Happy 10th birthday Bio2RDF and welcome to its 500th citation !

That is it, 10 years of being http://bio2rdf.org linked data service returning RDF from dereferenceable URIs according to the Linked data principles.

It all started in the November 23 2005




and here we are today with the 500th citations.

KaBOB VS Bio2RDF

KaBOB: ontology-based semantic integration of biomedical databaseshttp://www.biomedcentral.com/1471-2105/16/126/abstract

KaBOB recent paper describes how a mashup have been created using 14 ontologies and 18 data sources converted to RDF, all loaded into a triplestore which is not made public. Great work, a mashup well designed based on ontologies and data normalization a quality standard never really put into Bio2RDF's triplestores. Nice work but not available to the bioinformatician community and it is a lot of work to rebuild it from scratch.

The first step of my hackhaton project is to rebuil such a mashup from the dame data collection and expose it on the web as linked data, I will use the kabob.bio2rdf.org namespace for it.

In the past I would have created a triplestore for it, Virtuoso can easily handle 500 millions triples beast. I will try differently and will use Elasticsearch instead and Kibana as a user interface available at http://melina.bio2rdf.org.

KaBOB currently imports the following 14 ontologies:

1. Basic Formal Ontology (BFO) [9]
2. BRENDA Tissue / Enzyme Source (BTO) [10]
3. Chemical Entities of Biological Interest (ChEBI) [11] (54,838 from ONTOBEE)
4. Cell Type Ontology (CL) [12]
5. Gene Ontology including biological process, molecular function, and cellular component
(GO) [7] (42,807 from ONTOBEE)
6. Information Artifact Ontology (IAO) [6]
7. Protein-Protein Interaction Ontology (MI) [13]
8. Mammalian Phenotype Ontology (MP) [14]
9. NCBI Taxonomy [15]
10. Ontology for Biomedical Investigation (OBI) [16]
11. Protein Modification (MOD) [17]
12. Protein Ontology (PR) [18]
13. Relation Ontology (RO) [19]
14. Sequence Ontology (SO) [8]

KaBOB currently imports data from the following 18 data sources:

1. Database of Interacting Proteins (DIP) [20]
2. DrugBank [21] (19,844 from Bio2RDF)
3. Genetic Association Database (GAD) [22] ()
4. UniProt Gene Ontology Annotation (GOA) [23]
5. HUGO Gene Nomenclature Committee (HGNC) [24] (43,407 from Bio2RDF)
6. HomoloGene [25] (18,712 from Bio2RDF)
7. Human Protein Reference Database (HPRD) [26]
8. InterPro [27]  (25,272 from Bio2RDF)
9. iRefWeb [28]
10. Mouse Genome Informatics (MGI) [29] ()
11. miRBase [30]
12. NCBI Gene [31] (47,728 from Bio2RDF)
13. Online Mendelian Inheritance in Man (OMIM) [32] (14,609 from Bio2RDF)
14. PharmGKB [33] ()
15. Reactome [34] ()
16. Rat Genome Database (RGD) [35]
17. Transfac [36]
18. UniProt [37] (124,567)

In red is the number of document/graph loaded in ES.

Data source :

OBO : http://www.ontobee.org/sparql

Uniprot : http://beta.sparql.uniprot.org/sparql

and Bio2RDF corresponding SPARQL endpoints.

Bio2RDF 10th birthday this year, and I am back on the biohacking road

This weekend is the first biohackathon about BD2K in San Diego:

https://github.com/Network-of-BioThings/nob-hq/wiki/1st-BD2K-3rd-Network-of-BioThings-Hackathon

It is a good occasion to explore new avenue to expose RDF biological knowledge in the big data era. So let's try Elasticsearch... (https://www.elastic.co/products/elasticsearch)

it is free, fast and it scale. This would not be doable without the recent availability of the RDF version format in JSON, the JSON-LD project (http://json-ld.org/).

I will use the JSON-LD converter written by Peter Ansell, one of the major contributor to Bio2RDF, (https://github.com/jsonld-java).

So let's try to load some of Bio2RDF triples into ElasticSearch ! I have 24 hours to explore this new approach.

Here is what we will try to achieve :

1. RDF2ES : Bring KaBOB online as RDF REST services using ElasticSearch

1. Description.  KaBOB is a semantic integration of 18 different biomedically relevant knowledge sources.  The linked paper describes processes for instantiating it as RDF, but does not provide a functional implementation.  This is likely because of the significant challenges involved in stably hosting a very large SPARQL endpoint.  Perhaps SPARQL isn’t the best way to share this content.  This project is to figure out a way to the useful data integration work done in kaBOB available via a set of web services that are both fast and reliable.  Willing to sacrifice some of the flexibility of a full sparql endpoint to gain a functional app.  Perhaps using Elastic Search.
   
