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From: Scott C. <sc...@sc...> - 2016-10-26 15:34:12
|
Hi Shane, The loader module, lib/Bio/GMOD/DB/Adaptor.pm, is quite old and uses an ugly idiom that I'd rather not talk about but it's use has be deprecated in modern Perl. I don't have a working instance of Chado I can test with handy (later in the week I could spin something up on AWS, but I don't have time now), but I did commit this to github if you want to try it out: https://raw.githubusercontent.com/GMOD/Chado/fix_shift_if_defined/chado/lib/Bio/GMOD/DB/Adapter.pm Just download this and replace the one it's complaining about in /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm. Also, you won't be able to load the Relations Ontology via the make command. You'll need to download http://purl.obolibrary.org/obo/ro/subsets/ro-chado.obo and use the commands described in INSTALL.Chado. In brief: $ go2fmt.pl -p obo_text -w xml /path/to/obofile | \ go-apply-xslt oboxml_to_chadoxml - > obo_text.xml and $ stag-storenode.pl \ -d 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT' \ --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml Depending on how you installed DBIx::DBStag, the ".pl" on stag-storenode.pl might have to be removed. Good luck! Scott On Wed, Oct 26, 2016 at 8:57 AM, Shane McCoy <sha...@gm...> wrote: > > > Hello, > Using Chado VERSION=1.31 > I am getting this error when using the gmod bulk load for Chado: > >> $ gmod_bulk_load_gff3.pl --noexon --analysis --organism "stripedbass" --gfffile SBDraft_Full.nodna.gff --dbname apollo-db >> Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 498. >> Compilation failed in require at /usr/local/bin/gmod_bulk_load_gff3.pl line 13. >> BEGIN failed--compilation aborted at /usr/local/bin/ gmod_bulk_load_gff3.pl line 13. > > > I have bioperl 1.006925 installed. I did see that the make ontologies fails now, >> >> Which ontologies would you like to load (Comma delimited)? [0] 1,2,3,4 >> fetching files for Relationship Ontology >> +http://www.obofoundry.org/ro/ro.obo >> 404 Not Found (http://www.obofoundry.org/ro/ro.obo) >> fetching files for Sequence Ontology > > > I am using the https://cpt.tamu.edu/computer-resources/chado-prebuilt-schema/ recommended sql for this build. > > Any thoughts why this is failing? Thanks! > Shane M. > > > > > ------------------------------------------------------------------------------ > The Command Line: Reinvented for Modern Developers > Did the resurgence of CLI tooling catch you by surprise? > Reconnect with the command line and become more productive. > Learn the new .NET and ASP.NET CLI. Get your free copy! > http://sdm.link/telerik > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Shane M. <sha...@gm...> - 2016-10-26 12:57:59
|
Hello, Using Chado VERSION=1.31 I am getting this error when using the gmod bulk load for Chado: $ *gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> --noexon > --analysis --organism "stripedbass" --gfffile SBDraft_Full.nodna.gff > --dbname apollo-db* > Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at > /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 498. > > *Compilation failed in require at /usr/local/bin/gmod_bulk_load_gff3.pl > <http://gmod_bulk_load_gff3.pl> line 13.BEGIN failed--compilation aborted > at /usr/local/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> > line 13.* I have bioperl 1.006925 installed. I did see that the *make ontologies* fails now, > Which ontologies would you like to load (Comma delimited)? [0] *1,2,3,4* > fetching files for Relationship Ontology > +http://www.obofoundry.org/ro/ro.obo > 404 Not Found (http://www.obofoundry.org/ro/ro.obo) > fetching files for Sequence Ontology I am using the https://cpt.tamu.edu/computer-resources/chado-prebuilt-schema/ <https://cpt.tamu.edu/computer-resources/chado-prebuilt-schema/> recommended sql for this build. Any thoughts why this is failing? Thanks! Shane M. |
From: Stephen F. <spf...@gm...> - 2016-10-03 17:40:44
|
Hi Naama, That sounds like a good idea. Scott, any thoughts on starting up a new round of v1.4 Chado discussions? Stephen On 9/28/2016 8:57 AM, Naama Menda wrote: > this sounds good to me. > > I think we should have a dbpatch system, we could write every schema > change in a short SQL file, and then when all the changes are > officially in a new chado version all the new DDLs would go into one file > > -Naama > > > > Naama Menda > Boyce Thompson Institute for Plant Research > Tower Rd > Ithaca NY 14853 > USA > > (607) 254 3569 > Sol Genomics Network > http://solgenomics.net/ > nm...@co... <mailto:nm...@co...> > > On Wed, Sep 28, 2016 at 11:53 AM Stephen Ficklin <spf...@gm... > <mailto:spf...@gm...>> wrote: > > Hi Naama, > > I think the change is good. > > For us to not lose track of changes in Chado (for Tripal > compatibility) I think now might be a good time to define a formal > process for documenting, reviewing, accepting and incorporating > any change to Chado. > > We do have a good number of items left over from our Chado v1.3 > suggested changes document that we decided to push off to v1.4. > Perhaps we should restart that document, and maybe a new round of > discussions for v1.4 and add the nd_protocol.description column as > one of the items? > > Stephen > > > On 9/28/2016 8:42 AM, Naama Menda wrote: >> this table has just id and name fields. >> We would like to add a 'description' column >> This is similar to the DDL of other tables, such as db, project, >> genotype, and others. >> >> If there is no objection, I'll add the SQL >> >> thanks, >> -Naama >> >> >> Naama Menda >> Boyce Thompson Institute for Plant Research >> Tower Rd >> Ithaca NY 14853 >> USA >> >> (607) 254 3569 >> Sol Genomics Network >> http://solgenomics.net/ >> nm...@co... <mailto:nm...@co...> >> >> >> ------------------------------------------------------------------------------ >> >> >> _______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> <mailto:Gmo...@li...> >> https://lists.sourceforge.net/lists/listinfo/gmod-schema > |
