Re: [cellml-discussion] PMR categories
On 6/8/07, James Lawson <[EMAIL PROTECTED]> wrote: > So for example someone's trying to build a large model but the only > components (or data to build components) available are from non-matching > species? Yes. > So the LFID (I looked it up but it went over my head) provides > a way we can do that which is more precise and flexible than simply > referring to NCBI taxonomy? Read the paper I referenced, it has a very simple breakdown of LSID and the taxonomy naming issue. > > > > > The critical thing for us is that a single model will quite often > > contain elements that derive their mechanism or parameters from > > studies on different organisms, so we need to be quite rigorous in > > looking at all components in a model and identifying their origin. > > This is obviously one facet where imports should be helping us to put > > circles around species specific submodels. > > > ___ > 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
Re: [cellml-discussion] PMR categories
So for example someone's trying to build a large model but the only components (or data to build components) available are from non-matching species? So the LFID (I looked it up but it went over my head) provides a way we can do that which is more precise and flexible than simply referring to NCBI taxonomy? > > The critical thing for us is that a single model will quite often > contain elements that derive their mechanism or parameters from > studies on different organisms, so we need to be quite rigorous in > looking at all components in a model and identifying their origin. > This is obviously one facet where imports should be helping us to put > circles around species specific submodels. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
Yes, species attributes are important - especially where a model contains mixed data. We can use the species metadata, however I would like to extend the specification of that property to have other resources as possible values, not just simple strings, and to use something like the LSID formalism outlined in the following paper: TAXONOMIC NAMES, METADATA, AND THE SEMANTIC WEB : Biodiversity Informatics, 3, 2006, pp. 1-15 The paper explains in a pretty straightforward way why this is better than using names from a single source such as the NCBI Taxonomy (which we advocate in the metadata spec). The critical thing for us is that a single model will quite often contain elements that derive their mechanism or parameters from studies on different organisms, so we need to be quite rigorous in looking at all components in a model and identifying their origin. This is obviously one facet where imports should be helping us to put circles around species specific submodels. cheers Matt On 6/8/07, James Lawson <[EMAIL PROTECTED]> wrote: > Actually, I'd venture to say that the majority of them aren't models of > human biological systems. A lot of them are animal models or based on > experiments done in non-human cell lines (for example Xenopus oocytes > (frog) are commonplace for cell cycle experiments,) and there are also a > number of bacterial models. > > I agree, I think the metadata field for species (a lot of the models > already have this, I think,) would be a useful value to sort by. Perhaps > this should be on the advanced search page rather than on the front > page, however. > > Eventually, the plan is to be able to sort by pretty much any metadata > field that is contained in the models. > > In the future, perhaps we'll actually have specific sections devoted to > particular species. For example, the nematode work Caenorhabditis > elegans has only ~1000 cells, and every single cell and its function has > been mapped. The C. elegans neural system in particular has been mapped > in a lot of detail, with work by White, Brenner et al. (1986) mapping > all the synaptic connections between all of the neurons. Although I > haven't checked, I imagine there are efforts to model the whole > organism. While this isn't a human physiome project, animal models like > this are really important in developing frameworks to use for > modelling/studying larger systems. > > Randall Britten wrote: > > A separate phylogeny attribute is probably also needed. > > > > It is not clear whether all the models are meant to pertain to human > > physiology. One example certainly does not: "# Baylor, Hollingworth, > > Chandler, 2002, 'Comparison of Simulated and Measured Calcium Sparks > > in Intact Skeletal Muscle Fibers of the Frog'". > > > > > > ___ > > 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 > ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
