Re: BioRDF Telcon
Responses in line. 1. We have text mined much of the Affymetrix GEO data, curated it and imported it into ArrayExpress - there is now much better sample annotation than the native data in GEO. We also are running QC across all the data files so we know which should be excluded for future analyses. I think it's the right thing to do both to enrich data annotation and to enhance data quality. This will help data integration a lot. Currently, we are exploring query federation in the neuroscience context. It'd be great if we can use the neuroscience use case(s) to help drive your ontology development for text mining and data visualization. In addition to the NIH neuroscience microarray consortium, it may be possible to collaborate with the Neuroscience Information Framework (NIF) to see if we can utilize some of its resources (e.g., neuron ontology). Re-use of the neuron ontology is possible, but it depends on whether there is available data to annotate either in ArrayExpress or GEO. If you can get me a list of experiments accessions or pubmed ids I can see if this is feasible 3. We have summary level data of genes x conditions for ~30,000 hybs worth of data in our gene expression atlas with p values indicating relative under/over-expression. We are planning to export these as triples as soon as we publish the atlas - these may be of interest. www.ebi.ac.uk/gxa - there's an API at present, but it will be improved in the next month or so. It fits well with what we're currently exploring in terms of gene list representation and linking genes and samples to existing ontologies. It'd be great if we can download or fetch RDF triples from EBI atlas. We have a student starting work on this in a month, if you can produce concrete use cases for how you want to access these data we can do something. 4. If neuroscience data is of specific interest we could do a themed atlas release where we add datasets for a given community or project and make these available. These can be identified by ArrayExpress or GEO accession or pubmed and we can re-annotate the genes vs Uniprot/Ensembl, add GO terms, etc and curate the sample attributes and experimental variables. These pipelines are already in place as part of our production workflow. I think it's a great idea to do a themed atlas (e.g., neuro-atlas). I just played with gxa a little bit. It's nice! For example, I could find genes that are over-expressed in the hippocampus brain region across different experiments. However, when I tried to do the same thing for neurons, there are only a few neuron types that I can select. It'd be nice if we can have more neuron types, for instance. This is probably as we don't have data - here's a list of human experiments with the term neuron - if any of these are useful, then I can prioritise their curation and inclusion in an atlas release http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=neuronspecies=Homo+sapiensarray=exptype=pagesize=25sortby=releasedatesortorder=descending and brain http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=brainspecies=Homo+sapiensarray=exptype=pagesize=25sortby=releasedatesortorder=descending I'd be very happy to collaborate, and for this group to use our data, we spend a lot of time adding semantic value to it, so please let me know if this is of interest We are also looking into the possibility of establishing collaboration with the scientific discourse task force based on the microarray use case. We're planning to have a microarray-related presentation and discussion on Aug. 31 (Monday, 11 am EDT/5 pm CET). Details will be announced later. It'd be great if you can join the BioRDF call to participate in the discussion. Cheers, -Kei best regards Helen Kei Cheung wrote: The minutes for yesterday's BioRDF call are available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009-07-20_Conference_Call Thanks to Lena for scribing and Eric for retrieving the transcript from the IRC log. Cheers, -Kei Kei Cheung wrote: This is a reminder that the next BioRDF teleconf. will be held at 11 am EDT (5 pm CET) on Monday, July 20 (see details below). I created the following wiki page for discussing the microarray use case: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Cheers, -Kei == Conference Details == * Date of Call: Monday July 20, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 (HCLS) * IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call and introduction (Kei) * TCM data quick update (Jun, Kei) * Query
