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From: Chris M. <cj...@fr...> - 2007-01-18 22:46:08
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Hi Xianhua Note there is now a gmod-ajax list too. I think a RESTFUL architecture makes a lot of sense for an AJAX application. By the way, I think you mean "Chado". (try a google search for "define: chode" - I do hope chode doesn't catch on as another Chado mispronounciation!). On Jan 18, 2007, at 7:47 AM, Xianhua Liu wrote: > I am trying to build web interface to query and view data from > Chode with extension schema for bio-diversity data. I am planning > to use a 4-lawyer architecture as following: > > 1. AJAX: front-end > 2. WebService: web lawyer > 3. XXX: Middleware > 4. Chode: back-end > > Why WebService? > 1. independency of front-end on middleware. > 2. loose coupling > 3. easy data integration over web > 4. ... > > Challenges: > 1. standardization of web service interface > 2. federalization of data representation model exchanged through > the web service (XML Schema, Ontology, ...?) > 3. Performance? > > RESTful or SOAP: > I prefer to choose RESTful web service, because it is easy, direct > and light. > > If someone have already tried the same and similar thing, please > share your experience and lessons and tech choises. > > Welcome every one to send comments about the idea, and suggestions > about techniques, software packages and any other sources. > > Thanks, > > Xianhua > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV________________________________ > _______________ > Gmod-architecture mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-architecture |
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From: Ian H. <ih...@be...> - 2007-01-19 00:29:59
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Now that we have a full-time gmod-ajax person (in the form of Mitch) it's probably about time to kick off a discussion on how to move towards our goals of community annotation (and what this means exactly) and full browser functionality including search, rich display, etc (and to what extent this should be GBrowse-like). Chris, Andrew and I had a tete-a-tete a couple of months ago in which we scribbled some notes on the back of an envelope (or coffeeshop napkin). Andrew, do you have that napkin anywhere? Could we start by reprising those? I am running out the door right now but could dredge up my memory of the meeting if necessary. One thing is that Mitch is away for a week or so. So probably the discussion will have to wait a little while for him to get back, before it gets really productive. I. Chris Mungall wrote: > Hi Xianhua > > Note there is now a gmod-ajax list too. > > I think a RESTFUL architecture makes a lot of sense for an AJAX > application. > > By the way, I think you mean "Chado". (try a google search for > "define: chode" - I do hope chode doesn't catch on as another Chado > mispronounciation!). > > On Jan 18, 2007, at 7:47 AM, Xianhua Liu wrote: > >> I am trying to build web interface to query and view data from >> Chode with extension schema for bio-diversity data. I am planning >> to use a 4-lawyer architecture as following: >> >> 1. AJAX: front-end >> 2. WebService: web lawyer >> 3. XXX: Middleware >> 4. Chode: back-end >> >> Why WebService? >> 1. independency of front-end on middleware. >> 2. loose coupling >> 3. easy data integration over web >> 4. ... >> >> Challenges: >> 1. standardization of web service interface >> 2. federalization of data representation model exchanged through >> the web service (XML Schema, Ontology, ...?) >> 3. Performance? >> >> RESTful or SOAP: >> I prefer to choose RESTful web service, because it is easy, direct >> and light. >> >> If someone have already tried the same and similar thing, please >> share your experience and lessons and tech choises. >> >> Welcome every one to send comments about the idea, and suggestions >> about techniques, software packages and any other sources. >> >> Thanks, >> >> Xianhua >> >> >> ---------------------------------------------------------------------- >> --- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys - and earn cash >> http://www.techsay.com/default.php? >> page=join.php&p=sourceforge&CID=DEVDEV________________________________ >> _______________ >> Gmod-architecture mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-architecture > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Andrew U. <and...@gm...> - 2007-01-22 18:08:41
