BioSharing

GigaScience, GigaDB and BioSharing

2011-11-27T23:27:00.001-08:00

Revolutionizing data collection, dissemination and use, GigaScience launches the new integrated journal and database in collaboration with BGI and BioMed Central, and working closely with the BioSharing and the ISA commons communities to maintain the highest data and metadata standards.

The novel format ofpublishing integrates manuscript publication with the GigaDB public database, where dataset (i) gets a DOI to make them discoverable, trackable and citable, and (ii) are structured according to community standards, via the ISA tools.

Synergy force - The BioSharing community grows

2011-10-06T05:59:00.000-07:00

The BioSharing community keeps growing steadily!

In the last few months the BioCatalogue, Dryad, DataCite, the Digital Curation Centre (DCC), COMBINE, the National Cancer Research Institute (NCRI) Informatics Initiative have joined the BioSharing community.

These groups are recognized stakeholders with strong ties with their respective communities. A link with/among them is pivotal for the BioSharing mission and it will be essential also to continue developing and enriching the catalogue of standards.

Alsheikh-Ali et al Data Availability study published in PloS One

2011-10-05T02:22:00.000-07:00

Public Availability of Published Research Data in High-Impact Journals

Full Article

Alawi A. Alsheikh-Ali1,2#, Waqas Qureshi3#, Mouaz H. Al-Mallah4,5, John P. A. Ioannidis2,6,7,8,9*

Abstract

Background
There is increasing interest to make primary data from published research publicly available. We aimed to assess the current status of making research data available in highly-cited journals across the scientific literature.

Methods and Results
We reviewed the first 10 original research papers of 2009 published in the 50 original research journals with the highest impact factor. For each journal we documented the policies related to public availability and sharing of data. Of the 50 journals, 44 (88%) had a statement in their instructions to authors related to public availability and sharing of data. However, there was wide variation in journal requirements, ranging from requiring the sharing of all primary data related to the research to just including a statement in the published manuscript that data can be available on request. Of the 500 assessed papers, 149 (30%) were not subject to any data availability policy. Of the remaining 351 papers that were covered by some data availability policy, 208 papers (59%) did not fully adhere to the data availability instructions of the journals they were published in, most commonly (73%) by not publicly depositing microarray data. The other 143 papers that adhered to the data availability instructions did so by publicly depositing only the specific data type as required, making a statement of willingness to share, or actually sharing all the primary data. Overall, only 47 papers (9%) deposited full primary raw data online. None of the 149 papers not subject to data availability policies made their full primary data publicly available.

Conclusion
A substantial proportion of original research papers published in high-impact journals are either not subject to any data availability policies, or do not adhere to the data availability instructions in their respective journals. This empiric evaluation highlights opportunities for improvement.

BioSharing at COMBINE meeting - Community Standards for Systems Biology

2011-09-28T03:52:00.000-07:00

The 2nd COMBINE meeting was held on 2-7 September in gorgeous Heidelberg.

"The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards covering all the aspects of modeling in biology."

During the live streamed meeting, the core COMBINE community gave overview talks on the latest updates on the popular standards, SBML, SED-ML, BioPAX, SBGN and CellML. Brilliant keynote talks by Peer Bork (EMBL Heidelberg) and Michael White (University of Manchester) on their 20+ years of research in systems biology added to the memorability of the meeting.

A lecture on BioSharing was also given by Prof. Dawn Field, titled as "BioSharing: standards, policies and communication in bioscience".

All slides and posters are published in a Nature Precedings collection for COMBINE 2011.

Pistoia Alliance - Vocabulary Services Initiative and Information Ecosystem workshop

2011-09-26T10:39:00.000-07:00

BioSharing team works to engage closely with the Pistoia Alliance as new R&D business models demand successful integration of heterogeneous data from multiple providers and scientific domains. Here described are the Pistoia Alliance's activities BioSharing team is part of.

The Vocabulary Services Initiative (VSI) is the latest working group launched by the Pistoia Alliance to tackle the heterogeneous terminological landscape that makes expensive and hard to share, correlate and integrate data. VSI aims to address the issues and possible solutions around the precompetitive development of open research vocabularies will benefit information producers and consumers. The VSI working group, lead by Lee Harland (Connected Discovery) and Ian Dix (AstraZeneca), has developed a paper describing the need for shared services around vocabularies. Titled "Empowering Industrial Research with Shared Biomedical Vocabularies", the paper is to be published in Drug Discovery Today - most likely in the November 2011 issue.

Going one step further, Pistoia Alliance will explore the concept of the "Information Ecosystem" at a highly interactive workshop on 10 October 2011 in Hannover, Germany (the site of the Bio-IT World European meeting). "Delegates will describe the evolving information ecosystem in biomedical and pharmaceutical research and determine strategies for collaboratively shaping this ecosystem to maximum advantage... Even if you can't attend the meeting, we invite you to send use cases describing what scientists expect and need from this highly changeable environment".

Great RIN report on the use of and issues around data centres

2011-09-26T04:01:00.000-07:00

Data centres: their use, value and impact | Research Information Network
Great report examining the use of and issues around data centres.
In short: they work, more needed.

Also relevant/current:
Data centres at heart of UK data sharing culture (JISC news item)
How do we incentivise data sharing? On standards, support and ‘data Oscars’ (Sarah Porter, JISC)

Making the case for international data sharing

2011-09-16T15:56:00.000-07:00

The case for international data sharing, particularly overcoming challenges in developing countries, took centre stage at an international symposium that took place in Washington DC in April.

More

BioHackathon 2011 - Focus on Linked Data in life science

2011-08-20T21:58:00.000-07:00

Running since 2008 in Japan, the BioHackathon 2011 starts today in the beautiful city of Kyoto. This year's focus is generation and utilization of Linked Data in life science.

During this first live streamed open symposium day, a series of short presentations set the scene for the hands-on hackaton event that runs for the whole week (Aug 22-26). Presentations include:
- SPARQLing UniProt RDF (Jerven Bolleman)
- BioMart and semantic-web querying (Joachim Baran)
- SADI and semantic-web services (Mark Wilkinson)
Also BioSharing (Susanna-A Sansone) and the ISA infrastructure (Philippe Rocca-Serra) are also introduced, along with NCBO BioPortal (Trish Whetzel), MIRIAM Registry (Camille Laibe) and many others.

If you want to know what is going on during the whole week, here is how you can do it:

During a 'unconference' style session, driven by the participants, the problems to be addressed are discussed and listed;
Progresses are recoded live in a dedicated wiki page.

Following the hackathon:

A blog will posted at the BioMed Central Blog site;
A special issue will be published in JBMS, containing a series of articles describing specific topics in more detail.

Publishing Open Data Working Group and BioSharing

2011-08-08T10:14:00.000-07:00

On June 17th, BMC brought together authors, editors, publishers, librarians and funders under the Publishing Open Data Working Group to investigate the potential for developing widely-agreeable and transferable guidelines, processes and policies enabling reproducible and open data in the life sciences. "So rather than ‘why share data?’, the question now is ‘how?’", writes Iain Hrynaszkiewicz of BMC.

A detailed summary is now available, including mutually agreeable ways forward on all three of the meeting’s proposed goals. The next steps for the stakeholders also include to work together:

to identify more areas of science where there are no obvious places and formats to store data, for example by reviewing resources such the BioSharing list of data standards;
to include institutions to the BioSharing list of data sharing policies.

BioSharing at ISMB/ECCB 2011, Vienna

2011-07-21T06:44:00.000-07:00

At the 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2011) the BioSharing team and members of its community were present in full force!

During the Bio-Ontologies SIG, Susanna-Assunta Sansone (co-chair) explained the growth of the BioSharing catalogue's content, the need for the harmonization of standards and the creation of 'usability' and 'popularity' metrics. At the "Unifying Bio-Resources Descriptors" workshop, Susanna-Assunta Sansone, Dawn Field, Philippe Rocca-Serra (of BioSharing) and Pascale Gaudet (of the International Society of Biocuration) co-chaired a well attended discussion on BioDBcore. This is a strawman uniform system for describing databases, in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement. A panel with journals and representatives of bio-resources showed their support for BioSharing and the BioDBcore initiative; they include:

- Naomi Attar, BioMedCentral

- Adriaan Klinkenberg, Elsevier

- Rebecca Lawrence, F1000

- Francis Ouellette, DATABASE and Bioinformatics Links Directory

- Nicolas Le Novère, MIRIAM resource

- Jeffrey Grethe, Neuroscience Information Network

- Trish Whetzel, NCBO and Biositemaps

Agenda and presentations from these events will be available at the Nature Precedings' BioSharing Collection soon.

What is the right format for my data? Just look it up!

2011-07-08T07:52:00.000-07:00

BioMed Central works to support initiatives aimed at promoting transparency and reproducibility in research, and they strongly encourage data sharing and publication. They have developed improved article features and resources to better link journal articles to underlying data, and related standards to facilitate academic credit for data sharing.

Their latest blog on "Availability of supporting data’: crediting transparency and enhancing the literature" strengthen the role of the BioSharing catalogue...... "And what is the right format for my data? To help maximize potential for data reuse and increase the efficiency of science, shared data should be made available in formats that are widely agreed by the relevant scientific field – data standards. BMC Research Notes launched an initiative in 2010 to promote the awareness and use of data standards, and subsequently partnered with the BioSharing to achieve this shared goal. Journals that introduce the ‘Availability of supporting data’ section’ encourage authors to comply with available field-specific standards for the preparation and recording of data. We recommend authors check the BioSharing catalogue for information on best practice in their field for sharing of data, with particular attention to maintaining patient confidentiality."

What kind of community are you trying to build?

2011-06-21T07:56:00.000-07:00

A lot of data sharing is about overcoming not just technological bottlenecks, but also sociological hurdles (how to get people to work together towards a common goal). A key aspects of a lot of data sharing projects/initiatives is the creation of a suitable community to tackle or adopt a given solution.

Here is an interesting post that points out that we not only need to know what kind of community we need and are trying to build, but helps create a framework for thinking about community structure.

Crowd, Hub & Spoke, or Network? What kind of community do you have?

Community Structure is of course an increasingly well-defined concept in the analysis of a wide range of networks - from things to people.

Genomics Crowdsourcing - community pooling of data and analysis of deadly bug

2011-06-16T15:59:00.000-07:00

A link to a short post from TheOpenProcess blog describing one of the first examples of genomics data crowdsouring - may this happen far more often.

The brilliant Genome Analysis Crowdsourcing repository

The fourth data sharing policy in the BioSharing Collection is by the UK Natural Environment Research Council

2011-06-10T00:19:00.000-07:00

We are now pleased to announce that a (non-exclusive) copy of the data sharing policy of the UK Natural Environment Research Council (NERC) is now part of the Nature Precedings’ Biosharing Collection.

This is the fourth policy posted, along with those of the US Department of Energy (DOE) Genomic Science program Wellcome Trust and Biotechnology and Biological Sciences Research Council (BBSRC). All of the documents in this collection are also listed in the BioSharing catalogue which centralizes funders’ data policies well as standards documents from different research communities.

Nature Precedings's BioSharing Collection - Wellcome Trust and BBSRC join in!

2011-06-08T09:00:00.000-07:00

We are now pleased to announce that (non-exclusive) copies of the Wellcome Trust and Biotechnology and Biological Sciences Research Council (BBSRC) are now available at the Nature Precedings’ Biosharing Collection.

The BioSharing Collection works to house data policies from multiple funding agencies as well as standards documents from different research communities. The US Department of Energy (DOE) Genomic Science program was the early adopter of the Collection.

All of the documents in this collection are also listed in the BioSharing catalogue which centralizes funders’ data policies and works to link them to reporting standards (minimal information checklists, terminologies, exchange format) and relevant tools and data repositories, in collaboration with existing resources.

BioSharing featured in Nature Genetics' editorial on "Standard cooperating procedure"

2011-05-29T08:12:00.000-07:00

"Community review of proposed standards is a good strategy to broaden consensus on ways to conduct principled, ethical and efficient research" says the editorial on "Standard cooperating procedure" Nature Genetics' 43, 501 (2011).

"The Data Standards preprint server at Nature Precedings makes funder policies, data plans and standards documents citable for use and comment. Biosharing complements this by indexing and presenting them along with other related initiatives. By working together to maximize the visibility and inter-operability of policies, plans and standards, we will make them easier to develop and submit and improve their usefulness to researchers."

The collaboration between Nature Precedings and BioSharing has resulted in a new Collection, see related blog post.

BMJ Open updates its "Resources for data management and sharing" recommendations and includes BioSharing

2011-05-20T04:34:00.001-07:00

BMJ Open has updated its “Resources for data management and sharing” document to include more details about data sharing - including a link to the BioSharing Catalogue of policies and standards.