Second CfP: 2nd international workshop on Social Data on the Web (SDoW2009), colocated with ISWC2009
Apologies for cross-postings. Please forward to interested colleagues and mailing lists. *** Submissions deadline extended until August 10th *** CALL FOR PAPERS: SDoW2009 2nd International Workshop on Social Data on the Web (SDoW2009) October 25, 2009 collocated with ISWC-2009 Westfields Conference Center, near Washington, DC., USA Paper submission: August 10, 2009 http://sdow.semanticweb.org/2009/ The 2nd International Workshop on Social Data on the Web (SDoW2009), co-located with the 8th International Semantic Web Conference (ISWC2009), aims to bring together researchers, developers and practitioners involved in semantically-enhancing social media websites, as well as academics researching more formal aspect of these interactions between the Semantic Web and Social Web. Important dates --- * Submission deadline:Aug 10, 2009 * Notification of acceptance: Sep 04, 2009 * Camera-ready paper submission: Oct 02, 2009 * Camera-ready proceedings: Oct 09, 2009 * Workshop: Oct 25, 2009 Description --- Since its first steps in 2001, many research issues have been tackled by the Semantic Web community such as data formalism for knowledge representation, data querying and scalability, or reasoning and inferencing. More recently, Web 2.0 offered new perspectives regarding information sharing, annotation, and social networking on the Web. It opens new research areas for the Semantic Web which has an important role to play to lead to the emergence of a Social Semantic Web that should provide novel services to end-users, combining the best of both Semantic Web and Web 2.0 worlds. To achieve this goal, various tasks and features are needed from data modelling and lightweight ontologies, to knowledge and social networks portability as well as ways to interlink data between Social Media websites, levering proprietary data silos to a Giant Global Graph. Following the successful SDoW2008 workshop at ISWC2008, SDoW2009 aims to bring together Semantic Web experts and Web 2.0 practitioners and users to discuss the application of semantic technologies to data from the Social Web. Topics of interest -- Topics of interest include, but are not limited to: * Applications and tools using Social Semantic Web technologies * Creating RDF-based knowledge using social media services * Data Portability and Social Network Portability * Emerging semantic platforms for the Social Web * Enriching Social Web with semantic data - RDFa, microformats and other approaches * Linked Data on the Social Web - providing linked data from social media sites * Mining and analysis of Social Data * Ontologies for the Social Web - developing, using and extending lightweight ontologies/vocabularies for social media sites * Querying and mining social semantic data * Policies, authentication, security, and trust within collaborative scenarios * Producing Semantic Web data from social software applications * Reasoning for Social Web applications * Semantic blogging, wikis and social networks * Semantically-Interlinked Online Communities (SIOC) * Social and semantic bookmarking, tagging and annotation * Using Semantic Web technologies for Social Data integration Submissions --- The following types of contributions are welcomed: * Full technical papers, up to 12 pages. * Short technical papers and position papers, up to 6 pages. * Posters and Demos, 2-3 pages with a description of the application, ideally accompanied with a link to an online demo. Workshop Chairs --- * John Breslin, DERI, NUI Galway, Ireland * Uldis Bojārs, DERI, NUI Galway, Ireland * Alexandre Passant, DERI, NUI Galway, Ireland * Sergio Fernández, Fundación CTIC, Spain Program Committee - * Alessandra Toninelli, Università di Bologna, Italy * Chris Bizer, Freie Universität Berlin, Germany * Dan Brickley, FOAF project Vrije Universiteit Amsterdam, The Netherlands * Denny Vrandecic, DFKI, University of Karlsruhe, Germany * Diego Berrueta, Fundación CTIC, Spain * Eric Prud'hommeaux, MIT, USA / W3C, USA * Fabien Gandon, INRIA, France * Frederick Giasson, Zitgist, Canada * Gunnar Aastrand Grimnes, DFKI Knowledge Management Lab, Germany * Harry Halpin, University of Edinburgh, UK * Hideaki Takeda, National Institute of Informatics, Japan * Hugh Glaser, University of Southampton, UK * Jie Bao, Rensselaer Polytechnic Institute, USA * Jose E. Labra, University of Oviedo, Spain * Josephine Griffith, NUI Galway, Ireland * Kotaro Nakayama, The University of Tokyo, Japan * Li Ding, Rensselaer Polytechnic Institute, USA * Libby Miller, BBC, UK * Olaf Hartig, Humboldt-Universität zu Berlin,
