Re: [Obo-format] request for new tags: modified_by and modification_date

[Yu L. <lin...@gm...>]

Hi, all,

One thing encountered in our ontology development is that sometimes we
would like to know the history of one specific term. For example, in what
context or circumstances was it created. What kind of discussion did the
developers go through based on the definition and modeling of this term.
Different ontology developer groups may use mail list, issue trackers or
skype call memos for debating or discussing.

Sometimes one mail would lead to two or more different issues, and which is
hard to seperate.
Sometimes people don't put all the discussions into issue tracker.
Or sometimes people put the meeting memo in a webpage.

There must be a better organized way to coordinate all those efforts for a
sustainable ontology development.

What I want is a more focused method for tracking down all the references
of one specific term from one specific ontology, which is somehow narrower
that what KnowledgeBlog is doing.

I wonder if anybody has some ideas or suggestions on this.

Thanks,
Asiyah Yu Lin

On Thu, Nov 1, 2012 at 10:58 AM, Phillip Lord
<phi...@ne...>wrote:

>
>
> I would agree with this. Currently, we see publication as a way of
> describing work that has already been done. But writing short articles,
> explain design decision as you go, I think, it a very valuable thing.
>
> I've been using my own blog this way for a while; it's not quite a lab
> notebook; the articles are a little bit more abstracted from the
> immediate process of what I have done. The problem with this at the
> current time, is that this keeps the history of what has been done, but
> doesn't infer "credit" as science is still tied up with the idea that
> credit comes only from Impact Factor. Not much that can be done with
> this.
>
> I have some concerns about putting author information in too deeply into
> the ontology since this is going to produce potentially bloated work. I
> think we need to avoid duplicated the knowledge that is already being
> stored in the versioning system.
>
> Phil
>
> Chris Mungall <cjm...@lb...> writes:
> > 3. Any ontology contributions involving a piece of unique non-trivial
> biology
> > or ontology modeling is often deserving of at least a small article
> published
> > on a pre-print site. The ontogenesis kblog ( http://knowledgeblog.org/) is
> > ideal for this. The article can then be linked from the originating
> ontology,
> > or indeed from other ontologies, publications and so on. I recommend that
> > anyone involved in making ontologies (everyone on this list I expect)
> read
> > Robert Steven's and others excellent ontology articles published on this
> forum
> > ( http://ontogenesis.knowledgeblog.org/ ), and considers writing an
> article on
> > their own ontology for publication and community comments here.
> >
> > By all means follow the traditional publication route too but it's
> harder to
> > publish ontology papers and the traditional review process can be at
> odds with
> > the goal of getting comprehensive documentation out there, even in
> venues like
> > PLoS ONE.
> >
> > 4. As in software engineering, an ontology should include comprehensive
> > in-line documentation, stating why things are modeled a certain way. The
> > primary goal here is maintainability and long-term sustainability, but
> it also
> > serves as an audit trail and potential mechanism of credit. Note that
> there is
> > some level of overlap between 4 and 3 - it may be the case that these are
> > combined, with a high level summary article on the kblog accompanying
> detailed
> > ontology-specific documentation embedded in the ontology.
> >
> > As yet the mechanism for achieving #4 is under discussion, but inspired
> by
> > systems developed by David OS and Matt Brush, the basic idea is:
>