BMJ Open is an online-only, open access general medical journal, dedicated to publishing medical research from all disciplines and therapeutic areas. The journal publishes all research study types, from study protocols to phase I trials to meta-analyses, including small or potentially low-impact studies. Publishing procedures are built around fully open peer review and continuous publication, publishing research online as soon as the article is ready.

BMJ Open aims to promote transparency in the publication process by publishing reviewer reports and previous versions of manuscripts as pre-publication histories. Authors are asked to pay article-processing charges on acceptance; the ability to pay does not influence editorial decisions.

Resources for data management and sharing
Faster progress in improving health, better value for money and higher quality science were the three key benefits stressed by the UK's Medical Research Council, the Wellcome Trust, the US National Institutes of Health and others, who articulated their commitment to sharing data in a joint statement in 2011, and have developed policies and tools to assist their researchers to do so.

Read the Full document here

Nature Precedings's BioSharing Collection is live - DOE the early adopter!

2011-05-05T04:25:00.000-07:00

The Nature Precedings’ Biosharing Collection has been just launched and it is set to offer a focal point for stakeholders in data policy and provides a “one-stop shop” for those seeking data policy documents and standards for high-throughput genomics and functional genomic bioscience data, in particular.

Last year, Nature Precedings, the online archive for pre-publication research findings from Nature Publishing Group (NPG), began to host citable data management plans (marker papers) in order to encourage data sharing. This was soon followed by the addition of standards documents for best research practice, aiming for broad consensus via community review and comment, as described in the Nature Genetics editorial “Discussing Standards”.

The BioSharing Collection will house data policies from multiple funding agencies as well as standards documents from different research communities. We are now pleased to announce that the data policy of the US Department of Energy (DOE) Genomic Science program is an early adopter of the Collection and a (non-exclusive copy) of their document is now been posted!

Like other documents on Nature Precedings, these are citable (have DOIs) and can be rapidly versioned. Further, all of the documents in this collection will be listed by Biosharing.org in the BioSharing catalogue which centralizes funders’ data policies and works to link them to reporting standards (minimal information checklists, terminologies, exchange format) and relevant tools and data repositories, in collaboration with existing resources.

EPSRC launches a "Policy Framework on Research Data"

2011-05-05T04:05:00.000-07:00

The BioSharing catalogue now includes the UK Engineering and Physical Sciences Research Council (EPSRC) new policy framework (effective from 1st May 2011).

The framework covers the access to, and management of, research data arising from research sponsored by EPSRC. It is being introduced in recognition of the need for increased transparency of publicly funded research and availability of its outputs. It sets out our expectations arising from seven basic principles which align with the core RCUK principles on data sharing.

BMC Research Notes and BioSharing – collaboration changes everything

2011-04-11T07:51:00.000-07:00

Through the series on "Data standardization, sharing and publication", BMC Research Notes is building a growing network of experts on data standards from different communities – from genomics and proteomics, through to metabolomics and medical informatics.

BioSharing’s standards catalogue and BMC Research Notes’ series complement one another – standards groups can contribute educational data notes to the series which helps raise awareness of a specific standard, and which then can be linked to the BioSharing catalogue. Presenting an open dataset formatted in a standardized way (along with the corresponding preparation guidelines), each data note offers a great example of best practice in data standardization.

This partnership between BMC Research Notes and BioSharing will help both groups to reach a wider community and achieve our common goal more efficiently for a greater benefit to the scientific community. Read the full announcement on the BioMed Central Blog.

BioSharing catalogue of standards: release v1

2011-04-10T18:59:00.000-07:00

The first version of the BioSharing catalogue of standards has been released!

It classifies standards into three types:
- reporting requirements (minimal information checklists to report of the same core set of information)
- terminological artifacts (such as controlled vocabularies and ontologies to describe the information)
- exchange formats (to communicate the information)

The catalogue aims to
1. centralize community-developed bioscience standards, linking to other portals open access resources and, progressively, to lists of tools and databases implementing the standards;
2. develop and maintain a set of criteria for assessing the quality and formal rigor of the standards, but also the interoperability and relations among them;
3. foster interoperability, addressing overlaps and duplication of efforts that hamper their wider uptake and interfere with the creation of standards-compliant systems.

New communities join BioSharing

2011-04-09T05:25:00.000-07:00

The BioSharing community grows. In the last few months, BioMedCentral, Nature Precedings and Equator Network have joined BioSharing.

To enrich the catalogue of standards, the BioSharing team also work to establish new collaborations and links to other portals and open access resources that collect and publish documents on standards and their implementations.

ISCB Public Policy Statement

2011-03-08T11:07:00.000-08:00

The ISCB Board of Directors has published the "ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature" in both official journals of the Society, Bioinformatics and PLoS Computational Biology.

They now invite the community to be signatory to this policy statement (http://www.iscb.org/iscb-policy-statements/literature_open_access/signup).

The spread of BioWikis: wikis for biologists

2011-02-17T01:56:00.000-08:00

Here is a webpage/project with the admirable goal of collecting up information about the growing number of Wiki sites in biology. In addition to highlighting the number of sites now up and running, this webpage also gives key stats about the activity on these various sites, for example the total number of pages hosted in each of the listed wiki sites.

BioWiki

Developers and creators of wikis for biologists are encouraged to add/update information about their own site.

BioWiki: This page presents a table of BioWikis, wikis for biologists.

BioSharing in the news - Science 'Dealing with Data'

2011-02-11T06:00:00.000-08:00

BioSharing is featured in two Science Careers pieces, part of a "Special Online Collection: Dealing with Data" in Science.

Curators for Biology

2011-02-10T16:25:00.001-08:00

Another good article about the important role of expert curators in biology - originally published in the journal Nature as a for-fee article - the contents are freely available as a feature article on the Naturejobs website:

Bioinformatics: Curation generation

Katharine Sanderson

Nature 470, 295–296 (2011)

With biological databases growing in size and number, curators are needed to update and correct their contents. For those who prefer computers to pipettes, there are opportunities.

US defence advisory panel proposes a “Library of Congress” for pathogens

2011-02-04T07:27:00.000-08:00

From various news sources, a report from 2009 just released to the public:

http://www.fas.org/blog/secrecy/2011/02/microbial_forensics.html

I looked up the National Bioforensic Reference Collection mentioned but it is not known to Google. It appears to be hosted at the Battelle National Biodefence Institute.

Does this mean I can add "counter-terrorism" to my CV due to my involvement in microbial data cataloguing efforts? :-)

Summary:

In order to help determine the origins of microbial threats in terrorist incidents or epidemics, it would be useful to have a deep archive of various strains of lethal bacteria, the JASON defense advisory panel told the National Counterproliferation Center in a newly released 2009 report (pdf).

Because of the natural variation in the microbes of interest, “we believe that a ‘Library of Congress’ for microbial pathogens is needed,” the JASONs said.

“This library would consist of strains collected worldwide by methods that preserve sample properties, and capture all relevant data (e.g. geolocation, local environmental conditions). It should include laboratory isolates, natural isolates, and DNA sequence data.”

Minimum information about databases: BioDBCore

2011-01-18T13:36:00.002-08:00

Following the first BioSharing meeting, Pascale Gaudet, current
Chairperson of the International Society for BioCuration, took forward
an idea to create a minimum information standard to describe
databases. After initially discussing this idea with Amos Bairoch,
Dawn Field and Susanna Sansone, this idea was taken forward at the
community level by engaging a range of thought leaders in the field.
This 'minimum information' specification is now called BioDBCore and
has been described in the first instance in a pair of editorials

published in NAR and the Database journals (Gaudet et al, 2010).

The main website for the BioDBCore project is hosted by the ISB (http://biocurator.org/biodbcore.shtml).

The BioDBCore checklist is overseen by the International Society for
Biocuration (ISB) (http://biocurator.org/), in collaboration with the
BioSharing forum [http://www.biosharing.org/).

Towards BioDBcore: a community-defined information specification for
biological databases.
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK,
Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook
CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock
JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch
Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L,
Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T,
Whetzel PL, White O, Yamasaki C; on behalf of the BioDBCore working
group.

Gaudet et al, 2010 NAR (http://nar.oxfordjournals.org/content/early/2010/11/17/nar.gkq1173.abstract)

Gaudet et al, 2010 Database (http://database.oxfordjournals.org/content/2011/baq027)

The goals of the proposed BioDBCore checklist are given below:

Gather the necessary information to provide a general overview of the
database landscape, and compare and contrast the various resources.

Encourage consistency and interoperability between resources.

Promote the uptake and use of semantic and syntactic standards.

Provide guidance for users when evaluating the scope and relevance of
a resource, as well as details of the data access methods supported.

Ensure that the collective impact of these resources is maximized.

The BioDBCore working group is open to all interested parties. Please contact the ISB at intsocbio@gmail.com for more information.

Top 10 openness advances of 2010 - BioTorrents

2011-01-14T16:26:00.000-08:00

Peter Suber has published a top 10 list of 'openness advances of 2010.

The full list is here: http://www.earlham.edu/~peters/fos/newsletter/01-02-11.htm

For example, the list contains a mention of the Biotorrents project:

"The most exciting new open-data platform in 2010 was BioTorrents from Morgan Langille and Jonathan Eisen, a P2P data-sharing service for biology using BitTorrent. Something like this will be needed in every field where researchers need to share not just megabytes or gigabytes, but terabytes and petabytes."

Biotorrents is a way for scientists to upload and share data - it provides an alternative to FTP or HTTP and centralizes files for future sharing.

The Biotorrents papers has been published in PloS One and cites our 'omics data sharing paper.

BioTorrents: A File Sharing Service for Scientific Data - paper

BioSharing meeting report published in SIGS journal

2010-12-30T12:27:00.001-08:00

The meeting report from the inaugural BioSharing meeting is now out in the journal Standards in Genomic Sciences (SIGS). Thanks to everyone who contributed.

The Biosharing meeting report is part of a special issue of SIGS organized by the Genomic Standards Consortium (GSC) that includes nine meeting reports from five communities (the GSC, BioSharing, EMP, MIBBI and CAFAE).

Biosharing meeting report: HTML

New BioSharing website LAUNCHED

2010-12-23T10:37:00.000-08:00

The new site has been launched!
Two prototype catalogues centralize data policies and reporting standards. A draft set of core information are exposed in this first version; we plan, however, to enrich their content and enhance their functionalities iteratively.
A feedback form and a mailing list are available from the 'Contact' page for you to provide us with suggestions and comments, but als receive news and announcement of releases and related meetings.

New BioSharing prototype website soon

2010-12-15T14:46:00.000-08:00

The new prototype site will be launched on Wednesday 22nd of December, 2010. In line with "Statement of Purpose - Draft, Oct 2010" it will include “One-stop shop” catalogues to help centralizing information on bioscience data policies, standards and links to other related portals, and a communication forum to maintain linkages between stakeholders to enable flow of information and mutual support.

NSF Data Management Plan Requirements

2010-11-30T11:23:00.000-08:00

Beginning January 18, 2011, proposals submitted to NSF must include a supplementary document of no more than two pages labeled “Data Management Plan”. This supplementary document should describe how the proposal will conform to NSF policy on the dissemination and sharing of research results. See Grant Proposal Guide (GPG) Chapter II.C.2.j for full policy implementation.

Data Management & Sharing Frequently Asked Questions (FAQs) - updated November 30, 2010

NSF Data Sharing Policy

Investigators are expected to share with other researchers, at no more than incremental cost and within a reasonable time, the primary data, samples, physical collections and other supporting materials created or gathered in the course of work under NSF grants. Grantees are expected to encourage and facilitate such sharing. SeeAward & Administration Guide (AAG) Chapter VI.D.4.

Great data sharing talk

2010-10-19T04:02:00.001-07:00

Useful, interesting (and amusing) data sharing slides in this recent talk by Heather Piwowar: http://is.gd/g7Zke (slideshare).

Statement of Purpose - Draft, Oct 2010

2010-10-05T07:42:00.000-07:00

The overall objective of the BioSharing forum is to work at the global level to build stable linkages between funders, implementing data sharing policies, and well-constituted standardization efforts in the biosciences domain, to expedite the communication and the production of an integrated standards-based framework for the capture and sharing of high-throughput genomics and functional genomic bioscience data, in particular.

This overall objective has several components, each of which can be further decomposed:

1. Web site to centralize bioscience data policies, reporting standards and links to other related portals

Providing a “one-stop shop” for those seeking data sharing policy documents and information about the standards and technologies that support them.
Exposing core information on well-constituted, community-driven standardization efforts and link to their reporting standards (checklists, ontologies and file-formats), documentation, training material, news and contact point.
Linking to exiting portals or new resources (to be developed collaboratively with other groups and initiatives) for those seeking information on systems serving or implementing the standards.

2. Communication forum for funders and leaders of the standardization efforts to achieve harmonization and mutual support

Lobbying for intra-harmonization within the two stakeholders groups to promote
i. exchange of ideas and policy components among public and private funders, and between funders and potential fundees, to ensure the difference among the policies (such as the reporting standards supported) do not impede seamless interoperability of the data, ultimately;
ii. cross-project activities among the standardization efforts to create interoperable reporting standards and avoiding unnecessary overlaps, duplication of efforts and incompatible tools.
Identifying a mutual support system between the two stakeholders groups to ensure
i. funding agencies are abreast with challenges the standardization efforts face and can provide targeted funds to sustain their development and maintenance;
ii. ensure that when community-developed standards are mature and appropriate standards-compliant systems become available these are channelled to the appropriate funding agencies, that in turn endorse them in their data sharing policies, thus achieving wider harmonization of the data.

The BioSharing forum will have a combination or targeted and open-attendance meetings, normally as part of larger meetings so as to reach as broad an audience as possible especially potential fundees and therefore future users of standards. The forum will utilize all possible means to disseminate information (such as RSS feeds, position papers, presentation).

Fairly succinct MIBBI/standards proceedings paper

2010-09-28T02:27:00.001-07:00

MIBBI and its context were presented at the 4th Int'l Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations (ESCEC) in 2009, for which a short paper was also prepared, linked here.

Interesting poster abstract on attribution of re-used data

2010-09-21T02:24:00.000-07:00

Copied from: http://is.gd/fkWiz

Data citation in the wild
Valerie Enriquez, Sarah Walker Judson, Nicholas M. Weber, Suzie Allard, Robert B. Cook, Heather A. Piwowar, Robert J. Sandusky, Todd J. Vision, Bruce Wilson

Consistent attribution of research data upon reuse is necessary to reward the original data-producing investigators, reconstruct provenance, and inform data sharing policies, tool requirements, and funding decisions. Unfortunately, norms for data attribution are varied and often weak. As part of the DataONE 2010 summer internship program, three interns studied the policies, practice, and implications of current data attribution behavior in the environmental sciences. We found that few policies recommend robust data citation practices: in our preliminary evaluation, only one-third of repositories (n=26), 6% of journals (n=307), and 1 of 53 funders suggested a best practice for data citation. We manually reviewed 500 papers published between 2000 and 2010 across six journals; of the 198 papers that reused datasets, only 14% reported a unique dataset identifier in their dataset attribution, and a partially-overlapping 12% mentioned the author name and repository name. Few citations to datasets themselves were made in the article references section. In multivariate analysis, citation patterns were more correlated with repository (with citations to Genbank being most complete) than journal or datatype. Attribution patterns were found to be steady over time. Consistent with these findings, dataset reuse was difficult to track through standard retrieval resources. Searching by repository name retrieved many instances of data submission rather than data reuse, combing the citation history of data creation articles was time consuming, and searching citation databases for the few early-adopter dataset DOIs and HDLs in reference lists failed due to apparent limitations in database query capabilities and structured extraction of DOIs. We hope these descriptions of the current data attribution environment will highlight outstanding issues and motivate change in policy, tools, and practice. This research was done as open science (http://openwetware.org/wiki/DataONE:Notebook/Summer_2010): ask us about it!

BioSharing now on Twitter

2010-09-16T08:37:00.000-07:00

BioSharing now has a presence on Twitter, which we will use as part of our efforts to disseminate useful information to those with an interest in data sharing, and news about the project.

We would also like to promote the use of the #biosharing hashtag by people on Twitter making relevant comments, to facilitate discovery of conversations about data sharing.

BMC Research call for "Data Notes" and descriptions of community standards...

2010-09-16T04:29:00.000-07:00

Here is more information about this initiative from the BioMed Central blog.

"By publishing Data Notes (often called “data papers” by other publishers), authors in BMC Research can publish peer-reviewed articles that briefly describe a biomedical data set or database..."

A call for BMC Research Notes contributions promoting best practice in data standardization, sharing and publication
Iain Hrynaszkiewicz

BMC Research Notes 2010, 3:235

Published: 2 September 2010
Abstract (provisional)

BMC Research Notes aims to ensure that data files underlying published articles are made available in standard, reusable formats, and the journal is calling for contributions from the scientific community to achieve this goal. Educational Data Notes included in this special series should describe a domain-specific data standard and provide an example data set with the article, or a link to data that are permanently hosted elsewhere. The contributions should also provide some evidence of the data standard's application and preparation guidance that could be used by others wishing to conduct similar experiments. The journal is also keen to receive contributions on broader aspects of scientific data sharing, archiving, and open data.

You can read the full article here: Editorial

Great RIN/NESTA report on data sharing

2010-09-13T05:53:00.001-07:00

The research Information Network (RIN) and the National Endowment for Science Technology and the Arts (NESTA) have just put out a really interesting report on the reasons for and problems with data sharing, based on six case studies (direct link to PDF). Lots of the issues are things that come up time and again, though it's nice to see the case made less anecdotally than I normally manage :)

Nature Precedings expands scope to take data policy related documents

2010-08-31T03:32:00.001-07:00

From an Editorial entitled Cite Site in Nature Genetics (Nature Genetics 42, 729 (2010) doi:10.1038/ng0910-729) comes news that Nature Preceedings is now catering to the types of documents the BioSharing community wishes to promote.

"We now have adapted our preprint archive, Nature Precedings, to host project descriptions, community standards papers and funder policies. Citable project descriptions provide a guide to the resources available and create a mechanism to give data producers citation credit.

The US National Institutes of Health and National Science Foundation both now require their grantees to produce a project description document explaining their aims and the resources they hope to generate. We created an archive where these documents (often referred to as 'marker papers') can be publicly deposited and, if necessary, regularly updated. Project descriptions can function as guides to projects that are complex and that deposit disparate resources in several databases. They can also help data users keep track of differing and evolving conditions for data use (if any exist). Because the archive is citable, it can help data users and journal editors handle competing publications more fairly. Citations to project descriptions may also be tracked to ensure effective use of resources and to make recommendations for best research practice."

Read more here

The purpose of Nature Precedings:

"Nature Precedings connects thousands of researchers and provides a platform for sharing new and preliminary findings with colleagues on a global scale.

Post pre-print manuscripts, posters and presentations on Nature Precedings to claim priority and receive feedback on your findings prior to formal publication."

the latest list of planets - to share the data or not?

2010-08-19T05:34:00.000-07:00

An article in the New York Times called In the Hunt for Planets, Who Owns the Data? describes the debate over whether researchers have the right to hold back the best candidates for newly discovered planets.

"By agreement with NASA, the team is holding back data on its 400 brightest and best planet candidates, which the astronomers intend to observe themselves over a busy summer."

Here is a great excerpt from the article about science and data sharing in general:

The fate of data — who owns it and who gets to see it, and when — has become one of the more contentious issues in science, scientists say.

In the past, scientific data consisted of carefully inked notations in research notebooks, bound, with numbered pages, accumulating on a bookshelf in the office or lab, or photographic plates in yellowing envelopes sitting in a filing cabinet. And it was proprietary, meaning it was yours forever to publish or mull endlessly as you desired.

Today, it often consists of billions or trillions of 1’s and 0’s reposing in vast digital archives, whose capacity is measured in terabytes or petabytes, buttressed by the giant computer programs that process it and the reams of ancillary information, dubbed metadata, that give it context.

In the era of the Web, all this information can be sent around the globe at the click of a mouse, retrieved and manipulated by anyone who wants to use it to better understand the nature of dark matter, argue about the safety or desirability of nuclear power, or decide how much salt to put in her food.

“Science is more and more living in a glass house,” said Robbert Dijkgraaf, a physicist at the University of Amsterdam and co-chairman of the InterAcademy Council, a multinational organization of science academies that is reviewing the work of the Intergovernmental Panel on Climate Change at the request of the United Nations.

Phillip Sharp, a biologist at the Massachusetts Institute of Technology, led a National Academy of Sciences study last year that said rules for sharing data should be built into projects. In an interview, he said: “The time has past when a bunch of elite true-meaning experts could go into the next room and make conclusions. They have to be transparent. That’s a change in the culture.”

Read the whole article here

Governance of communities - non-profit organizations

2010-08-19T01:58:00.001-07:00

Gaining non-for-profit status has proven a major milestone in the formation of key scientific communities, including some listed on the BioSharing website. Academic non-profit organizations (NPOs) gain credibility, branding and the independence required to work collaboratively across traditional institutional boundaries.

The reasons why a research community goes down the route of becoming a NPO are varied and the ways they get there are different, but they are all unified by needing to have a mission and transparent mechanisms of operation.

In order to gain NPO status, a community has to define its mission, elect officers and form a Board with bylaws. The rules that govern the Board (community) are encapsulated in its bylaws (Good template and explanation here).

Bylaws (also called constitutions or the charters) are usually made public on a community's website. Below is a list of NPOs contributing to real-world data sharing and links to their bylaws:

SAGE Bionetworks - Bylaws - Sage Bionetworks is a new, not-for-profit medical research organization established in 2009 to revolutionize how researchers approach the complexity of human biological information and the treatment of disease.

International Society for Biocuration - Constitution and Governance Guidelines - The ISB is a non-profit organisation for biocurators, developers, and researchers with an interest in biocuration. The society promotes the field of biocuration and provides a forum for information exchange through meetings and workshops.

PISTOIA: Bylaws - The PISTOIA Alliance aims to provide an open foundation of data standards, ontologies and web-services to streamline the Pharmaceutical Drug Discovery workflow (Chemistry, Biological Screening, Logistics) through common business terms, relationships and processes

Other initiatives have gained NPO status through an association with a parent
NPO (or fiscal sponsor). Science Commons is an initiative run by Creative Commons (Bylaws). Also, OBO Foundry uses iCommons (Bylaws) as as its fiscal agent. iCommons is a legal entity in its own right and is a former subsidiary of Creative Commons based in the UK (i.e. was incubated by Creative Commons).

There are many, many NPOs that contribute to science and scientific research - a few more are listed below for contrast (three scientific societies and the internet giant, the Wikipedia Foundation).

CSM: Bylaws - The Canadian Society of Microbiologists seeks to advance microbiology in all its aspects and to faciliate the interchange of ideas between microbiologists.

AAAS: Constitution revisions of AAAS and its divisions - The American Association for the Advancement of Science, "Triple A-S" (AAAS), is an international non-profit organization dedicated to advancing science around the world by serving as an educator, leader, spokesperson and professional association. It is the world's largest general scientific society.

ISCB: Bylaws and governing policies - The International Society for Computational Biology (ISCB) serves over 2500 members from nearly 100 countries around the world by addressing scientific policies, providing access to high quality publications, organizing meetings, and serving as a portal to information about training, education, employment and news from related fields.

Wikipedia Foundation: Bylaws - The Wikimedia Foundation, Inc. is a nonprofit charitable organization dedicated to encouraging the growth, development and distribution of free, multilingual content, and to providing the full content of these wiki-based projects to the public free of charge.

Unlocking the Potential (of data)

2010-08-06T03:44:00.001-07:00

When we talk about the need to share biological data and outline the obstacles in the way we talk about too file formats, too much fragmentation, lack of standards, lack of tools, etc...

In doing so, we are just rephrasing the exact same issues that led to the creation of the internet - the ultimate tool for communication and information sharing.

Tim Berners-Lee invented the World Wide Web (i.e. URLs and HTML) exactly to overcome these problems and frustrations - as he says in this Ted Talk to "Unlock all this Potential".

See the beginning of this Ted.com "Ideas worth spreading" video for his thinking in developing the WWW 20 years ago:

Tim Berners-Lee on the next Web Tim Berners-Lee on TED.com

"Tim Berners-Lee invented the World Wide Web. He leads the World Wide Web Consortium, overseeing the Web's standards and development."

Now he's 'reframing' the world again by focusing on raw data and what can be done when it is made available on the internet.

Now he is calling for everyone to "put their data on the web". He argues that documents you read, data you can do all kinds of stuff with! As he says, data drives a huge amount of what goes on in our lives.

The technology underlying this new revolution in data on the web is the concept of "linked data" - including the relationships between data points (the design principles of this standard/technology are here).

This next Ted.com video gives examples of what can be done - including volunteer creation of maps following the earthquake in Haiti.

This is a glimpse of what will be done by the "Open Data Movement" in the future:

Tim Berners-Lee: The year open data went worldwide

Computers to generate new hypotheses from existing data?

