I don't think this is a good idea. - I think bioentity should be depreciated, it has not intrinsic semantic value. - If it is used currently, it should be left as its current minimum specification which is to label and point to other bioinformatics database IDs. - The problem is not 'biologically related paper's' per se, but one of identifying what was the primary publication or publications that motivated a model. - There is also the case where a single publication that contains a mathematical model is the one and only primary source for the model itself - a rather common case at the moment.
I would prefer that the primary publication(s) be identified as such, which covers the case in where there are some models in the repository built from general review papers of biology with no math. I would prefer references to other related publications to be bound explicitly to a comment in the model metadata - there should be a reason identified by the author/editor/reviewer as to why there has been such an association made. As an aside, we also need to determine whether the bqs schema provides enough detail to match publications across metadata instances for different models, and whether we should be complimenting bibliographic data with pubmed Ids and the like. cheers Matt On 3/29/07, Andrew Miller <[EMAIL PROTECTED]> wrote: > Hi, > > As discussed at the last CellML meeting, there are some models which > reference both the paper about the model, and a reference about the > biology. Since there is no way to determine between them, this creates > problems for CellML metadata processing tools which want to identify the > paper about the model (such as the CellML repository). However, it would > still be a good thing to include references about the biology / > experiments on which a model is based, as well as papers on underlying > mathematical techniques (and perhaps earlier papers?) > > The CellML Metadata specification already describes a predicate > cmeta:bio_entity, and another cmeta:math_problem. Although the cmeta > specification suggests that these be used to provide references to > identifiers for the biological entity a part of the model relates to, > and likewise for the mathematical problem, it would also be possible to > create a list of references inside the resource targeted by the > bio_entity or math_problem predicate. > > I would therefore suggest that the following be considered best practice: > 1) Only refer to the paper about the model from the metadata for the model. > 2) Any other papers should be in another resource referred to from the > bio_entity and math_problem entities. > > Does anyone else have any opinion on this? > > Best regards, > Andrew > > || > _______________________________________________ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > _______________________________________________ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