Actually, I'd venture to say that the majority of them aren't models of human biological systems. A lot of them are animal models or based on experiments done in non-human cell lines (for example Xenopus oocytes (frog) are commonplace for cell cycle experiments,) and there are also a number of bacterial models. I agree, I think the metadata field for species (a lot of the models already have this, I think,) would be a useful value to sort by. Perhaps this should be on the advanced search page rather than on the front page, however. Eventually, the plan is to be able to sort by pretty much any metadata field that is contained in the models. In the future, perhaps we'll actually have specific sections devoted to particular species. For example, the nematode work Caenorhabditis elegans has only ~1000 cells, and every single cell and its function has been mapped. The C. elegans neural system in particular has been mapped in a lot of detail, with work by White, Brenner et al. (1986) mapping all the synaptic connections between all of the neurons. Although I haven't checked, I imagine there are efforts to model the whole organism. While this isn't a human physiome project, animal models like this are really important in developing frameworks to use for modelling/studying larger systems. Randall Britten wrote: > A separate phylogeny attribute is probably also needed. > > It is not clear whether all the models are meant to pertain to human > physiology. One example certainly does not: "# Baylor, Hollingworth, > Chandler, 2002, 'Comparison of Simulated and Measured Calcium Sparks > in Intact Skeletal Muscle Fibers of the Frog'". > > > ___ > 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
Re: [cellml-discussion] PMR categories
A separate phylogeny attribute is probably also needed. It is not clear whether all the models are meant to pertain to human physiology. One example certainly does not: "# Baylor, Hollingworth, Chandler, 2002, 'Comparison of Simulated and Measured Calcium Sparks in Intact Skeletal Muscle Fibers of the Frog'". ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
Matt wrote: > I'm not sure what the physiome ontology is. Currently the anatomy > ontology is the one I've been working on and this has no physiological > processes in it yet. > > I was hoping I had been clear in my previous emails that I want the > current and future author supplied keywords to help drive the > ontology, not the other way around. > Authors will still be able to supply their own keywords to models, and if enough authors uses it of course it can be added to the main list of terms which forms the ontology. Tommy. > On 6/8/07, James Lawson <[EMAIL PROTECTED]> wrote: >> Peter Hunter wrote: >> It may be that the additional key words >>> should adhere to terms from an ontology as Matt suggests and should >> use the >>> predictive completion facility that Andre suggests. >> Will we use the Physiome ontology for this? It will require changing the >> current keywords that are defined in the metadata for many of the models >> so they fit an ontology. >> >> Should we be using ontology terms for the major categories as well? A >> quick flick through the Physiome ontology suggests that we might have >> trouble finding terms in it that would fit what we want. >> >> >> ___ >> 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 ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
David Nickerson wrote: > I really don't like the idea of giving a model a keyword of "other". > Hopefully the repository will be smart enough to automatically add > models to the "other" listing if they don't have any of the other > predefined key words. > I agree, and I don't think I will put an 'other' category, as giving a value to something where an absence of value should be will cause problems in the future. The main listing will of course have a choice to select 'other', where models not categorized with the main set of keywords will be shown. Tommy. > And then if "other" is taken out of this list of mandatory keywords you > can no longer make them mandatory - which I would also prefer. These > predefined keywords should simply be given as suggestions for the user > to choose from. I think we need to be careful not too present repository > users with the impression that only certain types of models are > acceptable in the repository - unless we *are* trying to restrict the > types of models going in there? One example that wouldn't fit any of the > current categories might be finite element basis function definitions > for use with fieldML models. > > > Andre. > > > Peter Hunter wrote: >> Dear All, >> >> The intention of this discussion was to decide on a list of items for a >> drop-down list of predefined terms that would be available when choosing >> 'key words' for a new model and which would be the list of terms used to >> display models on www.cellml.org/models (together with the default 'All >> models' item). The idea was that choosing one or more of these key words >> terms would be mandatory when defining model metadata but that one could >> also enter additional keywords for more advanced searching. It may be >> that the additional key words should adhere to terms from an ontology as >> Matt suggests and should use the predictive completion facility that >> Andre suggests. But I am keen to keep this first list of terms fairly >> short. My suggestion is the following list. I've checked through the >> repository and less than 10% of the models would end up solely under >> 'Other'. I am sure we will need to expand this list as the repository >> grows and I suggest we have a policy of keeping the number that end up >> solely in the 'Other' category to less than 10% of the total. We may >> also later need a policy to refine the classification when too many >> models are displayed under one term. >> >> Calcium dynamics >> Cell cycle >> Cell migration >> Circadian rhythms >> Electrophysiology >> Excitation-contraction coupling >> Gene regulation >> Mechanical constitutive laws >> Metabolism >> Myofilament mechanics >> Signal transduction >> Other (the default key word in the list of predefined terms) >> >> Let me know if you can think of other more appropriate terms or >> additional ones, then I'll ask Tommy to implement it. I'm happy to then >> go through and classify all current models in the repository into these >> categories. >> >> Cheers, >> Peter >> ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