From: Chris M. <cjm...@lb...> - 2016-09-28 23:36:46
|
On 12 Sep 2016, at 5:26, Brian Repko wrote: > Hi Chris, > > My understanding is that JSON is a representation of an object tree, > adding JSON Pointer gets you an object graph. Yes, technically it's a graph layered on a tree (json) representation > I guess what I'm asking is - what are the objects being represented? > Will they be nodes and edges or will they be terms and typedefs? In Chado terms, the nodes are terms and typedefs > If nodes and edges, then the model is some form of a graph model and > there probably isn't a need for a JSON Schema. > But if the objects modeled are terms and typedefs then you could also > make use of JSON Schema for that as well. > It's almost like GMOD Chado (cv module) is obo-relational-database - > which could be represented in JSON (tables/columns). > You have a obo-graph-model - represented in JSON. Perhaps, I'm what > I'm > thinking of is an obo-json project. ;-) Yes, that would have been equally good a name for it (though there is a structurally equivalent YAML if you want it) > I don't have super deep knowledge of the OBO model itself so please > forgive me if I'm missing something. > Didn't mean to criticize the project, I am just trying to understand > it's goals/vision. No worries, thanks > Cheers, > -brian > > ----- Original message ----- > From: Chris Mungall <cjm...@lb...> > To: Brian Repko <bri...@le...> > Cc: "gmod-schema List" <gmo...@li...> > Subject: Re: [Gmod-schema] obographs JSON > Date: Sun, 11 Sep 2016 16:20:12 -0700 > > Yes, it could. The oboformat library is a very direct translation of > OBO > syntax - it's not very convenient, but probably not too bad for the > purposes of writing a chado loader. And if what you have works there > is > no reason to rewrite it. > Although not sure I understand the last part: obographs give you the > convenience of JSON (no need for a special parser) but at the same > time, > it's graph oriented, in the way the cvterm_relationship table is. > > On Mon, Sep 5, 2016 at 12:03 PM, Brian Repko > <bri...@le...> wrote: >> __ >> Our use case is also a bit different as well since we have GMOD Chado >> as converted to Java / Liquibase (for mulitiple database support). We >> load obo files with BBOP's oboformat library. This gives us access to >> Term and Typedef objects directly and the data within them. Could >> obograph support that kind of model but in JSON vs a graph-oriented >> node/edge model? >> >> -brian >> >> ----- Original message ----- >> From: Scott Cain <sc...@sc...> >> To: Chris Mungall <cjm...@lb...> >> Cc: gmod tripal devel <gmo...@li...>, >> "GMOD >> Schema/Chado List" <gmo...@li...> >> Subject: Re: [Gmod-schema] obographs JSON >> Date: Fri, 2 Sep 2016 11:05:39 -0400 >> >> I think there a probably some people (besides me) using stag- >> storenode, but probably not many. The majority of Chado users these >> days are using Tripal, so we'd want to see the current Tripal >> ontology >> loader updated as well. I cc'ed the dev list to make sure they're >> aware of it too (though I imagine they're all on the Chado list too). >> >> >> On Fri, Sep 2, 2016 at 7:38 AM, Chris Mungall >> <cjm...@lb...> wrote: >>> >>> For a while there has been a need of a developer-friendly >>> replacement >>> for OBO format. While advanced applications should target OWL, >>> there a >>> number of things that make direct OWL consumption developer- >>> unfriendly >>> (especially perl and python developers) >>> >>> We have come up with a proposed JSON representation that is >>> intended to >>> have the simplicity of OBO, with optional extensions for advanced >>> OWL >>> axioms - in JSON or YAML: >>> https://github.com/geneontology/obographs >>> >>> The intent is for any replacements for stage-storenode.pl to >>> target this >>> (I'm not up to date on what people are currently using) >>> >>> It shouldn't be regarded as stable yet - I'd like feedback from >>> the GMOD >>> community first. Please email here or use the issue tracker with any >>> comments, thanks! >>> >>> --------------------------------------------------------------------- >>> --------- >>> _______________________________________________ >>> Gmod-schema mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema >>> >> >> >> >> >> -- >> ---------------------------------------------------------------- >> -------- >> Scott Cain, Ph. D. scott at >> scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> >> ---------------------------------------------------------------------- >> -------- >> _________________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> >> >> ---------------------------------------------------------------------- >> -------- >> >> _______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> |
From: Naama M. <nm...@co...> - 2016-09-28 15:57:55
|
this sounds good to me. I think we should have a dbpatch system, we could write every schema change in a short SQL file, and then when all the changes are officially in a new chado version all the new DDLs would go into one file -Naama Naama Menda Boyce Thompson Institute for Plant Research Tower Rd Ithaca NY 14853 USA (607) 254 3569 Sol Genomics Network http://solgenomics.net/ nm...@co... On Wed, Sep 28, 2016 at 11:53 AM Stephen Ficklin <spf...@gm...> wrote: > Hi Naama, > > I think the change is good. > > For us to not lose track of changes in Chado (for Tripal compatibility) I > think now might be a good time to define a formal process for documenting, > reviewing, accepting and incorporating any change to Chado. > > We do have a good number of items left over from our Chado v1.3 suggested > changes document that we decided to push off to v1.4. Perhaps we should > restart that document, and maybe a new round of discussions for v1.4 and > add the nd_protocol.description column as one of the items? > > Stephen > > On 9/28/2016 8:42 AM, Naama Menda wrote: > > this table has just id and name fields. > We would like to add a 'description' column > This is similar to the DDL of other tables, such as db, project, genotype, > and others. > > If there is no objection, I'll add the SQL > > thanks, > -Naama > > > Naama Menda > Boyce Thompson Institute for Plant Research > Tower Rd > Ithaca NY 14853 > USA > > (607) 254 3569 > Sol Genomics Network > http://solgenomics.net/ > nm...@co... > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > Gmod-schema mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > |
From: Stephen F. <spf...@gm...> - 2016-09-28 15:53:54
|
Hi Naama, I think the change is good. For us to not lose track of changes in Chado (for Tripal compatibility) I think now might be a good time to define a formal process for documenting, reviewing, accepting and incorporating any change to Chado. We do have a good number of items left over from our Chado v1.3 suggested changes document that we decided to push off to v1.4. Perhaps we should restart that document, and maybe a new round of discussions for v1.4 and add the nd_protocol.description column as one of the items? Stephen On 9/28/2016 8:42 AM, Naama Menda wrote: > this table has just id and name fields. > We would like to add a 'description' column > This is similar to the DDL of other tables, such as db, project, > genotype, and others. > > If there is no objection, I'll add the SQL > > thanks, > -Naama > > > Naama Menda > Boyce Thompson Institute for Plant Research > Tower Rd > Ithaca NY 14853 > USA > > (607) 254 3569 > Sol Genomics Network > http://solgenomics.net/ > nm...@co... <mailto:nm...@co...> > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema |
From: Naama M. <nm...@co...> - 2016-09-28 15:42:46
|
this table has just id and name fields. We would like to add a 'description' column This is similar to the DDL of other tables, such as db, project, genotype, and others. If there is no objection, I'll add the SQL thanks, -Naama Naama Menda Boyce Thompson Institute for Plant Research Tower Rd Ithaca NY 14853 USA (607) 254 3569 Sol Genomics Network http://solgenomics.net/ nm...@co... |
From: Scott C. <sc...@sc...> - 2016-09-23 15:12:43
|
Hello Genome Informaticians, The following survey is aimed at users (and potential users) of GMOD genome databases, especially the JBrowse genome browser. It will directly inform the priorities for renewal of the R01 that funds JBrowse software development and the GMOD helpdesk. We know surveys are thankless and dull. Your time in filling out this one is GREATLY appreciated. https://goo.gl/forms/1bKIuAMjGKrS0hUi1 Thanks & best wishes, The JBrowse team -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Brian R. <bri...@le...> - 2016-09-12 12:27:04
|
Hi Chris, My understanding is that JSON is a representation of an object tree, adding JSON Pointer gets you an object graph. I guess what I'm asking is - what are the objects being represented? Will they be nodes and edges or will they be terms and typedefs? If nodes and edges, then the model is some form of a graph model and there probably isn't a need for a JSON Schema. But if the objects modeled are terms and typedefs then you could also make use of JSON Schema for that as well. It's almost like GMOD Chado (cv module) is obo-relational-database - which could be represented in JSON (tables/columns). You have a obo-graph-model - represented in JSON. Perhaps, I'm what I'm thinking of is an obo-json project. ;-) I don't have super deep knowledge of the OBO model itself so please forgive me if I'm missing something. Didn't mean to criticize the project, I am just trying to understand it's goals/vision. Cheers, -brian ----- Original message ----- From: Chris Mungall <cjm...@lb...> To: Brian Repko <bri...@le...> Cc: "gmod-schema List" <gmo...@li...> Subject: Re: [Gmod-schema] obographs JSON Date: Sun, 11 Sep 2016 16:20:12 -0700 Yes, it could. The oboformat library is a very direct translation of OBO syntax - it's not very convenient, but probably not too bad for the purposes of writing a chado loader. And if what you have works there is no reason to rewrite it. Although not sure I understand the last part: obographs give you the convenience of JSON (no need for a special parser) but at the same time, it's graph oriented, in the way the cvterm_relationship table is. On Mon, Sep 5, 2016 at 12:03 PM, Brian Repko <bri...@le...> wrote: > __ > Our use case is also a bit different as well since we have GMOD Chado > as converted to Java / Liquibase (for mulitiple database support). We > load obo files with BBOP's oboformat library. This gives us access to > Term and Typedef objects directly and the data within them. Could > obograph support that kind of model but in JSON vs a graph-oriented > node/edge model? > > -brian > > ----- Original message ----- > From: Scott Cain <sc...@sc...> > To: Chris Mungall <cjm...@lb...> > Cc: gmod tripal devel <gmo...@li...>, "GMOD > Schema/Chado List" <gmo...@li...> > Subject: Re: [Gmod-schema] obographs JSON > Date: Fri, 2 Sep 2016 11:05:39 -0400 > > I think there a probably some people (besides me) using stag- > storenode, but probably not many. The majority of Chado users these > days are using Tripal, so we'd want to see the current Tripal ontology > loader updated as well. I cc'ed the dev list to make sure they're > aware of it too (though I imagine they're all on the Chado list too). > > > On Fri, Sep 2, 2016 at 7:38 AM, Chris Mungall > <cjm...@lb...> wrote: >> >> For a while there has been a need of a developer-friendly replacement >> for OBO format. While advanced applications should target OWL, >> there a >> number of things that make direct OWL consumption developer- >> unfriendly >> (especially perl and python developers) >> >> We have come up with a proposed JSON representation that is >> intended to >> have the simplicity of OBO, with optional extensions for advanced OWL >> axioms - in JSON or YAML: >> https://github.com/geneontology/obographs >> >> The intent is for any replacements for stage-storenode.pl to >> target this >> (I'm not up to date on what people are currently using) >> >> It shouldn't be regarded as stable yet - I'd like feedback from >> the GMOD >> community first. Please email here or use the issue tracker with any >> comments, thanks! >> >> --------------------------------------------------------------------- >> --------- >> _______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> > > > > > -- > ---------------------------------------------------------------- > -------- > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > ---------------------------------------------------------------------- > -------- > _________________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > ---------------------------------------------------------------------- > -------- > > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > |
From: Chris M. <cjm...@lb...> - 2016-09-11 23:20:23
|
Yes, it could. The oboformat library is a very direct translation of OBO syntax - it's not very convenient, but probably not too bad for the purposes of writing a chado loader. And if what you have works there is no reason to rewrite it. Although not sure I understand the last part: obographs give you the convenience of JSON (no need for a special parser) but at the same time, it's graph oriented, in the way the cvterm_relationship table is. On Mon, Sep 5, 2016 at 12:03 PM, Brian Repko <bri...@le... > wrote: > Our use case is also a bit different as well since we have GMOD Chado as > converted to Java / Liquibase (for mulitiple database support). We load obo > files with BBOP's oboformat library. This gives us access to Term and > Typedef objects directly and the data within them. Could obograph support > that kind of model but in JSON vs a graph-oriented node/edge model? > > -brian > > ----- Original message ----- > From: Scott Cain <sc...@sc...> > To: Chris Mungall <cjm...@lb...> > Cc: gmod tripal devel <gmo...@li...>, "GMOD > Schema/Chado List" <gmo...@li...> > Subject: Re: [Gmod-schema] obographs JSON > Date: Fri, 2 Sep 2016 11:05:39 -0400 > > I think there a probably some people (besides me) using stag-storenode, > but probably not many. The majority of Chado users these days are using > Tripal, so we'd want to see the current Tripal ontology loader updated as > well. I cc'ed the dev list to make sure they're aware of it too (though I > imagine they're all on the Chado list too). > > > On Fri, Sep 2, 2016 at 7:38 AM, Chris Mungall <cjm...@lb...> wrote: > > > For a while there has been a need of a developer-friendly replacement > for OBO format. While advanced applications should target OWL, there a > number of things that make direct OWL consumption developer-unfriendly > (especially perl and python developers) > > We have come up with a proposed JSON representation that is intended to > have the simplicity of OBO, with optional extensions for advanced OWL > axioms - in JSON or YAML: > https://github.com/geneontology/obographs > > The intent is for any replacements for stage-storenode.pl to target this > (I'm not up to date on what people are currently using) > > It shouldn't be regarded as stable yet - I'd like feedback from the GMOD > community first. Please email here or use the issue tracker with any > comments, thanks! > > ------------------------------------------------------------ > ------------------ > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > ------------------------------------------------------------ > ------------------ > *_______________________________________________* > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > |
From: Brian R. <bri...@le...> - 2016-09-05 19:23:08
|
Our use case is also a bit different as well since we have GMOD Chado as converted to Java / Liquibase (for mulitiple database support). We load obo files with BBOP's oboformat library. This gives us access to Term and Typedef objects directly and the data within them. Could obograph support that kind of model but in JSON vs a graph-oriented node/edge model? -brian ----- Original message ----- From: Scott Cain <sc...@sc...> To: Chris Mungall <cjm...@lb...> Cc: gmod tripal devel <gmo...@li...>, "GMOD Schema/Chado List" <gmo...@li...> Subject: Re: [Gmod-schema] obographs JSON Date: Fri, 2 Sep 2016 11:05:39 -0400 I think there a probably some people (besides me) using stag-storenode, but probably not many. The majority of Chado users these days are using Tripal, so we'd want to see the current Tripal ontology loader updated as well. I cc'ed the dev list to make sure they're aware of it too (though I imagine they're all on the Chado list too). On Fri, Sep 2, 2016 at 7:38 AM, Chris Mungall <cjm...@lb...> wrote: > > For a while there has been a need of a developer-friendly replacement > for OBO format. While advanced applications should target OWL, > there a > number of things that make direct OWL consumption developer- > unfriendly > (especially perl and python developers) > > We have come up with a proposed JSON representation that is > intended to > have the simplicity of OBO, with optional extensions for advanced OWL > axioms - in JSON or YAML: > https://github.com/geneontology/obographs > > The intent is for any replacements for stage-storenode.pl to > target this > (I'm not up to date on what people are currently using) > > It shouldn't be regarded as stable yet - I'd like feedback from > the GMOD > community first. Please email here or use the issue tracker with any > comments, thanks! > > --------------------------------------------------------------------- > --------- > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -------------------------------------------------------------------- ---------- _________________________________________________ Gmod-schema mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-schema |
From: Scott C. <sc...@sc...> - 2016-09-02 15:05:49
|
