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Re: [Obo-discuss] Draft of an OBO about write-up
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From: Alan R. <ala...@gm...> - 2007-12-29 22:40:48
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On Dec 29, 2007, at 2:17 PM, Judith Blake wrote: > Hi Suzi and all, > > This seems pretty straight-forward to me as to content. > > Here are my confusions. > > 1. The paper does not address the relationship of the OBO Foundry > to either the NCBO BioPortal that refers to the OBO Foundry or the > CaBIG effort that refers to ontology standards as would be > addressed by a NCBO librarian checking in an ontology through the > BioPortal to the OBO Foundry. Since the intersections are not > addressed, I am left to think that this document reflects an > independent OBO Foundry that is not in collaboration with the NCBO > or NCI. I think a sentence at the start to place OBO Foundry > within context of community biomedical ontologies would alleviate > that confusion. An earlier draft of the document started with a sentence I added: Within the larger effort that is the Open Biomedical Ontologies (OBO), the objective of the OBO Foundry is to collect a family of ontologies.. By which I was trying to do that. But this is a good point about checking in to Bioportal. Certainly, being part of the larger set of OBO, they would be put there, but in this document we don't say that the procedure for joining is to give something to an NCBO librarian. So to make explicit my understanding, which should be corrected as appropriate, I understand the Foundry process to not be associated with the BioPortal, except to the extent that it uses the BioPortal as a vehicle for dissemination and a source of tools. The BioPortal isn't an ontology development effort, but rather and attempt to support such. I don't understand there to be a formal connection to CaBIG either, currently, other than that they are an important customer and a supporter of some of our efforts. I understand the Foundry to be one initiative in the space of biomedical ontologies, with specific goals and a certain take on the biomedical ontology building business. Anyways, all, please correct, confirm, or shape this. > 2. This paper reflects much of what was published in the Nature > Biotechnology pub [Nov 2007 vol 25, 12511255]. How or is this > document meant to supplement the pub? Is it the on-line working doc? My understanding of the intention was to be more specifically about the process mechanics, elaborating more specifically on what it means to participate in the "collaborative experiment", and design a transparent process for governing the entity. It was somewhat unclear, without this, exactly how decisions would be made, and where accountability for those decisions would lie. > 3. I had to read the second sentence several times to get the > context of 'use'. I would suggest changing that sentence to read > "...and good practive in ontology development and implementation > (sssxxx). I think the sense of "use" - "principles of use" was to address how the ontology is used after it has been developed, things like what an annotation means and how to annotate consistently so that annotations can be meaningfully shared, or how to make true statements using an ontology. So 2 questions: 1) (to the other drafters) Do I have that right? 2) (to Judy) Is this what you mean by implement? -Alan > > Best, > Judy > > > > Suzanna Lewis wrote: >> Happy new year everyone, >> >> In the spirit of new beginnings a few of us (myself and those on >> the cc line above) have -drafted- a write-up that describes what >> the OBO Foundry is all about and how we want it to work. We did >> this because there have been a lot of questions and some confusion >> about what we're attempting here. This is an attempt to answer >> these questions and to make everything more clear. >> >> However, this write-up is not done. For that, we need everyone to >> be involved. If you can find the time to peruse this, and give us >> feedback to be incorporated, it would be fantastic. >> >> Is it clear? >> >> Are there questions that aren't answered? Any missing bits? >> >> Can it be made shorter (or broken into >1 documents)? (started out >> hoping for a one-pager) >> >> Where and what are the contentious bits? What explanations would >> make these more clear? >> >> Any other advice (or new year's resolutions)? >> >> I'll try to get this on the web site for download soon and put a >> notice up that it is there. >> >> Have at it! >> >> -S and all >> >> >> >> >> --------------------------------------------------------------------- >> --- >> >> --------------------------------------------------------------------- >> ---- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2005. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> --------------------------------------------------------------------- >> --- >> >> _______________________________________________ >> Obo-discuss mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-discuss >> > > |