I'm not sure what the physiome ontology is. Currently the anatomy ontology is the one I've been working on and this has no physiological processes in it yet. I was hoping I had been clear in my previous emails that I want the current and future author supplied keywords to help drive the ontology, not the other way around. On 6/8/07, James Lawson <[EMAIL PROTECTED]> wrote: > Peter Hunter wrote: > It may be that the additional key words > > should adhere to terms from an ontology as Matt suggests and should > use the > > predictive completion facility that Andre suggests. > > Will we use the Physiome ontology for this? It will require changing the > current keywords that are defined in the metadata for many of the models > so they fit an ontology. > > Should we be using ontology terms for the major categories as well? A > quick flick through the Physiome ontology suggests that we might have > trouble finding terms in it that would fit what we want. > > > ___ > 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
Re: [cellml-discussion] PMR categories
Peter Hunter wrote: It may be that the additional key words > should adhere to terms from an ontology as Matt suggests and should use the > predictive completion facility that Andre suggests. Will we use the Physiome ontology for this? It will require changing the current keywords that are defined in the metadata for many of the models so they fit an ontology. Should we be using ontology terms for the major categories as well? A quick flick through the Physiome ontology suggests that we might have trouble finding terms in it that would fit what we want. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
I think that list is a good start for a top level set of terms. I
agree with Andre that other should not be a selectable term. I would
probably offer a primary keyword which forces a selection from the
current list of terms ('none of these') being one of the items, and
then a dynamic set of free text keyword fields (by using say the
DataGridField plone product http://plone.org/products/datagridfield)
so that Authors can add their own (especially if they don't fit into
one of the primaries). There can be a note to say that if you don't
fit into a primary your model will be listed under other, but to point
out that it is important for them to add the free form keywords so
that 'we' can look over the models that end up in other and perhaps
add another primary keyword option if something looks as if it should
be.
I really want to be able to capture author coined keywords since this
is the best input for trying to organise an ontology of keywords
(including synonyms etc that come up).
cheers
Matt
On 6/7/07, Peter Hunter <[EMAIL PROTECTED]> wrote:
>
> Dear All,
>
> The intention of this discussion was to decide on a list of items for a
> drop-down list of predefined terms that would be available when choosing
> 'key words' for a new model and which would be the list of terms used to
> display models on www.cellml.org/models (together with the default 'All
> models' item). The idea was that choosing one or more of these key words
> terms would be mandatory when defining model metadata but that one could
> also enter additional keywords for more advanced searching. It may be that
> the additional key words should adhere to terms from an ontology as Matt
> suggests and should use the predictive completion facility that Andre
> suggests. But I am keen to keep this first list of terms fairly short. My
> suggestion is the following list. I've checked through the repository and
> less than 10% of the models would end up solely under 'Other'. I am sure we
> will need to expand this list as the repository grows and I suggest we have
> a policy of keeping the number that end up solely in the 'Other' category to
> less than 10% of the total. We may also later need a policy to refine the
> classification when too many models are displayed under one term.
>
> Calcium dynamics
> Cell cycle
> Cell migration
> Circadian rhythms
> Electrophysiology
> Excitation-contraction coupling
> Gene regulation
> Mechanical constitutive laws
> Metabolism
> Myofilament mechanics
> Signal transduction
> Other (the default key word in the list of predefined terms)
>
> Let me know if you can think of other more appropriate terms or additional
> ones, then I'll ask Tommy to implement it. I'm happy to then go through and
> classify all current models in the repository into these categories.
>
> Cheers,
> Peter
>
>
> David Nickerson wrote:
> One thing I have found useful in other taxonomy/keyword type web
> interfaces (e.g., see drupal) is that when entering such keywords the
> interface dynamically completes the terms and/or presents alternatives
> based on what the user enters. I'd imagine such an interface would work
> well at pulling terms out of the ontologies Matt is talking about.
>
>
> David.
>
>
> Tommy Yu wrote:
>
>
> Just had a discussion with Peter, Randall and James about this.