I think there a probably some people (besides me) using stag-storenode, but probably not many. The majority of Chado users these days are using Tripal, so we'd want to see the current Tripal ontology loader updated as well. I cc'ed the dev list to make sure they're aware of it too (though I imagine they're all on the Chado list too). On Fri, Sep 2, 2016 at 7:38 AM, Chris Mungall <cjm...@lb...> wrote: > > For a while there has been a need of a developer-friendly replacement > for OBO format. While advanced applications should target OWL, there a > number of things that make direct OWL consumption developer-unfriendly > (especially perl and python developers) > > We have come up with a proposed JSON representation that is intended to > have the simplicity of OBO, with optional extensions for advanced OWL > axioms - in JSON or YAML: > https://github.com/geneontology/obographs > > The intent is for any replacements for stage-storenode.pl to target this > (I'm not up to date on what people are currently using) > > It shouldn't be regarded as stable yet - I'd like feedback from the GMOD > community first. Please email here or use the issue tracker with any > comments, thanks! > > ------------------------------------------------------------ > ------------------ > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Chris M. <cjm...@lb...> - 2016-09-02 11:38:37
|
For a while there has been a need of a developer-friendly replacement for OBO format. While advanced applications should target OWL, there a number of things that make direct OWL consumption developer-unfriendly (especially perl and python developers) We have come up with a proposed JSON representation that is intended to have the simplicity of OBO, with optional extensions for advanced OWL axioms - in JSON or YAML: https://github.com/geneontology/obographs The intent is for any replacements for stage-storenode.pl to target this (I'm not up to date on what people are currently using) It shouldn't be regarded as stable yet - I'd like feedback from the GMOD community first. Please email here or use the issue tracker with any comments, thanks! |
From: Stephen F. <spf...@gm...> - 2016-06-14 03:33:43
|
Hi All, FYI.... Tripal has a new Twitter account (with a nod to GMOD): https://twitter.com/TripalProject. We'll post updates, announcements and interesting things Tripal related for those interested. Stephen |
From: Cannon, E. K [C. S] <ekc...@ia...> - 2016-06-02 20:06:58
|
Thanks Chris and Pankaj! I had just arrived at the sinking realization about part 1 below literally seconds before your notes arrived. Not a trivial task, and not one I want to attempt independently of the Planteome project. Ethy ________________________________________ From: Jaiswal, Pankaj - OSU <jai...@sc...> Sent: Thursday, June 2, 2016 2:39 PM To: Chris Mungall; Cannon, Ethalinda K [COM S] Cc: gmo...@li...; gmo...@li... Subject: Re: [Gmod-schema] GRIN into Chado On 6/2/2016 12:30 PM, Chris Mungall wrote: > Hi Ethy, > > I believe there are two parts here > > 1. Extracting relevant info for GRIN, including mapping their > descriptors onto TO terms > 2. Loading this into Chado > > I believe the bulk of the work would be in 1. This is something we > have been looking into in the Planteome project. Pankaj, is this > something we're going to tackle soon? We don't want to duplicate > effort here > Yes. As soon as Plant Disease work is done by Jorrit, he can move on to mapping GRIN descriptors. Pankaj > Once 1 is done, it can pipe the results to 2 in a format like GAF or > Phenopackets (phenopackets.org). There is a GAF loader for Chado, but > no phenopackets one yet. Either way part 2 should be turning the handle. > > On 2 Jun 2016, at 11:48, Cannon, Ethalinda K [COM S] wrote: > >> Has anyone tried loading GRIN data into Chado? I seem to recall >> mention of this having been done or planned to be done, but don't >> remember by whom. >> >> >> Ethy >> >> ------------------------------------------------------------------------------ >> >> What NetFlow Analyzer can do for you? Monitors network bandwidth and >> traffic >> patterns at an interface-level. Reveals which users, apps, and >> protocols are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning reports. >> https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema -- Pankaj Jaiswal, PhD Associate Professor Dept. of Botany and Plant Pathology 2082 Cordley Hall Oregon State University Corvallis, OR, 97331 USA Ph.: +1-541-737-8471 Fax: +1-541-737-3573 email: jai...@or... Web: http://jaiswallab.cgrb.oregonstate.edu http://icbo-conference.org |
From: Jaiswal, P. - O. <jai...@sc...> - 2016-06-02 19:54:21
|
On 6/2/2016 12:30 PM, Chris Mungall wrote: > Hi Ethy, > > I believe there are two parts here > > 1. Extracting relevant info for GRIN, including mapping their > descriptors onto TO terms > 2. Loading this into Chado > > I believe the bulk of the work would be in 1. This is something we > have been looking into in the Planteome project. Pankaj, is this > something we're going to tackle soon? We don't want to duplicate > effort here > Yes. As soon as Plant Disease work is done by Jorrit, he can move on to mapping GRIN descriptors. Pankaj > Once 1 is done, it can pipe the results to 2 in a format like GAF or > Phenopackets (phenopackets.org). There is a GAF loader for Chado, but > no phenopackets one yet. Either way part 2 should be turning the handle. > > On 2 Jun 2016, at 11:48, Cannon, Ethalinda K [COM S] wrote: > >> Has anyone tried loading GRIN data into Chado? I seem to recall >> mention of this having been done or planned to be done, but don't >> remember by whom. >> >> >> Ethy >> >> ------------------------------------------------------------------------------ >> >> What NetFlow Analyzer can do for you? Monitors network bandwidth and >> traffic >> patterns at an interface-level. Reveals which users, apps, and >> protocols are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning reports. >> https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema -- Pankaj Jaiswal, PhD Associate Professor Dept. of Botany and Plant Pathology 2082 Cordley Hall Oregon State University Corvallis, OR, 97331 USA Ph.: +1-541-737-8471 Fax: +1-541-737-3573 email: jai...@or... Web: http://jaiswallab.cgrb.oregonstate.edu http://icbo-conference.org |