Re: Can RDFa be used on XML: pharma information
I am sorry if I come into this thread very late. Additionally to what Ralph just said, the RDFa distiller running on the W3C site: http://www.w3.org/2007/08/pyRdfa/ should actually work with an arbitrary XML file, although only SVG is 'announced' there (which is probably my mistake). If there is a problem then, well... it is my bug:-( Ivan Ralph R. Swick wrote: At 10:48 PM 6/23/2009 +1000, Rick Jelliffe wrote: I see that the 2008 draft http://www.w3.org/2006/07/SWD/RDFa/rdfa-overview says RDFa itself is intended to be a technique that allows for adding metadata to any (XML) markup document, including SMIL, RSS, SVG, MathML, etc. Note, however, that in the current state, RDFa is being defined only for the (X)HTML family of languages. The RDFa specification was designed with the intent that other languages than XHTML could take advantage of RDFa markup. (The terminology host language was used in some drafts to signal this direction.) The charter under which the group was operating was specific to XHTML, thus the wording in the W3C Recommendation. So I think I will go ahead and add some RDFa markup to the XML, By all means, reuse the RDFa vocabulary if it seems appropriate for your application. -- Ivan Herman, W3C Semantic Web Activity Lead Home: http://www.w3.org/People/Ivan/ mobile: +31-641044153 PGP Key: http://www.ivan-herman.net/pgpkey.html FOAF: http://www.ivan-herman.net/foaf.rdf smime.p7s Description: S/MIME Cryptographic Signature
LODD Telcon Minutes
Minutes from today's LODD telcon are now available. http://esw.w3.org/topic/HCLSIG/LODD/Meetings/2009-07-22_Conference_Call Thanks to Anja for scribing. Susie
Early Bird Registration ends 31st July - 5th i-Semantics 2009/4th AIS SigPrag Int. Pragmatic Web
[Call for Participation - apologies for cross-posting] Dear Colleagues, We would like to invite you to participate in the 5th International Conference on http://i-semantics.tugraz.at/ Semantic Systems (i-Semantics 2009) and the 4th http://www.pragmaticweb.info/index.php?option=com_contenttask=viewid=51I temid=1 AIS SigPrag International Pragmatic Web Conference Track (ICPW 2009) which will be held at together with the i-Know 2009, 2 - 4 September 2009, Messecongress|Graz, Austria. i-Semantics 2009: http://i-semantics.tugraz.at/ Pragmatic Web: http://www.pragmaticweb.info/index.php?option=com_content http://www.pragmaticweb.info/index.php?option=com_contenttask=viewid=51I temid=1 task=viewid=51Itemid=1 The early-bird registration will end 31 July 09 - http://i-semantics.tugraz.at/registration We are building a highly interesting program. Highlights of the program - - 3 Keynotes x Peter Kropsch (CEO Austrian Press Agency) When technologies are drivers, integrated concepts are needed for success! x Paolo Traverso (Director of the Center for Information Technology - IRST) Towards a Future Internet of Services and Content x Professor Eric Tsui (Associate Director of the Knowledge Management Research Centre, The Hong Kong Polytechnic University, China) KM education, adoption and research in Hong Kong: The KMRC perspective - 4th AIS SigPrag Pragmatic Web Conference Track x Pragmatic Web Panel Discussion x Pragmatic Web Tutorial by Ronald Stamper (Professor (retired) University of Twente) about Organizational Semiotics and Pragmatic Web - 3rd International Cooperation-Event - LINKED OPEN DATA Triplification Challenge - Exibition - Semantic Web Industry Day - Podiumsdiskussion - Paper Presentations All together we received 128 submissions from which 20 full papers and 9 short papers were selected for i-Semantics 2009 and 5 full papers and 5 short papers were selected for the Pragmatic Web conference track. You will be offered an exciting venue to exchange new ideas and learn more about Semantic Web, Pragmatic Web, Corporate Semantic Web, Linked Open Data Web, Social Semantic Web, Organizational Semiotics, as well as practical developments, standards and experiences in latest industry technologies in these fields. The full i-Semantics/Pragmatic Web program is available at: http://i-semantics.tugraz.at/program The registration page is available at: http://i-semantics.tugraz.at/registration We are looking forward to welcome you in Graz! Your i-Semantics/Pragmatic Web team
