Re: [cellml-discussion] PMR categories
Tommy Yu wrote: David Nickerson wrote: Actually they are. Keywords are defined in the CellML metadata specifications and are already being used in various files. Feel free to check the CellML files of the old repository and scroll down the to keyword section. An example follows. From http://www.cellml.org/examples/models/beeler_reuter_model_1977.html: !-- Keyword(s) -- bqs:reference rdf:parseType=Resource dc:subject rdf:parseType=Resource bqs:subject_typekeyword/bqs:subject_type rdf:value rdf:Bag rdf:liventricular myocyte/rdf:li rdf:lielectrophysiological/rdf:li /rdf:Bag /rdf:value /dc:subject /bqs:reference I do understand it may be different from the full CellML metadata specification as found in http://www.cellml.org/specifications/metadata/cellml_metadata_1.0#sec_bqs, but all other models pretty much follow this RDF format and so I wound up having to follow the above format to pick up the keyword metadata. does this mean that keywords described using the RDF specified in the CellML Metadata Specification will not be picked up? or is the above allowed in addition to following the specification? And are there any plans to standardise on one or the other of these? I believe as per the metadata specification status, it is only a draft. I did not develop the specifications and I did not coded the model, and since the current usage is not following the specification I have not much of a choice and so I did not follow the draft specification. I can of course make adjustment to the keyword code. As for standardization of the keyword metadata, I am not the best person to answer that. I'd suggest that since you are deciding how keywords are extracted, edited, and put back into the models that you are the best person to answer that. Otherwise there should have been some discussion on this mailing list as to how to handle this issue. David. ___ 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'd suggest that since you are deciding how keywords are extracted, edited, and put back into the models that you are the best person to answer that. Otherwise there should have been some discussion on this mailing list as to how to handle this issue. Okay, I've re-read the metadata specification, specifically the RDF schema draft section at the bottom of the document, and the RDF schema for Dublin Core (which was related). bqs:reference rdf:parseType=Resource dc:subject rdf:parseType=Resource bqs:subject_typekeyword/bqs:subject_type rdf:value rdf:Bag rdf:liventricular myocyte/rdf:li rdf:lielectrophysiological/rdf:li /rdf:Bag /rdf:value /dc:subject /bqs:reference This method of defining a keyword uses the straight dublin core subject while using the bqs:subject_type property to label this instance of dc:subject property as 'keyword', it is consistent with the standards defined, but not specifically to the definition of the CellML metadata. Perhaps those keywords were coded in before keywords were defined, and nobody raised any issue about the need to convert the old format to the new format until today. If we use the metadata specification it may look like this: |bqs:reference rdf:parseType=Resource| | ||bqs:keyword| |||rdf:Seq| || rdf:liventricular myocyte/rdf:li rdf:lielectrophysiological/rdf:li |||||/rdf:Seq||| | ||/bqs:keyword| |||/bqs:reference| || Since the specification is already written to accomodate the keywords I think it is better to keep to it, even though the common usage (as defined by the number of files with this RDF to describe keywords used by the old and current repositories) does not follow it. I must admit I let this issue slipped through my head as I didn't think too much about it. Thank you for correcting me. However, my inspection of the metadata specification revealed some issues, such as this: | !--Subject Type-- rdf:Property rdf:about=amp;bqsns;subject_type rdfs:labelsubject type/rdfs:label rdfs:comment Defines the topic of a resource. /rdfs:comment rdfs:subPropertyOf rdf:resource=dcns;subject / rdfs:isDefinedBy rdf:resource=bqsns; / /rdf:Property !--Subject Type:Keyword-- rdf:Property rdf:about=bqsns;keyword rdfs:labelkeyword/rdfs:label rdfs:comment Defines the topic of a resource using keywords. /rdfs:comment rdfs:type rdf:resource=dcns;subject_type / rdfs:isDefinedBy rdf:resource=bqsns; / /rdf:Property | The specification have||| subject_type prefixed with both the dublin core namespace and the bqs|| namespace. Dublin Core does not define subject_type, so that needs to be corrected, perhaps the author meant to use bqsns;subject_type where s/he wrote dcns;subject_type. It also had double escaped ampersand (||amp;bqsns;subject_type should probably be just ||bqsns;subject_type) and other mistakes at other places. I also think keyword be limited constrained to certain domains (via rdf schema), such as limiting it to within the bqs:reference class so users knows specifically where to place it, and machines know where to read it.|| I supposed this topic about formalizing the RDF schema and issues with the metadata specification should probably be discussed in a different discussion thread.||| || ||Tommy. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