From: Chris M. <cjm...@lb...> - 2016-06-02 19:31:05
|
Hi Ethy, I believe there are two parts here 1. Extracting relevant info for GRIN, including mapping their descriptors onto TO terms 2. Loading this into Chado I believe the bulk of the work would be in 1. This is something we have been looking into in the Planteome project. Pankaj, is this something we're going to tackle soon? We don't want to duplicate effort here Once 1 is done, it can pipe the results to 2 in a format like GAF or Phenopackets (phenopackets.org). There is a GAF loader for Chado, but no phenopackets one yet. Either way part 2 should be turning the handle. On 2 Jun 2016, at 11:48, Cannon, Ethalinda K [COM S] wrote: > Has anyone tried loading GRIN data into Chado? I seem to recall > mention of this having been done or planned to be done, but don't > remember by whom. > > > Ethy > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and > protocols are > consuming the most bandwidth. Provides multi-vendor support for > NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. > https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema |
From: Cannon, E. K [C. S] <ekc...@ia...> - 2016-06-02 19:21:14
|
Has anyone tried loading GRIN data into Chado? I seem to recall mention of this having been done or planned to be done, but don't remember by whom. Ethy |
From: Naama M. <nm...@co...> - 2016-05-26 20:28:21
|
hi Chris, I can make the changes in git and send a pull request. These changes have been in the works for a couple of years now, but no one really wanted to touch the phenotype module until now. The idea is to separate phenotype values from the cvterms, as it is structured no in the phenotype table, allowing to store any number of cvterms linked with one phenotype value (using phenotype_cvterm) + adding the ability to group those cvterms if needed (phenotype_clause) The suggested schema is vary abstract, and the examples with EQ statements is just a use-case . It would work well for any post-composition of cvterms that describe a phenotype , quantitative or qualitative. So yes, we'd like to have flexible 'slots' for phnoetypes, and the type_id field in phenotype_cvterm is optional in cases such as making an EQ statement that requires indicating if the cvterm is PE1, PE2, etc. as shown in the example, or any other semantics that may be needed -Naama Naama Menda Boyce Thompson Institute for Plant Research Tower Rd Ithaca NY 14853 USA (607) 254 3569 Sol Genomics Network http://solgenomics.net/ nm...@co... On Thu, May 26, 2016 at 3:52 PM Chris Mungall <cjm...@lb...> wrote: > Thanks Naama > > Do you intend to make a pull request for the schema changes? I'm not sure > what the current GMOD policy is but this works well on other standards > projects, with stakeholders giving +1s etc, and having the discussion > linked to the commit trail > > If I could attempt a brief summary, sorry if this doesn't fully capture > it: you are moving from the old schema where phenotypes have a fixed number > of slots were available to a flexible number of slots. > > Standardization of the slot fields (what you have as PE1, PE2, etc) is key > to successful interoperability. There are a few options here. One way is to > use RO relations. Another way is to treat these as a different layer from > the biological object graph, and to treat them as slots that may have > different meanings in different contexts. > > This is actually quite well aligned with the Dead Simple OWL Design > patterns approach that a number of ontologies are switching to. See > https://github.com/dosumis/dead_simple_owl_design_patterns > > For some example trait patterns, see > > https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns > > I think it would be a good idea to align the cvterms you use with the ones > we are using here. Sorry if this sounds a little opaque, I'll try and > provide more details later. > > > > On Thu, May 26, 2016 at 10:44 AM, Naama Menda <nm...@co...> wrote: > >> There are some proposed changes for allowing to post-compose cvterms >> linked to one phenotype >> >> http://gmod.org/wiki/Chado_Post-Composed_Phenotypes >> >> The detailed chnages are in the doc for proposed changes in Chado >> >> https://docs.google.com/document/d/1IZ3VMpIoG1hhpbHYi6rbChImLgrlmbyy7Ewms-EpaeU/edit >> >> This schema has minimal changes (only 1 new table and 2 new columns in >> phenotype_cvterm) and works well for simple EAV and complex EQ >> statements, as well as with post and pre-composed cvterms. >> >> We'd like to use some of these new features in our breeders databases, so >> if you are using the phenotype module please read those pages and send your >> input >> >> >> Thanks! >> >> >> Naama Menda >> Boyce Thompson Institute for Plant Research >> Tower Rd >> Ithaca NY 14853 >> USA >> >> (607) 254 3569 >> Sol Genomics Network >> http://solgenomics.net/ >> nm...@co... >> >> >> ------------------------------------------------------------------------------ >> Mobile security can be enabling, not merely restricting. Employees who >> bring their own devices (BYOD) to work are irked by the imposition of MDM >> restrictions. Mobile Device Manager Plus allows you to control only the >> apps on BYO-devices by containerizing them, leaving personal data >> untouched! >> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j >> _______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> >> > |
From: Chris M. <cjm...@lb...> - 2016-05-26 19:52:58
|
