nodalpoint.org

One of the crucial aspects of any 6 day marathon conference is plentiful strong coffee, ISMB2003 got this right, however ISMB2005 coffee leaves a lot to be desired. Anyway on to more weighty matters. I'm sitting in on the BioOntologies panel discussion, they seem to have a jokey kind of vibe going on here which is cool. The participants on the panel are Mark Musen (MM), Larry Hunter (LH), Judith Blake (JB) and Eric Neumann (EN), they are trying to get input on the following statements (responses follow):

We should be more authoritarian and less liberal in the building of Bio-ontologies ?

MM: Too many standards and issues yet to be sorted out with languages and representations, thus is too difficult to be too authoritarian.
MM: Content is different we can do something about this ?
MM: We can't force particular distinctions or ways of thinking on people
MM: This is why Upper Level Ontologies don't really work, there are many ULO that don't agree with each other.
MM: Let 1000 flowers bloom, experiment, and see what comes out of the process and
MM: Let's have education ? Learning from one another ?

My question is does this mean we should have primers on currently implemented technologies ? How should this work ?

JB: Apply gentle persuasion, lead by example,
JB: Respond to community, bridge between standardization of information and the working biologist.
JB: Role to play for providing biomedical ontologies and mappings between ontologies for working biologists.
JB: Open to suggestions ? Keep an open mind
JB: Beware the big gorilla, we can dictate standards only mentor... example of gene names... work to wards common standards but they will only BE standards if they are adopted and used by the working biological scientists.
JB: Disconnection between communities, must provide intersections...
JB: Message: not authoritarian...

LH: We need government for this, resources are scarce, build ontology for life, enormous effort,

I think this is garbage, people working biologists are the resources necessary, see the tagging discussion on nodalpoint ?

LH: Having a consistent ontology allows you to do more productive things rather than dealing with the inconsistencies
LH: We have to do it right, pay attention process, but not like the OMG or W3C, responsive to the domain experts

These guy's are a little alienated from biologists ?

EN: Ontologies embody many different kinds of applications, many different approaches
EN: Different levels of ontologies, starting points, needs for large scale ontologies
EN: In addition to big initiatives, there are local needs, smaller ontologies as bridges
EN: (ROOM for everyone)... driven by community needs
EN: Need to negotiate meaning, take the time to negotiate, how to develop fluid negotiation ?
EN: Negotiation process is important

Audience questions:

Lot's of questions about funding ??

What about mappings ?

Efficiency, limited resources,

Just because it's first doesn't mean it's best ?

More talk about governments ? What about wikipedia ?

MM: Semantic web expects many many many ontologies, how will that all work ?

LH: Issues in bio-ontologies are different than semantic web issues ?

LH seems to thing that there is "one right view of biology" a core that is right ? Seems to contradict himself by suggesting that we need one core ontology that doesn't change, but says this needs to change and we need to be flexible about how we do it. There is a kind of theme that there is a core of biology that doesn't change. I think the idea should be more like the infrastructure or framework should be very robust and allow for evolution of ontologies, mapping of ontolgoies, because the "biological knowledge" always changes... i.e. our conception of how biological systems changes. It seems that this will ultimately be done in a vacuum, talking about how to fund it etc. when there are excellent models that exist now for community based ontology development e.g. delicious... and tags on humbed etc. people just DON'T get this ?? Why ? Right now I would like to get up and mention this but I KNOW that no one will get it. I decide to make a comment about collaborative ontologies, folksonomies, tags, wikipedia etc. but the sensible tan slacks PI crows is hogging the discussion ? My comment on all this is that no one group is authoritative on all topics, trust your community...

They announce the second statement but discussion has wandered off...

MM: Visionary... some meta application that helps us think about biology because it know about biology to and all the facts ontolgies can help in this respect...

EN: Discusses slides from TBLs bio-it world talk...
EN: Multiple bio-ontolgoies (existing) used together right now... My poster discusses this (not to self to put this online).

In conclusion I would say that there is a core group of ontologists that have vested (funding) interests in being the arbiters of what does and does not go into bioontologies. The reason I feel this is because a few people were at pains to suggest that the issue of bioontologies are different from ontologies in the semantic web (which has been demonstrated not to be the case). The semantic web is an excellent frame work for doing more collaborative ontology work.