Ugh, looks like Thunderbird clobbered my last message when I told it to converted html to plain text. This is my reply. Okay, I've re-read the metadata specification, specifically the RDF schema draft section at the bottom of the document, and the RDF schema for Dublin Core (which was related). bqs:reference rdf:parseType=Resource dc:subject rdf:parseType=Resource bqs:subject_typekeyword/bqs:subject_type rdf:value rdf:Bag rdf:liventricular myocyte/rdf:li rdf:lielectrophysiological/rdf:li /rdf:Bag /rdf:value /dc:subject /bqs:reference This method of defining a keyword uses the straight dublin core subject while using the bqs:subject_type property to label this instance of dc:subject property as 'keyword', it is consistent with the standards defined, but not specifically to the definition of the CellML metadata. Perhaps those keywords were coded in before keywords were defined, and nobody raised any issue about the need to convert the old format to the new format until today. If we use the metadata specification it may look like this: bqs:reference rdf:parseType=Resource bqs:keyword rdf:Seq rdf:liventricular myocyte/rdf:li rdf:lielectrophysiological/rdf:li /rdf:Seq /bqs:keyword /bqs:reference Since the specification is already written to accomodate the keywords I think it is better to keep to it, even though the common usage (as defined by the number of files with this RDF to describe keywords used by the old and current repositories) does not follow it. I must admit I let this issue slipped through my head as I didn't think too much about it. Thank you for correcting me. However, my inspection of the metadata specification revealed some issues, such as this: !--Subject Type-- rdf:Property rdf:about=amp;bqsns;subject_type rdfs:labelsubject type/rdfs:label rdfs:comment Defines the topic of a resource. /rdfs:comment rdfs:subPropertyOf rdf:resource=dcns;subject / rdfs:isDefinedBy rdf:resource=bqsns; / /rdf:Property !--Subject Type:Keyword-- rdf:Property rdf:about=bqsns;keyword rdfs:labelkeyword/rdfs:label rdfs:comment Defines the topic of a resource using keywords. /rdfs:comment rdfs:type rdf:resource=dcns;subject_type / rdfs:isDefinedBy rdf:resource=bqsns; / /rdf:Property The specification have subject_type prefixed with both the dublin core namespace and the bqs namespace. Dublin Core does not define subject_type, so that needs to be corrected, perhaps the author meant to use bqsns;subject_type where s/he wrote dcns;subject_type. It also had double escaped ampersand (amp;bqsns;subject_type should probably be just bqsns;subject_type) and other mistakes at other places. I also think keyword be limited constrained to certain domains (via rdf schema), such as limiting it to within the bqs:reference class so users knows specifically where to place it, and machines know where to read it. I supposed this topic about formalizing the RDF schema and issues with the metadata specification should probably be discussed in a different discussion thread. Tommy. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
Matt wrote: On 6/11/07, Tommy Yu [EMAIL PROTECTED] wrote: Matt wrote: I have concluded that they are now talking about the web site and not keywords in general. My assumption was that the category field selections are not persisted in the model metadata at all. Actually they are. Keywords are defined in the CellML metadata specifications and are already being used in various files. Feel free to check the CellML files of the old repository and scroll down the to keyword section. An example follows. You are talking about keywords, I was talking about these new things Peter brought up called Categories. I will say it again. Categories are not 'new things'. It is something specific to the CellML Repository I was told to implement. The options in the category are keywords themselves. Items there are not 'new things'. They are just keywords hand-picked by Peter to show up in the drop box that happens to be labeled as categories. Nothing more. Before you ask further, I only did what I was told. From http://www.cellml.org/examples/models/beeler_reuter_model_1977.html: !-- Keyword(s) -- bqs:reference rdf:parseType=Resource dc:subject rdf:parseType=Resource bqs:subject_typekeyword/bqs:subject_type rdf:value rdf:Bag rdf:liventricular myocyte/rdf:li rdf:lielectrophysiological/rdf:li /rdf:Bag /rdf:value /dc:subject /bqs:reference I do understand it may be different from the full CellML metadata specification as found in http://www.cellml.org/specifications/metadata/cellml_metadata_1.0#sec_bqs, but all other models pretty much follow this RDF format and so I wound up having to follow the above format to pick up the keyword metadata. It's different, but says the same thing, even though the graph comes out different. Personally I think we should probably dump bqs; the rdf schema we advertise is non-standard and broken. I very much agree, it was not easy working with and around it, especially given the pile of cruft that is already in place that I have to deal with... Dublin core is not the easiest thing to follow, but at least it is standard and used in the world, so we should at least keep that. If someone come up with a proper metadata specification based only on industry standard with everyone in the community agreeing with use it I would be happy as it should make my life easier when dealing with CellML metadata. Also, I don't want to be dealing