What does swine flu look like?

If you have been following all the major news reports, such as the ones on the BBC then you will have probably have been bombarded  with images of a spherical virus with lots of spikes, as an image of what swine flu looks like. This would not be entirely correct. The first high resolution electron microscopy images of the swine flu virus have been released which show that the virus is not spherical but rahter oblong in shape, as shown in the image below.

Attribution vs Citation: Do you know the difference?

This is a cross-posted , two-author item available both from this and Allyson’s blog.

Often the words “attribution” and “citation” are used interchangeably. However, in the context of ensuring your work gets the referencing it deserves when others make use of it, it is important that the differences between these two concepts are clear. This article outlines the differences between attribution and citation, and suggests that what most scientists are interested in is not attribution, which can be ensured via licensing restrictions, but instead citation, which is a much tougher nut to crack.

At ISMB last week, there were a number of conversations about the difference between attribution and citation. This topic was brought up again yesterday in a conversation between the two authors of this post, Frank and Allyson. It is an important distinction which is explored in this post.

First, some definitions for attribution and citation. These are not the only definitions possible, but for the purposes of this discussion, please keep these in mind.

Attribution: Acknowledgement of the use of someone else’s information, data, or other work. Crucially, while Wikipedia has a fairly straightforward definition of citation, it does NOT mention even common ways that attribution should be implemented (see Wikipedia attribution page).

Citation: When you publish a paper that makes use of someone else’s information (data, ontology, etc.), you include in that paper a reference to the work of that other person or group. Wikipedia states that it is a “reference to a published or unpublished source” whose prime purpose is of “intellectual honesty”.

Distinguishing between attribution and citation.
You can imagine that citation is a specific type of attribution, but attribution itself can be performed in any number of ways. For scientists, citation is much more useful to their careers as a result of the publish or perish environment.

So, what could attribution consist of? First, let’s take as an example the re-use of someone else’s ontology or specific sub-parts or classes of that ontology. Each class in an ontology is identified by a URI. Therefore, is importing the URI enough? With a URI is it clear where you got the class from? If it’s not enough, where do you put that reference or statement that you are re-using other classes: within the overall metadata of your own ontology? Alternatively, when attributing data is a reference to the originating paper or URL from where you downloaded the data enough? Where do you put that reference: within the metadata of your own document? As a citation? How much is enough attribution?

These questions cannot easily be answered.

A common-sense answer to the question of properly fulfilling requirements is to, at a minimum, first cite their information in your paper, and second include URL(s)/URI(s) in your metadata. But here we get to the crux of the matter: we’ve now stated that a useful way to ensure attribution is to cite the other person. But, if you think carefully, what’s more important for your impact assessments, and your work? It’s actually the citation itself. Sure, acknowledgement via extra referencing in the metadata of the person using your information is great, but what you really need is a citation in their work. If we aren’t careful, we will all make the easy mistake of conflating citation in papers with importing a licensed piece of information and how to mark its inclusion: the former is what we often are scored on and what we would really like, while the latter is the only thing a license enforces. Licensing with attribution requirements is not citation; you can make use of a licensed ontology, but this does not require you to cite it in a paper.

Attribution: the legal entity.

Important point: It’s easy to use a license such as the CC-BY, thinking that you’ll ensure citation, when in fact all you’re doing is ensuring attribution.

What are the implications of attribution? It can quickly get out-of-control and difficult to manage.
By requiring attribution in an ontology or data file, if someone imports information (such as a class from an ontology) into their own document, the new one must attribute the original. Continuing the ontology analogy, if there are 20-30 ontologies being used for a single project (which is not inconceivable in the coming years), there could be great difficulty in maintaining attribution for them all.

Important point: While licenses such as the CC-BY allow the attribution to be performed “in the manner specified by the author or licensor”, this could lead to 30 different licensors requiring potentially 30 different methods of attribution, and attribution stacking isn’t pretty.

Citation: the gentlemen’s club.

Can citation be assured? No. Well, maybe.
You can imagine citation as a gentlemen’s club, as propriety dictates that you should cite another’s work that you use, but there is no legal requirement to do so. Indeed, many believe that citation should not be enforced anyway. In contrast, attribution as required by licenses is a legal statement. However, let’s revisit the clause in CC-BY that states the author/licensor can specify the manner in which the attribution is given.

