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
Monday, July 20, 2009
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
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
Wednesday, July 01, 2009
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
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.
http://www.slideshare.net/fbelleau/bio2rdf-w3c-hcls2009
Thanks to the organizers of the event.
Bio2RDF @ W3C HCLS2009
View more presentations from Belleau François.
Monday, June 29, 2009
0.6.1 bug fix release now available
A maintenance release, version 0.6.1 was released today on sourceforge [1]. There were a few coding bugs in the 0.6.0 release relating to the namespace match method "all", the rdf rule order was not being imported from the configuration properly resulting in queries which relied on more than one rule not getting any results back, and included static RDF/XML sections were not being included. There was also a fix related to default providers that eliminates duplicate queries for namespaces where a namespace was assigned to a default provider for a query that allowed default providers.
The configuration files have also been updated, although people using the live configuration method (the default) would have received the configuration changes already. Some performance improvements related to logging have also been made that in some circumstances will dramatically improve the performance of the package, although the majority of the overall request latency is still related to internet latency related to the SPARQL queries.
From this version on, I will also be releasing MD5 hashes for each of the downloaded files so people can check that their downloaded file matches the release on sourceforge.
[1] https://sourceforge.net/project/platformdownload.php?group_id=142631
The configuration files have also been updated, although people using the live configuration method (the default) would have received the configuration changes already. Some performance improvements related to logging have also been made that in some circumstances will dramatically improve the performance of the package, although the majority of the overall request latency is still related to internet latency related to the SPARQL queries.
From this version on, I will also be releasing MD5 hashes for each of the downloaded files so people can check that their downloaded file matches the release on sourceforge.
[1] https://sourceforge.net/project/platformdownload.php?group_id=142631
Tuesday, June 23, 2009
Version 0.6.0 of the Bio2RDF server software released
The next version of the Bio2RDF software, version 0.6.0 was released today on sourceforge [1]
It has some major feature additions over the previous version, with the highlights being an RDF based configuration, the ability to update the configuration while the server is running, and support for sophisticated profiles so that users can pick and choose sources without having to change the basic configuration sources that are shared between different users. If users want to add or subtract from the base configuration they can create a small RDF file on their server and use that file to pick which sources they want to use and which queries they want to be able to execute.
If anyone wants to check out the example [2] and use it as a guide to mock up some SPARQL queries or definitions for endpoints that go with the queries it would be great to see what other resources we can combine into the global Bio2RDF configuration. If you need pointers in how to get your own configuration working feel free to ask me.
[1] https://sourceforge.net/project/platformdownload.php?group_id=142631
[2] http://bio2rdf.wiki.sourceforge.net/sample+configuration
It has some major feature additions over the previous version, with the highlights being an RDF based configuration, the ability to update the configuration while the server is running, and support for sophisticated profiles so that users can pick and choose sources without having to change the basic configuration sources that are shared between different users. If users want to add or subtract from the base configuration they can create a small RDF file on their server and use that file to pick which sources they want to use and which queries they want to be able to execute.
If anyone wants to check out the example [2] and use it as a guide to mock up some SPARQL queries or definitions for endpoints that go with the queries it would be great to see what other resources we can combine into the global Bio2RDF configuration. If you need pointers in how to get your own configuration working feel free to ask me.
[1] https://sourceforge.net/
[2] http://bio2rdf.wiki.
Friday, May 08, 2009
Version 0.5.0 of the Bio2RDF server software released
The next version of the server software has been released on sourceforge. [1]
It contains a number of changes that will hopefully make it more useful for the tasks we want to do with linked rdf queries.
One major one is the introduction of content negotiation, which has been tested for N3 (using text/rdf+n3) and RDF/XML (using application/rdf+xml). It was made possible this quickly after the last release by the use of the content negotiation code from Pubby, the driver behind the DBpedia web interface and URI resolution mechanism. It is also possible to explicitly get to the N3 format currently by prefixing the URL with /n3/ See [2] for an example. The ability to explicitly get to the RDF/XML will be added in future.
Another change that will hopefully be useful is the introduction of clear RDF level error messages when either the syntax of a URI is not recognised, or the syntax was recognised but there were no providers that were relevant to the URI. See [3], [4] and [5] for a demonstration of the error messages.
There is also the ability to page through the results, which is necessary when there are more than 2000 results to a query from a particular endpoint. To use the paging facility the URI needs to be prefixed by /pageoffsetNN/, where NN is a number indicating which page you would like to look at. The queries are not ordered currently, but in the short term it would be reasonable to believe that they should be consistent enough to get through all of the results. Ordered queries take a lot longer than unordered queries, so it is unlikely that the public mirrors will ever introduce ordered queries. An example of the paging URL could be [6] or [7].