>
> The keywords are in the metadata for the models, and there is no limit to
> what can go in there. The concern about that is the list could get too big
> (for minor categories), or variations in the name (electrophysiology vs
> electrophysiological), or just spelling in general. What was decided is to
> have the same category list, but it would act as a "blessed" list of
> keywords that will serve as a guide to what should be added to the model,
> and as a broad category filter for the main repository listing. Users would
> still be able to add or search by other keywords (from the advance search
> interface) if they wish.
>
> Tommy.
>
> Matt wrote:
>
>
> On 6/6/07, David Nickerson <[EMAIL PROTECTED]> wrote:
>
>
> James Lawson wrote:
>
>
> David Nickerson wrote:
>
>
> Would I be correct in assuming that these terms will be key words added
> to the model metadata and that the division into categories on the main
> repository page will be assembled from queries on each of these
> predefined key words?
>
> Well potentially, there could be many many different keywords, so Peter
> suggested that we might not necessarily want to base the categories on
> just the keywords. At the moment, Tommy's sorting function is based on
> keywords but he suggested that we could have both a keyword and a more
> general category selection system.
>
> not sure I like the idea of a separate category, seems to me adding some
> special piece of metadata to models just to make a repository dump look
> pretty isn't the way to go. It would be nicer to make use of the
> keywords (which are genuinely useful metadata to more than just the
> model repository), p
Re: [cellml-discussion] PMR categories
I really don't like the idea of giving a model a keyword of "other". Hopefully the repository will be smart enough to automatically add models to the "other" listing if they don't have any of the other predefined key words. And then if "other" is taken out of this list of mandatory keywords you can no longer make them mandatory - which I would also prefer. These predefined keywords should simply be given as suggestions for the user to choose from. I think we need to be careful not too present repository users with the impression that only certain types of models are acceptable in the repository - unless we *are* trying to restrict the types of models going in there? One example that wouldn't fit any of the current categories might be finite element basis function definitions for use with fieldML models. Andre. Peter Hunter wrote: > Dear All, > > The intention of this discussion was to decide on a list of items for a > drop-down list of predefined terms that would be available when choosing > 'key words' for a new model and which would be the list of terms used to > display models on www.cellml.org/models (together with the default 'All > models' item). The idea was that choosing one or more of these key words > terms would be mandatory when defining model metadata but that one could > also enter additional keywords for more advanced searching. It may be > that the additional key words should adhere to terms from an ontology as > Matt suggests and should use the predictive completion facility that > Andre suggests. But I am keen to keep this first list of terms fairly > short. My suggestion is the following list. I've checked through the > repository and less than 10% of the models would end up solely under > 'Other'. I am sure we will need to expand this list as the repository > grows and I suggest we have a policy of keeping the number that end up > solely in the 'Other' category to less than 10% of the total. We may > also later need a policy to refine the classification when too many > models are displayed under one term. > > Calcium dynamics > Cell cycle > Cell migration > Circadian rhythms > Electrophysiology > Excitation-contraction coupling > Gene regulation > Mechanical constitutive laws > Metabolism > Myofilament mechanics > Signal transduction > Other (the default key word in the list of predefined terms) > > Let me know if you can think of other more appropriate terms or > additional ones, then I'll ask Tommy to implement it. I'm happy to then > go through and classify all current models in the repository into these > categories. > > Cheers, > Peter > > David Nickerson wrote: >> One thing I have found useful in other taxonomy/keyword type web >> interfaces (e.g., see drupal) is that when entering such keywords the >> interface dynamically completes the terms and/or presents alternatives >> based on what the user enters. I'd imagine such an interface would work >> well at pulling terms out of the ontologies Matt is talking about. >> >> >> David. >> >> >> Tommy Yu wrote: >> >>> Just had a discussion with Peter, Randall and James about this. >>> >>> The keywords are in the metadata for the models, and there is no limit to >>> what can go in there. The concern about that is the list could get too big >>> (for minor categories), or variations in the name (electrophysiology vs >>> electrophysiological), or just spelling in general. What was decided is to >>> have the same category list, but it would act as a "blessed" list of >>> keywords that will serve as a guide to what should be added to the model, >>> and as a broad category filter for the main repository listing. Users >>> would still be able to add or search by other keywords (from the advance >>> search interface) if they wish. >>> >>> Tommy. >>> >>> Matt wrote: >>> On 6/6/07, David Nickerson <[EMAIL PROTECTED]> wrote: > James Lawson wrote: > >> David Nickerson wrote: >> >>> Would I be correct in assuming that these terms will be key words added >>> to the model metadata and that the division into categories on the main >>> repository page will be assembled from queries on each of these >>> predefined key words? >>> >> Well potentially, there could be many many different keywords, so Peter >> suggested that we might not necessarily want to base the categories on >> just the keywords. At the moment, Tommy's sorting function is based on >> keywords but he suggested that we could have both a keyword and a more >> general category selection system. >> > not sure I like the idea of a separate category, seems to me adding some > special piece of metadata to models just to make a repository dump look > pretty isn't the way to go. It would be nicer to make use of the > keywords (which are genuinely useful metadata to more than just the > model reposit
