Archive for category MIBBI
Content, Syntax and Semantics
Posted by peanutbutter in bioinformatics, computer science, conference, MIBBI on May 2, 2009
These are the slides I gave at a DCC workshop entitled, “Digital curation 101″ which aimed to give and overview of what to consider regarding data curation and management in the context of applying for research funding. The presentation starts with definitions of content syntax and semantics, and example of how these concepts are being applied in the life-sciences, specifically proteomics.
MIAPE: Gel Informatics is now available for Public Comment
Posted by peanutbutter in bioinformatics, data standards, Journals Publishing, MIBBI, Proteomics on August 18, 2008
The MIAPE: Gel Informatics module formalised by the Proteomics Standards Initiative (PSI) now available for Public Comment on the PSI Web site. Typically alot of this information will be contained in the image analysis software, so we would especially encourage software vendors to review the document. 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.
If you have comments that you would like to make but would prefer not to make public, please email the PSI editor Norman Paton.
Double standards in Nature biotechnology
Posted by peanutbutter in bioinformatics, data standards, Journals Publishing, MIBBI on August 7, 2008
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.
The First MIBBI workshop: Day 2
Posted by peanutbutter in conference, conference report, data standards, MIBBI on April 7, 2008
The second day of the MIBBI workshop was more “free flowing” compared to the first day. During the second day we focussed on the process of MIBBI, house-keeping, infrastructure and the website.
The main focus of the day was discussing what it means to be registered on the MIBBI site and be a member of the Foundry. As a straw man, rather than starting from scratch, we used the OBO foundry principles to see if they could be applied to reporting check-lists, and came up with a draft set of principles. A full “official” report of the workshop should be forthcoming.
As a break from the rigorous standards development and process of reporting check-lists we went to a local restaurant and experienced anarchy when it came to understanding the menu. The meal itself was brilliant, however some degree of semantic extraction had to be applied to the menu to actually understand what we were ordering – No fancy algorithms were applied here, other than aksing the staff so explain it in English! And we think we have problems in the life-sciences! An example of the menu can be seen in the photo graphs which also include the delegates the meal and the venue.
|First MIBBI workshop 2-3rd April 2008|
The First MIBBI Workshop: Day 1
Posted by peanutbutter in bioinformatics, CARMEN, conference, conference report, data standards, FuGE, MIBBI, neuroinformatics, ontology, open data, open science on April 2, 2008
MIBBI is a registry of scientific experiment reporting guidelines with the idea to foster a foundry of best practice to further develop and encourage modular development and re-use of reporting guidelines. The first workshop is being held at the EBI on the 2nd – 3rd April 2008 and is a relatively closed workshop to those developers and guidelines that are registered on the site. The schedule for day one is a whistle stop tour consisting of 5 min talks (adjusting for an academics interpretation of what 5 minutes means) for all the guidelines that exist, their scope and the people behind them. Due to this I am not going to comment on individual talks. I presented two talks during the day. One on CARMEN and the development of the MINI: Electrophysiology reporting guidelines, and one, standing in for Andy Jones on FuGE.
I tried sharing these slides via google presentation, they looked quite nice. However, wordpress does not seem to allow them to embed. So I put them on slide share instead. These set the tone for the discussions for the afternoon and tomorrow.