Matt wrote: > I don't think this is a good idea. > > - I think bioentity should be depreciated, it has not intrinsic semantic > value. > It does, unfortunately, seem to usually target a literal node at the moment. It would be nice for this to at least be a resource, which could provide further information about the biological entity (or if we decide not to do that, at least a resource, with a dictionary and a process for adding new words to the dictionary to avoid duplication).
It seems that GO(Gene Ontology) has terms for cell types, biological compartments, and so on, which would offer a better way to provide this information. I still think that this metadata is useful, even if the automated interpretation of it is currently difficult. > - 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. > There are three layers of information here: Layer 1: What biological entity are we describing? (could be answered with a GO term). Layer 2: What information about that biological entity are we using? (could be answered with a reference to a paper, and perhaps even a reference to raw experimental data). Layer 3: How was that information translated into a model (could be answered with a reference to a paper on the model). Layer 3 is clearly information about the model, and should be described by as an arc of the model resource. Layer 1 is described by a literal at the moment. Layer 2 is therefore a gap, which we don't have any proper way to represent now. > - 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. > The publication which motivated the expression of a model in CellML, or the publication which motivated the creation of the model? Most of the models in the repository were motivated by a paper about a model which was not initially expressed in CellML. However, the way that the metadata specification works now is that the paper which describes the model (not the paper which motivated it) is referenced from the information about the model (not information about the CellML file). > - 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. > This is what most models in CellML should aim to attain. Models can be submitted prior to publication as a model, but the step of going from the biology to a model is something which does need peer review. > 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. > If a model is built in that way, it should reference the review papers as information about the biology, and the author should ideally submit it for publication, at which point the reference to the paper could be filled in. > 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. > The problem with this is that the comment is not machine readable, so there is then no way to get aggregate statistics on why models are linked. There is also a potential for significant duplication of information, as opposed to a set of standardised predicate terms for linking to a set of models. > 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. > I think that the PUBMED ID is always useful, because it allows CellML processing software (e.g. the repository) to link directly to the Entrez / PUBMED page. We could build links based on searches for authors and titles, but a unique ID is much cleaner. It seems that many repository models do have PUBMED IDs on them. Best regards, Andrew _______________________________________________ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
