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[Obi-devel] definition_source vs. definition_citation
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From: Daniel S. <sc...@eb...> - 2008-01-22 15:12:18
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Hello all I created a wiki page at https://wiki.cbil.upenn.edu/obiwiki/index.php/ActionItems/Votes#definition_source_vs._definition_citation where Alan and I list our pros and cons for our proposals for this annotation property name. Please have a look. Cheers, Daniel Schober Alan Ruttenberg wrote: > I tried to update the page, but the wiki is down. Here is my text. > Melanie, perhaps you could update the page with this tomorrow? > > Thanks, > Alan > > === Pro 'definition_citation' (Alan) === > > There are three issues: what the contents of the field should be, what > it should be named, and the status of > http://obi.sourceforge.net/ontologyInformation/MinimalMetadata.html > > 1. Contents of the field > > We discussed the contents of the field in these developers meetings > * http://obi.sourceforge.net/notes/developers/200702/28Feb2007.txt > * http://obi.sourceforge.net/notes/developers/200703/07Mar2007.txt > > In this meeting we receive the coordinators call decision on the > proposal: String format adopted, instance representation not to be in > all versions of OBI, but to be in ones intended for Semantic Web use > * http://obi.sourceforge.net/notes/developers/200704/18Apr2007.txt > > Documentation is here: > * http://esw.w3.org/topic/OBI_Definition_Source > > 2. Name of the field > > * http://obo-discuss.googlegroups.com/web/OBO%20policies%20v8_AR.doc : > "We view publishing an open ontology as analogous to publishing an > open-access scientific paper in many respects" > > * http://library.duke.edu/research/citing/within/ "Citing Sources > Within Your Paper: Whenever you quote, paraphrase, summarize, or > otherwise refer to the work of another, you are required to cite its > source" > > Our current definition for definition_citation is: "formal citation, > e.g. identifier in external database to indicate / attribute source(s) > for the definition. Free text indicate / attribute source(s) for the > definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki > uri on 31.01.2007" > > In other words, the traditional way one identifies a source in a > research paper is a citation, publishing ontologies in the foundries > are analogous to publishing research papers, and name that most > clearly suggests this is definition_citation. That the definition > starts out with "formal citation" further reinforces this. > > 3. Status of > http://obi.sourceforge.net/ontologyInformation/MinimalMetadata.html > > * We use a property called "example_of_usage" not "example" as noted > on the page > * We recently decided to use the representation of alternative tags is > to follow the specification given on > http://esw.w3.org/topic/OBI_Definition_Source, obsoleting the fields > alternative_term_tag, alternative_term_source > > In other words, the page is out of date - these things happen. > > > > > > > On Jan 21, 2008, at 7:14 AM, Daniel Schober wrote: > >> Hello Alan, >> As agreed on the last OBI call, I have put reasons to keep using >> 'definition_source' onto the wiki at >> >> https://wiki.cbil.upenn.edu/obiwiki/index.php/ActionItems/Votes#definition_source_vs._definition_citation >> >> Please add in and state your arguments for 'definition_citation'. >> We 2 could have a skype call on this as well (I am available the >> whole day today). Otherwise we let people vote on it based on what is >> on the wiki. >> Cheers, >> Daniel. >> >> Alan Ruttenberg wrote: >> >>> Here's what we said we would do. >>> Relevant to the discussion is that we decided to go ahead with the >>> proposal I made for alternative term tags, which was part of the >>> definition source proposal. >>> >>> So, why don't we take a couple of passes passing back and forth our >>> summaries and then send them both out in a note. >>> >>>> As Alan said, we decided during the last call to talk about this. >>>> As Daniel also said, this has been talked about several times already. >>>> In the interest of not having the same discussion again, I would >>>> like to propose the following: >>>> - Alan and Daniel prepare a short summary of their proposal and >>>> why the other one doesn't satisfy them >>>> - we could then post this on the wiki/dev list and give people >>>> some time to think about it and see if new issues arise >>>> - we can then schedule some time in a call to see if we reached an >>>> agreement, if it is not the case we can then put the issue to a vote. >>> >>> >>> >>> -Alan >>> >>> On Jan 15, 2008, at 10:12 AM, James Malone wrote: >>> >>>> Hi, >>>> >>>> Daniel do you want to do this then since you raised it? We should >>>> just complete this so we can make everything consistent. There's >>>> enough 'discussion' on the lists at moment, people may go mad if >>>> we go over this again; OK some of us are already there... :) >>>> >>>> J >>>> >>>> >>>> >>>> >>>> Daniel Schober wrote: >>>> >>>>> Hi all, >>>>> As mentioned a few times now, we have already agreed to use >>>>> definition_source (see my obi dev list email of 11.12.07). Also >>>>> that is what we have on the community approved minimal metadata >>>>> pages and in our skos-submitted requirements list. I think >>>>> changing to definition_citation >>>>> >>>>> * will set the owl file out of sync with the obi webpages, which >>>>> might confuse people that are aware of our webpages >>>>> * might mislead people: The word 'citation' to me is more >>>>> restrictive than 'source', and we do not want to quote a >>>>> definition, but rather indicate what we took as a source. I >>>>> believe 'citation' would make it more difficult to align >>>>> definitions to the OBO Foundry needs. >>>>> * will cause unnessesary work to update all the OBI web pages.I >>>>> think it is easier to edit the properties.owl file and >>>>> substitute definition_citation with definition_source and then >>>>> we are in sync with what is on the websites again >>>>> >>>>> So I still think it is plausible and also the easier way to >>>>> update the owl file to use definition_source. >>>>> >>>>> Maybe we can vote on this issue once and for all , e.g. per >>>>> 'hands up' on tomorrows OBI centra call. >>>>> Cheers, >>>>> Daniel. >>>>> >>>>> James Malone wrote: >>>>> >>>>>> Hi Guys, >>>>>> >>>>>> I thought this was sorted on a dev call I was on a few weeks >>>>>> ago. I thought the general view was just use >>>>>> definition_citation since there is no definition_source and Alan >>>>>> can correct this is we really feel the urge to using a script? >>>>>> Also, within citation you would just put either a paper citation >>>>>> (reference), website uri (e.g. wikipedia, NCI) or fialing that >>>>>> the editor name(s) if the first two methods failed (i.e. if you >>>>>> can't find a good definition in literature or other online >>>>>> resources) Please feel free to correct me if I'm wrong and this >>>>>> is not what you are looking to discuss :) >>>>>> >>>>>> James >>>>>> >>>>>> >>>>>> Daniel Schober wrote: >>>>>> >>>>>>> Hi Alan, >>>>>>> I don't care much, we can also have a call (now?) with just us >>>>>>> two about it, or discuss it tomorrow at the OBI call. What >>>>>>> would you prefer? >>>>>>> Cheers, Daniel. >>>>>>> . >>>>>>> >>>>>>> >>>>>>> Alan Ruttenberg wrote: >>>>>>> >>>>>>> >>>>>>>> Why would you discuss citation versus source, which is not >>>>>>>> specific to Instrument branch, over use cases, which is >>>>>>>> needed for the workshop? >>>>>>>> -Alan >>>>>>>> >>>>>>>> On Jan 15, 2008, at 5:22 AM, Daniel Schober wrote: >>>>>>>> >>>>>>>> >>>>>>>>> Discuss metadata name issues on citation vs source and >>>>>>>>> cardinality >>>>>>>>> if time also... >>>>>>>>> Instrument use case discussion >>>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> _____________________________________________________________________ >>>>> _____________________ >>>>> >>>>> Dr. Daniel Schober >>>>> >>>>> NET Project - Ontologist >>>>> >>>>> The European Bioinformatics Institute email: sc...@eb... >>>>> <mailto:sc...@eb...> >>>>> EMBL Outstation - Hinxton direct: +44 (0)1223 494410 >>>>> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 >>>>> Cambridge CB10 1SD, UK Room: A3-141 >>>>> (extension building) >>>>> >>>>> Project page: www.ebi.ac.uk/net-project >>>>> <http://www.ebi.ac.uk/net-project> >>>>> >>>>> Personal page: http://www.ebi.ac.uk/Information/Staff/ >>>>> person_maint.php?s_person_id=734 >>>>> Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ >>>>> >>>>> >>>> >>>> >>>> -- >>>> European Bioinformatics Institute, Wellcome Trust Genome Campus, >>>> Hinxton, Cambridge, CB10 1SD, United Kingdom >>>> Tel: + 44 (0) 1223 494 676 >>>> Fax: + 44 (0) 1223 492 468 >>> >>> >> >> -- >> __________________________________________________________________________________________ >> >> Dr. Daniel Schober >> >> NET Project - Ontologist >> >> The European Bioinformatics Institute email: sc...@eb... >> <mailto:sc...@eb...> >> EMBL Outstation - Hinxton direct: +44 (0)1223 494410 >> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 >> Cambridge CB10 1SD, UK Room: A3-141 (extension building) >> >> Project page: www.ebi.ac.uk/net-project >> <http://www.ebi.ac.uk/net-project> >> >> Personal page: >> http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 >> Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ >> >> > -- __________________________________________________________________________________________ Dr. Daniel Schober NET Project - Ontologist The European Bioinformatics Institute email: sc...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 494410 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK Room: A3-141 (extension building) Project page: www.ebi.ac.uk/net-project Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ |