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Peanutbutter has been spread for the last time. Long live jam

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On looking at the date on my last post, shamefully I realised I have not posted for over a year. Most, well all, of my activity has been via twitter and FriendFeed. The reason for the lack of posts is also related to why I started bloging in the first place. I created this blog when I was a Phd student and maintained it while I was a postdoc to discuss work, ideas and problems. With my move to the biotech industry I was not able to post so freely on work related issues.

I have now moved from being in the biotech industry to the publishing industry (see About page) and I think I am in a position to blog a bit more freely than I have been previously. So with this in mind I have been doing some housekeeping. I have updated my about page accordingly. I have updated my publication page via referencing my Mendeley public profile, as opposed to referencing my CiteULike profile.

However, the main change is that I have retired the “peanutbutter” meme  (hence the title for this post) and replaced it with (the jam). Hopefully wordpress will work its magic and maintain the mapping for all the subscriptions, but just incase, if you want to, please update your feed subscriptions to

Maybe my top referring search term “is peanutbutter good for you health” will start to be replaced with more informatics relevant topics.

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A trip to Cambridge in June

I’m taking a trip to Cambridge between June 7th and June 12th.

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A trip to London in May

I’m taking a trip to London on May 14th.

I will be at the Molecular Regulation of Cardiac Disease Symposium May 14-15 2009, London, UK. Hosted by Abcam

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A trip to Manchester in May

I’m taking a trip to Manchester between May 11th and May 13th.

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PSI AnalysisXML Enters Public Comment

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The HUPO Proteomics Standards Initiative aims to develop community data standards for proteomics, that are developed, accepted and implemented by the proteomics community.  To this end,  The “AnalysisXML: exchange format for peptides and proteins identified from mass spectra” is now available for Public Comment on the PSI Web site.

The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process.

This message is to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal.

If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI.

Announcement via the PSI editor, Norman Paton

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The OBI winter workshop 2009

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The OBI winter workshop 2009 has just been held in Vancouver. This was the first of the 2009 bi-annual face-to-face workshops concerned with the development of the ontology for biomedical investigations. The first session, on the first day, covered some administration and developmental policy issues;

Namespace –  should other communities who wish to integrate with OBI retain their namespace within OBI or loose it and gain an OBI one instead? The general consensus was that there should be only one namespace within OBI and that the source of the term/community should be described in the annotation property of each class.

Defined classes – a general development policy is that classes should not be asserted under defined classes (classes with Necessary and Sufficient conditions) this is to avoid multiple inheritance and to allow the reasoner to infer the hierarchy.

Quick ID – I presented the current status of the Quick ID policy to allow rapid term submission to the ontology. The documentation is still in a draft stage and will change, available from here.

Quick term – similar to the quick id process but concerns submission of classes which are composites (intersection of) classes that exist across multiple resources.


Several people presented use-cases on how they are either using or intend to make use of OBI.  James presented  a talk on how Genepattern software would like to use OBI. Bjoern presented how he would like to use OBI for the immune epitope database (IEDB) and Jennifer outlined potential for the CEBS. This was very interesting and encouraging that there is definitely a demand for OBI and pressure to release something.

The remaining sessions were concerned with specific branch development describing important classes that exist and any issues that were outstanding that required a broader impact from the consortium, in order to reach a conclusion. I presented reports on both the instrument branch and the relations branch status.

On the final day we dealt with the OBI manuscript, incorporating the use-cases that were presented and assigning sections to individuals for completion and the different flavours of OBI releases that our users would require. We finished with presentations from NCBO Bioportal 2.0 demonstrating new features and soliciting feedback, and from Larisa on the robot scientist which uses there own ontology for experiments to drive the robot.

All in all it was a very productive, but tiring workshop which provided the ground work for further OBI development and work on the manuscript, between now and the next workshop  Summer 2009 OBI workshop (back2back with 2nd OBO Foundry workshop), EBI, Cambridge, UK, June 2-6, 2009 (OBO Foundry 7-8; OBI 9-12)

For a full outline of the agenda (now incorporated with action items) see here.

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All change in 2009, no more academia

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Last week I completed what was my first week of working in academia in 2009 and also my last for the foreseeable future. I have decided to leave academia, as well as Newcastle to take a position in a Biotech company in Cambridge.

I have certainly enjoyed just over 5 years working in Newcastle encompassing my PhD and a postdoc. Within that time my research interests have developed from representing scientific data, to data standards to ontology development. I am still maintaining some of my research interests in my new position. I will be working for an antibody company called Abcam, and as part of my role I will be investigating how to represent their product catalogue as an ontology and how users can have a more direct interaction with it.

I am really looking forward to this fresh challenge. I don’t know how this change of position will effect the content of this blog, although I expect it to still largely reflect my interests on the representation of scientific data and open science. I think its probably safe to assume there might be the odd post about antibodies as well.

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Dopplr and my first trip

I have just signed up to Dopplr to track my travel and to keep a record of my trips. I am not sure how much use I will get out of it or how much of a benefit it will be, however I thought I would give it a go.

I’m taking a trip to Vancouver between January 31st and February 8th. which will be for the OBI developers workshop.

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What is your data sharing statement?

More and more funding bodies asking to make the findings of publicly funded scientific research freely available. However typically they provide limited infrastructure or recommendations as to how this should actually happen. I was wondering what type of data sharing statement researchers are (or should) be including within their grant proposals? Below is an example of how this could look. However, it provides no indication of how this could actually take place, for example via wikis, hosting on sourceforge, google code etc. It also does not imply timing, for example, this happens live, or when the grant is finished. Should the infrastructure and timing also be included?

  1. The protocols, methods and algorithms developed will be made available under the Creative Commons Attribution 3.0 License
  2. The data produced will be made available via the Science Commons, Protocol for Implementing Open Access Data.
  3. All source code developed will be made available under an open source license.


Proteomics Standards Initiative recommendations

Several new standard artefacts have progressed through the public consultation process of the PSI. They are the MIAPE Column Chromatography document and the Mass Spectrometer Markup Language Specification (mzML).

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