with five different graphs that says the same thing. I have enough headaches dealing with constructing multiple versa queries to pull relevant data as it is. I would have liked some indication that the 'categories' used also end up in the model keywords attributed to the model in addition to the keywords supplied by the author when creating or uploading the model. That is already the case, the 'categories' *are* keywords that are chosen by Peter as a selectable choice in the filtering drop box for the repository listing. You need to make sure the keywords then are ordered collections so that you can create some rule for your 'category' interpretation. Not really. I don't care what they are ordered. If it exists it gets highlighted as per demand. I don't like this special attention that certain keywords gets. They get no further treatment aside from the special attention which is to limit the listing of keywords. Peter does not want that list to be filled with over 100 keywords. A condensed listing was desired and I implemented with keywords as those keywords used must exactly describe what the models we have in the repository (and the old repository) are about. Feel free to check these links out. http://www.cellml.org/examples/repository/index.html - Under Table of Contents - Basically the same list of categories. http://www.cellml.org/models/pmr_search - Feel free to see/search by all keywords with the 'Keywords' selection box. It works exactly the same as the category filter found on top of the main listing except the short list found on the main listing is a predefined list of keywords. Again, having the special category listing that only includes the few chosen keywords is intended to be an usability aid for the filtering of the major types of models we deal with, which happens to be described via the keyword metadata. If you still think category describes something new (at least in the way it is implemented by the CellML repository), I don't know what else to convince you that it isn't. I would like there to be as many keywords allowed as the author/uploader wants (perhaps just a lines field will do for now for this). Constraining them to a single extra keyword in addition to a selected category makes no sense to me. In the Edit Keyword interface, any keyword of the model that matches one of the 'blessed' keywords
Re: [cellml-discussion] PMR categories
Matt wrote: I have concluded that they are now talking about the web site and not keywords in general. My assumption was that the category field selections are not persisted in the model metadata at all. Actually they are. Keywords are defined in the CellML metadata specifications and are already being used in various files. Feel free to check the CellML files of the old repository and scroll down the to keyword section. An example follows. From http://www.cellml.org/examples/models/beeler_reuter_model_1977.html: !-- Keyword(s) -- bqs:reference rdf:parseType=Resource dc:subject rdf:parseType=Resource bqs:subject_typekeyword/bqs:subject_type rdf:value rdf:Bag rdf:liventricular myocyte/rdf:li rdf:lielectrophysiological/rdf:li /rdf:Bag /rdf:value /dc:subject /bqs:reference I do understand it may be different from the full CellML metadata specification as found in http://www.cellml.org/specifications/metadata/cellml_metadata_1.0#sec_bqs, but all other models pretty much follow this RDF format and so I wound up having to follow the above format to pick up the keyword metadata. I would have liked some indication that the 'categories' used also end up in the model keywords attributed to the model in addition to the keywords supplied by the author when creating or uploading the model. That is already the case, the 'categories' *are* keywords that are chosen by Peter as a selectable choice in the filtering drop box for the repository listing. I would like there to be as many keywords allowed as the author/uploader wants (perhaps just a lines field will do for now for this). Constraining them to a single extra keyword in addition to a selected category makes no sense to me. In the Edit Keyword interface, any keyword of the model that matches one of the 'blessed' keywords will be highlighted in the category list. All other keywords will be in the lines field editor. Feel free to log into the site (I assume you have an account) and try out the editing interface. I do agree it is currently slightly clunky, but James has no complaints with it and he has already added/verified keyword for half the curated models (I think) of the repository. Again, the category field is a *subset* of keywords to limit the number of choices in the filtering menu and not a distinct entity. Hope this clear things up. Tommy. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