RE: BioRDF Telcon
hi kei and helen, like helen, i've been following the HCLS working groups with great interest. as one of the designers, with helen, of the MAGE-ML and MAGE-TAB specs i might be able to provide a little technical insight into the formats. (from helen) This is probably as we don't have data - here's a list of human experiments with the term neuron - if any of these are useful, then I can prioritize their curation and inclusion in an atlas release kei, are the NIH Neuroscience Microarry Consortium exeriments you've cited and others like them in GEO or ArrayExpress? a set of those could be a good starting point for helen. first, MAGE-ML is based on a DTD[1], not an XSD. in early 2002 as the OMG Gene Expression specification[1] was being finalized, XSD was still in its infancy so we weren't comfortable at that point generating a XSD. the MAGE-OM UML[2], in a very early XMI format from Rational Rose and UniSys, was used to generate the DTD with code we wrote ourselves[3]. the UML model was designed to capture the flow of a microarray experiment and how the resulting arrays were organized in the experiment based on how the samples were treated and/or on the samples' phenotypes for the purpose of a reviewer understanding the methodology and for a researcher replicating and/or re-analyzing the results. some of the details of the flow may not be of much interest, i.e. it might be worth simply connecting the BioSource elements with their gene expression data and not worrying about how the hybridization was performed. but that depends on what you want to do and you know that better than i. also, the data itself are specified in external files, typically in a white-space delimited format where the column headers are specified in the MAGE-ML file in the QuantitationTypeDimension element and the identifiers of the row specified in one of the three DesignElementDimension elements, Feature, Reporter, CompositeSequence, depending on how derived the data is. Also the data can be in a vendor specific format such as the Affymetrix CEL (since the CEL file internally specifies the dimensions often they are left out of the MAGE-ML document). the ExperimentalFactor elements are certainly relevant and if you've looked at some of the examples you will noticed that the BioSource elements, in particular, and other elements are annotated by OntologyEntry elements. from the gene expression specification: OntologyEntry A single entry from an ontology or a controlled vocabulary. For instance, category could be 'species name,' value could be 'homo sapiens' and ontology would be taxonomy database, NCBI. for the element an ontology entry element is annotating, we looked at it as a way of specifying something like the object identified by the element is an instance of the class/individual specified by the OntologyEntry so from kitm-affy-droso-176167 one sees that the BioSource is an instance of Drosophila, whole animal, whole head and an age of 3 days: BioSource identifier=arrayconsortium.tgen.org::biosource.181527 name=Oregon R head 3d Characteristics_assnlist OntologyEntry category=Organism value=Drosophila description=Drosophila OntologyReference_assn DatabaseEntry accession=#Organism URI=http://mged.sourceforge.net/ontologies/MGEDontology.php#Organism; Database_assnref Database_ref identifier=MO/ /Database_assnref /DatabaseEntry !-- snip -- /OntologyReference_assn /OntologyEntry OntologyEntry category=OrganismPart value=whole animal description= OntologyReference_assn DatabaseEntry accession=#OrganismPart URI=http://mged.sourceforge.net/ontologies/MGEDontology.php#OrganismPar t Database_assnref Database_ref identifier=MO/ /Database_assnref /DatabaseEntry /OntologyReference_assn !-- snip -- /OntologyEntry OntologyEntry category=OrganismPartRegion value=whole head description= !-- snip -- /OntologyEntry !-- snip -- OntologyEntry category=Age value=Age OntologyReference_assn DatabaseEntry accession=#Age URI=http://mged.sourceforge.net/ontologies/MGEDontology.php#Age; Database_assnref Database_ref identifier=MO/ /Database_assnref /DatabaseEntry /OntologyReference_assn Associations_assnlist OntologyEntry category=has_measurement value=has_measurement OntologyReference_assn DatabaseEntry accession=#has_measurement
