June 19, 2009

Nettab 2009 Day Three: Semantic Integration

Catania ElephantA brief report (well just some scribbled notes, bullet points and links really) on the third and final day of Network Applications and Tools in Biology (NETTAB) 2009 in Catania, Sicily. There was a special section on Methods and Tools for RNA Structure and Functional Analysis. Disclaimer: RNA mania isn’t really my thing – so the RNA presentations and papers are grossly under-represented in this mini-report (sorry).

  • Keynote: Semantically Integrated eCommunities in Biomedicine: Next-Generation Models of Biomedical Communication, Tim Clark Massachusetts General Hospital and Harvard Medical School, Boston. His presentation opened by asking: What do the following have in common?

    1. Alzheimer’s Disease
    2. Huntington’s Disease
    3. Nicotine Addiction
    4. Schizophrenia
    5. Bipolar Disorder
    6. Autism
    7. Parkinson’s Disease
    8. ALS (Amyotrophic lateral sclerosis)
    9. Neuropathic Pain
    10. Major Depressive Disorder
    11. Cancer (multiple forms)


    1. Highly complex disorders
    2. Much information, incomplete understanding
    3. Inadequate treatment options
    4. Huge cost in human suffering
    5. Multi-factorial causality
    6. Require multi-disciplinary collaboration for progress to understanding and cure

    Tim discussed using The Science Collaboration Framework (SCF) a reusable, semantically-aware toolkit for building on-line communities. These make heavy use of Open Linked Data, controlled vocabularies and  Drupal to build websites to tackle the above disorders. For example pdonlineresearch.org (Parkinson’s Disease), StemBook.org (Harvard Stem Cell Institute) and alzforum.org (Alzheimers) [1]. The controlled vocabulary and ontology approach works well for understood stuff (where named entities are known) but not so good at the outer boundaries of our knowledge. Reusable framework for building web communities, Uses shared ontologies/vocabularies, Open source, freely available.

  • Michaela Guendel (Leaf Bioscience) presented DC-THERA Directory: A Knowledge Management System to Support Collaboration on Dendritic Cell and Immunology Research,  using cell type ontology, dendritic cell ontology, chebi, obi. Project involves Andrea Splendiani, Ciro Scognamiglio and Marco Brandizi
  • GePh-CARD: an information exchange application for an Hub & Spoke Network for Skeletal Dysplasias was presented by M. Mordenti & L. Sangiorgi
  • Panel Discussion: Collaborative and Social Bioinformatics Research and Development: Why, When, Who and How? Alex Bateman, Tim Clark, Duncan Hull and all participants. This panel discussion concentrated on Who? (experts vs. non experts, crowds vs. individuals, how to motivate and reward people to contribute to online communities. community annotation of data only possible when curators cede control of data) and then Where? (open wikis vs. closed ones, private vs. public data, wikis often not suitable for highly structured data, centralised vs. distributed systems)
  • Keynote: Bacterial Phylogeny and Taxonomy in the High-Throughput Sequencing World, Gabriel Valiente
  • Magdalena Musielak (has worked with Piotr Byzia) presented RNA tertiary structure prediction with ModeRNA,
  • Olivier Perriquet presented Improved heuristic for pairwise RNA secondary structure prediction,
  • Giampaolo Bella talked about Analysing microRNA by Theorem Proving. qualitative logic proving before quantitative experimental measures e.g. “shall we go to restaurant” before “how much does it cost”?
  • Mapping miRNA genes on human fragile sites and translocation breakpoints Alfredo Ferro et al.
  • Keynote: Computational challenages in the study of small RNAs Doron Betel, memorial sloan-kettering cancer center
  • microrna.gr. a suite of web based tools for elucidating microrna function was presented by Giorgo L. Papadopoulous, DIANA bioinformatics lab, biomedical Science research center, Alexander Fleming, Vari, Athens, Greece
  • Last but not least there was miRScape: a cytoscape plugin to annotate biological networks with microRNAs

The Tenth NETTAB (2010) Workshop will be in Rome, where the theme will be Oncology Bioinformatics and will be held at the end of  May or beginning of  June 2010.


  1. Das, S., Girard, L., Green, T., Weitzman, L., Lewis-Bowen, A., & Clark, T. (2009). Building biomedical web communities using a semantically aware content management system Briefings in Bioinformatics, 10 (2), 129-138 DOI: 10.1093/bib/bbn052

May 31, 2007

Google Metabolic Maps

Google in the Palm of my HandThese days, new Google products and code seem to appear on a weekly basis. Take, for example, Google Gears which takes advantage of SQLite, mentioned on nodalpoint recently. They certainly don’t hang about at the Googleplex in Mountain View, California. Wouldn’t it be great if Google applied some of that engineering expertise and agility to science and bioinformatics? Just imagine: we could have Google Metabolic Maps, a virtual globe of the cell for scientists everywhere…

Scientists have been drawing metabolic maps for a very long time, but unfortunately when it comes to charting and understanding metabolic pathways, we’re still at the “here be dragons” stage of bio-cartography. I’m obviously not the first person to dream of this, but imagine maps of metabolic pathways looked more like Google Earth or Google Maps, than the old fashioned style maps, many life scientists will be familiar with. Now imagine just a little more, that these maps weren’t just available on conventional screens, but we’re given the Minority Report treatment, courtesy of Mr Bill Gates and his wizzy surface magic at Microsoft. Wouldn’t that be great? Metabolic maps on an interactive tabletop computer. Just like Tom Cruise in the movies, we’d be able to effortlessly swish around metabolism (or the metabolome / proteome / genome / [insert-your-favourite]ome). Imagine if it was all open-source too, no boundaries, no passports…

Now, you may say that I’m a dreamer, but I’m not the only one [1,2,3].


  1. Zhenjun Hu, Joe Mellor, Jie Wu, Minoru Kanehisa, Joshua M. Stuart and Charles DeLisi (2007) Towards zoomable multidimensional maps of the cell Nature biotechnology 25 (5), 547-54. DOI:10.1038/nbt1304
  2. Hiroaki Kitano, Akira Funahashi, Yukiko Matuoka and Kanae Oda (2005) Using process diagrams for the graphical representation of biological networks Nature biotechnology 23 (8), 961-6. DOI:10.1038/nbt1111
  3. John Lennon and Yoko Ono (1971) Imagine
  4. this post originally published on nodalpoint with comments

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