Dear All, Poul and I have looked at the discussion on this thread and to best encompass the various suggestions we've decided to ask Tommy to do the following: 1. Include both a category field with predefined terms (Tommy has this in now) and an additional general 'key word' field. A model can be in multiple categories. 2. The sort facility on the repository will have three ways of sorting: The 1st is the above list of categories, the 2nd is a drop down list that provides more options (see next point), and the 3rd is the curation level. 3. The 2nd sort facility will present several options such as keyword search, species, cell type, etc, and access to more extensive boolean searches (author, year, etc). Cheers, Peter Matt wrote: 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 begin:vcard fn:Peter Hunter FRS n:Hunter;Peter org:University of Auckland;Auckland Bioengineering Institute (ABI) email;internet:[EMAIL PROTECTED] title:Director tel;work:+649 3737599 x88395 tel;fax:+649 367 7157 version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
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'
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 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
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), possibly with the addition of a guided part of the
metadata editing workflow which prompts the user to
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'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
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
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
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
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
Some of those are subsets of others. You might want to generalise a bit more and then fit some of the useful specifics into that. I would be interested to see what you come up with. cheers Matt On 6/6/07, James Lawson [EMAIL PROTECTED] wrote: Hi folks, Tommy is currently working on a sorting function for the main model list of the PMR. Peter is looking for some ideas on what categories people think should be included (with respect to biology, not curation - that will be separate, coming soon!) The old repository obviously has models listed under categories. Do we want to keep those categories? We don't want too many categories, so what is important? As well as just biological function, perhaps the model type is important too. Particularly when the repository goes 1.1 we'll start getting multiscale models. Here's a list I compiled, which represents most of the models we currently have. Multiscale Cardiobiology/Cardiophysiology Neurobiology/Neurophysiology Beta Cells/Insulin Electrophysiology Biomechanics Biochemistry Pharmacology Signal Transduction/Signalling Metabolism Energy Metabolism Cell Cycle Immunology Virology HIV Circadian Rhythms Calcium Dynamics Protein Structure Function Please discuss. Kind regards, James Lawson ___ 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
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? And if so, I'm gonna further assume that there are no issues with having a model in more than one category, right? And what are the consequences for a model not fitting into any of these categories? I'd suggest that multiscale is a bit too general to be useful in this sort of setting, as its conceivable that pretty much every model in the repository is multiscale in some sense. David. James Lawson wrote: Hi folks, Tommy is currently working on a sorting function for the main model list of the PMR. Peter is looking for some ideas on what categories people think should be included (with respect to biology, not curation - that will be separate, coming soon!) The old repository obviously has models listed under categories. Do we want to keep those categories? We don't want too many categories, so what is important? As well as just biological function, perhaps the model type is important too. Particularly when the repository goes 1.1 we'll start getting multiscale models. Here's a list I compiled, which represents most of the models we currently have. Multiscale Cardiobiology/Cardiophysiology Neurobiology/Neurophysiology Beta Cells/Insulin Electrophysiology Biomechanics Biochemistry Pharmacology Signal Transduction/Signalling Metabolism Energy Metabolism Cell Cycle Immunology Virology HIV Circadian Rhythms Calcium Dynamics Protein Structure Function Please discuss. Kind regards, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
Hi I agree with David, 'Multiscale' looks out of place because it is a description of what kind of model it is, rather than what aspect of biology/physiology is being modelled. Edmund 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? And if so, I'm gonna further assume that there are no issues with having a model in more than one category, right? And what are the consequences for a model not fitting into any of these categories? I'd suggest that multiscale is a bit too general to be useful in this sort of setting, as its conceivable that pretty much every model in the repository is multiscale in some sense. David. James Lawson wrote: Hi folks, Tommy is currently working on a sorting function for the main model list of the PMR. Peter is looking for some ideas on what categories people think should be included (with respect to biology, not curation - that will be separate, coming soon!) The old repository obviously has models listed under categories. Do we want to keep those categories? We don't want too many categories, so what is important? As well as just biological function, perhaps the model type is important too. Particularly when the repository goes 1.1 we'll start getting multiscale models. Here's a list I compiled, which represents most of the models we currently have. Multiscale Cardiobiology/Cardiophysiology Neurobiology/Neurophysiology Beta Cells/Insulin Electrophysiology Biomechanics Biochemistry Pharmacology Signal Transduction/Signalling Metabolism Energy Metabolism Cell Cycle Immunology Virology HIV Circadian Rhythms Calcium Dynamics Protein Structure Function Please discuss. Kind regards, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:Dr Edmund J. Crampin n:Crampin;Edmund org:The University of Auckland;Auckland Bioengineering Institute adr:Auckland Mail Centre;;Private Bag 92019;Auckland;;1142;New Zealand email;internet:[EMAIL PROTECTED] title:Senior Lecturer tel;work:+64 9 373 7599 ext. 88168 tel;fax:+64 9 367 7157 x-mozilla-html:TRUE url:http://www.bioeng.auckland.ac.nz/people/crampin/ version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