1. First we will load part of Kabob data source for human into an ElasticSearch cluster. (OMIM, GO, CHEBI, Drugbank, OBO ontologies, Reactome, Uniprot and entrez gene)
2. Second we will build REST services to access it, there will be available for hacking.
3. Third we will explore this data using Kibana tool.
4. Finally, we will illustrate how a Talend workflow consuming RDF data can replace a complex SPARQL query. The querying workflow will be exposed at MyExperiments.
2. input.  Instructions for integrating 18 different biological data sources + code at: https://github.com/UCDenver-ccp/datasource https://github.com/drlivingston/kr https://github.com/drlivingston/kabob I will use bio2rdf version of kabob selected dataset.
   
   If someone has access to Kabob RDF data, we could load it into ES triplestore.

output. web services that provide useful answers to questions about genes, biological process, and diseases, Those REST services will be created the way Bio2RDF API have been done, they are generated using Talend ESB tool (http://bio2rdf.org/test) and virtuoso triplestore will be replaced by ES storage.

We will try to create a type ahead user experience over those dataset, a feature that Bio2RDF have always been missing. (bio2rdf.org)

Finally, we will explore the data visualisation potential of the Kabina tool over ElasticSearch data in JSON-LD format.

Biocuration 2010 presentation

Here is the presentation given at Biocuration 2010 , October 13th

W4 4 marc-alexandre-nolin-v2

View more presentations from nolmar01.

Bio2RDF return to Japan

Bio2RDF is returning in Japan again this year. We will give a talk about Bio2RDF at Biocuration 2010 . Biocuration is from October 11th to October 14th at Odaiba, Tokyo.

Bio2RDF Cognoscope presentation at BioHackathon 2010 in Tokyo

François Belleau from the Bio2RDF project was invited as an early Semantic Web technology adopter to present the Bio2RDF project at the annual BioHackathon 2010 held each year in Tokyo.

Bio2RDF@BH2010

View more presentations from François Belleau.

Linking Open Drug Data wins the Triplify challenge

Congratulations to Kei's group and their Linking Open Drug Data (LODD) project for winning the Triplify challenge.

http://blog.aksw.org/2009/triplification-challenge-2009-winners/

http://triplify.org/files/challenge_2009/LODD.pdf

It is a new contribution to the LOD cloud and they have linked those new datasets to Bio2RDF and DBpedia URIs. That is the right way to do it !

The story so far of Linked Data, Bio2RDF is part of it !

In the latest publication of Tim Berner-Lee, he tells the recent story of emerging Linked Data, Bio2RDF is mentioned as an important Biology contributor. This paper is a must for anyone interested in this fantastic new approach.

http://tomheath.com/papers/bizer-heath-berners-lee-ijswis-linked-data.pdf

In this map of Linked Data, Bio2RDF contribution is shown in purple. The corresponding SPARQL endpoints are available here :

http://delicious.com/tag/bio2rdf:sparql

Bio2RDF is now using Virtuoso 6 and its new facet browser

Bio2RDF is moving from Virtuoso 5 to Virtuoso 6 server. The new software support facet browsing in real time.

We invite you to explore our graph with a full text search query for hexokinase. Once the results list is shown try the options in the right menu. Enjoy the discovery experience.

Try the 2009 version of "Atlas about Human and Mouse" :

http://atlas.bio2rdf.org/fct/

the graph can also be queried in sparql :

http://atlas.bio2rdf.org/sparql

The list of the Bio2RDF converted graph will be published and updated here :

The facet browsers list :
http://delicious.com/tag/bio2rdf:fct
The sparql endpoints list :
http://delicious.com/tag/bio2rdf:sparql

Bio2RDF visit at HCLS annual meeting

Bio2RDF team members Marc-Alexande Nolin, Michel Dumontier and Francois Belleau, have been invited to present actual state of the Bio2RDF project at the annual face to face meeting of the HCLS community. Here is a link to the presentation :

http://www.slideshare.net/fbelleau/bio2rdf-w3c-hcls2009

Thanks to the organizers of the event.

Bio2RDF @ W3C HCLS2009

View more presentations from Belleau François.

2,4 billions triples of Bioinformatics RAW DATA NOW

In his recent talk at TED, Tim Berner Lee invited the data provider to make available data in RDF format to help the building process of linked data web. He asked them to offer RAW DATA NOW.



We totally share this approach in the Bio2RDF community, our goal is to make public datasets from the bioinformatics community available in RDF format via standard SPARQL endpoints (Virtuoso server is used for that). We strongly believe in the semantic web approach to solve science problem but we do not want to wait for data provider to do the RAW DATA conversion job. Converting data to RDF is not fun, we did a lot of this dirty job, and here are the results for actual Bio2RDF release of 34 data sources.

Our current datasets in N3 format are available here :

http://quebec.bio2rdf.org/download/n3/

We invite semantic search engine provider to index these files.

