Posts Tagged Biology

The Semantic Web of Life Science

This summary was born out of a question  on Twitter and percolated to FriendFeed, which was “Who is using RDF and integrating other resources at the minute and what are those resources? From this question, several resources were highlighted.

UniProt. The comprehensive resource of protein information is available as an RDF distribution and each Protein record has a corresponding RDF download option.

Phil pointed out Semantic Systems Biology, As systems biology is largely concerned with representing networks and interactions at a systems level, a language like RDF would seem an obvious choice to represent this type of knowledge, to aid semantic description and data integration.

Melanie pointed out the following resources such as Bio2RDF. This project aims to RDF-ize numerous public life-science resources using what they call a three step approach which they have developed. The following image illustrates some of the resources that are included in Bio2RDF.

Bio2RDF Cloud

Bio2RDF Cloud

The NeuroCommons project seeks to make all scientific research materials – research articles, annotations, data, physical materials – as available and as usable as they can be. As a result they have an RDF triple store which they encourage you to either contribute to or download and use.

For a more general overview of resources that exist as an RDF implementation, the Linked Open Data cloud provides a graphical summary of the resources that exists and the relationships between them.

If you know of any more life-science resources or projects using RDF, then please do comment below.  Egon has indicated he is working on RDF-ing the NMRShiftDB and ChEMBL’s Starlight, and Andrew Clegg is considering a project proposal involving RDF. As a result a very interesting discussion ensued on FF.

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The BioSysBio conference 2009

The Genomics GTL Pictorial Program.
Image via Wikipedia

The premise of the BioSysBio conference is to

bring together the best young researchers working in Synthetic Biology, Systems Biology and Bioinformatics, providing a platform to hear and discuss the most recent and scientific advances and applications in these fascinating fields.

This years BioSysBio 09 has just taken place in Cambridge, UK. The program was more slanted towards synthetic biology rather than more traditional systems biology, which I think reflects the growing momentum that synthetic biology has gained in the past year. I think this is a good progress and  I was secretley glad as I did not want to spend 3 days looking at massive network diagrams squashed onto power point slides.

This was the first conference I had been to that the organisers actually requested that we use the BioSysBio FriendFeed room and Twitter to communicate, so I did. Half way through the first day the organisers demonstrated the FF room, which seemed to exist solely of Allyson’s posts, and questions were asked if she was a blogging bot. When we did confirm there was actually a female at an engineering conference, she was thereafter known as the BioSysBio poster girl.

As ever Ally was monumental in her blogging during the conference and all her posts can be found here. At one stage Simon did try to blog her talk to the same detail and speed, but he just kept coming up withe excuses about the wifi being slow – eventually he got there.

This was the first time I attended BioSysBio and I thoroughly enjoyed the experience. In general all of the talks were of a high standard most notable for me were Allyson Lister’s talk on Saint: a lightweight SBML annotation integration environment, Christina Smolke on  Programming RNA Devices to Control Cellular Information Processing, Piers Millet on Why Secure Synthetic Biology? and Drew Endy on Building a new Biology. It was also good to hear about improvements for the Registry of standard biological parts by Randy Rettberg and the wiki style community building of the product catalogue, or data sheet about each part.

There is no point in me re-posting coverage that has already been documented, so if you would like to follow what happened you can follow the #biosysbio twitter stream, the biosysbio FreindFeed Room, or if you want a more comprehensive overview, Ally’s blog.

This was also the first time I had used twitter (via tweetdeck) instead of Friendfeed to microblog a conference. This approach certainly generated alot of noise and random soundbites, and was probably a fast way to make notes. However, although everything is grouped under the #biosysbio tag, they are not grouped around a particular talk or discussion thread. I can’t help thinking that microblogging via FriendFeed would be more focused around a specific talk and provide a more focused discussion, as opposed to just covering what was happening second by second.

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Double standards in Nature biotechnology

OK, So that is a relatively inflammatory and controversial headline, edging on the side of tabloid sensationalism. What is refers to is probably a situation that I may never find myself in again, which is in this months edition of Nature Biotechnology I am an author on two, biological standards related publications.

The first is a letter advertising the PSI’s MIAPE Guidelines for reporting the use of gel electrophoresis in proteomics. This letter is also accompanied by letters referring to the  MIAPE guidelines for Mass Spectrometry, Mass Spectrometry Informatics and protein modification data.

The second is a paper on the Minimum Information about a Biomedical or Biological Investigations (MIBBI) registry entitled Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

The following press release describes this paper in more detail.

More than 20 grass-roots standardisation groups, led by scientists at the European Bioinformatics Institute (EMBL-EBI) and the Centre for Ecology & Hydrology (CEH), have combined forces to form the “Minimum Information about a Biomedical or Biological Investigation” (MIBBI) initiative. Their aim is to harmonise standards for high-throughput biology, and their methodology is described in a Commentary article, published today in the journal Nature Biotechnology.

Data standards are increasingly vital to scientific progress, as groups from around the world look to share their data and mine it more effectively. But the proliferation of projects to build “Minimum Information” checklists that describe experimental procedures was beginning to create problems. “There was no way of even finding all the current checklist projects without days of googling,” says the EMBL-EBI’s Chris Taylor, who shares first authorship of the paper with Dawn Field (CEH) and Susanna-Assunta Sansone (EMBL-EBI). “As a result, much of the great work that’s going into developing community standards was being overlooked, and different communities were at risk of developing mutually incompatible standards. MIBBI will help to prevent them from reinventing the wheel.

The MIBBI Portal already offers a one-stop shop for researchers, funders, journals and reviewers searching for a comprehensive list of minimum information checklists. The next step will be to build the MIBBI Foundry, which will bring together diverse communities to rationalise and streamline standardisation efforts. “Communities working together through MIBBI will produce non-overlapping minimal information modules,” says CEH’s Dawn Field. “The idea is that each checklist will fit neatly into a jigsaw, with each community being able to take the pieces that are relevant to them.” Some, such as checklists describing the nature of a biological sample used for an experiment, will be relevant to many communities, whereas others, such as standards for describing a flow cytometry experiment, may be developed and used by a subset of communities.

“MIBBI represents the first new effort taking the Open Biomedical Ontologies (OBO) as its role model”, says Susanna-Assunta Sansone. “The MIBBI Portal operates in a manner analogous to OBO as an open information resource, while the MIBBI Foundry fosters collaborative development and integration of checklists into self-contained modules just like the OBO Foundry does for the ontologies”.

There is a growing understanding of the value of such minimal information standards among biologists and an increased willingness to work together across disciplinary boundaries. The benefits include making experimental data more reproducible and allowing more powerful analyses over diverse sets of data. New checklist communities are encouraged to register with MIBBI and consider joining the MIBBI Foundry.

Press release issued by the EMBL-European Bioinformatics Institute and the Centre for Ecology and Hydrology, UK.
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