Working Groups/Science/swat4ls hackathon/participants

=Participants= ''Registered as of Dec. 1st, 2011. In random order.''

Peter Murray-Rust
Open Bibliography #quixote Open Computational Chemistry Chemical Markup Language #bkn Bibliographic Knowledge network #blueobelisk Community for open Source chemistry

David Shotton
Member of original Open Research Reports team. Interested in publishing open infectious disease information   With Tanya Gray, I have developed MIIDI, the Minimum Information standard for reporting an Infectious Disease Investigation, and a MIIDI Editor that can form the basis for Open Research Reports. This has been funded by the JISC as part of the Dryad-UK Project for which I was PI. This followed from semantic publishing work on an infectious disease paper: See links below    http://www.miidi.org  http://www.miidi.org:8080/input-form  Semantically enhanved infectious disease paper: http://imageweb.zoo.ox.ac.uk/pub/2008/plospaper/latest/  Papers describing this work:  Shotton D, Portwin K, Klyne G, Miles A (2009). Adventures in semantic publishing: exemplar semantic enhancement of a research article. PLoS Computational Biology 5: e1000361. http://dx.doi.org/10.1371/journal.pcbi.1000361. Shotton D (2009). Semantic Publishing: The coming revolution in scientific journal publishing. Learned Publishing 22: 85-94. http://dx.doi.org/10.1087/2009202

Tanya Gray
Researcher   To contribute to the Open Research Reports initiative. MIIDI - Minimum Information about an Infectious Disease Investigation MIIDI Editor   www.miidi.org

Gilles Frydman
Patients access to full text articles

Jenny Molloy
Coordinator of Open Data in Science Working Group at the Open Knowledge Foundation. Not a coder/developer so I'll be an ideas/communications person during the hackathon.

Alf Eaton
Mendeley Web Library

Juha Muilu
Semantic data standards for Life Science, particularly for describing genetic variation. GEN2PHEN - Genotype to Phenotype Project. http://gen2phen.org VarioML Data Standard http://varioml.org VarioML Data Standard http://varioml.org VarioML is a data integration solution that creates a layer of meaning above the many variation standards and formats used across labs and clinics, enabling them to be integrated and made sense of as a whole

Achille Zappa
LOGVD Linked Open Gene Variation Data (http://bioinformatics.istge.it/logvdsparql/ & http://bioinformatics.istge.it/logvd/). The research topic relevant to my doctoral research is related to semantic data integration for translational research in oncology. At the moment my work is focused on gene mutations and variations for humans. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework. [not a real coder for now ;)]

Robert Cox
RIKEN BASE

David Gifford
Biological Linked Open Data   www.scinets.org www.biolod.org

Koro Nishikata
I am interested in researches and development of Semantic Web applications and tools, and Linked Open Data related to life science area. The BioLOD.org project   Web site: http://biolod.org  BioLOD.org provides biological open data according to the W3C LOD standard format of the Linking Open Data project similar to DBpedia and Bio2RDF. The BioLOD.org project is supported by the National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (JST), and RIKEN Institute of Physical and Chemical Research. BioLOD.org is developed and maintained by RIKEN BASE (Bioinformatics And Systems Engineering Division)

Norio KOBAYASHI
BioSPARQL

Tetsuro Toyoda
RIKEN

James Dodd
I'm about to begin a software development project as part of a Computer Science masters at Birkbeck, and I'm keen to get lots of ideas.

Jacek Grzebyta
Phi base website, domain model

Brian Hole
REWARD - Researchers using Established Workflows to Archive Research Data   http://www.ucl.ac.uk/reward I also work at Ubiquity Press, where we are about to release a new platform of data journals. ORRs are a good example of a data, or metadata paper for this platform, so we are very interested in how we can incorporate MIIDI metadata in these.

Götz Fabian
DOG4DAG, a tool for semi-automatic ontology generation and extension. DOG4DAG stands for Dresden Ontology Generator for Directed Acyclic Graphs. Here's a website to our tool, containing links to the Protégé and OBO-Edit plugins: http://www.biotec.tu-dresden.de/research/schroeder/dog4dag/

M. Scott Marshall
The Life Sciences and Health Care Semantic Web is blossoming!

Clinic - a good launching pad for Semantic Web
I believe that the life sciences Semantic Web will get the most initial traction (no pun intended!) in the clinic with patient data and CDS. At the moment, simple forms of information retrieval from hospital IT (e.g. "How many liver patients checked in on Tuesday?") require an API contortionist! Other nice drivers: biobanking, personalized medicine, data sharing in general. UK just announced 70M pounds support for ELIXIR.

RDF representations and tool support for key data types
I think that the best way to encourage uptake is to create RDF representations for data types and instrumentation (and its metadata), as well as to create builtin support for early semantic commitment at the point of experimental design in the tools that scientists use the most (see, for example, Rightfield). So, as another example, we are planning to build support for the expression RDF (in #1 below )into R tools - Jim McCusker (Yale/RPI) has already done this to some extent.