2010-08-04T14:45:00.001-07:00

Everyone is talking about how we are now overwhelmed with available data, including an ever increasing number of scientific publications. Humans just can not keep up. There is now a growing effort to use computers to make sense of all this data, even to the point of using computers to generate new scientific hypotheses. If computers can logic out the patterns, for example, in the published literature between different discplines, they may be able to suggest new avenues of research.

This is the subject of nice article in the Guardian:

Web-crawling computers will soon be calling the shots in science
Within a decade, computers will be able to plough through scientific data looking for patterns and connections – then tell scientists what they should do next

The articles is a response to an article in Science by James Evans and Andrey Rzhetsky of the University of Chicago called "Machine Science".

Distributed-thinking projects

2010-08-04T14:29:00.000-07:00

The open availability of data is made all the more appealing to many by the idea of the associated problems.

The idea of scavenging CPU cycles from home computers is now well embedded in popular culture following the success of efforts like SETI@home. More recently, researchers created the same kind of home computing software to do computationally time-consuming protein folding problems. Surprisingly, some volunteers fed back to the project that they thought they could solve the folding problems quicker/better than the computer. This led to the creation of the FoldIt program - and people took on the challenge.

Such projects are now called distributed-thinking projects and their numbers are growing.

Read this Nature article for more: Citizen Science: People Power

Benefits and incentives for data sharing

2010-07-22T03:48:00.000-07:00

This interesting article in PloS ONE by Heather Piwowar and colleagues presents a compelling argument for providing open access to data that perhaps shouldn't come as too much of a surprise - an increase in citations for the original publication.

The authors examined the citation history of 85 cancer microarray clinical trial publications with respect to the availability of their data. Publications where the data was made publicly available were significantly associated with a 69% increase in citations.

---

Piwowar HA, Day RS & Fridsma DB. Sharing Detailed Research Data Is Associated with Increased Citation Rate. PLoS ONE 2(3): e308.
doi:10.1371/journal.pone.0000308

Biosharing meeting presentations available online

2010-07-16T04:04:00.000-07:00

The inaugural BioSharing meeting was held at ISMB this year within the GSC's M3 SIG. Thanks to everyone who participated! There was clear interest in formalizing a BioSharing community among community representatives and this came through, in particular, in the great Panel discussion at the end of the day-long meeting. Thanks to all the speakers who sat the panel and talked about what the vision of a future BioSharing community might look like. A workshop report will be generated, but for now all speakers presentations have been posted onto the agenda.

Speaker presentations

The dark side of data sharing

2010-07-16T03:20:00.000-07:00

There is a super post on "How to build a bad biological database" on the "Wood for the Trees" blog.

By making a tongue in cheek list of how to build a terrible database, the author hits many of the essential criteria for supporting good data sharing practice at the database level.

Enthusiastic comments include one from Mike Galperin that he will make it essential reading for all authors to the Database special issue of Nucleic Acids Research!

Here are the top three tips - see the full list here.

TIP ONE Make submission difficult

TIP TWO Have a support service that is available 9-5 Mon to Fri GMT

TIP THREE Don’t let your file formats interconvert

Read more

Data Sharing International Conference 2010

2010-06-10T01:59:00.000-07:00

Data Sharing International Conference September 2010
September 20- 22, St Hugh's College, Oxford

The provisional agenda is now up and includes a BioSharing talk.

Go to the conference site here: Data Sharing International Conference

The conference is hosted by the Centre for Health, Law and Emerging Technologies (HeLEX) at Oxford.

Researching law, policy and practice in the governance of health and emerging technologies HeLEX is an interdisciplinary research centre, based at the Department of Public Health at the University of Oxford.

OVERVIEW

With the aid of technology and the support of funders, data sharing is now possible on a scale that has not been possible before with genome sequence and research datasets located in different countries easily available to researchers online. Sequence data produced by projects such as the Human Genome Project have accelerated advances in scientific knowledge. On the basis of this, national funders are now encouraging the deposition of many different kinds of research data for use by all; the building of research infrastructure to network biobanks; and have funded large international consortia to share samples and information from thousands of research participants to understand the effect of DNA on disease.

Whilst these developments have potential great benefits for science, they raise a number of practical and procedural issues, but also broader questions about fairness, equity and justice.

How should data-generators be rewarded for their efforts to the scientific community?

Can we promise anonymity of research participants when whole sequences data and phenotypic data are being used for research purposes?

Should participants be fed back individual findings?

Are our national research governance systems adequate to cope with global data sharing?

What innovative IT solutions can be brought into this field to address these challenges and further promote data sharing?

The purpose of this conference is to bring together leaders in the field to discuss the issues raised by data sharing in genomics as well as bringing experts from other domains to add a new dimension to these debates.

SeaDataNet Data Policy

2010-06-07T09:13:00.001-07:00

Here is a good example of a public data policy distilled from many more specific policies that enables a wide range of collaborators to work together efficiently.

"SeaDataNet has federated open digital repositories to manage, access and share data, information, products and knowledge originating from oceanographic fleets, new automatic observation systems and space sensors."

The SeaDataNet Data Policy

"SeaDataNet has defined an overarching SeaDataNet Data policy, that aims to strike a balance between the rights of investigators and the need for widespread access through the free and unrestricted sharing and exchange of SeaDataNet data, meta-data and data products. The final goal of this policy is to serve the scientific community, public organisations, and environmental agencies, and to facilitate the production of advice and status reports by stating the conditions for data submission, access and use. This policy applies to data managed by SeaDataNet partners for providing access to data managed in the SeaDataNet distributed systems."

Read more about the SeaDataNet project and its data policy on the SeaDataNet homepage: http://www.seadatanet.org/

New members to BioSharing...

2010-06-02T03:04:00.000-07:00

The BioSharing image map found on each page of this website is a visual representation of the "BioSharing universe" that is naturally starting to form in the scientific community. Its spokes are the types of activities that are required to bring about real-world data sharing and the communities represented on those spokes (icons) are experts and champions of those areas. The real vision for a future BioSharing universe is where all these communities intersect....and interact. Bringing these communities together is the purpose of the upcoming BioSharing meeting.

It is the collaborative intersection of the many spokes around the ring that holds the promise and many of these groups area already building these 'cross-over' points as a natural part of their evolution.

All of the icons are on the 'wheel' following discussions with representatives of each group.

We'd like to now welcome SAGE, a data sharing effort that we recently blogged about.

SAGE, like many of the other representatives in this image do not belong on just one spoke of this wheel - they are also an open repository for example. No doubt, this image will evolve.

In this same sense, the Genomic Standards Consortium (GSC), which is hosting the first BioSharing meeting, has now also been put into this universe, as well as the Protein Standards Initiative (PSI). Both GSC and PSI are founding members of the MIBBI consortium - already on the wheel - for their work promoting checklists in the areas of genomics/metagenomics and proteomics, respectively. Both both groups also work at many of the intersections of the BioSharing wheel as domain-level expert groups of researchers.

We welcome new members and look forward to seeing how this data-sharing landscape changes after the first BioSharing meeting.

Journals taking data sharing seriously: Dryad

2010-05-24T15:58:00.000-07:00

As previously blogged, journals are increasingly taking an active role in data sharing.

This includes building partnerships will next-generation data repositories for data accompanying publications. This is the function of the Dryad repository.

Dryad: http://www.datadryad.org/

"Dryad is being developed by the National Evolutionary Synthesis Center and the University of North Carolina Metadata Research Center, in coordination with a large group of Journals and Societies in evolutionary biology and ecology. The National Evolutionary Synthesis Center is a joint effort of Duke University, the University of North Carolina, and North Carolina State University."

There is a Dryad Fact Sheet and a Blog.

MICheckout is live

2010-05-19T03:34:00.000-07:00

The first version of MICheckout is up, linked from the MIBBI front page, allowing the compilation of MIBBI Foundry modules into made-to-measure sets of guidelines. Now stuffing with MIBBI Foundry content (lots to go, but enough in there already to warrant the announcement). Big thanks to Eamonn Maguire for the GUI and for plumbing everything in.

A minimum data sharing policy?

2010-04-21T16:37:00.001-07:00

To follow up on the post about the 12 steps to creating a new data policy, here is a first set of thought of what a high-level template for a data sharing policy might look like.

All data policies provide guidelines for adhering to the principle that data sharing is a good thing. While the particular rules of sharing might be different for a variety of reasons, the general tenets are largely the same.

Might it be possible to encapsulate these basic tenets into a terse minimum data sharing policy that could fit many (all?) situations?

This was in fact one of the recommendation of our Omics data sharing paper:

"We recommend that a single, brief, high-level consensus guideline serve as a template for policy documents at the funder, community, and project levels. At its heart should be the public and timely release of data. It should be based on the principle that funders and the research community must work together to develop best practice."

If such a high level general policy is possible it could contain simple content like this:

A minimum data policy

As an initiative/project/research scientist you will:

- continuously seek to comply with best practices in data sharing
- comply with relevant policies of funders
- strive to share your data with your colleagues and the wider world
- comply with relevant reporting standards
- cite any and all use of public data
- support Open Access publishing and Open Source software solutions
- cost appropriate resources into your grants to cover basic
data management and data sharing best practices
- participate in community efforts when you have opinions,
expertise to contribute
- work with funding agencies to help support you (the community) in complying with this policy

Of course, authors would then add relevant details to these basic statements to make their specific stance explicit.

Right now these statements combine both principles (data sharing should be part of the fabric of research) and practices (use standards as far as possible).

While a data policy based just on practices could easily be distilled from such a general guideline, policies that included strong principles would best start to bring about real-world data sharing.

Scientific Data Sharing Project

2010-04-18T11:43:00.000-07:00

Here is another data sharing project, that like the SAGE project, is focusing first on improving human health, through sharing of scientific data.

The "Scientific Data Sharing Project's" mission is:

"The Data Sharing Project seeks to expedite research breakthroughs by helping make scientists’ raw data freely available to other researchers. Focusing first on the field of medicine, the project’s aim is to expand data sharing in a way that can lead to discoveries that increase people's chances of living longer and healthier lives. The project website will be a key resource for the airing of all aspects of data sharing, including its promise and the cultural and technological obstacles in its path."

Their Links page lists a wide range of organizations relevant to the future of data sharing in this domain.

Getting scientific data out there for the public good

2010-04-14T14:23:00.000-07:00

The SAGE effort is attracting increasing attention due to its admirable goal of trying to make more scientific data public in the hopes of eradicating disease.

Here is a nice article about the SAGE mission from the Wall Street Journal describing some of these efforts and focusing on the question of why much of the scientific community still finds it hard to make data public, quickly.

"My data, your data, our data"

Here is the opening sentence:

"In the age of Facebook, Twitter, and Wikipedia, it is hard to believe there is still one group that prefers to be more circumspect about sharing: scientists."

Here is the vision statement from SAGE:

"Create an open access, integrative bionetwork evolved by contributor scientists working to eliminate human disease"

Here is more background on SAGE from the homepage:

"Sage Bionetworks is a new, not-for-profit medical research organization established in 2009 to revolutionize how researchers approach the complexity of human biological information and the treatment of disease. Sage’s objectives are:

- to build and support an open access platform and databases for building innovative new dynamic disease models
- to interconnect scientists as contributors to evolving, integrated networks of biological data"

M3 & BioSharing SIG at ISMB 2010

2010-03-11T10:44:00.000-08:00

Date: July 9-10, 2010
Venue: Boston, Mass, USA
ISMB 2010

This event marks the inaugural meeting of the BioSharing community.

The first day is dedicated to the Genomics Standards Consortium (GSC) that will hold the second Metagenomics, Metadata and Metaanalysis (M3) workshop after a successful event at ISMB in 2009.

Here, more information on the event.

Register through the ISMB 2009 registration page here. Note that you do NOT have to register to the ISMB conference itself to attend a SIG meeting. You need to register for a two-day SIG meeting in order to attend the M3 / Biosharing 2010 SIG.

Organizers
Co-chairs:
Ed DeLong, Massachusetts Institute of Technology
Owen White, University of Maryland
Dawn Field, NERC Centre for Ecology and Hydrology, UK
Susanna-Assunta Sansone, European Bioinformatics Institute
Program committee
Lynette Hirschman, MITRE, USA
Frank Oliver Gloeckner, MPI Bremen, Germany
Lynn Schriml, University of Maryland, USA
George Garrity, Michigan State University, USA
Jack Gilbert, Plymouth Marine Labs, UK
John Wooley, University of California, San Diego
Iddo Friedberg, Miami University, Ohio, USA
Guy Cochrane, EMBL European Bioinformatics Institute, Cambridge
Peter Sterk, Wellcome Trust Sanger Institute, UK
Amanda Collis, BBSRC, UK
Pascale Gaudet, Northwestern University
Suzi Lewis, Lawrence Berkeley National Laboratory, Berkeley, USA

A survey of live blogging technology for covering scientific conferences

2010-03-05T00:09:00.000-08:00

There are many ways of openly disseminating scientific information on the Internet. The technologies now available are particularly important for conferences, where expansive sharing policies such as those from recent conferences (e.g. ISMB/ECCB 2009, Science Online London 2009, and Science Online 2010) helped people work together and aid information flow within the community. For instance, FriendFeed has been successfully used to kick-start collaborative research efforts resulting in publications. In addition, the live blogging of ISMB/ECCB 2009 resulted in two papers in PLoS Computational Biology: one providing a number of guidelines for the creation of live blogging conference policy; the second describing the implementation of those guidelines at ISMB/ECCB 2009. This post describes the technologies commonly in use by today's life scientists, and is intended as a companion to the two PLoS Computational Biology articles cited above.

Current Web Platforms for Live Coverage

A number of platforms are potentially suitable for live coverage of conferences. The most common ones are compared in the table below, and include dedicated services such as CoverItLive or ScribbleLive as well as other more general platforms such as wikis, blogs, Twitter, FriendFeed or the upcoming Google Wave. This article covers non-audio/video coverage of live conferences; for further information on these areas, please see the FriendFeed discussion. Additionally, a constantly-updated list of online tools used by scientists is available via its FriendFeed thread.

Platform	Pros	Cons
Dedicated conference coverage services (e.g. CoverItLive or ScribbleLive)	· Designed for covering conferences	· High barrier of entry: need separate accounts · Geared towards centralized coverage provided by a dedicated blogging team
Wikis	· Familiar technology · Multiple users	· In practice, only one person can edit at a time · Editing and saving cycles are slow
Twitter	· Low barrier of entry · Provides rapid coverage · Commonly-used as a forum for personal opinions and spontaneous remarks	· 140 characters per message not enough to convey the meaning of scientific talks · Unless special tags ("hashtags") are used, difficult to aggregate
Personal Blogs	· Commonly-used as a forum for personal opinions · Room for detailed commentary	· Difficult to aggregate unless bloggers submit links to their posts to a central location
FriendFeed	· Low barrier of entry · Enables collaborative editing	· Limited format: one heading followed by a long list of plain-text comments
Google Wave	· Enables collaborative editing · Advanced editing features, such as automatic spelling correction · Extensible through 3^rd party applications or “robots”, e.g. automatic insertion of chemical diagrams, etc.	· Not released yet

Blogs have been used for a long time to report and reflect on conference talks. Blog posts usually have only one author and are posted after the talk. In contrast, recently emerging services such as Twitter and FriendFeed provide the opportunity for instant coverage of the conference from many angles, broadcast to a world-wide audience. Twitter is a micro-blogging service which allows 140-character long "tweets". While this method of microblogging encourages succinct, direct statements, a single tweet is generally too short to convey the meaning of a scientific talk. Twitter is difficult to use as the main microblogging platform for a conference without overwhelming followers with a multitude of messages.

FriendFeed is a service that enables users to aggregate their "lifestream", i.e. to bundle their posts from sites like blogs, Twitter, bookmarking services and other items of interest from RSS feeds. These bundles are then shared with each user’s followers. Many scientists have adopted FriendFeed, focusing on scientific feeds of interest, such as science or technology blogs or papers saved in repositories such as CiteULike and Connotea. FriendFeed also features "rooms", discussion forums dedicated to a certain topic to which users can subscribe. For example, there is a thriving community of scientists on FriendFeed in the Life Scientists room (http://friendfeed.com/the-life-scientists) and many conferences have created their own rooms. The current use of FriendFeed as a platform to cover conferences began entirely accidentally, as an outcome of the existing community of scientists using the service.

Irrespective of the technology chosen, record permanence is an important unsolved issue. There is no straightforward answer as to how long FriendFeed comments will be stored, and it is noteworthy that FriendFeed was acquired by Facebook in August 2009, making the long-term future of the service as-yet unclear. Twitter does not have an archive, and users are reliant upon third-party tools (http://printyourtwitter.com/, http://twapperkeeper.com/) to keep a longer-term record of what has been said. While conference organizers could strive to create and provide an archive of live blogging efforts, it is unclear if such efforts should be their responsibility.

Future Developments
The ideal conference coverage platform should have a low barrier of entry to allow for efficient collaboration between bloggers. It should also be possible to make room for personal comments and questions next to the more objective transcript of the talk. FriendFeed has currently proven to be the most versatile, but as it only allows for a linear stream of comments without special formatting, it has been mostly used to generate a transcript of the talk. Upcoming developments such as Google Wave merge collaborative editing with information dissemination, document versioning and task automation, effectively combining the power of email, chat-based environments and wikis. Scientists are already working on uses of Google Wave for collaborative research activities. Real-time editing should minimize the duplication of content frequently encountered in FriendFeed coverage, as multiple attendants covering the same talk can observe each other’s actions, edit existing comments and add corrections as needed. Repository 'robots' (automated participants in a Wave) would allow for the merger of multiple Waves into a coherent summary of a conference, or allow for parallel but connected streams of coverage. This is how Mathias Uhlen's keynote at ISMB/ECCB 2009 looks on FriendFeed (http://ff.im/4Hk76):

It could instead be parallelized with one thread displaying factual reporting of the talk and the other covering personal comments and discussion. Factual reporting and personal comments are separated yet connected. For the transcript section, author names are hidden, while they are shown for the section containing personal statements. Separate posts from the FriendFeed thread have been merged, taking advantage of real-time editing facilities.

However, only actual use will determine if such technologies would be too distracting or even work under the conditions of conference network infrastructure. It is noteworthy, however, that the Google Wave protocol is designed to be open and allow multiple servers to offer Waves. Thus, conference organizers could supply their own Wave server within the conference network for faster access times. The success of Google Wave and similar services will ultimately depend on their acceptance within the scientific community, but initial reception has been positive (http://blog.openwetware.org/scienceintheopen/2009/07/19/sci-bar-foo-etc-part-iii-google-wave-session-at-scifoo, http://network.nature.com/people/mfenner/blog/2009/07/18/using-google-wave-for-a-week-its-still-great) and the first citation manager robots are being tested. Additional robots such as those handling automatic semantic annotation of abstracts and commentary should be easy to embed and are being actively discussed, but so far lack reported results from actual field tests.

This article is an expanded version of Text S1 of the PLoS Computational Biology article "Live Coverage of Scientific Conferences Using Web Technologies" by Listeret al., is approved by the authors of that paper and has been modified from the original by two of the original authors (Michael Kuhn and Allyson Lister).

The Panton Principles: Principles for Open Data in Science

2010-02-24T13:33:00.000-08:00

A group has published what they are calling the Panton Principles (The Panton Arms is a pub in Cambridge, UK).

Individuals and institutions can sign up to endorse the use of these open data principles in science. Visitors are also encouraged to leave comments.

"Science is based on building on, reusing and openly criticising the published body of scientific knowledge. For science to effectively function, and for society to reap the full benefits from scientific endeavours, it is crucial that science data be made open. Formally, we recommend adopting and acting on the following principles:"

Visit the Panton Principles website to view the four recommendations.

The Panton Principles were authored by

Peter Murray-Rust, University of Cambridge (UK)
Cameron Neylon, STFC (UK)
Rufus Pollock, Open Knowledge Foundation and University of Cambridge (UK)
John Wilbanks, Science Commons (USA)

With help from the Open Knowledge Foundation's Working Group on Open Data in Science.

Fun blog post on why data sharing is a good thing

2010-02-17T02:58:00.000-08:00

Responding to a fairly negative piece in The Scientist, the author rebuts and runs through some positives for data sharing: CLICK ME

12 Steps to creating a Data Sharing Policy

2010-02-08T04:57:00.001-08:00

The Omics data sharing publication that gave rise to this BioSharing website reviewed the data policies of a range of major funders. It also outlined some of the aspects of best practice that were used in the development of those policies. Specifically, a checklist of steps for developing data sharing policies was presented in supplementary information.

These steps are presented again below to put them fully in the public domain (the paper is free at Science but this list is in the Supplementary Online Materials Section). They are general guidelines but passing through these explicit stages makes sure a new policy is based on consensus and meets the needs of the community it is set to serve.

The final result will be a consensus-driven short document, developed by an appropriate policy working group, ready for circulation and posting to an official website for reference. Like all policies, it should be open to challenge and improvement over time especially as technologies that underpin data sharing shift and change.

How does one create a data sharing policy in practice?

Below is a 12‐step checklist outlining the process by which data sharing policies are generated in practice. This checklist is suitable for the development of policy at all levels but is based on experiences gained by major funders of 'omics research (See Supplementary Online Material Box 1 of Field et al, 2009).

The list of policies from which this checklist is derived is found here: data policies

While policies are most often generated by funding agencies, it is good practice for institutions and large consortia to also create explicit data sharing policies. Most policies are only a few pages long, and some of the best are only 1 page - any more detailed information should be contained in a larger 'information guidebook' or other documentation.

The data policy should put into words the general rules of engagement surrounding the data being generated and used and provide explicit expectations for all parties involved.

A 12-Step Checklist for Developing a New Data Policy

1. Identify science driver(s) necessitating a formal data policy for a particular research community

2. Create a working body to bring the data policy to fruition

3. Conduct an initial poll of researcher and funder priorities with respect to data policy development (i.e., confirm the relative importance of data management compared to sharing)

4. Identify the full range of stakeholders

5. Research current policies and draw from them and the literature

6. Draft a straw man document and define key aspects of the policy:

* scope of policy (data types covered, appropriate standards and repositories)

* applicability (which data falls under the policy), rules of data sharing, compliance to standards, submission to appropriate repositories

* funding levels to support implementation and compliance and the consequences of noncompliance

7. Subject straw man to internal and then external round(s) of consultation followed by iterative improvement

8. Obtain formal sign‐off or endorsement by the organization of a final draft and post final draft onto appropriate public website and publicize (launch)

9. Set into motion support for policy:

* Could include: creation/extension of data centers, physical archives, facilities, institutions, or ring‐fenced funds for competitive award programs, development of standard and repositories, education, outreach, etc

10. Monitor compliance and enforce policy

11. Extend policy to cover sub‐areas of science/data as required (create child policies)

12. Evolve or deprecate policy, or component parts, as required

Discussion of microbial genome annotation standards

2010-02-01T06:25:00.001-08:00

Amongst other things, some people discussing microbial genome annotation standards on FriendFeed.

Data Archiving in Ecology and Evolution

2010-01-17T16:40:00.000-08:00

To promote the preservation and fuller use of data, The American Naturalist, Evolution, the Journal of Evolutionary Biology, Molecular Ecology, Heredity, and other key journals in evolution and ecology will soon introduce a new data‐archiving policy. The policy has been enacted by the Executive Councils of the societies owning or sponsoring the journals. For example, the policy of The American Naturalist will state:

This journal requires, as a condition for publication, that data supporting the results in the paper should be archived in an appropriate public archive, such as GenBank, TreeBASE, Dryad, or the Knowledge Network for Biocomplexity. Data are important products of the scientific enterprise, and they should be preserved and usable for decades in the future. Authors may elect to have the data publicly available at time of publication, or, if the technology of the archive allows, may opt to embargo access to the data for a period up to a year after publication. Exceptions may be granted at the discretion of the editor, especially for sensitive information such as human subject data or the location of endangered species.

Journal 'OMICS' recommends MIBBI

2009-12-16T02:31:00.001-08:00

The Liebert journal 'OMICS: A journal of Integrative Biology' now endorses MIBBI. "OMICS also recommends that all publications in 2010 follow relevant community-wide standards and, specifically, will be MIBBI-compliant (Minimum Information for Biological and Biomedical Investigations, www.mibbi.org)" wrote Editor in Chief Eugene Kolker in his December 15 editorial.

Listorius: OpenScience

2009-11-27T10:23:00.000-08:00

Jonathan Eisen has started a compilation of the best openscience sources on Twitter. See it here and suggest new sources:

openscience

"People who tweet about open science, open access, open source, etc"

DOIs for all: DataCite

2009-11-18T08:18:00.000-08:00

DataCite - International Initiative to Facilitate Access to Research Data

A group of leading research libraries and technical information providers have established a partnership to improve access to research data on the internet.

The German National Library of Science and Technology (TIB), the British Library, the Library of the ETH Zurich, the French Institute for Scientific and Technical Information (INIST), the Technical Information Center of Denmark, the Dutch TU Delft Library, Canada Institute for Scientific and Technical Information (CISTI), the Australian National Data Service (ANDS) and the California Digital Library (CDL) all signed a Memorandum of Understanding to this effect.

The goal of this cooperation is to establish a not-for-profit agency that enables organisations to register research datasets and assign persistent identifiers to them, so that research datasets can be handled as independent, citable, unique scientific objects.

BioCurator Forum on future funding of databases

2009-11-04T00:58:00.000-08:00

The International Society for BioCuration has recently launched and held elections to formally establish the ISB Executive Board.

The mission of ISB is to advance the art of Biocuration and recognize the highly skilled researchers who do this invaluable work.

Most recently they have launched a discussion forum.

Following on from the recent post on how to sustain databases, ISB have launched a discussion on the same topic.

See and join the discussion here: ISB database funding forum

Bionumbers database - a fun reminder of the value of open data agrgregation

2009-10-30T08:16:00.000-07:00

A colleague just pointed out the BioNumbers database to me at a meeting - what a great idea!

It is a database of important numbers in biology. You can contribute to it and post comments on already catalogued numbers.

It is still early days for this database but it does remind one how much data really is out there and how powerful it can be when the scientific community is given new tools to allow open data aggregation.

This is perhaps the best page to start with if you want to have an overview of the why and what of the site -Resources - or have a look at this 1 page 'handout' with a bunch of interesting numbers.

How to sustain databases?

2009-10-29T18:27:00.001-07:00

Public databases are essential for data sharing. An open access journal called "Database" launched in 2009.

"Huge volumes of primary data are currently archived in numerous open-access databases, and with new generation technologies becoming more common in laboratories, large datasets will become even more prevalent than today. The archiving, curation, analysis and understanding of all of this data is a challenge. Database: The Journal of Biological Databases and Curation provides a platform for the presentation of novel ideas in database research surrounding biological information, and aims to help strengthen the bridge between database developers and users."

A paper by the CASIMIR group, which recently published on post-publication data sharing, has now published a paper on models for sustaining biological databases.

Models for financial sustainability of biological databases and resources

Christina Chandras¹, Thomas Weaver², Michael Zouberakis¹,Damian Smedley³, Klaus Schughart⁴, Nadia Rosenthal⁵,John M. Hancock⁶, George Kollias¹, Paul N. Schofield⁷ andVassilis Aidinis¹^,*

¹Institute of Immunology, Biomedical Sciences Research Center Alexander Fleming, 34 Fleming Street, 16672 Athens, Greece, ²MRC Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, ³European Bioinformatics Institute, EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK, ⁴Experimental Mouse Genetics, Helmholtz Centre for Infection Research & University of Veterinary Medicine, Hannover, Inhoffenstrabe 7, D-38124 Braunschweig, Germany, ⁵EMBL-Monterotondo Outstation, Via Ramarini 32, 00015 Monterotondo-Scalo (RM), Italy, ⁶Bioinformatics Group, MRC Harwell, Harwell, Oxfordshire, OX11 0RD and ⁷Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK

*Corresponding author: Tel: +30 210 9654382; Fax: +30 210 9654210; Email: v.aidinis@fleming.grCorrespondence may also be addressed to Paul N. Schofield. Tel: +44 1223 333878; Fax: +44 1223 333840; Email: ps@mole.bio.cam.ac.uk

	Abstract

Top Abstract Introduction Data and biological resources Problems encountered Models examined The role of industry... A model with potential:... The role of consortia Recommendations for the mouse... Discussion Funding References

Following the technological advances that have enabled genome-wideanalysis in most model organisms over the last decade, therehas been unprecedented growth in genomic and post-genomic sciencewith concomitant generation of an exponentially increasing volumeof data and material resources. As a result, numerous repositorieshave been created to store and archive data, organisms and material,which are of substantial value to the whole community. Sustainedaccess, facilitating re-use of these resources, is essential,not only for validation, but for re-analysis, testing of newhypotheses and developing new technologies/platforms. A commonchallenge for most data resources and biological repositoriestoday is finding financial support for maintenance and developmentto best serve the scientific community. In this study we examinethe problems that currently confront the data and resource infrastructureunderlying the biomedical sciences. We discuss the financialsustainability issues and potential business models that couldbe adopted by biological resources and consider long term preservationissues within the context of mouse functional genomics effortsin Europe.

Legalese and data sharing

2009-10-27T19:20:00.000-07:00

Lawyers and legal experts have a very important role to play is paving the way for improved access to data that benefits both providers and consumers within a sustainable framework.

One tutorial on some of these issues was presented at the recent ISWC meeting. The ISWC is the major international forum where the latest research results and technical innovations on all aspects of the Semantic Web are presented.

The 8th International Semantic Web Conference (ISWC 2009) was held 25-29 October 2009 near Washington, DC.

This tutorial is one such example of the increasing exchange between the legal and scientific worlds. The slides presentations have been posted to the web (at SlideShare) for reference.

ISWC 2009 Tutorials/Legal and Social Frameworks for Sharing Data on the Web

Sunday, 25th October, 14:00- 18:00

Abstract

The Linked Data movement is gathering momentum and its principles are beginning to be adopted outside of the core Semantic Web community. To date the emphasis has rightly been on communicating key technology principles, but sustainable use of Semantic Web resources, particularly within a commercial context, requires that a broader range of issues are addressed. For example, what legal issues relate to the collection and republication of data from existing resources, and how do these vary internationally? Can incorrectly applied rights statements hamper reuse of data? How should community norms, like attribution, be fostered within a global community of data reusers? Many Semantic Web developers do not have the experience to address these questions, with the result that sustained growth of the Linked Data web may be hindered. This tutorial will address this education need, providing participants with an understanding of the broader range of issues relevant to global data publishing. The tutorial will review existing legal frameworks that support open data publishing, and provide guidance on their reuse. The social aspects of data sharing will also be introduced, using the Science Commons as an exemplar of open, international data sharing through creation of a public data commons.

NIH to Update Data-Sharing Policy for Sequence and Related Genomic Data

2009-10-25T07:26:00.000-07:00

The NIH has released a notice that it will update its data sharing policy.

Notice Number: NOT-HG-10-006

Key Dates
Release Date: October 19, 2009

Issued by
National Human Genome Research Institute (NHGRI), (http://www.genome.gov/)

Purpose

The purpose of this Notice is to inform the research community of plans by the National Institutes of Health (NIH) to:

1. Update data sharing policies for NIH supported research, including extramural and intramural projects, involving sequence and related genomic data obtained with advanced sequencing technology (e.g., medical resequencing data, sequence data from non-human species, including microorganisms, transcriptomic and epigenomic data, as well as data needed for interpretation, including associated clinical, other phenotype and metadata, such as supporting study documents and methodologies);
2. Encourage investigators and IRBs to consider the potential for broad sharing of sequence and related genomic data in developing informed consent processes and documents for such studies involving human sequence data; and,
3. Communicate the agency’s intent and current underlying considerations related to developing a policy pertaining to the deposition of these large datasets into centralized databases, such as the GenBank Short Read Archive (SRA) or the Database of Genotypes and Phenotypes (dbGaP), so that they are available as broadly and rapidly as possible to a wide range of scientific investigators.

Read the full notice here: http://grants.nih.gov/grants/guide/notice-files/NOT-HG-10-006.html

Or read more about it at Genome Web:

The National Institutes of Health plans to update its data-sharing policies for sequence and related genomic data obtained with "advanced sequencing technology", and to encourage investigators and institutional review boards "to consider the potential for broad sharing of sequence and related genomic data" when developing informed consent protocols for studies that involve human sequence data, according to a recent notice from the National Human Genome Research Institute.

According to the document, "very large" sequence data sets that allow for new biological insights "are not only valuable for addressing the questions that the experiments were designed to ask, but also have added scientific value when combined with other large data sets."

Full Story: http://www.genomeweb.com/sequencing/nih-update-data-sharing-policy-sequence-and-related-genomic-data

Explain Science Commons in 2 minutes? Yes we can.

2009-10-25T07:18:00.000-07:00

Here is a great two minute video about the Science Commons and their aim of making scientific information free and open to promote scientific discovery. If you don't know anything about the Science Commons yet its a good place to start. If you are familiar with their work and goals you can appreciate it is a nice two minute overview that captures the importance of this effort!

The Science Commons in 2 minutes: http://blog.ted.com/2008/12/explain_science.php

Science Commons homepage: http://sciencecommons.org/

Making the Web Work for Science

Science Commons designs strategies and tools for faster, more efficient web-enabled scientific research. We identify unnecessary barriers to research, craft policy guidelines and legal agreements to lower those barriers, and develop technology to make research, data and materials easier to find and use.

Our goal is to speed the translation of data into discovery — unlocking the value of research so more people can benefit from the work scientists are doing.

'Omics Data Sharing' article published in Science

2009-10-09T02:09:00.001-07:00

The BioSharing website was launched to accompany this paper which appeared today in Science. It is "free to access" - you just have to be signed up to view the free content at Science.

It can also be found here for free at UKPubmed Central: Omics Data Sharing

Dawn Field, Susanna-Assunta Sansone, Amanda Collis, Tim Booth, Peter Dukes, Susan Gregurick, Karen Kennedy, Patrik Kolar, Eugene Kolker, Mary Maxon, Sian Millard, Alexis-Michel Mugabushaka, Nicola Perrin, Jacques Remacle, Karin Remington, Philippe Rocca-Serra, Chris Taylor, Mark Thorley, Bela Tiwari, John Wilbanks 2009. Science. 326:234-236.

The BioSharing website was launched to accompany the publication of the below article on the role of data policies in supporting scientific research. This website is dedicated to centralizing and giving higher profile to bioscience data policies and standards. Its offers a focal point for the various stakeholders in data policy by fulfilling two main roles: (i) Providing a ‘one-stop-shop’ for those seeking data policy documents and related information (including information about the standards and technologies that support them) and (ii) Encouraging the exchange of ideas and policy components amongst funders, and between funders and potential fundees, ultimately to harmonize policy components where feasible.

Science 9 October 2009:
Vol. 326. no. 5950, pp. 234 - 236
DOI: 10.1126/science.1180598

POLICY FORUM

MEGASCIENCE:

'Omics Data Sharing

Dawn Field,¹^,*^,^, Susanna-Assunta Sansone,¹^,2^, Amanda Collis,³^, Tim Booth,¹ Peter Dukes,⁴Susan K. Gregurick,⁵ Karen Kennedy,⁶ Patrik Kolar,⁷ Eugene Kolker,⁸ Mary Maxon,⁹ Siân Millard,¹⁰Alexis-Michel Mugabushaka,¹¹ Nicola Perrin,¹² Jacques E. Remacle,⁷ Karin Remington,¹³Philippe Rocca-Serra,¹² Chris F. Taylor,¹² Mark Thorley,¹⁴ Bela Tiwari,¹ John Wilbanks¹⁵

Development of high-throughput genomic and postgenomic technologies has caused a change in approaches to data handling and processing (1). One biological sample might be used to generate many kinds of "big" data in parallel, such as genome sequence (genomics), patterns of gene and protein expression (transcriptomics and proteomics), and metabolite concentrations and fluxes (metabolomics). Extensive computer manipulations are required for even basic analyses of such data; the challenges mount further when two or more studies' outputs must be compared or integrated.

¹ U.K. Natural Environment Research Council (NERC), Environmental Bioinformatics Centre.
² European Molecular Biology Laboratory (EMBL) Outstation, The European Bioinformatics Institute (EBI).
³ U.K. Biotechnology and Biological Sciences Research Council.
⁴ U.K. Medical Research Council.
⁵ U.S. Department of Energy.
⁶ Genome Canada and Wellcome Trust Sanger Institute.
⁷ Unit for Genomics and Systems Biology, European Commission.
⁸ Seattle Childrens Hospital.
⁹ Marine Microbiology Initiative, Gordon and Betty Moore Foundation.
¹⁰ U.K. Economic and Social Research Council.
¹¹ European Science Foundation.
¹² The Wellcome Trust.
¹³ U.S. National Institute of General Medical Science, NIH.
¹⁴ NERC.
¹⁵ Science Commons.

^* Full author affiliations are available on Science Online.

These authors contributed equally to this article.

Author for correspondence. E-mail: dfield@ceh.ac.uk

Read the Full Text

The Changing face of our data landscape

2009-10-08T04:42:00.000-07:00

The BBSRC has just run an interesting article on data sharing : "The changing face of our data landscape. The article exposes both the benefits and the obstacles to data sharing through examples including how public access to H1N1 data resulted in a Nature publication detailing the origins and evolution of the H1N1 outbreak in Mexico a mere 8 weeks after it started.