Thanks Naama Do you intend to make a pull request for the schema changes? I'm not sure what the current GMOD policy is but this works well on other standards projects, with stakeholders giving +1s etc, and having the discussion linked to the commit trail If I could attempt a brief summary, sorry if this doesn't fully capture it: you are moving from the old schema where phenotypes have a fixed number of slots were available to a flexible number of slots. Standardization of the slot fields (what you have as PE1, PE2, etc) is key to successful interoperability. There are a few options here. One way is to use RO relations. Another way is to treat these as a different layer from the biological object graph, and to treat them as slots that may have different meanings in different contexts. This is actually quite well aligned with the Dead Simple OWL Design patterns approach that a number of ontologies are switching to. See https://github.com/dosumis/dead_simple_owl_design_patterns For some example trait patterns, see https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns I think it would be a good idea to align the cvterms you use with the ones we are using here. Sorry if this sounds a little opaque, I'll try and provide more details later. On Thu, May 26, 2016 at 10:44 AM, Naama Menda <nm...@co...> wrote: > There are some proposed changes for allowing to post-compose cvterms > linked to one phenotype > > http://gmod.org/wiki/Chado_Post-Composed_Phenotypes > > The detailed chnages are in the doc for proposed changes in Chado > > https://docs.google.com/document/d/1IZ3VMpIoG1hhpbHYi6rbChImLgrlmbyy7Ewms-EpaeU/edit > > This schema has minimal changes (only 1 new table and 2 new columns in > phenotype_cvterm) and works well for simple EAV and complex EQ > statements, as well as with post and pre-composed cvterms. > > We'd like to use some of these new features in our breeders databases, so > if you are using the phenotype module please read those pages and send your > input > > > Thanks! > > > Naama Menda > Boyce Thompson Institute for Plant Research > Tower Rd > Ithaca NY 14853 > USA > > (607) 254 3569 > Sol Genomics Network > http://solgenomics.net/ > nm...@co... > > > ------------------------------------------------------------------------------ > Mobile security can be enabling, not merely restricting. Employees who > bring their own devices (BYOD) to work are irked by the imposition of MDM > restrictions. Mobile Device Manager Plus allows you to control only the > apps on BYO-devices by containerizing them, leaving personal data > untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > |
From: Naama M. <nm...@co...> - 2016-05-26 17:44:23
|
There are some proposed changes for allowing to post-compose cvterms linked to one phenotype http://gmod.org/wiki/Chado_Post-Composed_Phenotypes The detailed chnages are in the doc for proposed changes in Chado https://docs.google.com/document/d/1IZ3VMpIoG1hhpbHYi6rbChImLgrlmbyy7Ewms-EpaeU/edit This schema has minimal changes (only 1 new table and 2 new columns in phenotype_cvterm) and works well for simple EAV and complex EQ statements, as well as with post and pre-composed cvterms. We'd like to use some of these new features in our breeders databases, so if you are using the phenotype module please read those pages and send your input Thanks! Naama Menda Boyce Thompson Institute for Plant Research Tower Rd Ithaca NY 14853 USA (607) 254 3569 Sol Genomics Network http://solgenomics.net/ nm...@co... |
From: Dave C. <cle...@ga...> - 2016-05-16 17:21:22
|
Hello all, *GMOD will be holding a community meeting on June 30th and July 1st <http://gmod.org/wiki/Jun_2016_GMOD_Meeting> in Bloomington, Indiana, United States.* GMOD Meetings <http://gmod.org/wiki/Meetings> are a mix of user and developer presentations, and are a great place to find out what is happening in the project, what's coming up, and what others are doing. *Early bird registration <https://gmod2016.eventbrite.com/> ends May 21, this Saturday.* *For those who would like to present a talk or poster, the meeting registration form includes a section for submitting the presentation title and abstract.* If you have any suggestions or requests for the meeting, please contact the GMOD help desk <he...@gm...>. *GCC2016* The GMOD Meeting is immediately after the 2016 Galaxy Community Conference (GCC2016) <https://gcc2016.iu.edu/>, also in Bloomington (and sharing housing and venue). If you are interested in Galaxy, *GCC2016 has a number of deadlines this Friday, May 20*. See below. Galaxy is a part of the GMOD project and there are several presentations at GCC2016 that cover the GMOD integration: - Moving data from the warehouse to the workbench: a bridge to Galaxy from the Tripal community genome database software platform, <http://sched.co/743X> talk presented by Margaret Staton - Apollo: Collaborative Manual Annotation for Genomic Sequencing Projects <http://sched.co/743i>, talk presented by Nathan Dunn (Apollo will have a poster and demo) - Hardwood Genomics Database (HGD): a web portal and database resource for hardwood tree genomic and genetic research, poster presented by Ming Chen and Margaret Staton (posters are not online yet) More posters and demos are in the works. Thanks, and hope to see you in Bloomington, Dave C ---------- Forwarded message ---------- From: Dave Clements <cle...@ga...> Date: Mon, May 16, 2016 at 9:09 AM Subject: GCC2016 Deadlines this Friday & Conference schedule To: Galaxy Announcements List <gal...@li...>, Galaxy Dev List <gal...@li...> Hello all, This is just a reminder that* there are some key deadlines this Friday, May 20:* - Early registration ends <https://gcc2016.iu.edu/registration/index.php>. After Friday registration rates go up by over 40%. - Poster abstracts <https://gcc2016.iu.edu/abstracts/index.php> are due. - Demo abstracts <https://gcc2016.iu.edu/abstracts/index.php> are due. These are new this year and can complement a poster abstract or stand on their own. If you are wondering what's happening at GCC2016, the training and conference schedules <https://gcc16.sched.org/> are now online, featuring 21 accepted talks <https://gcc16.sched.org/overview/type/Conference> and 31 training sessions <https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any>. And, thanks to Jetstream <http://jetstream-cloud.org/> IU's newest National Science Foundation-funded project (and in which Galaxy is a partner), and the National Center for Genome Analysis Support <http://ncgas.org/> at IU are sponsoring an opening reception on Monday evening <http://sched.co/72bN> at the IU Cyberinfrastructure Building. The first ever GCC opening reception will feature local wine/beer, morsels from local eateries, and demonstrations of the 15 million+ pixel IQ-Wall, IU's Data Center, Science on a Sphere, and other IU-centric IT. Hope to see you there, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ |
From: David E. <em...@mo...> - 2016-04-15 19:45:16
|
Hi All, FlyBase has implemented the Group Module in our chado instance and we're quite happy with it. (And in case we didn't say it before: complements and many thanks, Mara!) Here's some details on what we're using it for: http://flybase.org/static_pages/feature/previous/articles/2015_05/gene_groups.html And anyone who wants to have a look under the hood can grab the pg dump of the current FlyBase release here: ftp://ftp.flybase.net/releases/current/psql/ Best, -Dave On Fri, Apr 15, 2016 at 2:27 PM, Joe Carlson <jwc...@lb...> wrote: > Hi, > > There is a need for a module like this. The existing solutions and work > around are a bit messy. I’ve been trying out this module for representing > our protein families. And trading some email with Mara Kim, the author. > > I had a couple of suggestions about nomenclature and syntax (for example, > in feature_grpmember, the column grpmember_id references grp and not > grpmember.) > > I also think that a couple more fields in grp are needed: dbxref_id to > reference the primary dbxref and an is_obsolete boolean. > > This also seems to me to be a case where table inheritance may be useful. > I know there can be some performance problems with table inheritance but it > might be useful if there are many different types of ‘things’ that people > want to put into groups. > > Joe > > On Apr 15, 2016, at 9:50 AM, Stephen Ficklin <spf...@gm...> wrote: > > Hi Sofia, > > The Group Module is a candidate module for inclusion in a future release > of Chado. I'm CC'ing my response to the Chado schema mailing list for input > from others who have implemented it. Currently, there is not Tripal > module to support it. Although I believe there are some Tripal sites that > may be using it and have some support. If they read this and respond they > may be able to share some insights. > Stephen > > On 4/8/2016 8:57 AM, Sofia Robb wrote: > > Hello All, > > I am still working on adding gene groups to one of my tripal installs. I > found this chado module: > > http://gmod.org/wiki/Chado_Group_Module > > Is there a recommended way to add these modules to the chado in tripal? > > > Thanks, > Sofia > > > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > Gmod-tripal mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gmod-tripal > > > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications > Manager > Applications Manager provides deep performance insights into multiple > tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z_______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications > Manager > Applications Manager provides deep performance insights into multiple > tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > |
From: Joe C. <jwc...@lb...> - 2016-04-15 18:28:08
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Hi, There is a need for a module like this. The existing solutions and work around are a bit messy. I’ve been trying out this module for representing our protein families. And trading some email with Mara Kim, the author. I had a couple of suggestions about nomenclature and syntax (for example, in feature_grpmember, the column grpmember_id references grp and not grpmember.) I also think that a couple more fields in grp are needed: dbxref_id to reference the primary dbxref and an is_obsolete boolean. This also seems to me to be a case where table inheritance may be useful. I know there can be some performance problems with table inheritance but it might be useful if there are many different types of ‘things’ that people want to put into groups. Joe On Apr 15, 2016, at 9:50 AM, Stephen Ficklin <spf...@gm...> wrote: > Hi Sofia, > > The Group Module is a candidate module for inclusion in a future release of Chado. I'm CC'ing my response to the Chado schema mailing list for input from others who have implemented it. Currently, there is not Tripal module to support it. Although I believe there are some Tripal sites that may be using it and have some support. If they read this and respond they may be able to share some insights. > Stephen > > On 4/8/2016 8:57 AM, Sofia Robb wrote: >> Hello All, >> >> I am still working on adding gene groups to one of my tripal installs. I found this chado module: >> >> http://gmod.org/wiki/Chado_Group_Module >> >> Is there a recommended way to add these modules to the chado in tripal? >> >> >> Thanks, >> Sofia >> >> >> >> >> ------------------------------------------------------------------------------ >> >> >> _______________________________________________ >> Gmod-tripal mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-tripal > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z_______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema |
From: Stephen F. <spf...@gm...> - 2016-04-15 16:50:17
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Hi Sofia, The Group Module is a candidate module for inclusion in a future release of Chado. I'm CC'ing my response to the Chado schema mailing list for input from others who have implemented it. Currently, there is not Tripal module to support it. Although I believe there are some Tripal sites that may be using it and have some support. If they read this and respond they may be able to share some insights. Stephen On 4/8/2016 8:57 AM, Sofia Robb wrote: > Hello All, > > I am still working on adding gene groups to one of my tripal > installs. I found this chado module: > > http://gmod.org/wiki/Chado_Group_Module > > Is there a recommended way to add these modules to the chado in tripal? > > > Thanks, > Sofia > > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > Gmod-tripal mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal |