My latest research is focused on cluster/list annotation in biology. Given a cluster or list of genes or proteins that were grouped together using some metric (expression profile, sequence or structure similarity, interactions, etc), how can you discover descriptive terms or labels for that cluster? This seems to be a common question, and yet I've had trouble finding tools that help you do what I am specifically trying to do (investigation of a list of biological entities). I've found many that can give you tons of information for single genes or proteins, which I don't consider that helpful, and a few that can give you information for a group, but these are either organism specific or limited to one or two types of data (e.g. GO terms).
Since I am developing a method to do this based on text, I'd like to be able to compare my method to existing ones that solve the same problem. What I am looking for is two or three available methods that give you information relevant to a list of biological entities from multiple species, at least one of which uses literature or text-mining. Does anyone know of such methods, or have ideas of where to look? Various PubMed and Google searches have failed me!
Unrelated, but also done today: Submitted the PSB proposal to Nature Precedings as per several of your requests. Will update once word is back from their review process.
Showing posts with label psb proposal. Show all posts
Showing posts with label psb proposal. Show all posts
Tuesday, February 26, 2008
Friday, January 25, 2008
Is the danger of being scooped field-dependent?
The students in my program get together once in a while for what we call "Researchome", also known fondly as "dinner-ome", originally conceived as a casual forum in which students could present their research or other topics of interest to other students, while getting dinner for free. But without someone to present, there is no justification to have Researchome, so rather than deprive a dozen grad students of free food, I threw together a quick presentation of Open Science and my proposal for PSB for our Researchome last night.
Biomedical informatics students are a smart bunch, so there was some great discussion. Naturally, the concern over getting scooped came up, and while I was quick to pooh-pooh it as a naive/narcissistic fear, the others were fairly adamant that it was a valid concern. Several gave personal anecdotes. And the picture that started to emerge was one where the danger of being scooped was highly dependent on the field you were in - theoretical vs. applied, basic vs. translational, science vs. medicine, all of which may put different emphasis on the idea vs. the implementation.
According to one of the students at the Researchome, in theoretical disciplines such as math or physics, credit is given as soon as an idea is recorded. But in fields like cell biology, just having the idea for an experiment or a hypothesis is not enough; instead, you must conduct the experiment and demonstrate successful results through a peer-reviewed publication before credit is given. Because of this, people in these fields are more reluctant to be open about their research before it has been published, and getting scooped can have real consequences for someone's career and funding. In my limited explorations of the world wide open science web, it seems as if a significant portion of those participating are chemists. Is getting scooped less of a concern in chemistry than it is in, say, molecular biology, and, if so, why? If there is a discrepancy between fields in the danger of being scooped, how should this be addressed as the open science community moves forward? Is it possible to change the standards by which success and intellectual credit are determined?
Aside from this interesting issue, some valid points were brought up concerning the proposal for an open science session at PSB. One is that the audience at PSB is by and large composed of scientists who don't generate their own data, but use the data generated by others. A lot of high-throughput, -omics, and bioinformatics-minded people. Therefore, open data and open source will probably be of greater interest to them than the more overarching idea of open notebook science. Focusing on standards, exchange formats, and tools and methodologies for conducting open science may be a good approach.
The other consensus that the students came to was that open science is so broad and important a topic that it should be featured as a session at a much larger conference, such as ISMB or AMIA. Many were bemused as to why I chose what is arguably a niche conference as a venue for open science. My rationale at this point is that it is the soonest we could possibly organize a meeting on open science jointly with an established conference, and I think the audience is relevant enough for it to be productive. Being smaller, it may also be a good stepping stone towards a bigger meeting, and I wouldn't be surprised if some efforts began for that before PSB 2009 comes around.
Many thanks to the students who attended the Researchome for their feedback. I'll be working on a draft of the proposal over the next couple days.
Biomedical informatics students are a smart bunch, so there was some great discussion. Naturally, the concern over getting scooped came up, and while I was quick to pooh-pooh it as a naive/narcissistic fear, the others were fairly adamant that it was a valid concern. Several gave personal anecdotes. And the picture that started to emerge was one where the danger of being scooped was highly dependent on the field you were in - theoretical vs. applied, basic vs. translational, science vs. medicine, all of which may put different emphasis on the idea vs. the implementation.
According to one of the students at the Researchome, in theoretical disciplines such as math or physics, credit is given as soon as an idea is recorded. But in fields like cell biology, just having the idea for an experiment or a hypothesis is not enough; instead, you must conduct the experiment and demonstrate successful results through a peer-reviewed publication before credit is given. Because of this, people in these fields are more reluctant to be open about their research before it has been published, and getting scooped can have real consequences for someone's career and funding. In my limited explorations of the world wide open science web, it seems as if a significant portion of those participating are chemists. Is getting scooped less of a concern in chemistry than it is in, say, molecular biology, and, if so, why? If there is a discrepancy between fields in the danger of being scooped, how should this be addressed as the open science community moves forward? Is it possible to change the standards by which success and intellectual credit are determined?
Aside from this interesting issue, some valid points were brought up concerning the proposal for an open science session at PSB. One is that the audience at PSB is by and large composed of scientists who don't generate their own data, but use the data generated by others. A lot of high-throughput, -omics, and bioinformatics-minded people. Therefore, open data and open source will probably be of greater interest to them than the more overarching idea of open notebook science. Focusing on standards, exchange formats, and tools and methodologies for conducting open science may be a good approach.
The other consensus that the students came to was that open science is so broad and important a topic that it should be featured as a session at a much larger conference, such as ISMB or AMIA. Many were bemused as to why I chose what is arguably a niche conference as a venue for open science. My rationale at this point is that it is the soonest we could possibly organize a meeting on open science jointly with an established conference, and I think the audience is relevant enough for it to be productive. Being smaller, it may also be a good stepping stone towards a bigger meeting, and I wouldn't be surprised if some efforts began for that before PSB 2009 comes around.
Many thanks to the students who attended the Researchome for their feedback. I'll be working on a draft of the proposal over the next couple days.
Subscribe to:
Posts (Atom)