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Ian et all... I've transferred all our ideas to the wiki a long time ago, they can be found here: http://biowiki.org/view/GBrowse/WishList Andrew On 1/18/07, Ian Holmes <ih...@be...> wrote: > Now that we have a full-time gmod-ajax person (in the form of Mitch) > it's probably about time to kick off a discussion on how to move towards > our goals of community annotation (and what this means exactly) and full > browser functionality including search, rich display, etc (and to what > extent this should be GBrowse-like). > > Chris, Andrew and I had a tete-a-tete a couple of months ago in which we > scribbled some notes on the back of an envelope (or coffeeshop napkin). > Andrew, do you have that napkin anywhere? Could we start by reprising > those? I am running out the door right now but could dredge up my memory > of the meeting if necessary. > > One thing is that Mitch is away for a week or so. So probably the > discussion will have to wait a little while for him to get back, before > it gets really productive. > > I. > > > > Chris Mungall wrote: > > Hi Xianhua > > > > Note there is now a gmod-ajax list too. > > > > I think a RESTFUL architecture makes a lot of sense for an AJAX > > application. > > > > By the way, I think you mean "Chado". (try a google search for > > "define: chode" - I do hope chode doesn't catch on as another Chado > > mispronounciation!). > > > > On Jan 18, 2007, at 7:47 AM, Xianhua Liu wrote: > > > >> I am trying to build web interface to query and view data from > >> Chode with extension schema for bio-diversity data. I am planning > >> to use a 4-lawyer architecture as following: > >> > >> 1. AJAX: front-end > >> 2. WebService: web lawyer > >> 3. XXX: Middleware > >> 4. Chode: back-end > >> > >> Why WebService? > >> 1. independency of front-end on middleware. > >> 2. loose coupling > >> 3. easy data integration over web > >> 4. ... > >> > >> Challenges: > >> 1. standardization of web service interface > >> 2. federalization of data representation model exchanged through > >> the web service (XML Schema, Ontology, ...?) > >> 3. Performance? > >> > >> RESTful or SOAP: > >> I prefer to choose RESTful web service, because it is easy, direct > >> and light. > >> > >> If someone have already tried the same and similar thing, please > >> share your experience and lessons and tech choises. > >> > >> Welcome every one to send comments about the idea, and suggestions > >> about techniques, software packages and any other sources. > >> > >> Thanks, > >> > >> Xianhua > >> > >> > >> ---------------------------------------------------------------------- > >> --- > >> Take Surveys. Earn Cash. Influence the Future of IT > >> Join SourceForge.net's Techsay panel and you'll get the chance to > >> share your > >> opinions on IT & business topics through brief surveys - and earn cash > >> http://www.techsay.com/default.php? > >> page=join.php&p=sourceforge&CID=DEVDEV________________________________ > >> _______________ > >> Gmod-architecture mailing list > >> Gmo...@li... > >> https://lists.sourceforge.net/lists/listinfo/gmod-architecture > > > > > > ------------------------------------------------------------------------- > > Take Surveys. Earn Cash. Influence the Future of IT > > Join SourceForge.net's Techsay panel and you'll get the chance to share your > > opinions on IT & business topics through brief surveys - and earn cash > > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > _______________________________________________ > > Gmod-ajax mailing list > > Gmo...@li... > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Ian H. <ih...@be...> - 2007-01-22 22:01:28
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ah, apologies. thank you. Andrew Uzilov wrote: > Ian et all... > > I've transferred all our ideas to the wiki a long time ago, they can > be found here: > > http://biowiki.org/view/GBrowse/WishList > > > Andrew > > > On 1/18/07, Ian Holmes <ih...@be...> wrote: >> Now that we have a full-time gmod-ajax person (in the form of Mitch) >> it's probably about time to kick off a discussion on how to move towards >> our goals of community annotation (and what this means exactly) and full >> browser functionality including search, rich display, etc (and to what >> extent this should be GBrowse-like). >> >> Chris, Andrew and I had a tete-a-tete a couple of months ago in which we >> scribbled some notes on the back of an envelope (or coffeeshop napkin). >> Andrew, do you have that napkin anywhere? Could we start by reprising >> those? I am running out the door right now but could dredge up my memory >> of the meeting if necessary. >> >> One thing is that Mitch is away for a week or so. So probably the >> discussion will have to wait a little while for him to get back, before >> it gets really productive. >> >> I. >> >> >> >> Chris Mungall wrote: >>> Hi Xianhua >>> >>> Note there is now a gmod-ajax list too. >>> >>> I think a RESTFUL architecture makes a lot of sense for an AJAX >>> application. >>> >>> By the way, I think you mean "Chado". (try a google search for >>> "define: chode" - I do hope chode doesn't catch on as another Chado >>> mispronounciation!). >>> >>> On Jan 18, 2007, at 7:47 AM, Xianhua Liu wrote: >>> >>>> I am trying to build web interface to query and view data from >>>> Chode with extension schema for bio-diversity data. I am planning >>>> to use a 4-lawyer architecture as following: >>>> >>>> 1. AJAX: front-end >>>> 2. WebService: web lawyer >>>> 3. XXX: Middleware >>>> 4. Chode: back-end >>>> >>>> Why WebService? >>>> 1. independency of front-end on middleware. >>>> 2. loose coupling >>>> 3. easy data integration over web >>>> 4. ... >>>> >>>> Challenges: >>>> 1. standardization of web service interface >>>> 2. federalization of data representation model exchanged through >>>> the web service (XML Schema, Ontology, ...?) >>>> 3. Performance? >>>> >>>> RESTful or SOAP: >>>> I prefer to choose RESTful web service, because it is easy, direct >>>> and light. >>>> >>>> If someone have already tried the same and similar thing, please >>>> share your experience and lessons and tech choises. >>>> >>>> Welcome every one to send comments about the idea, and suggestions >>>> about techniques, software packages and any other sources. >>>> >>>> Thanks, >>>> >>>> Xianhua >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> --- >>>> Take Surveys. Earn Cash. Influence the Future of IT >>>> Join SourceForge.net's Techsay panel and you'll get the chance to >>>> share your >>>> opinions on IT & business topics through brief surveys - and earn cash >>>> http://www.techsay.com/default.php? >>>> page=join.php&p=sourceforge&CID=DEVDEV________________________________ >>>> _______________ >>>> Gmod-architecture mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-architecture >>> >>> ------------------------------------------------------------------------- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to share your >>> opinions on IT & business topics through brief surveys - and earn cash >>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to share your >> opinions on IT & business topics through brief surveys - and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Mitch S. <li...@ar...> - 2007-01-27 19:50:21
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On Fri, 2007-01-19 at 11:20 +1100, Ian Holmes wrote: > Now that we have a full-time gmod-ajax person (in the form of Mitch) > it's probably about time to kick off a discussion on how to move towards > our goals of community annotation (and what this means exactly) and full > browser functionality including search, rich display, etc (and to what > extent this should be GBrowse-like). As far as community annotation goes, I'm going to try and summarize the different things I've heard and read and thought so far. Hopefully this is not retreading heavily covered ground too much - There are three kinds of community annotation that have been talked about: 1. Bulk annotation upload. Lots of people have GFF/BED/etc. files that they'd like to see rendered. We ought to make this dead simple. Existing examples include Santa Cruz's upload functionality: http://genome.ucsc.edu/cgi-bin/hgCustom and GBrowse's: http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/htdocs/annotation_help.html As I see it, the fundamental difference between "annotation upload" as currently implemented and "community annotation" like Ian's talking about above is that with annotation upload the uploader is the only one looking at their annotations, while with community annotation potentially everyone else is looking at them as well. This immediately raises a number of questions, like how to manage all the uploaded tracks. These will obviously vary in usefulness, and we don't want to clutter up the display too much; on the other hand we don't want to make people pick from a huge list as a prerequisite to using the browser. This suggests that we'll want to have a list of "blessed" or "default" tracks, but then you have the problem of choosing those. Or we could have a track ranking mechanism where we show the top n highest ranked tracks, but then we have the problem of coming up with the track rankings. One option would be a moderation system (e.g., "Digg this track [+/-]"). In the fancy extreme we could even have a collaborative filtering mechanism where we "recommend" tracks to people based on their previous moderations. In any case, making annotation upload work is a prerequisite to everything else, so that's the first priority IMO. The main things we have to do differently from current annotation upload are kicking off a pre-rendering or primitive database fill operation and coming up with some way of notifying the user when their track is ready to view. Anything else? 2. Individual feature creation/editing. It would be neat to be able to "draw" and "resize" features by clicking and dragging with the mouse. I believe this is possible to do in the browser, but it is fairly fancy and might be difficult to do in a cross-browser way. Suzi Lewis and Chris Mungall at Berkeley BOP seem to think that this need is adequately served by fatter clients like Apollo. Can anyone think of a use case where someone would want to be able to adjust feature boundaries but would be a casual enough user to not want to install Apollo? I would imagine that most people who want to e.g. edit gene models would be involved enough to install some software but my experience here is limited. If no one can come up with a compelling use case for having this on a web browser I'd be tempted to leave this out entirely, or at least leave it until the other community annotation things are implemented. 3. Feature "commenting". Not sure what to call this (annotation annotation?), but I'm sure there are lots of biologists out there who know a lot about a relatively small number of genes. This is the kind of knowledge that wouldn't be a good fit for creating an entire track with (so it doesn't fit well into the bulk annotation upload mechanism), but would work better for adding information about features on an existing track. Examples that I can imagine include adding GO terms to existing annotations, adding information about where a certain gene is expressed, what pathways a gene is involved in, literature references, etc. Some of these things could be stored in Chado (how much?) but in general the kinds of information that would go here are hard to predict IMO, so I'd like to have the option of storing it in something less structured. On the unstructured side, we could have a wiki with a page for each gene, transcript, protein, whatever. One moderately-structured option would be to use a semantic wiki like Semantic MediaWiki: http://wiki.ontoworld.org/index.php/Semantic_MediaWiki I like the idea of having this information available in RDF, and the URI-based named attribute and typed link structure fits fairly well with the DAS/2 feature/prop mechanism AFAICS. In the short term I'm thinking of generating a semantic wiki page for each annotation (directly from Chado or using Bio::DB) and having that be (one of) the link(s) in the feature mouseover popup. Per the discussion here from last November, I'd like to implement those popups with DAS/2, which ought to be reasonably straightforward to access from javascript. I'll be putting this up as a page on biowiki.org and updating it with any discussion from the list. Regards, Mitch |
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From: Ian H. <ih...@be...> - 2007-02-01 04:10:55
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Thanks for this Mitch. As you say, my opinion is that we should get (crude) prototypes of community annotation and search working quickly (ideally by, say, RECOMB), if only because people can clearly SEE that we are working on GUI development, but community annotation (in particular) is currently just a twinkle in the eye (or, less prosaically, a few lines in a grant proposal). If we can get something even quite simple going, like UCSC-style GFF/BED upload, I think it will really help in providing some direction. I'm inclined to agree that drawing features on the genome is difficult to do well & better served by Apollo etc, although I don't really know enough about who uses GMOD to understand the use case. I recall Lincoln was into this at one point so perhaps he has some idea. Can you let us know when you've posted this email up on a biowiki page... I suggest we try to set a date to talk about this stuff in more detail on a GMOD conference call -- ideally in a couple of weeks or so when I'm back in Berkeley (so I don't have to get up at some bleary-eyed hour in order to participate from Australia) cheers Ian Mitch Skinner wrote: > On Fri, 2007-01-19 at 11:20 +1100, Ian Holmes wrote: >> Now that we have a full-time gmod-ajax person (in the form of Mitch) >> it's probably about time to kick off a discussion on how to move towards >> our goals of community annotation (and what this means exactly) and full >> browser functionality including search, rich display, etc (and to what >> extent this should be GBrowse-like). > > As far as community annotation goes, I'm going to try and summarize the > different things I've heard and read and thought so far. Hopefully this > is not retreading heavily covered ground too much - > > There are three kinds of community annotation that have been talked > about: > 1. Bulk annotation upload. Lots of people have GFF/BED/etc. files that > they'd like to see rendered. We ought to make this dead simple. > Existing examples include Santa Cruz's upload functionality: > http://genome.ucsc.edu/cgi-bin/hgCustom > and GBrowse's: > http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/htdocs/annotation_help.html > > As I see it, the fundamental difference between "annotation upload" as > currently implemented and "community annotation" like Ian's talking > about above is that with annotation upload the uploader is the only one > looking at their annotations, while with community annotation > potentially everyone else is looking at them as well. > > This immediately raises a number of questions, like how to manage all > the uploaded tracks. These will obviously vary in usefulness, and we > don't want to clutter up the display too much; on the other hand we > don't want to make people pick from a huge list as a prerequisite to > using the browser. This suggests that we'll want to have a list of > "blessed" or "default" tracks, but then you have the problem of choosing > those. Or we could have a track ranking mechanism where we show the top > n highest ranked tracks, but then we have the problem of coming up with > the track rankings. One option would be a moderation system (e.g., > "Digg this track [+/-]"). In the fancy extreme we could even have a > collaborative filtering mechanism where we "recommend" tracks to people > based on their previous moderations. > > In any case, making annotation upload work is a prerequisite to > everything else, so that's the first priority IMO. The main things we > have to do differently from current annotation upload are kicking off a > pre-rendering or primitive database fill operation and coming up with > some way of notifying the user when their track is ready to view. > Anything else? > > 2. Individual feature creation/editing. It would be neat to be able to > "draw" and "resize" features by clicking and dragging with the mouse. I > believe this is possible to do in the browser, but it is fairly fancy > and might be difficult to do in a cross-browser way. Suzi Lewis and > Chris Mungall at Berkeley BOP seem to think that this need is adequately > served by fatter clients like Apollo. Can anyone think of a use case > where someone would want to be able to adjust feature boundaries but > would be a casual enough user to not want to install Apollo? I would > imagine that most people who want to e.g. edit gene models would be > involved enough to install some software but my experience here is > limited. If no one can come up with a compelling use case for having > this on a web browser I'd be tempted to leave this out entirely, or at > least leave it until the other community annotation things are > implemented. > > 3. Feature "commenting". Not sure what to call this (annotation > annotation?), but I'm sure there are lots of biologists out there who > know a lot about a relatively small number of genes. This is the kind > of knowledge that wouldn't be a good fit for creating an entire track > with (so it doesn't fit well into the bulk annotation upload mechanism), > but would work better for adding information about features on an > existing track. Examples that I can imagine include adding GO terms to > existing annotations, adding information about where a certain gene is > expressed, what pathways a gene is involved in, literature references, > etc. Some of these things could be stored in Chado (how much?) but in > general the kinds of information that would go here are hard to predict > IMO, so I'd like to have the option of storing it in something less > structured. > > On the unstructured side, we could have a wiki with a page for each > gene, transcript, protein, whatever. One moderately-structured option > would be to use a semantic wiki like Semantic MediaWiki: > http://wiki.ontoworld.org/index.php/Semantic_MediaWiki > I like the idea of having this information available in RDF, and the > URI-based named attribute and typed link structure fits fairly well with > the DAS/2 feature/prop mechanism AFAICS. > > In the short term I'm thinking of generating a semantic wiki page for > each annotation (directly from Chado or using Bio::DB) and having that > be (one of) the link(s) in the feature mouseover popup. Per the > discussion here from last November, I'd like to implement those popups > with DAS/2, which ought to be reasonably straightforward to access from > javascript. > > I'll be putting this up as a page on biowiki.org and updating it with > any discussion from the list. > > Regards, > Mitch > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Mitch S. <mit...@be...> - 2007-02-06 02:06:10
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Ian Holmes wrote: > Can you let us know when you've posted this email up on a biowiki page... > I finally did this: http://biowiki.org/view/GBrowse/CommunityAnnotation Mitch |
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