Important point: Could you use a license such as CC-BY, and state that the attribution must come in the form of, at a minimum, citation in the paper which describes the work being performed by the licensee?

Bottom line: which one is more important to you, as a scientist? Depends on the context.
This is difficult to answer. There aren’t very many guidelines available for us to analyse. The OBO Foundry does have a set of principles, the first of which states that “their [the ontology(ies) and their classes] original source is always credited and that after any external alterations, they must never be redistributed under the same name or with the same identifiers”. However, how this credit is attained is unclear, as described in various blog posts (Allyson, Frank, Melanie). As a result, the following conclusions came out of the OBO Foundry workshop this summer (Monday outcomes): it is “unclear if each ontology should develop their own bespoke license or use develop ‘CC-by’; how to give attribution? Generally use own judgment, here MIREOT mechanism can help when importing external terms into an ontology, giving class level attribution” (MIREOT web page, see also OWLED 2008 paper). Therefore, while they are aware of the problem, they don’t offer a consensus solution(s).

The flipside of this is that in order to use an ontology, you first have to write a paper and cite the classes you wish to import, then get on with the work. If you never get a paper and therefore a citation, is you ontology/data illegal? If you take the example of OBI, which imports several other ontologies and is an open community of developers, would a license restriction requiring citation actually prevent the work starting? This is probably a bit of a chicken-and-egg scenario, if it were ever to come a reality. In short, while there are some tempting possibilities, there doesn’t yet seem to be a useful solution.

In summary, it’s generally not attribution that people want (which can be licensed, even if you don’t like the layers of attribution that will require once you’re using multiple sources) but citation, which isn’t so easily licensed – yet. When deciding what sort of license to use (e.g. an open one like CC0 or an attribution-based one like CC-BY), you need to take into account expected usage. In some cases, for a leaf ontology, perhaps CC-BY is appropriate, as it isn’t intended to be imported by others, but you never know when your leaf will turn into something others import. Science Commons also believes that attribution is a very different beast, and shouldn’t be required when licensing data. They provided me with an answer to how to license ontologies recently that favored CC0.

So, if you really want citation and not attribution, consider an open license such as CC0 and make a gentlemanly (gentle-science-person-ly) request that if someone uses it AND publishes a paper on it, please cite it in the way you suggest. Alternatively, I’d be interested to hear if it would be possible to use an attribution-based license such as CC-BY and then require the attribution method be citation in a paper. Would this method work, and would it be polite? Your comments, please.

The OBO foundry principles

This week, is a week long ontology building week, consisting of two days at the OBO Foundry workshop followed by 4 days at the OBI workshop, all hosted at the EBI. In advance of the meeting (even though I am writing this during the meeting) Duncan asked “how can the ontology development principles be improved“. Ally and Melanie responded commenting on each principle, and I would pretty much agree with every issue the ontology ladies raise. These principles should be used to guide ontology developers to build a consistent resource and which are used to “peer-review” the ontology. However, my concern is that there is no indication or recommended methodology in how these principles could be met, during the development process. This was my motivation for reviewing all the existing documented methodologies are assess there applicability (shameless plug), as I think it is important to remember that the members of the OBO Foundry are not the first people in the world to build ontologies and we should make use of known and documented expertise where possible instead of re-inventing the wheel.   These are my take on the principles below. However, I would recommend reading Ally’s and Melanie’s first as I have tried not to repeat what they have already said. Although, as Duncan and the ontology ladies have independently arrived at mostly the same conclusions, there is a very real need to address or more explicitly state, these set of principles.

1.The ontology must be open and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers.

Licenses – This is always a touchy subject, within the life-sciences and IMHO largely due to a mis-understanding of what a license is actually for. Being open in the sciences is often mis-interpreted as “you can use it, but you have to attribute me”. This is actually not being open. The attribution aspect is actually a restriction. The principle of the OBO foundry  is that there will be hundreds of separate and orthogonal ontologies that will all refer and reference each other. If every single ontology has to be attributed this will become a large overhead. In addition, if we do insist on attribution, how do we acknowledge the use?  An official statement? Is importing the URI enough?  This aspect of the principles really needs to be explicit and clearly stated. Making use of  licenses that already exist may be a good starting point, rather than trying to define a bespoke OBO Foundry license. Two possibilities are Creative Commons – Attribution or CCO. The current OBO principles seem to merge these two licenses together. An explicit statement on licenses  is  really needed. Ally covers this in more detail on her post.

2. The ontology is in, or can be expressed in, a common shared syntax. This may be either the OBO syntax, extensions of this syntax, or OWL.

mm, this is confusing “expressed in a common shared syntax”, but you can use either OBO or OWL that would be two different syntax – no? Either the OBO foundry are in a shared syntax, or they are in OBO or OWL.

3. The ontologies possesses a unique identifier space within the OBO Foundry.

I would be good just to tighten this up a bit. A clear statement of the identification schema would be helpful

4. The ontology provider has procedures for identifying distinct successive versions.

This is a good statement and version of ontologies definitely need to be identified. As Ally mentions, we probably do not want to legislate which versioning system to use (svn, git etc). However maybe a recommendation of which to use and what constitutes a change may be helpful.

5. The ontology has a clearly specified and clearly delineated content.

How would you describe this to your users or developers? In ontology development this is traditionally called defining your scope. Your scope can be described by competency questions – questions your ontology should answer.

6.The ontologies include textual definitions for all terms.

A definition of a class in the ontology is its assertion in the hierarchy and all the logical restrictions, it can also include a natural language definition. I would re-word this to ” The classes in the ontology shoud have a natural language definition which reflection the logical definition of the class”.

7.The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.

Same comment as Ally

8. The ontology is well documented.

Not really sure what this actually means or how to implement it. There are a set of naming recommendations within the OBO Foundry, is this what it is referring to? There are also metadata recommendation from OBI, is this the same thing?

9.The ontology has a plurality of independent users.

Why is this important as a principle for inclusion? Is listing on the OBO Foundry not an attempt to gain wider use? Are the computational users? is a user an individual, a  lab, a project, community?

10.The ontology will be developed collaboratively with other OBO Foundry members.

Why? Is this really a guiding development policy? What does collaboratively mean? In terms of the license? Does branching in a versioning repository count as collaborative development? I would suggest that if we get the terms of the license explicit an the idea of the Foundry then this principle is probably not necessary to be stated.

These comments are more a mix questions for debate rather than any clear cut corrections.

Developing ontologies in decentralised settings

I have placed a e-prints of a manuscript, on Nature preceedings, that I have been working on, in collaboration with the authors listed on the manuscript. It presents a review of the available published ontology engineering methodologies, and then assess their suitability when applied to community ontology development (the decentralised setting).

It is a lengthy document. Here is the abstract:

This paper addresses two research questions: “How should a well-engineered methodology facilitate the development of ontologies within communities of practice?” and “What methodology should be used?” If ontologies are to be developed by communities then the ontology development life cycle should be better understood within this context. This paper presents the Melting Point (MP), a proposed new methodology for developing ontologies within decentralized settings. It describes how MP was developed by taking best practices from other methodologies, provides details on recommended steps and recommended processes, and compares MP with alternatives. The methodology presented here is the product of direct first-hand experience and observation of biological communities of practice in which some of the authors have been involved. The Melting Point is a methodology engineered for decentralised communities of practice for which the designers of technology and the users may be the same group. As such, MP provides a potential foundation for the establishment of standard practices for ontology engineering.

Content, Syntax and Semantics

These are the slides I gave at a DCC workshop entitled, “Digital curation 101″ which aimed to give and overview of what to consider regarding data curation and management in the context of applying for research funding. The presentation starts with definitions of content syntax and semantics, and example of how these concepts are being applied in the life-sciences, specifically proteomics.

A trip to Cambridge in June

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

A trip to London in May

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

I will be at the Molecular Regulation of Cardiac Disease Symposium May 14-15 2009, London, UK. Hosted by Abcam http://www.abcam.com/index.html?pageconfig=resource&rid=11503&sc_ql=1595&intGoUser=15

A trip to Manchester in May

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

The Semantic Web of Life Science

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

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

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

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

Bio2RDF Cloud

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

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

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

HUPO PSI-PAR: standard format for protein affinity reagents

Image via Wikipedia

HUPO PSI-PAR: standard format for protein affinity reagents is now available for Public Comment on the PSI Web site for the next 30 days. The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process. This message is to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal. If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI. If you have comments that you would like to make but would prefer not to make public, please email the PSI-Editor directly.