Re: [cellml-discussion] PMR categories
Dear All, The intention of this discussion was to decide on a list of items for a drop-down list of predefined terms that would be available when choosing 'key words' for a new model and which would be the list of terms used to display models on www.cellml.org/models (together with the default 'All models' item). The idea was that choosing one or more of these key words terms would be mandatory when defining model metadata but that one could also enter additional keywords for more advanced searching. It may be that the additional key words should adhere to terms from an ontology as Matt suggests and should use the predictive completion facility that Andre suggests. But I am keen to keep this first list of terms fairly short. My suggestion is the following list. I've checked through the repository and less than 10% of the models would end up solely under 'Other'. I am sure we will need to expand this list as the repository grows and I suggest we have a policy of keeping the number that end up solely in the 'Other' category to less than 10% of the total. We may also later need a policy to refine the classification when too many models are displayed under one term. Calcium dynamics Cell cycle Cell migration Circadian rhythms Electrophysiology Excitation-contraction coupling Gene regulation Mechanical constitutive laws Metabolism Myofilament mechanics Signal transduction Other (the default key word in the list of predefined terms) Let me know if you can think of other more appropriate terms or additional ones, then I'll ask Tommy to implement it. I'm happy to then go through and classify all current models in the repository into these categories. Cheers, Peter David Nickerson wrote: One thing I have found useful in other taxonomy/keyword type web interfaces (e.g., see drupal) is that when entering such keywords the interface dynamically completes the terms and/or presents alternatives based on what the user enters. I'd imagine such an interface would work well at pulling terms out of the ontologies Matt is talking about. David. Tommy Yu wrote: Just had a discussion with Peter, Randall and James about this. The keywords are in the metadata for the models, and there is no limit to what can go in there. The concern about that is the list could get too big (for minor categories), or variations in the name (electrophysiology vs electrophysiological), or just spelling in general. What was decided is to have the same category list, but it would act as a "blessed" list of keywords that will serve as a guide to what should be added to the model, and as a broad category filter for the main repository listing. Users would still be able to add or search by other keywords (from the advance search interface) if they wish. Tommy. Matt wrote: On 6/6/07, David Nickerson <[EMAIL PROTECTED]> wrote: James Lawson wrote: David Nickerson wrote: Would I be correct in assuming that these terms will be key words added to the model metadata and that the division into categories on the main repository page will be assembled from queries on each of these predefined key words? Well potentially, there could be many many different keywords, so Peter suggested that we might not necessarily want to base the categories on just the keywords. At the moment, Tommy's sorting function is based on keywords but he suggested that we could have both a keyword and a more general category selection system. not sure I like the idea of a separate category, seems to me adding some special piece of metadata to models just to make a repository dump look pretty isn't the way to go. It would be nicer to make use of the keywords (which are genuinely useful metadata to more than just the model repository), possibly with the addition of a guided part of the metadata editing workflow which prompts the user to choose at least one of the predefined "category" keywords and a filter smart enough to put models without one of the special keywords into an "other" category. This way the main repository page layout could be easily changed to add or remove keywords that get pulled out as categories without having to change the models. It would also be nice if we can analyse all the repository searching to keep track of the most popular keywords and adjust the categories on the main page accordingly :-) Well, I'm hoping to steal all the keywords and lay them out in the physiome ontology and then put them back in as bioentities (or math related) metadata pointing into this. So the long term relationship between keywords and this "ontology" metadata is where my thinking lies. I like the idea of reflecting this information into keywords, e.g. for 'cardiovascular' the bioentity would be some big long uri pointing into the instance of the term 'cardiovascular'