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. And if so, I'm gonna further assume that there are no issues with having a model in more than one category, right? right And what are the consequences for a model not fitting into any of these categories? We create an 'other' category? I'd suggest that multiscale is a bit too general to be useful in this sort of setting, as its conceivable that pretty much every model in the repository is multiscale in some sense. Fair enough, multiscale can be a pretty abstracted term. David. Thanks, your comments are always helpful. James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
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 :-) ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
On 6/6/07, David Nickerson [EMAIL PROTECTED] 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? I would hope so. And if so, I'm gonna further assume that there are no issues with having a model in more than one category, right? I would hope so. And what are the consequences for a model not fitting into any of these categories? It has to fit somewhere, I don't think the list is easily determined from the top down like this. I would prefer that keywords were added for each model and then we look at the accumulation of terms post this process and work out sets and subsets and maybe places where merging or specialisation can occur. I'd suggest that multiscale is a bit too general to be useful in this sort of setting, as its conceivable that pretty much every model in the repository is multiscale in some sense. Yeah, it's too vague a term at the moment. David. James Lawson wrote: Hi folks, Tommy is currently working on a sorting function for the main model list of the PMR. Peter is looking for some ideas on what categories people think should be included (with respect to biology, not curation - that will be separate, coming soon!) The old repository obviously has models listed under categories. Do we want to keep those categories? We don't want too many categories, so what is important? As well as just biological function, perhaps the model type is important too. Particularly when the repository goes 1.1 we'll start getting multiscale models. Here's a list I compiled, which represents most of the models we currently have. Multiscale Cardiobiology/Cardiophysiology Neurobiology/Neurophysiology Beta Cells/Insulin Electrophysiology Biomechanics Biochemistry Pharmacology Signal Transduction/Signalling Metabolism Energy Metabolism Cell Cycle Immunology Virology HIV Circadian Rhythms Calcium Dynamics Protein Structure Function Please discuss. Kind regards, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] ___ 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
And what are the consequences for a model not fitting into any of these categories? It has to fit somewhere, I don't think the list is easily determined from the top down like this. I would prefer that keywords were added for each model and then we look at the accumulation of terms post this process and work out sets and subsets and maybe places where merging or specialisation can occur. yep - that sounds like a very good approach to me also. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
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' in the ontology, so it would be nice if the keywords were at least dynamically generated from the labels of these ontological term instances. ___ 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
I think you need to re-read my last email. Ontologies are blessed lists at the most simple interpretation. I don't care too much about different terms for the same thing at the moment, the impetous should be to retrieve all the current keywords, then 'bless the list and update the keywords and add others, then give this list to me to try and formalize in the ontology. On 6/6/07, Tommy Yu [EMAIL PROTECTED] 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' in the ontology, so it would be nice if the keywords were at least dynamically generated from the labels of these ontological term instances. ___ 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 ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
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' in the ontology, so it would be nice if the keywords were at least dynamically generated from the labels of these ontological term instances. ___ 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 -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