There is also the ability to get an RDF document describing what actions would be taken for a particular query. It is interoperable with the /n3/ and /pageoffsetNN/ URI manipulations so URI's like [8] can be made up and resolved. This RDF document is setup to contain all of the necessary information for the client to then complete the query with their own network resources if necessary. In future, clients should be able to patch into this functionality without having to keep a local copy of the configuration on hand, although a distributed configuration idea is also in the works for sometime in the future. Currently the distribution is readonly from [9]. The [9] URL has also been made content negotiable for HTML/RDFXML/N3 content types, with a default to HTML if the content type is not recognised by the Sesame Rio library, but it can still be accessed in a particular format without content negotiation by appending /html /n3 or /rdfxml .
Since the last release the GeoSpecies dataset has also been partially integrated, although it doesn't seem to have a sparql endpoint so currently it is only available for basic construct queries. [10] Not all of the namespaces inside the geospecies dataset have rules for normalisation to Bio2RDF URI syntax, but the rest will be integrated eventually.
The order of normalisation rules is now respected when applying them, with lower numbers being applied before higher numbers. Numbers with the same order cannot be relied on to be applied in a consistent manner if they overlap syntactically.
The MyExperiment SPARQL endpoint [11] has also been integrated into Bio2RDF since the last release, so for instance, a user in the MyExperiment system can be resolved using [12], but there are also other things like workflows which could in the future provide valuable interconnections for the linked rdf web. Further integration with MyExperiment would be invaluable to the future of the Bio2RDF network I think.
Partial support for INCHI resolution has also made it into this release, although there are some syntax bugs with rdf.openmolecules.net that stop Sesame being able to parse the resulting RDF/XML so the inchi's are only being resolved using pubchem so far. Some INCHI's, particularly those which contain + signs will also be unresolvable for the current time because the Apache HTTPD and Apache Tomcat and URLRewrite stack we are using unurlencodes the plus signs to spaces somewhere along the line and it is hard to figure out what configuration is needed to avoid it happening. It was hard enough figuring out how to make encoded slashes (%2F) usable inside identifiers (they need to be double encoded as %252F to avoid detection by the HTTPD/Tomcat/URLRewrite algorithms), so I am not sure what progress will be made with the plus signs in the near future.
DOI resolution has also been integrated from both the Uniprot Citations database and the BioGuid.info, but will likely only be fully useful for science related DOI's I think.
There are currently 368 namespaces known by the server software for Bio2RDF, with 231 information provider configurations (although the real number of providers is less than this due to duplication on a few providers to enable reverseconstruct, and unpercentencoded queries where necessary) The number of combinations that are currently encapsulated by the server configuration can be found at [13]
It is hard to believe so much could be packed into a new release two weeks after the last release!
See the complete list of changes at [14].
If anyone has alternative configurations that they have made up using the software I am more than willing to include them in the distribution so others can utilise them. The configuration file syntax is still in flux, and won't likely become stable until the 1.0 release, but it is mostly additions to support new features, so configurations based on older software versions are still useful and able to be migrated to the new scheme.
[1] https://sourceforge.net/project/platformdownload.php?group_id=142631
[2] http://qut.bio2rdf.org/n3/geneid:14456
[3] http://qut.bio2rdf.org/dummyquery/go:0004535
[4] http://qut.bio2rdf.org/image/geneid:14936
[5] http://qut.bio2rdf.org/GO:0004535
[6] http://qut.bio2rdf.org/n3/pageoffset2/chr:10090-chr14
[7] http://qut.bio2rdf.org/pageoffset2/chr:10090-chr14
[8] http://qut.bio2rdf.org/n3/queryplan/pageoffset2/chr:10090-chr14
[9] http://qut.bio2rdf.org/admin/configuration
[10] http://qut.bio2rdf.org/geospecies_bioclass:13
[11] http://rdf.myexperiment.org/sparql
[12] http://qut.bio2rdf.org/myexp_user:1177
[13] http://qut.bio2rdf.org/admin/namespaceproviders
[14] http://bio2rdf.wiki.sourceforge.net/Road+map
It contains a number of changes that will hopefully make it more useful for the tasks we want to do with linked rdf queries.
One major one is the introduction of content negotiation, which has been tested for N3 (using text/rdf+n3) and RDF/XML (using application/rdf+xml). It was made possible this quickly after the last release by the use of the content negotiation code from Pubby, the driver behind the DBpedia web interface and URI resolution mechanism. It is also possible to explicitly get to the N3 format currently by prefixing the URL with /n3/ See [2] for an example. The ability to explicitly get to the RDF/XML will be added in future.
Another change that will hopefully be useful is the introduction of clear RDF level error messages when either the syntax of a URI is not recognised, or the syntax was recognised but there were no providers that were relevant to the URI. See [3], [4] and [5] for a demonstration of the error messages.
There is also the ability to page through the results, which is necessary when there are more than 2000 results to a query from a particular endpoint. To use the paging facility the URI needs to be prefixed by /pageoffsetNN/, where NN is a number indicating which page you would like to look at. The queries are not ordered currently, but in the short term it would be reasonable to believe that they should be consistent enough to get through all of the results. Ordered queries take a lot longer than unordered queries, so it is unlikely that the public mirrors will ever introduce ordered queries. An example of the paging URL could be [6] or [7].
There is also the ability to get an RDF document describing what actions would be taken for a particular query. It is interoperable with the /n3/ and /pageoffsetNN/ URI manipulations so URI's like [8] can be made up and resolved. This RDF document is setup to contain all of the necessary information for the client to then complete the query with their own network resources if necessary. In future, clients should be able to patch into this functionality without having to keep a local copy of the configuration on hand, although a distributed configuration idea is also in the works for sometime in the future. Currently the distribution is readonly from [9]. The [9] URL has also been made content negotiable for HTML/RDFXML/N3 content types, with a default to HTML if the content type is not recognised by the Sesame Rio library, but it can still be accessed in a particular format without content negotiation by appending /html /n3 or /rdfxml .
Since the last release the GeoSpecies dataset has also been partially integrated, although it doesn't seem to have a sparql endpoint so currently it is only available for basic construct queries. [10] Not all of the namespaces inside the geospecies dataset have rules for normalisation to Bio2RDF URI syntax, but the rest will be integrated eventually.
The order of normalisation rules is now respected when applying them, with lower numbers being applied before higher numbers. Numbers with the same order cannot be relied on to be applied in a consistent manner if they overlap syntactically.
The MyExperiment SPARQL endpoint [11] has also been integrated into Bio2RDF since the last release, so for instance, a user in the MyExperiment system can be resolved using [12], but there are also other things like workflows which could in the future provide valuable interconnections for the linked rdf web. Further integration with MyExperiment would be invaluable to the future of the Bio2RDF network I think.
Partial support for INCHI resolution has also made it into this release, although there are some syntax bugs with rdf.openmolecules.net that stop Sesame being able to parse the resulting RDF/XML so the inchi's are only being resolved using pubchem so far. Some INCHI's, particularly those which contain + signs will also be unresolvable for the current time because the Apache HTTPD and Apache Tomcat and URLRewrite stack we are using unurlencodes the plus signs to spaces somewhere along the line and it is hard to figure out what configuration is needed to avoid it happening. It was hard enough figuring out how to make encoded slashes (%2F) usable inside identifiers (they need to be double encoded as %252F to avoid detection by the HTTPD/Tomcat/URLRewrite algorithms), so I am not sure what progress will be made with the plus signs in the near future.
DOI resolution has also been integrated from both the Uniprot Citations database and the BioGuid.info, but will likely only be fully useful for science related DOI's I think.
There are currently 368 namespaces known by the server software for Bio2RDF, with 231 information provider configurations (although the real number of providers is less than this due to duplication on a few providers to enable reverseconstruct, and unpercentencoded queries where necessary) The number of combinations that are currently encapsulated by the server configuration can be found at [13]
It is hard to believe so much could be packed into a new release two weeks after the last release!
See the complete list of changes at [14].
If anyone has alternative configurations that they have made up using the software I am more than willing to include them in the distribution so others can utilise them. The configuration file syntax is still in flux, and won't likely become stable until the 1.0 release, but it is mostly additions to support new features, so configurations based on older software versions are still useful and able to be migrated to the new scheme.
[1] https://sourceforge.net/project/platformdownload.php?group_id=142631
[2] http://qut.bio2rdf.org/n3/geneid:14456
[3] http://qut.bio2rdf.org/dummyquery/go:0004535
[4] http://qut.bio2rdf.org/image/geneid:14936
[5] http://qut.bio2rdf.org/GO:0004535
[6] http://qut.bio2rdf.org/n3/pageoffset2/chr:10090-chr14
[7] http://qut.bio2rdf.org/pageoffset2/chr:10090-chr14
[8] http://qut.bio2rdf.org/n3/queryplan/pageoffset2/chr:10090-chr14
[9] http://qut.bio2rdf.org/admin/configuration
[10] http://qut.bio2rdf.org/geospecies_bioclass:13
[11] http://rdf.myexperiment.org/sparql
[12] http://qut.bio2rdf.org/myexp_user:1177
[13] http://qut.bio2rdf.org/admin/namespaceproviders
[14] http://bio2rdf.wiki.sourceforge.net/Road+map
Tuesday, April 21, 2009
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.
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.
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