The way we produce them is documented in our Wiki at SourceForge in the Cookbook section :

http://bio2rdf.wiki.sourceforge.net/Namespace%27s+update

The actual list of SPARQL endpoints in the linked data cloud is hosted here :

http://esw.w3.org/topic/TaskForces/CommunityProjects/LinkingOpenData/DataSets/Statistics

Bio2RDF 2,4 billions triples graph of linked data represents 51 % of the actual global linked data graph size.

Finally, this is what this highly connected knowledge world look like.



I would take this occasion to thanks all the enthusiast biologist and researcher who invest themselves by annotating article, protein and gene product. Without this essential work of connecting documents and concepts together, this project would not have been possible.

For the 20th anniversary of the web, I would also want to thanks Tim Berner Lee for his inspiring vision. Bio2RDF may not be the awaited killer app of the life science to demonstrate the semantic web potential, but let's say that it is only the beginning of the linked data cloud build by and for scientists.

The WWW2009 workshop Linked Data on the Web (LDOW2009) was held today, I would like to say how important the work of this community is. Finally a last word to congratulate Virtuoso team and especially Orri Erling for his fantastic work with the new Virtuoso 6.0 server soon to be released. I cannot wait to see Bio2RDF data into this amazing engine.

Bio2RDF's map new graphic representation

This word net represents the actual namespace connection between Bio2RDF SPARQL endpoints. RDF datasets which were analyzed comes from Bio2RDF's download page. These representations are generated with Many Eyes visualization tools.


Static version.

This graph represent connections between namespaces of Bio2RDF's network graph of SPARQL endpoints, highlighted orange dots corresponds to Bio2RDF rdfised database.


Static version.

Bio2RDF and Semantic Web Pipes

The Bio2RDF Servlet has been packaged with Semantic Web Pipes. It provides runtime support for pipes, without the designer. Pipes you design at either the public pipes website, or your own pipes webapp, will run inside your Bio2RDF server, providing another method for scripting your queries.

Once you download and install the Servlet you will be able to access the pipes functionality using URL's which look like the following:

http://localhost:8080/pipes/bio2rdf_subject_object_slicing/namespace=keywords/identifier=11

Each of the Parameter's in the pipe are entered using "name=value" combinations and put together using "/".

Download the latest Bio2RDF Servlet to experiment.

Bio2RDF's contribution to the GGG is on the map

I am very pleased to see that Bio2RDF contribution is now on the GGG map of linked data. A big thanks to all the data provider and the active members of the Bio2RDF group. All the SPARQL endpoints we provides are not there yet but it is a great beginning.

When Bio2RDF meets Taverna

Try this Taverna workflow to explore the possibilities of building a mashup on the fly from Bio2RDF's sparql endpoints.

What is known about HIV using Bio2RDF's SPARQL endpoints ?

Tabulator and Bio2RDF sparql point a new integrated way to surf genomic knowledge

Try the Tabulator generic data browser to surf the 2 billions triples from Bio2RDF sparql points network. Install the FireFox plugin and strart from here :

http://bio2rdf.org/demo

Semantic Web Challenge 2008 participation

The Bio2RDF team is presenting a demo at the Semantic Web Challenge 2008.

http://challenge.semanticweb.org/

Good luck to Marc-Alexandre, Michel and Peter and all the others team member.

The paper is available here.

Bio2RDF Network Of Linked Data

Bio2RDF OWL ontology finaly available

This is the new OWL ontology file description of Bio2RDF project. It is a rough description of most types and predicates in the new Bio2RDF network of sparql graph.

http://bio2rdf.org/bio2rdf-2008.owl

A nice way to discover it is by using Protege tool and the Ontoviz plugin.

Here is what 2 billions triples from 40 datasources looks like :

2,3 Billions triples made available by Bio2RDF 27 SPARQL endpoints

27 public SPARQL endpoints build with a Virtuoso server are made available to the scientific community. Enjoy.

The list of databases is available here :

http://www.freebase.com/view/user/bio2rdf/public/sparql

For example the followings SPARQL endpoints offer a complete copy of the corresponding databases :

http://biocyc.bio2rdf.org/sparql
http://kegg.bio2rdf.org/sparql
http://geneid.bio2rdf.org/sparql
http://go.bio2rdf.org/sparql
http://iproclass.bio2rdf.org/sparql
http://mesh.bio2rdf.org/sparql
http://obo.bio2rdf.org/sparql
http://reactome.bio2rdf.org/sparql
http://uniprot.bio2rdf.org/sparql

Bio2RDF project's litterature review

Those links brings you to the actual Bio2RDF publications available.

The presentation are on SlideShare.

Bio2RDF: Towards a mashup to build bioinformatics knowledge systems published in Journal of Biomedical Informatics. Its pubmed entry pubmed:18472304.

The initial version presented at WWW2007 HCLS Workshop.

Bio2RDF : A Semantic Web Atlas of Post Genomic Knowledge about Human and Mouse part of Data Integration in the Life Sciences 5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008.

And a look in Google Scholar for citations.