The BBSRC has a strong data sharing policy and it can be seen here: Data Policies

New Wiki for Academics

2009-10-06T15:27:00.001-07:00

Wikipedia has changed the world. The wiki concept has spawned several academic wikis aiming to openly share information, for example about a genes and pathways (Wikigenes). Now AcaWiki has launched. Its tagline is "Democratization of Academic Knowledge".

"AcaWiki is like "Wikipedia for academic research" designed to increase the impact of scholars, students, and bloggers by enabling them to share summaries and discuss academic papers online. AcaWiki turns research hidden in academic journals into something more dynamic and accessible."

New RIN report: Communicating knowledge: how and why researchers publish and disseminate their findings

2009-09-29T05:39:00.000-07:00

"This report looks at how researchers publish and why, including the motivations that lead them to publish in different formats and the increase in collaboration and co-authorship. It also explores how researchers decide what to cite and the inﬂuence of research assessment on their behaviours and attitudes."

Toronto and Rome Data Sharing Workshops Publish Reports

2009-09-26T08:31:00.000-07:00

The “Toronto”(1) and “Rome” (2) data sharing workshops have published their meeting reports (as free content in the journal Nature) outlining how the community can advance its thinking and actions on sharing of pre- and post-publication data.

The organizers of these workshops sought to bring together researchers and funders to try to build upon the highly influential Bermuda Principles (3) and the Fort Lauderdale report (4).

The workshop reports are accompanied by the Nature Editorial "Data's Shameful Neglect".

Nature supported the publication of each of these reports with a discussion forum.

Discussion on Toronto Statement - including responses from Ewan Birney, a leader of the workshop.

Discussion on the Rome Agenda

REFERENCES

1. Toronto International Data Release Workshop Authors. Prepublication data sharing. Ewan Birney et al. Nature. 461:168-70. (2009)

2. Schofield, P.N. et al. Post-publication sharing of data and tools Nature. 461:171-3. (2009)

3. Summary of Principles Agreed at the First International Strategy Meeting on Human Genome Sequencing Bermuda, 25–28 February 1996 (HUGO, 1996); available at http://www.ornl.gov/sci/techresources/Human_Genome/research/bermuda.shtml

4 Sharing Data from Large-scale Biological Research Projects: A System of Tripartite Responsibility (Wellcome Trust, 2003); available at http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf

BioSharing Site MakeOver

2009-09-20T14:55:00.000-07:00

Thanks to Eamonn Maguire in Susanna Sansone's group at the EBI for adding some style to the layout and design of this blog! He's also created a BioSharing icon.

OSCON 2009 coming up

2009-07-14T03:16:00.000-07:00

Even for those (like me) who can't make it over to the conference, O'Reilly OSCON is well worth following especially as most talks are available to watch on-line.
This year David Dooling (The Genome Center at Washington University in St. Louis) is giving a talk on Friday 24th July entitled "The Freedom to Cure Cancer: Open Source Software in Genomics".

"This presentation will provide an insiders look at a high-through sequence generation and analysis facility, focusing on how it leverages FLOSS. Specifically, the enterprise IT infrastructure and software architecture will be detailed."

http://en.oreilly.com/oscon2009/public/schedule/detail/7985

I'll link to the video if and when it appears.

TIM

MIBBI @ ISMB 2009: Highlights talk

2009-07-02T15:16:00.000-07:00

ISMB highlights talk went well (imho). Posted it at

http://tinyurl.com/nvyb57

Why share data?

2009-06-15T15:09:00.000-07:00

A thread is developing on Nature Network on why we should share data. Read it here: http://network.nature.com/groups/genuine_article/forum/topics/4749?page=1

It is part of a larger topic "Scientific findings in a digital world: What is the genuine article?"

Moderators:

This is a forum to discuss issues surrounding scientific communication in a digital age – the focus of the upcoming Talkscience on the evening of 22nd July 2009.

The topic will be introduced by John Wilbanks of Science Commons and you can click here now to book tickets.

Informal Knowledge Sharing in Science via Social Networking

2009-04-30T03:41:00.001-07:00

Recently, more and more biologists, bioinformaticians, and scientists in general have been discovering the usefulness of social networking, microblogging, and blogging for their work. Increasingly, social networking applications such as FriendFeed and Twitter are becoming popular for the discovery of new research in a timely manner, for interactions and possible collaborations with like-minded researchers, and for announcing work that you're doing. Sharing data and knowledge in biology should not just be limited to formal publications and databases. "Biosharing" can also be informal, and social networking is an important tool in informally conveying scientific knowledge. But how should you get started in this new world? Here are my experiences with it, together with some links to and thoughts to help you get started.

I created my FriendFeed account in Fall 2008 and my Twitter account last month. Why did I start using these social networking sites? Well, with FriendFeed, I had noticed many of my work colleagues starting to use it, but had no real understanding as to why they were so evangelical about it. With Twitter, I held out longer but eventually realised it was a really quick and easy way to get my messages across. The reason I did it and why they are useful to me comes down to a simple answer.

I am interested in sharing knowledge. Social networking promotes an informal sharing of knowledge in a way complementary to more traditional, formal methods of knowledge sharing.

And if you're interested in knowledge sharing, then you should look into social networking. My research focuses on semantic data integration. I have a further interest in common data formats to enable data / knowledge sharing. As I am quite vocal about getting people interested in formal methods of knowledge sharing such as the triumvirate of MIBBI, OBI, and FuGE / ISA-TAB for experimental data¹ (and many, many more), it behooved me to learn about the informal methods.

Social Networking: Day-To-Day

But what convinced me that social networking for science was useful? By December I had a realisation: this social networking stuff was giving me more information directly useful to my research than any other resource I had used in the past. Period. You can see my happiness in this blog post from December, where I showed how, these days, I get more useful citations of papers I'm interested in via my friends' citeulike feeds on FriendFeed than I ever have managed from the PubMed email alerts. What convinced me is not a what, but a who.

Social networking for science is an informal data integrator because of the people that are in that network.

It's all about the people. I have met loads of new friends that have similar research interests via the "big 2" (FriendFeed and Twitter). I get knowledge and stay up to date on what's happening in my area of the research world. I make connections.

What is FriendFeed? At its most basic definition, it is an "personal" RSS Aggregator that allows comments on each item that is aggregated. For instance, I've added slides, citations, my blogs, my SourceForge activity and more to FriendFeed:

: A screenshot of the services page of my FriendFeed account

There are loads of other RSS feeds you can add to FriendFeed. Then, when people add your feed to their accounts, they can see your activity and comment on each item. You gradually build up a network of like-minded people. Additionally, you can post questions and statements directly to FriendFeed. This is useful as a form of microblogging, or posting short pieces of useful information quickly.

: A screenshot of my Twitter feed

What is Twitter? It's a bit like instant messaging to the world. You can say whatever you like in 140-characters or less, and it is published on your page (here's mine). Just like with FriendFeed, you can follow anyone else's Twitter feed. You can even put your Twitter feed into FriendFeed. People have a tendency to over-tweet, and write loads of stuff. I use it, but only for work, and only for things that I think might be relevant for quick announcements. If Doug Kell tweets, shouldn't you? ;)

Other people have posted on how FriendFeed is useful to them in their scientific work, such as Cameron Neylon (who has some practical advice too), Deepak Singh and Neil Saunders who talk about specific examples, and Simon Cockell who has written about his experiences with FriendFeed and Twitter. I encourage you to have a read of their posts.

You don't have to spend ages on FriendFeed and Twitter to get useful information out of it. Start simply and don't get social networking burnout.

Ask questions about science you can't answer in your own physical network at the office (Andrew Clegg did it, and have a look at the resulting discussion on FriendFeed and blog summary from Frank Gibson!). Post interesting articles. Ignore it for a week or more if you want: interesting stuff will be "liked" by other people in your network and will stay at the top of the feed. Trust the people in your network, and make use of their expertise in sending the best stuff to the top, if you don't have the time to read everything. Don't be afraid to read everything, or to read just the top two or three items in your feed.

Social Networking: Conferences and Workshops

These "big 2" social networking apps are really useful when it comes to conferences, where they are used to microblog talks, discussions, and breakout sessions. For detailed information on how they are used in such situations, see the conference report for ISMB 2008 in PLoS Computational Biology by Saunders et al. BioSysBio 2009 also used these techniques (FriendFeed room, Twitter hashtag).

Social Networking: What should I use?

Other social networking sites, billed as "especially for scientists", have been cropping up left, right and centre in the past year or two. There are "Facebooks for Scientists"² (there are more than 20 listed here, just to get you started, and other efforts more directed at linking data workflows such as myExperiment). So, should we be using these scientist-specific sites? I certainly haven't tried them all, so I cannot give you anything other than my personal experience.

As you can see from my FriendFeed screenshot, I belong to "Rooms" in FriendFeed as well as connecting directly with people's feeds. Rooms such as The Life Scientists, with over 800 subscribers, gets me answers to sticky questions I wouldn't otherwise know how or where to ask (see here for an example). These, and the people I choose to link with directly, give me all of the science-specific discussions I could want.

The more general the social networking application is and the larger the user-base it has, the more likely it is to be around next year.

Right now, I don't need any of the specialty features I'd get with a scientist-specific social networking application. I think the big names are more likely to reach a wider audience of like-minded folk.

Final Thoughts

Remember you're broadcasting to the world. Only put stuff in that you think others will be interested in. This is a public face for you and your career.

I am a strong believer in keeping the personal parts of my life private (the entire world doesn't need - or want - to know about my cat or see the pictures of my nephew) while at the same time making sure that I am really easy to reach for work-related discussions and collaborations. Through my blog, and my social networking, I am gaining a fuller appreciation of the work going on in the research community around me and contributing to the resulting large experiment in informal data integration.

It is fun: I meet new people and have interesting conversations. It is useful to my career: my blogging has resulted in an invitation to co-author two conference reports, and shows me new things happening in my field earlier than before. I'm all about sharing biological knowledge. I'm researching the formal side of data integration and sharing, and I'm using informal knowledge sharing to help me do my work.

I hope to see you there soon! Look me up!

Footnotes

For a very nice overview of these standards, see Frank Gibson's blog.
While I am on Facebook, I do not use it for work purposes, and therefore cannot comment on its applicability for scientists.

Allyson Lister's regular blog can be found at http://themindwobbles.wordpress.com. This is a cross-posted item available from both sites.

Aggregate spending on genomics research from 34 funding sources averaged around $2.9 billion in 2003-2006

2009-04-22T17:01:00.000-07:00

Genomics research: world survey of public funding.

BACKGROUND: Over the past two decades, genomics has evolved as a scientific research discipline. Genomics research was fueled initially by government and nonprofit funding sources, later augmented by private research and development (R&D) funding. Citizens and taxpayers of many countries have funded much of the research, and have expectations about access to the resulting information and knowledge. While access to knowledge gained from all publicly funded research is desired, access is especially important for fields that have broad social impact and stimulate public dialogue. Genomics is one such field, where public concerns are raised for reasons such as health care and insurance implications, as well as personal and ancestral identification. Thus, genomics has grown rapidly as a field, and attracts considerable interest. RESULTS: One way to study the growth of a field of research is to examine its funding. This study focuses on public funding of genomics research, identifying and collecting data from major government and nonprofit organizations around the world, and updating previous estimates of world genomics research funding, including information about geographical origins. We initially identified 89 publicly funded organizations; we requested information about each organization's funding of genomics research. Of these organizations, 48 responded and 34 reported genomics research expenditures (of those that responded but did not supply information, some did not fund such research, others could not quantify it). The figures reported here include all the largest funders and we estimate that we have accounted for most of the genomics research funding from government and nonprofit sources. CONCLUSION: Aggregate spending on genomics research from 34 funding sources averaged around $2.9 billion in 2003-2006. The United States spent more than any other country on genomics research, corresponding to 35% of the overall worldwide public funding (compared to 49% US share of public health research funding for all purposes). When adjusted to genomics funding intensity, however, the United States dropped below Ireland, the United Kingdom, and Canada, as measured both by genomics research expenditure per capita and per Gross Domestic Product.

See this abstract in Pubmed: Pubmed

Data sharing in genomics--re-shaping scientific practice

2009-04-22T16:38:00.000-07:00

Data sharing in genomics--re-shaping scientific practice.

Funding bodies have recently introduced a requirement that data sharing must be a consideration of all funding applications in genomics. As with all new developments this condition has had an impact on scientific practice, particularly in the area of publishing and in the conduct of research. We discuss the challenges that must be addressed if the full benefits of data sharing, as envisaged by funders, are to be realized.

See this abstract in Pubmed: Pubmed

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy - A Summit Report

2009-04-22T16:35:00.000-07:00

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy - A Summit Report

Policies supporting the rapid and open sharing of genomic data have directly fueled the accelerated pace of discovery in large-scale genomics research. The proteomics community is starting to implement analogous policies and infrastructure for making large-scale proteomics data widely available on a pre-competitive basis. On August 14, 2008, the National Cancer Institute (NCI) convened the "International Summit on Proteomics Data Release and Sharing Policy" in Amsterdam, the Netherlands, to identify and address potential roadblocks to rapid and open access to data. The six principles agreed upon by key stakeholders at the summit addressed issues surrounding 1) timing, 2) comprehensiveness, 3) format, 4) deposition to repositories, 5) quality metrics, and 6) responsibility for proteomics data release. This summit report explores various approaches to develop a framework of data release and sharing principles that will most effectively fulfill the needs of the funding agencies and the research community.

Go to Pubmed Abstract seen above: Pubmed

M3 meeting hosted by the Genomic Standards Consortium

2009-04-22T13:21:00.000-07:00

There are an increasing number of events being hosted by groups working in the area of biostandards. The Genomic Standards Consortium is holding a "Special Interest Group" (SIG) meeting at ISMB 2009.

This "Metagenomics, Metadata and MetaAnalysis" SIG will be held on June 27th, 2009 in Stockholm. It will focus on the collection and use of metadata in the comparative genomic analysis of metagenomic data.

Here is more information about the workshop:

A tag cloud of all the submitted abstracts: blog post at Byte Size Biology

Link to the meeting on the GSC homepage: M3

Link to all the SIGs for this year from the ISMB homepage: List of SIGs

Registration for the M3 SIG: Register

BioCurator 2009 meeting in Berlin

2009-04-17T12:44:00.000-07:00

I was invited this year to the 3rd International BioCuration Conference in Berlin to talk about the Genomic Standards Consortium (GSC, http://gensc.org).

I've really enjoyed the meeting and I'm pleased to see that the BioCurator community is establishing a new society, the International Society for Biocuration (ISB). The mission of the society is here.

There were many great talks including plenary sessions by Janet Thorton and Phil Bourne. Here is a link to the full agenda. Topics of sessions and tutorials included scholarly publishing, text mining, genomic annotation, training of new biocurators and standards. There was much talk about changes afoot in scholarly publishing - in particular its nice to see the concept of hubs and collections of papers from Open Access journals starting to emerge in reality. In his talk about many great tools and concepts pushing the envelope of merging publications and databases Phil Bourne pointed out that there is a new BioCuration Collection from PloS Comp Biology. It only has an editoral and two papers thus far, but new papers are welcomed.

BioCurators perform play an invaluable role in the research community - and this role is growing despite the need to continually move towards automated mark up of data to keep up with the massive influx of information (Phil Bourne said 50,000 new publications are indexed by PubMed each month).

Here is the start of the wikipedia entry containing a definition of a Biocurator (from http://en.wikipedia.org/wiki/Biocurator):

"A biocurator is a professional scientist who collects, annotates, and validates information that is disseminated by biological and model organism databases. The role of a biocurator encompasses quality control of primary biological research data intended for publication, extracting and organizing data from original scientific literature, and describing the data with standard annotation protocols and vocabularies that enable powerful queries and biological database inter-operability."

BioStandards: Big Data require Big Standards

2009-03-31T14:44:00.000-07:00

The term Big Data is increasingly being used. In late 2008 it was used as the title of a special issue of Nature.

Here is a great quote from an Editorial in the issue entitled "Community cleverness required":

"The lack of standards, for instance, confounds many a researcher seeking to harness the diversity of knowledge now available on any chosen topic. All credit, then, to those in the vanguard of interoperability."

Coping with Big Data requires Big Standards - big in the latter sense, meaning widely adopted, not extensive, standards. In fact, a common approach is to define a 'minimum' standard.

BioStandards: The three pillars of reporting standards are scope, semantics and syntax.

A large part of ensuring that data can be shared is defining common ways to do so. Reporting standards are composed of three aspects - scope, semantics and syntax. In other words, checklists, controlled vocabularies and ontologies and formats. In yet more words, checklists are text documents that describe the scope of a particular area of knowledge to be captured in a standardized way, cvs and ontologies are shared vocabularies that help semantically express that knowledge and file formats define a syntax that can be used to physically capture and exchange that information.

Reporting Standards allow sharing of data and promote interoperability

There are an increasing number of "minimum information" checklist projects in biology. This projects are defining essential - or minimal - descriptors for reporting different types of data. These communities have self-organized into a community called MIBBI - this stands for "Minimum Information about a Biological or Biomedical Investigation".

MIBBI: http://mibbi.org

A similar and more mature community exists for ontology development. The OBO Foundry now contains over 60 community-driven ontology development projects.

OBO Foundry: http://www.obofoundry.org/

Likewise there are an increasing number of format projects but they have yet to come together into a joined-up community. We have therefore simple started to collect up projects here on this page that we, for now, call the BioFormat community.

Formats: http://biosharing.org/2009/03/data-formats.html

Data-intensive science - a new paradigm

2009-03-31T11:06:00.000-07:00

Doug Kell maintains an excellent blog and has recently posted on the emergence of a fourth paradigm of generating new knowledge through scientific research.

His post entitled The fourth paradigm of scientific knowledge generation – data-intensive science describes a recent paper by Bell, Hey and Szalay entitled "Computer science. Beyond the data deluge".

The first two paradigms have long been recognized - theoretical and experimental. More recently there are an increasing number of computer simulation studies.

Now with the growth of the internet, increased computing power, and improved aggregation of data - along with new highthroughput technologies - it is possible to do science by grabbing the vast quantities of data that are already out there.

YouTube launched YouTube.edu

2009-03-31T07:29:00.001-07:00

To follow up briefly on a past post called "Videos promote the sharing of scientific data" YouTube has now launched YouTube.edu. This specialized version of the YouTube's is full of videos from the best universities in the world - MIT, Stanford, Harvard, UC Berkeley, etc - and the choice of subjects continues to expand. Some universities now offer whole courses online in this fashion.

Data Formats

2009-03-30T15:07:00.000-07:00

This is a list of 'format' projects that is referred to in a subsequent post entitled "Big Data requires Big Standards".

For now there is no formal umbrella community for format projects in the same sense as the MIBBI umbrella project for checklists.

We would like to suggest that such a community could form, for example under a "BioFormats" banner and we are currently discussing this with the leads of the below projects.

UML, XML or tabular representations

UML is an excellent generic data modelling language, XML is ideal for data exchange and tabular formats ready for import and processing in spreadsheet packages are ideal for biologists who want to easily access and analyze data. Therefore formats taking advantages of the strengths of these different approaches have been developed. There are now increasing efforts to support both XML (for bioinformaticians) and tabular (for biologists) through the use of converters (e.g. XLST).

Universal and Domain specific formats

There is increasing interest in harmonizing multi-omic studies. To do so ideally requires the ability to represent multiple checklists in a single format. From work on domain-specific formats two interoperable format are emerging, FUGE and ISATAB. After these two, domain-specific formats are listed.

Universal Formats

Functional Genomics Experiment (FuGE) (UML/XML): http://fuge.sourceforge.net/

Investigation / Study / Assay (ISA) tab-delimited (TAB) format (Tabular): http://isatab.sourceforge.net/

Both projects are being developed through extensions to cover an increasing range of biological investigations.

Domain-specific formats

Transcriptomics

MAGE-TAB : http://www.mged.org/mage-tab/

Genomics and Metagenomics (16S studies)

GCDML: http://gensc.org

Proteomics

HUPO-PSI XMls: http://www.psidev.info

System Biology
SMBL: http://sbml.org

UHTS Applications

Short Read Format (SRF): http://srf.sourceforge.net/

ESRC Sharing Research Data Workshop

2009-03-09T04:49:00.000-07:00

The Economic and Social Data Service will be holding a workshop entitled "Sharing Research Data: Pioneers, Policies and Protocols"

Friday 13 March 2009

Park Crescent Conference Centre, London, W1W 5PNESRC workshop

Overview

Agenda

Slides: All of the presentations from the workshop are found at the bottom of this page.

NEBC Data Policy: A Case Study

2009-03-02T16:25:00.001-08:00

Continuing on the theme of the need for a repository of links to current data policies, here is the first link to an existing policy along with a brief description. Hopefully more will follow.

The NERC Environmental Bioinformatics Centre (NEBC) has a data policy to cover 'omics data. NEBC's primary means of support its policy is through its EnvBase data catalogue.

Here is a breakdown of the structure of the policy.

The first section sets the frame of reference. This policy inherits most of its top level principles from the NERC Data Policy, its parent document. The document is generally brief and most of the detail is given in the four appendices.

The appendices cover:

1. Timeline for submission of data

2. Submission to public databases and compliance to recognized standards

3. Guidelines on submitting specific file formats

4. Terms of reference for the policy

The timeline in Appendix 1 includes the recommendation that researchers contact NEBC early with a grant to establish an baseline description of the data they expect to generate.

Appendix 2 lists all routine data types generated along with the appropriate public repositories and standards when available.

Appendix 3 covers accepted (recommended) file formats for submitting data directly to EnvBase for which a public repository is not available.

Appendix 4 describes the specific services available to NERC researchers funded under NERC Science Programmes that have 'bought into' the services provided by NEBC.

A Repository of Data Policies is Needed

2009-03-02T15:02:00.000-08:00

In developing a new data policy, it is most effective and wise to look around for existing policies that can be adopted in part or whole or at least modified. Good policies should already promulgate consensus on best practice in a particular community or for a specific data type.

Finding data policies on the web is not simple...They are dispersed - when they exist - and finding them is time-consuming.

In a previous post, we centralized links to the top level policies of a range of funding bodies. This is an obvious first step, but data policies can be generated by Institutions, Data Centres and Projects.

To help promote awareness of these policy and supoprt the development of new policies based upon them, it would be useful to have a centralized listing.

We are currently research existing policies, no matter how small, and aim to post a collection here. In the mean time, please feel free to email me links (dfield 'at' ceh.ac.uk).

Data Policies of Major Funding Agencies

2009-03-02T06:44:00.000-08:00

Note: This is an updated version of Table 1 in the publication "Omics Data Sharing" (2009).

A range of funding agencies have published data policies. These documents are dispersed across the internet, normally being posted within the website of each funding agency. Here is a collection of data policies for funders in the US and the UK that support 'omics research.

Economic and Social Research Council Data Policy

Natural Environmental Research Council (NERC) Data Mangement Policy

National Institute of Health Data Sharing Policy

Gordon and Betty Moore Foundation Data Sharing Policy and Implementation Guidance (2005),

Data Sharing Philosophy and Plan (2008)

Genome Canada Data Release and Resource Sharing Policy

Medical Research Council Data Sharing and Preservation Policy

Biotechnology and Biological Sciences Research Council (BBSRC) Data Sharing Policy

Wellcome Trust Policy on Data Management and Sharing

Genomics: GTL Program (Office of Biological and Environmental Research) Information and Data Sharing Policy

Content of Open Research Workshop at PSB 2009 online

2009-02-25T01:41:00.000-08:00

This post is to highlight that the full contents of the recent Open Research Workshop at PSB 2009 are available on the web. It is also to highlight a great example of the growing use (and utility) of social networking on the Web to communicate science, debate issues and build communities. Specifically PSB 2009 illustrates the use of FriendFeed to capture real-time information about the meeting.

We all know that the openness and transparency of the internet is revolutionizing modern life, and as part of this, scientific research as well. The growing willingness of researchers to engage in social networking and internet publishing phenomenon is having a positive impact on the quantity and quality of information available.

For example, I now follow several blogs and have recently noted with great interest that Doug Kell is now maintaining a highly polished blog in his new role as the CE of the BBSRC entitled "News, thoughts and facts from the Chief Executive of the Biotechnology and Biological Sciences Research Council".

Times are changing.

The concept of 'information at your fingertips' now more and more means finding the right stream of information direct from source - and in almost 'real time'.

The PSB 2009 meeting is an excellent example of this as Neil Saunders highlighted this in his post about joining the 2009 PSB meeting virtually through FriendFeed.

"...attend the 2009 Pacific Symposium on Biocomputing via the magic of FriendFeed."

Of particular note is the use of FriendFeed to add an extra dimension to the information now archived from the workshop. Details of the whole meeting, as covered on FriendFeed, can be found here in the PSB 2009 Room.

For example, here is the 'transcript' of the salient points of the "discussion session of the Open Research workshop".

Even if you weren't there, you get more of a 'feel' of the meeting in a way that can not be expressed by access to a program and set of talk slides alone.