2rdf.org/geneid:19> <http://bio2rdf.org/geneid_vocabulary:has_description> "ATP-binding cassette, sub-family A
(ABC1), member 1" .
<http://bio2rdf.org/geneid:19> <http://bio2rdf.org/geneid_vocabulary:has_taxid> <http://bio2rdf.org/taxon:9606> .
Query: Get taxonomic identifier and description for a specific gene symbol
PREFIX gene_vocab: <http://bio2rdf.org/geneid_vocabulary:>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
SELECT ?gene ?geneDescription ?taxid
WHERE {
?gene gene_vocab:has_symbol "ABCA1" .
?gene gene_vocab:has_description ?geneDescription .
?gene gene_vocab:has_taxid ?taxid .
}
9. EXAMPLE: CONSTRUCT
Data from Bio2RDF Gene dataset:
<http://bio2rdf.org/geneid:19> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/geneid_vocabulary:Gene>
.
<http://bio2rdf.org/geneid:19> <http://bio2rdf.org/geneid_vocabulary:has_symbol> "ABCA1" .
<http://bio2rdf.org/geneid:19> <http://bio2rdf.org/geneid_vocabulary:has_description> "ATP-binding cassette, sub-family A
(ABC1), member 1" .
<http://bio2rdf.org/geneid:19> <http://bio2rdf.org/geneid_vocabulary:has_taxid> <http://bio2rdf.org/taxon:9606> .
Query: Construct dc:identifier triple for an NCBI gene from description
PREFIX dc:http://purl.org/dc/terms/
PREFIX gene_vocab: <http://bio2rdf.org/geneid_vocabulary:>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
CONSTRUCT {
?gene dc:description ?geneDescription .
} WHERE {
?gene rdf:type gene_vocabulary:Gene .
?gene gene_vocab:has_symbol "ABCA1" .
?gene gene_vocab:has_description ?geneDescription .
}
10. EXAMPLE: ASK
Data from Bio2RDF DrugBank dataset:
<http://bio2rdf.org/drugbank_resource:DB00072_DB00563> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http:
//bio2rdf.org/drugbank_vocabulary:Drug-Drug-Interaction .
<http://bio2rdf.org/drugbank_resource:DB00072_DB00563> <http://www.w3.org/2000/01/rdf-schema#label> "DDI between
Trastuzumab and Methotrexate - Trastuzumab may increase the risk of neutropenia and anemia. Monitor closely for signs and
symptoms of adverse events. [drugbank_resource:DB00072_DB00563]" .
<http://bio2rdf.org/drugbank:DB00072> <http://bio2rdf.org/drugbank_vocabulary:is-ddi-interactor-in> <http://bio2rdf.
org/drugbank_resource:DB00072_DB00563> .
<http://bio2rdf.org/drugbank:DB00563> <http://bio2rdf.org/drugbank_vocabulary:is-ddi-interactor-in> <http://bio2rdf.
org/drugbank_resource:DB00072_DB00563> .
Query: Is there a drug-drug interaction between trastuzumab and methotrexate?
PREFIX drugbank_vocab: <http://bio2rdf.org/drugbank_vocabulary:>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
ASK WHERE {
?ddi rdf:type drugbank_vocab:Drug-Drug-Interaction .
<http://bio2rdf.org/drugbank:DB00072> drugbank_vocab:is-ddi-interactor-in ?ddi .
<http://bio2rdf.org/drugbank:DB00563> drugbank_vocab:is-ddi-interactor-in ?ddi .
}
12. Bio2RDF summary metrics can be
used to develop SPARQL queries
● Each Bio2RDF endpoint contains summary
metrics about the dataset, including:
○ unique predicate-object links and their frequencies
○ unique predicate-literal links and their frequencies
○ unique subject type-predicate-object type links and
their frequencies
○ unique subject type-predicate-literal links and their
frequencies
● These can inform SPARQL query
development by describing the links that
exist between entities of a given type
13. Bio2RDF summary metrics can be
used to develop SPARQL queries
http://download.bio2rdf.org/release/2/drugbank/drugbank.html
14. Bio2RDF summary metrics can be
used to develop SPARQL queries
PREFIX drugbank_vocabulary: <http://bio2rdf.
org/drugbank_vocabulary:>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?ddi ?d1name
WHERE {
?ddi a drugbank_vocabulary:Drug-Drug-Interaction .
?d1 drugbank_vocabulary:ddi-interactor-in ?ddi .
?d1 rdfs:label ?d1name .
?d2 drugbank_vocabulary:ddi-interactor-in ?ddi .
?d2 rdfs:label ?d2name .
FILTER (?d1 != ?d2)
}
Results: http://bit.ly/14qGfUh
16. Bio2RDF query: Retrieve diseases
associated with the BRCA1 gene
PREFIX ctd_vocab: <http://bio2rdf.org/ctd_vocabulary:>
SELECT ?disease ?diseaseLabel
FROM <http://bio2rdf.org/ctd>
WHERE {
?assoc rdf:type ctd_vocab:Gene-Disease-Association .
?assoc ctd_vocab:gene <http://bio2rdf.org/geneid:672> .
?assoc ctd_vocab:disease ?disease .
?disease rdfs:label ?diseaseLabel .
}
Results: http://bit.ly/162NM9L
17. Bio2RDF federated query: Retrieve GO function
labels from BioPortal for a gene in NCBI gene
SELECT *
WHERE {
<http://bio2rdf.org/geneid:3253304> <http://bio2rdf.
org/geneid_vocabulary:function> ?goFunction .
SERVICE <http://bioportal.bio2rdf.org/sparql> {
?goFunction rdfs:label ?label .
}
}
Results: http://bit.ly/13D20SR
18. Bio2RDF query: Count all the biochemical
reactions in the BioModels database involved in
"protein catabolic process"
SELECT ?go ?label count(distinct ?x)
WHERE {
{
# get all the biochemical reactions specifically labelled with protein catabolic
process
?go rdfs:label ?label .
FILTER regex(?label, "^protein catabolic process")
service <http://biomodels.bio2rdf.org/sparql> {
?x <http://bio2rdf.org/biopax_vocabulary:identical-to> ?go .
?x a <http://www.biopax.org/release/biopax-level3.owl#BiochemicalReaction> .
}
} UNION {
# get all the biochemical reactions that are more specific than "protein catabolic
process"
?go rdfs:label ?label .
?go rdfs:subClassOf ?tgo OPTION (TRANSITIVE) . # get all the subclasses of the
target to term
?tgo rdfs:label ?tlabel .
FILTER regex(?tlabel, "^protein catabolic process")
service <http://biomodels.bio2rdf.org/sparql> {
?x <http://bio2rdf.org/biopax_vocabulary:identical-to> ?go .
?x a <http://www.biopax.org/release/biopax-level3.owl#BiochemicalReaction> .
}
}
}
Results: http://bit.ly/14qGWwC
19. Use the VOS Faceted Browser to
explore Bio2RDF data
● Explore types and attributes
● Free text search
20. Explore Bio2RDF data on
your own!
http://download.bio2rdf.org/release/2/release.html