HCLS
Just finished a three year charter as co-chair of the W3C Health Care and Life Sciences Interest Group. Can still see my blogs here: http:// http://www.w3.org/blog/hcls/

In HCLS, we've just had an article accepted to Future Medicine's Pharmacogenomics journal "Semantically enabling pharmacogenomic data for the realization of personalized medicine". In followup work, we are creating a SPARQL endpoint for dbSNP and incorporating it into a Clinical Decision Support (CDS) system that makes use of the Translational Medicine Ontology (now extending for the representation of biomarkers, and other relevant concepts). We are also wrapping up two Interest Group notes (W3C notes are persistent online documents) that summarize 1) Draft approaches to representing expression studies in RDF and 2) Draftlinked data and RDF approaches to life sciences and clinical data. http://staff.science.uva.nl/~marshall/

Deyan Peychev
LinkedLifeData

Andrea Splendiani
I'm involved in a few projects related to the Life Sciences Semantic Web (and beyond). PHI-base (host pathogen interaction database) modeling in RDF, Ondex (the semantic web bits of it), RDFScape (needs update!), BioPAX (needs time!) and many others, including SWAT4LS (which is not a meta project, to be in theme)

Helena Deus
I am interested in developing applications for life sciences that make use of semantic web technologies. Granatum - A social collaborative working space semantically interlinking biomedical researchers, knowledge and data for the design and execution of in-silico models and experiments in cancer chemoprevention   http://granatum.org/    Yes    One of the most pressing issues for enabling interoperability of data in life sciences is the need to ensure that researchers producing data can decide in who can access it and which part of the datasets can be shared. As such, I would be interested in giving a lightning talk about the importance of permission management for enabling discovery of data and services in the life sciences and how this can be addressed by knowledge organization systems for the life sciences

Jerven Bollemam
I work on UniProt data in RDF. Which includes among other things a subset of pubmed data, NCBI/UniProt taxonomy, goa. Also has notes on Proteins involved in disease as well as links to many biological databases.

I am interested in large triple stores and federated queries. As well as using reasoners and rules to validate data.

Nick Juty
Interest in data standards and integration   MIRIAM Registry / identifiers.org    http://www.ebi.ac.uk/miriam/ http://identifiers.org

Luke McCarthy
SADI (Semantic Automated Discovery and Integration)   SADI is a set of standards-compliant best practices that simplify interoperability between Semantic Web Services. sadiframework.org

Mark Wilkinson
SADI - Semantic Automated Discovery and Integration   http://sadiframework.org  http://www.jbiomedsem.com/content/2/1/8

Reinout van Schouwen
Web services; text mining; semantic web technologies

Trish Whetzel
National Center for Biomedical Ontology (NCBO)   http://www.bioontology.org/ I am interested in the application of ontologies to solve biomedical and clinical research issues. Skills: Perl, Java, PHP, SQL

Tim Richardson
open data > open science ? The semantic web

Natalia Diaz Rodriguez
The research topics relevant to my doctoral research are Semantic Web and Semantic Web programming, frameworks for context-aware application programming, Smart Spaces, Ubiquitous Computing, Ambient Intelligence, Ambient Assisted Living, Device Interoperability, Ontologies, Object Oriented Programming. Project DIEM (Devices and Interoperability Ecosystem, www.diem.fi). Python, Smart-M3 semantic platform ( http://sourceforge.net/projects/smart-m3/)

Guoqian Jiang
My research areas are focused on the biomedical ontologies, data standards and Semantic web technologies. ADEpedia: A scalable and standardized knowledge base of adverse drug events using semantic web technology. (see http://adepedia.org )

Przemyslaw Nowak
I would like to participate in Hackathon, I'm interested in semantic web based solutions. Semantic web based expert system for grain drying.

Tomasz Kluza
I would like to participate in the hackathon and work in a group that will gather the www resources about the given topic of the project and then transform that knowledge to the Semantic Web space.

Graham Steel
Patient Advocacy generally and Open Access. Patients Participate   http://blogs.ukoln.ac.uk/patientsparticipate/

Justin Preece
I am attending this event to scout for technologies that exploit semantic reasoning of ontologies in association with curated biological data. Areas of interest: Semantic MediaWiki, Semantic Forms, ontologies, plant genome annotation data, genomics, semantic reasoning/inference.
 * Skills of use at the hackathon: Relational database architecture (MySQL), data and object modeling, web UI design, Perl, PHP, XML/RDF, some Java, some JSON
 * Skills not of use at the hackathon: C#, MS SQL, .NET platform, orchestral percussion, drum set, marimba

Dare Talvitie
Finnish Museum of Natural history, sysadmin roped into doing some development, working on a collection management system for Finnish museums of natural history based on a semantic web.